Re: [ccp4bb] CCP4-6.4.0 Update 018
CCP4BB list, Today I tried to install update 018, however I have lost the ability to do it from the GUI. Menu for checking available installation have disappeared mysteriously. Any clue not related to something I probably did between previous installation and this one will be welcomed. I do brute force reinstallation right now and hope it will work. FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Jun 13, 2014, at 23:07 , Andrey Lebedev andrey.lebe...@stfc.ac.uk wrote: Dear CCP4 Users An update for the CCP4-6.4.0 series has just been released, consisting of the following changes • refmac5 (all platforms): – Fixed restraints for M- and P-peptides – Fixed SAD scaling issue • monomers (all): – Fixed description for M- and P-peptides and some other entries • pointless (all): – Update to 1.9.10 fixing a long-standing bug in reindexing files with different (permuted) unit cells • aimless (all): – Fix to explicit run definitioin Note that auto-updates work only with CCP4 6.4.0 series, therefore please upgrade if necessary. The Update Manager is now included in the package so you do not need to install it separately. In addition, all available updates will be installed automatically if you are using Setup Manager for CCP4 installation. Please report any bugs to c...@stfc.ac.ukmailto:c...@stfc.ac.uk. Many thanks for using CCP4. The CCP4 Core Team -- Scanned by iCritical.
Re: [ccp4bb] CCP4-6.4.0 Update 018
Success (relative, as such things does not have to happened). The only thing I know that after about two weeks of not using CCP4, temporary directory which is defined in /tmp/myuser have disappeared and I opened it again manually After re-installation “Manage updates” menu reappeared :-/ Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Jun 14, 2014, at 12:21 , Felix Frolow mbfro...@post.tau.ac.il wrote: CCP4BB list, Today I tried to install update 018, however I have lost the ability to do it from the GUI. Menu for checking available installation have disappeared mysteriously. Any clue not related to something I probably did between previous installation and this one will be welcomed. I do brute force reinstallation right now and hope it will work. FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Jun 13, 2014, at 23:07 , Andrey Lebedev andrey.lebe...@stfc.ac.uk wrote: Dear CCP4 Users An update for the CCP4-6.4.0 series has just been released, consisting of the following changes • refmac5 (all platforms): – Fixed restraints for M- and P-peptides – Fixed SAD scaling issue • monomers (all): – Fixed description for M- and P-peptides and some other entries • pointless (all): – Update to 1.9.10 fixing a long-standing bug in reindexing files with different (permuted) unit cells • aimless (all): – Fix to explicit run definitioin Note that auto-updates work only with CCP4 6.4.0 series, therefore please upgrade if necessary. The Update Manager is now included in the package so you do not need to install it separately. In addition, all available updates will be installed automatically if you are using Setup Manager for CCP4 installation. Please report any bugs to c...@stfc.ac.ukmailto:c...@stfc.ac.uk. Many thanks for using CCP4. The CCP4 Core Team -- Scanned by iCritical.
Re: [ccp4bb] baverage: no tables were found in this file
Possibility to have file names with the spaces is a curse put on the community by Microsoft, and it will be a big mistake to introduce this to CCP4 (my opinion). I guess there are much more important things new CCP4 GUI should deal with. If CCP4 GUI will start to go this way, file names with spaces will become file names with spaces and multilingual, in some these languages writing is going in the different direction. In my introduction to UNIX, I teach in the beginning of practical protein crystallography my first demand from student is to forget about spaces in the fie names and the life will be much easier. No fix is needed for that, concentrate on more important problems :-) Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Jun 3, 2014, at 14:47 , Eugene Krissinel eugene.krissi...@stfc.ac.uk wrote: I take this chance to to confirm once more, as publicly as possible, that file paths with spaces are discouraged in today's CCP4. This inconvenience originates from ancient times in computing when good half of CCP4 was written and when spaces were disallowed on file system nodes. Please take a notice of this fact as CCP4 core still receives (albeit infrequent) bug reports, where surprising behaviour is due to using file paths with white spaces. Fixing this has proved to be a hard problem, purely because of technical choices made quite a number of years ago. But good news are that this limitation will be removed in new CCP4 Gui under development. Eugene On 3 Jun 2014, at 08:23, Mark J van Raaij wrote: This also occurred to me once where the file path had a space,(/Google Drive/), when I moved the file somewhere else it worked. I was using baverage from the CCP4i GUI. Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 3 Jun 2014, at 09:20, Tim Gruene wrote: Dear Bing, can you post the exact command you were using, please? Also please check with a different PDB file. In case you are using baverage from the command line, can you make sure you are actually using the program from ccp4 by typing 'which baverage' at the command prompt? Regards. Tim On 06/02/2014 10:16 PM, Wang, Bing wrote: Hi CCP4, Recently when I input my pdb file and run the baverage in the ccp4 suit to check the temperature factor, it always tell me No tables were fund in this file. Could you tell me how to fix this problem? Or is there another software instead of baverage I could use to check the temperature factor? Thanks! Bing -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -- Scanned by iCritical.
[ccp4bb] List of projects
I have 350 projects under CCP4 roof. It become difficult to navigate between them as Change Project pop-up menu is running out of window and is unmovable on my Mac laptop. How community solve such problem? FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608
Re: [ccp4bb] puzzle of reference zone in HKL2000
these are symmetry alternative choices of the cell axes they sure are the same as there are 14 Bravais lattices I guess it is not space group related. they were introduced to maintain a precision of calculationI guess, so to choose and alternative orientation were trigonometric parameters are in the region were small change in angle does not bring large change in the trigonometric function (or vice versa) FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On May 13, 2014, at 23:19 , 林世强 linshiqiang1...@gmail.com wrote: Hi everybody! I met with a problem when I was reading the HKL2000 online manual. It's the reference zone setup in the Step 11: What is the reference zone? How is this useful? (page 38, figure 38). Does anybody know the definition of reference zone, and why the reference zone setup window seems always contain the same 10 options, h0l, hk0, l0h, kh0, ..., 0-kl? Thanks. Best regards, Shiqiang Lin
[ccp4bb] TER in PDB file
Community! I am in the process of PDB deposition. I have used for refinement Refmac. I enter to refinement cycle PDB file with TER separators. After refinement they disappear. PDB validation server (option 1 with geometrical parameters report ) DEMAND TER separator. In my structure there are 28 hetero-mers. Is it sane: To demand such thing? Not to supply such thing? Do I miss something ? Does community punch in TER cards manually ? FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608
Re: [ccp4bb] TER in PDB file
Phenix does even more, it adds TER after ions and ligands, so again manual messing is needed. However they may have a jiffy to fix it. FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On May 14, 2014, at 07:23 , Robbie Joosten robbie_joos...@hotmail.com wrote: Dear Felix, I recently had the same problem. I didn't think TER records were a big deal. I never had a program that did weird thing because of missing TER records. But well, orders are orders, so we need TER records for deposition. It would be nice if all refinement programs would write those. AFAIK, Phenix already does. Rather then putting them in manually, I ended up using pdb_extract to convert my pdb file to mmCIF. A nice bonus is that you can throw in the log files from indexing and phasing which saves a lot of typing later in the deposition process. Cheers, Robbie Sent from my Windows Phone Van: Felix Frolow Verzonden: 13-5-2014 23:26 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] TER in PDB file Community! I am in the process of PDB deposition. I have used for refinement Refmac. I enter to refinement cycle PDB file with TER separators. After refinement they disappear. PDB validation server (option 1 with geometrical parameters report ) DEMAND TER separator. In my structure there are 28 hetero-mers. Is it sane: To demand such thing? Not to supply such thing? Do I miss something ? Does community punch in TER cards manually ? FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608
Re: [ccp4bb] metals disapear
Are these metals there in the beginning to experiment before radiation damage “destroy” them? Easy to check if X-ray fluorescence facility is installed on the beam line you are measuring. It is sensitive technique and we constantly use it in the beginning of every measurement. FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On May 1, 2014, at 04:03 , Sanishvili, Ruslan rsanishv...@anl.gov wrote: The question about metal sensitivity to radiation cannot be answered in general; it needs to be discussed in specific chemical coordination context. Agreed. The author of the original question should have provided more details about the metal in question, about the samples and the way experiment was carried out. The advice about using helical scan is horrible in this context. The diffraction collected by such method represents state of crystal exposed to constant high dose. If anything, the helical scan method is more suitable to study radiation damaged state of the crystal. I am afraid the advise was horribly misunderstood. A crystal during helical data collection doesn't have to be exposed to constant high dose. The exposure level is selected by the experimenter and is not intrinsic feature of helical data collection. The advise comprised a four-step program and it started by determining (in the first step) a lower dose that would still allow making valid enzymologic (or mechanistic) conclusions. Then further steps instructed how to lower this dose even more by using multiple crystals (if necessary due to poor crystals quality - 2nd step), or by spreading the same low dose over a larger volume using helical data collection - step 4. I suspect the misunderstanding is based on a misconception that if one is using helical data collection, one necessarily is using small beam and high intensity, but it is not so at all. The beam size to be used is dictated by the size of the well-diffracting volume (advised to determine in step #3). If one has large well-diffracting volume, large beam can be used for helical data collection as well (if the volume is larger than the beam size). Hope it clarifies things little better. Cheers, N. Ruslan Sanishvili (Nukri) Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov From: zbys...@work.swmed.edu [zbys...@work.swmed.edu] Sent: Wednesday, April 30, 2014 10:33 AM To: Sanishvili, Ruslan Cc: ccp4bb@jiscmail.ac.uk Subject: Re: [ccp4bb] metals disapear If metal ion will be sensitive to radiation depends on its redox chemistry and not its X-ray properties. For a metal to be affected by radiation dose it needs to be reduced by free radicals. However, such metals are rarely (by gene counts or deposits in PDB) present in catalytic sites of enzymes. The most frequently occurring metal ions in catalytic sites e.g. Mg++, Ca++, Zn++, Fe++, Mn++ lack oxidation state to which they could be reduced by a single radical. For this reason these metals tend to be very stable upon radiation and they are last to go. Copper is the counterexample where radiation sensitivity is much more likely to be expected. Unfortunately, the original question and part of the discussion involved generic category of metals involved in catalysis, rather then specific one. Magnesium is by far the the most frequently encounter metal in catalytic sites. In redox reaction the most frequent cofactors are not metals, but NAD or FAD. Iron is most often present in Fe-S clusters rather than as standalone Fe++ ion. These clusters are structurally diverse and do not necessarily participate in catalysis. If they have similar or diverse sensitivity to radiation is not clear to me. The question about metal sensitivity to radiation cannot be answered in general; it needs to be discussed in specific chemical coordination context. Separate issue: The advice about using helical scan is horrible in this context. The diffraction collected by such method represents state of crystal exposed to constant high dose. If anything, the helical scan method is more suitable to study radiation damaged state of the crystal. Zbyszek Otwinowski Dear Dean, You have already received excellent insight into radiation effects on metals. From personal experience, it doesn't take long for the metal occupancy to go down to 80%. Of course it is not anywhere near disappearing but then again, we don't know the details of your data collection and of how disappeared are your disappeared metals. I will only add that you can use modern
Re: [ccp4bb] error in starting imosflm
Hi Tim,
What can be a reason to work with an obsolete version of CCP4?
I remember reading somewhere that 6.3.0 version is obsolete.
FF
Dr Felix Frolow
Professor of Structural Biology and Biotechnology, Department of Molecular
Microbiology and Biotechnology
Tel Aviv University 69978, Israel
Acta Crystallographica F, co-editor
e-mail: mbfro...@post.tau.ac.il
Tel: ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608
On Apr 28, 2014, at 19:01 , Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Sreetama, dear Ian,
I avoid sourcing both version 6.3 and 6.4 in the same terminal. If I
need to work with 6.3 I modify my .bashrc from 6.4 to 6.3 and then
open a new terminal to make sure everything refers to v6.3 and vice versa.
Best,
Tim
On 04/28/2014 04:51 PM, Ian Tickle wrote:
Harry,
I've run into this problem before with other programs when I switch
between v6.3 v6.4. I think the problem is this code in
ccp4.setup-sh:
if [ `expr :${PATH}: : .*:${dir}:` -eq 0 ]; then if test
$ccp4_first_in_path -eq 1; then PATH=${dir}:${PATH} else
PATH=${PATH}:${dir} fi fi
Ignore the 'ccp4_first_in_path' business, unless the user has
hacked the script it always takes the 'then' clause of the 'if' so
it's actually doing this:
if [ `expr :${PATH}: : .*:${dir}:` -eq 0 ]; then if test
$ccp4_first_in_path -eq 1; then PATH=${dir}:${PATH} fi fi
So what happens is that the first time you source the setup for
v6.4 it prepends the directories for that version. If you then
source the setup for v6.3 it prepends the directories for that and
you will use the v6.3 executables. So far so good. Now what
happens if you source the setup for v6.4 again? The code above
ensures that the v6.4 directory is NOT prepended again and so it
will continue to use v6.3 until you logout in again reset the
path.
Cheers
-- Ian
On 28 April 2014 14:54, Harry Powell ha...@mrc-lmb.cam.ac.uk
wrote:
Hi Sreetama
That's the problem - sourcing the old ccp4 6.3 distro has set up
MOSFLM_EXEC to point to an old copy of ipmosflm that will not run
with the latest iMosflm.
Mosflm version 7.0.9 for Image plate and CCD data 14th May
2012
which cannot be used with iMosflm 7.1.0.
So it looks like there might be an issue with the ccp4 6.4 setup
not over-writing the environment variable MOSFLM_EXEC as it
should. The immediate way round this would be to not source ccp4
6.3 in any terminal that you want to run iMosflm from.
Can you send me c...@stfc.ac.uk (*not* to the ccp4bb, please)
the output of
echo $PATH which $MOSFLM_EXEC
(1) before you source ccp4-6.3 (2) after you source ccp4-6.3
(3) after you source ccp4-6.4
So that we can get a clear idea of what is happening to your PATH
when you do each of these three things.
On 28 Apr 2014, at 14:38, sreetama das wrote:
Dear Sir, If I sorce ccp4-6.3, and then change in the bashrc
file
source ccp4-6.4, (and source the modified .bashrc file in either
case) but don't close the previous terminal, then opening imosflm
gives the aforementioned error. After closing the imosflm GUI, if
I type at the terminal, I get the following:
sreetama@sreetama-laptop:~/data $ $MOSFLM_EXEC BFONT
COLOR=#FF!--SUMMARY_BEGIN-- html !-- CCP4 HTML
LOGFILE -- hr !--SUMMARY_END--/FONT/B
Mosflm version 7.0.9 for Image plate and CCD data
14th
May 2012 ***
Andrew Leslie and Harry Powell, MRC Laboratory of Molecular
Biology, Hills Road, Cambridge CB2 0QH, UK E-mails:
and...@mrc-lmb.cam.ac.uk, ha...@mrc-lmb.cam.ac.uk References:
Mosflm: A.G.W. Leslie and H.R. Powell (2007), Evolving Methods
for Macromolecular Crystallography, 245, 41-51 ISBN
978-1-4020-6314-5
New auto-indexing based on DPS: I. Steller R. Bolotovsky and
M.G.
Rossmann
(1997) J. Appl. Cryst. 30, 1036-1040 New iMosflm GUI: T.G.G.
Battye, L. Kontogiannis, O. Johnson, H.R.
Powell
and A.G.W. Leslie.(2011) Acta Cryst. D67, 271-281)
How much of this information is useful in diagnosing user problems?
Mosflm run on Monday, April 28 2014 at 19:01 by sreetama
Compiler command: gfortran Compiler version: GNU Fortran (GCC)
4.4.7 Copyright (C) 2010 Free
Software Foundation, Inc. GNU Fortran comes with NO WARRANTY, to
the extent permitted by law. You may redistribute copies of GNU
Fortran under the terms of the GNU General Public License. For
more informatio
Executable type: ELF 32-bit LSB executable, Intel 80386,
version
1 (SYSV), dynamically linked (uses shared libs), not stripped
This executable was built by ccb on Thursday, June 28 2012 at
09:33
MOSFLM =
Also the terminal refuses to close if I type exit. Forcibly
closing the
terminal , and typing imosflm in a new terminal solves
Re: [ccp4bb] small molecule crystallography
Dear Tim, I am sure your statement is too general and is not very precise. 10 deg oscillation range is as precise as 0.1 deg. Positions of diffraction spots on the area detector have defined position on rotation axis within the precision/accuracy of the stepping motor and the spacial resolution of the area detector and NOT defined by oscillation range. If it does, change your setup. We need sometimes 10 deg to have enough reflections for indexing. Obviously we need some reflections to define the orientational matrix and cell dimensions. FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Mar 25, 2014, at 10:26 , Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear David, I dare claim that rather you do not know how to use the listed programs in the case for small molecule data rather than none of them were optimised. E.g. 10degree frames loose all the possible accuracy in the phi-direction so I am not surprised you had trouble indexing. There is no reason for that, if you know which parameters to modify. In addition to that, concluding from one single data set that programs are not optimised may be a little overinterpreted. In my experience, this interpretation does not hold. Best, Tim On 03/24/2014 10:03 PM, David Schuller wrote: Coincidentally, I just spent my day trying to index a lattice of ~ 10 x 10 x 11 A. Mounting samples: if the compound is stable, just glue it to the end of a steel pin. No muss, no fuss. We had to attenuate our synchrotron beam heavily to make it work; motors can only turn so fast. We did 10 degree rotations to get enough spots per frame per imaging. Detector setup allowed for ~ 1 A resolution. Indexing was a challenge for many of the samples, heavily overloaded spots and streaks seemed to be causing the most problems. We tried various of the usual macromolecular programs for indexing; HKL2000, iMosFlm, XDS, DPS. None of them seem to be optimised for this, but some of them actually worked in some instances. On 03/24/14 14:04, Andreas Förster wrote: Dear all, I've been approached by a materials student with a petri dish full of big, sturdy, salty, yellow crystals. He claims I have the best kit for single-crystal diffraction on campus. I would very much appreciate advice on how to deal with this, anything in the range from won't work to use software X to analyze data in space group P-43N would be welcome. Thanks. Andreas -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
Re: [ccp4bb] small molecule crystallography
Dear Tim, My most experience is with HKL2000 which during the index doing something quite mysterious and not very well described such as a brute search for the correct reciprocal lattice. I do not know where initially the reflections are placed by HKL2000, but finally it converges. In the moment we know our orientational matrix (for small molecules we need get enough reflections for that doing 5-10 deg oscillation, again if we intend to use HKL2000), nothing matters (oscillation range etc.) but only stepping motors, stability of goniostat, detector spatial resolution and refinement of parameters. However I will be very glad to be corrected if I am wrong. FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Mar 25, 2014, at 10:55 , Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear Felix, as far as I understand we are talking about the frame width, not the total data range for indexing (10 degree rotations to get enough spots per frame). I have used 180degrees of data for indexing. At least XDS places the reflection at the centre of the frame so that with a 10deg frame width the position is know within +/-5 degree - it is not surprising indexing fails here. Regards, Tim On 03/25/2014 09:41 AM, Felix Frolow wrote: Dear Tim, I am sure your statement is too general and is not very precise. 10 deg oscillation range is as precise as 0.1 deg. Positions of diffraction spots on the area detector have defined position on rotation axis within the precision/accuracy of the stepping motor and the spacial resolution of the area detector and NOT defined by oscillation range. If it does, change your setup. We need sometimes 10 deg to have enough reflections for indexing. Obviously we need some reflections to define the orientational matrix and cell dimensions. FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Mar 25, 2014, at 10:26 , Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear David, I dare claim that rather you do not know how to use the listed programs in the case for small molecule data rather than none of them were optimised. E.g. 10degree frames loose all the possible accuracy in the phi-direction so I am not surprised you had trouble indexing. There is no reason for that, if you know which parameters to modify. In addition to that, concluding from one single data set that programs are not optimised may be a little overinterpreted. In my experience, this interpretation does not hold. Best, Tim On 03/24/2014 10:03 PM, David Schuller wrote: Coincidentally, I just spent my day trying to index a lattice of ~ 10 x 10 x 11 A. Mounting samples: if the compound is stable, just glue it to the end of a steel pin. No muss, no fuss. We had to attenuate our synchrotron beam heavily to make it work; motors can only turn so fast. We did 10 degree rotations to get enough spots per frame per imaging. Detector setup allowed for ~ 1 A resolution. Indexing was a challenge for many of the samples, heavily overloaded spots and streaks seemed to be causing the most problems. We tried various of the usual macromolecular programs for indexing; HKL2000, iMosFlm, XDS, DPS. None of them seem to be optimised for this, but some of them actually worked in some instances. On 03/24/14 14:04, Andreas Förster wrote: Dear all, I've been approached by a materials student with a petri dish full of big, sturdy, salty, yellow crystals. He claims I have the best kit for single-crystal diffraction on campus. I would very much appreciate advice on how to deal with this, anything in the range from won't work to use software X to analyze data in space group P-43N would be welcome. Thanks. Andreas -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
[ccp4bb]
Very reasonable structure, I guess in the direction perpendicular to your picture you will have next donut etc. You can call this - nan-pore ;-) Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Mar 19, 2014, at 18:37 , Eleanor Dodson eleanor.dod...@york.ac.uk wrote: How pretty - I love circular molecules! Eleanor On 19 March 2014 15:58, Yarrow Madrona amadr...@uci.edu wrote: Thank you to everyone for their input. I am posting a picture to some of the symmetry related molecules shortly. There are six dimers related by symmetry (60 degrees) with a donut hole in the middle. This was troubling to me as I have solved mostly tighter packing structures (monoclinic or orthorhombic) in the past. If expanded further there are a bunch of tightly packed donut holes (though I didn't show these). I want to know if this is really a viable solution. The crystals are huge (300microns X 300microns) and this would maybe explain why they are only diffracting to 3.2 angstroms. Thank you! https://www.dropbox.com/s/r01u37owbkz9pon/donut.png -Yarrow On Wed, Mar 19, 2014 at 6:59 AM, Yarrow Madrona amadr...@uci.edu wrote: Yes in the first couple of rounds of refinement it refines very well for a 3.2 angstrom structure (Now at 30%/24% Rfree/R). Everything Packs contiguously except for a donut hole in between six dimers that are related by symmetry. Trying to put a molecule there disrupts the symmetry and leads to clashes. I have a synchrotron trip next week, hopefully this should help clear things up a bit. On Wed, Mar 19, 2014 at 12:17 AM, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: I think you have solved it! That is an excellent LLG and if you can't see anything else in the map, then there s prob. not another molecule. Does it refine? If you look at the maps following refinement any missing features should become more obvious. Solvent content of 65% is not uncommon. Eleanor On 19 Mar 2014, at 03:46, Yarrow Madrona wrote: Hello CCP4 Users, I recently collected data in-house on an Raxis IV and am trying to solve a 3.2 angstrom structure. I have obtained only partial solutions using Phaser and would like some help. I believe I only have two molecules in the ASU instead of three as suggested by the mathew's calculation. I believe I have two molecules in the ASU with a space group of P312 despite a high solvent content. I have outlined by line of reasoning below. 1. Indexes as primitive hexagonal 2. Self rotation function (MolRep) gives six peaks for chi = 180. (I'm assuming chi is equivalent to kappa for Molrep) supporting the 2 fold axis in the P312 space group. See this link, https://www.dropbox.com/s/sj7c28pvuz7fei2/031414_21_rf.pdf 3. Scaling in P3 gives 6 molecules/ASU predicted by Mathew's calculation. Phaser gives solutions for only 4 molecules. 4. Scaling in P312 gives 3 molecules/ASU predicted by Mathew's calculation. Phaser gives solutions for only 2 molecules. Mathews calculation for data scaled in P312: For estimated molecular weight 44000. Nmol/asym Matthews Coeff %solvent P(3.20) P(tot) 1 6.8482.03 0.00 0.00 2 3.4264.07 0.18 0.13 3 2.2846.10 0.81 0.86 4 1.7128.13 0.01 0.01 5 1.3710.17 0.00 0.00 Phaser Stats: Partial Solution for data scaled in P312: RFZ=11.7 TFZ=27.4 PAK=0 LLG=528 TFZ==18.8 RF++ TFZ=52.1 PAK=0 LLG=2374 TFZ==30.3 6. No peaks in patterson map (No translational symmetry). 5. Very strong 2fo-fc density for two ligands in each monomer (Heme and 4 bromo-phenyl Immidazole) despite not including them in the search model. 6. There is only one black hole where it would be possible place another subunit but there is not much interpretable density and the symmetry of the space group would be broken if this was done. Six Dimers are arranged around this hole. I can post a picture if anyone wants to see it. 6. Early refinement of the partial solution gives an Rwork/Rfee ~ 24%/31% for a 3.2 angstrom data set. Probably over parameterized judging by the gap in R/Rfree but still better than I would guess if I had only 2/3 of the ASU composition. My belief is that there really is only two molecules in the ASU and that there just happens to be a very large solvent channel giving a 65% solvent content. I would like help in determining whether this is likely or if I have
Re: [ccp4bb] Phasing with Many Monomers/AU
Francis, It can happened We have (not yet published) P1 with 24 molecules. When we cut His-tag we get P1 with 32 molecules. In our case we believe it is dictated by very strong interaction between two monomers, and strong interaction between dimers with build a flattish tetramer. Probably such formations is more difficult to oaks than globular oligomers. In this moment I do not recall what we see in solution, I have to check. Relating to structure solution, P1 is very convenient space group. I would go for determination this structure by SAD (SHELXC/D/E pipe, PHENIX or SHARP). For the native - molecular replacement. In our time after tremendous developments in Refmac and Phenix and development o DM refinement is 3-3.4 Ang. Is not very difficult. I would use in addition to NCS restraints in refinement also multi crystal averaging. Roumors say it is the most strongest phasing method (attributed to Eleanor Dodson, myself never used it). FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Jan 19, 2014, at 08:48 , Francis Reyes francis.re...@colorado.edu wrote: You sure about this space group? 24 monomers in P1 is unusual (at least to me) F On Jan 18, 2014, at 9:14 AM, Chris Fage cdf...@gmail.com wrote: Hello Everyone, I am currently trying to phase a structure with an asymmetric unit predicted to contain 20-24 monomers (space group P1). The native crystals, while beautiful in appearance (see attached), only diffract to ~3.4-3.0 angstroms at best, and SeMet-derived crystals grow with poor morphology (small needles). Also, based a fluorescence scan, I know that mercury does not bind appreciably. Other than screening for a new space group, what options might I have for phasing this many monomers at lower resolution? Is there any real chance of solving the structure in this space group? Thank you in advance for any suggestions! Regards, Chris Crystals.jpg
[ccp4bb] NCS edits in COOT
I have a very large complex of proteins and I would like to use COOT to apply NCS edits in the case where the “master copy” is not chain A of my complex but any given chain. The script that I currently use (example only, actual number of molecules is much larger) (copy-residue-range-from-ncs-master-to-chains 0 A 1 500 (list B C D E)) works only for A but for this I need to temporarily rename molecules, making any molecule I wish to be master also to be A. It is O.K. to do this renaming once or twice, but not convenient if the extensive rebuilding of the complex is considered. Q1. Is there currently a possibility to use a different chain as the master for the NCS edits in COOT? Q2. If so, could someone please let me know how? Q3. If not, would it be possible to program this into Coot for the future for complicated cases? Q4. Is there another option, not COOT? Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608
Re: [ccp4bb] largest protein crystal ever grown?
Well if we start recalling rumours, I have heard that in UC San Diego in the laboratory of George Feher there was (is) a tetragonal hen egg white lysozyme crystal which weighted between 0.5 - 1.0 kg. It grew suspend on a mountain boots shoelace of the read colour. I have never visited George laboratory, but maybe among the society there are some who can shed some light on that…. FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Oct 25, 2013, at 12:18 , Boaz Shaanan bshaa...@bgu.ac.il wrote: Hi, Referring to the Hb crystal that Bill Scott saw in the MRC crystal growing room (by now tho old one I guess), is that the one that was sitting in the largest part of the Pasteur pipette? I recall this one and I keep telling my students about it when they ask about crystal size limits. Cheers, Boaz הודעה מקורית מאת: simon.phill...@rc-harwell.ac.uk תאריך: אל: CCP4BB@JISCMAIL.AC.UK נושא: Re: [ccp4bb] largest protein crystal ever grown? Hi Derek, That brings back memories. I am pretty certain that is the myoglobin crystal that was already on Benno's shelf at Brookhaven when I went there in 1980 to collect my oxymyoglobin neutron data. It would the metmyoglobin crystal Benno got the early neutron data from. He just kept it on the shelf because there was, of course, no degradation in the beam and a crystal is a pretty stable way to store a protein. Whenever he wanted more data he took it off the shelf and put it back on the beamline. If Benno is reading this bulletin board I am sure he could tell us more. Simon Simon E.V. Phillips Director, Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email: susan.jo...@rc-harwell.ac.uk Direct email: simon.phill...@rc-harwell.ac.uk Tel: +44 (0)1235 567701 (direct) +44 (0)1235 567700 (sec) +44 (0)7884 436011 (mobile) www: www.rc-harwell.ac.uk -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Derek Logan Sent: 24 October 2013 19:08 To: ccp4bb Subject: Re: [ccp4bb] largest protein crystal ever grown? Hi, Last spring I visited the Protein Crystallography Station at Los Alamos. On a shelf, in a capillary in a serious exhibition-quality glass dome, was a crystal of myoglobin some 50 mm**3, if I remember correctly. I was told it had been made by Benno Schoenborn some decades earlier and had been exposed to most of the neutron sources in the world (radiation damage - forget about it!) Paul Langan or Zoë Fisher can correct me if I've exaggerated the size or age. Anyway, as I already lost the record several times over for having seen the biggest protein crystal ever, I can share with you the surprise and delight of having to centre the crystals using a telescope mounted on a tripod on the other side of the room. Apparently the magnification on the microscope on the diffractometer (visible in this photo, and maybe the giant crystal too? http://www.lanl.gov/_assets/php/flickrImage.php?photo_id=5033219363secret=291f519124) was too high, so any neutron-size crystals would filled the whole field of view even if they were not well-centered. FWIW, my crystals (somewhat optimistically 0.4 mm**3) didn't diffract neutrons even after a 24h exposure :-) Derek Derek Logan tel: +46 46 222 1443 Associate Professor mob: +46 76 8585 707 Dept. of Biochemistry and Structural Biology www.cmps.lu.se Centre for Molecular Protein Science www.maxlab.lu.se/node/307 Lund University, Box 124, 221 00 Lund, Sweden On 24 Oct 2013, at 18:35, Victor Lamzin vic...@embl-hamburg.de wrote: Also following on from John's comment - back to the times of my PhD I was repeatedly growing crystals of bacterial formate dehydrogenase (80 kDa) of a size about 7x1.5x1 mm. I thought that was quite normal and did not even think of making a photo of 'just a protein crystal'. Victor This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell
Re: [ccp4bb] largest protein crystal ever grown?
I guess that this crystal was never tested with any X-ray source. After all George is a physicist who study photosynthesis processes by spectroscopic methods. However (unrelated but connected) I have collected once a data set from a see urchin needle which was 1 cm long, about 3 mm across (protein mass was dissolved), it was a single crystal despite a complicated and beautiful architecture, and mosaicity was about 0.5 deg on a Rigaku AFC5 diffractometer (mounted on a rotating anode with Ni filter. So I would not bet on the large crystal - big mosaicity formula. FF This remarkable hollow Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Oct 25, 2013, at 16:54 , Derek Logan derek.lo...@biochemistry.lu.se wrote: Hi Felix, What was the mosaicity of this crystal? The absorption correction must have been challenging too... Derek On 25 Oct 2013, at 13:23, Felix Frolow mbfro...@post.tau.ac.il wrote: Well if we start recalling rumours, I have heard that in UC San Diego in the laboratory of George Feher there was (is) a tetragonal hen egg white lysozyme crystal which weighted between 0.5 - 1.0 kg. It grew suspend on a mountain boots shoelace of the read colour. I have never visited George laboratory, but maybe among the society there are some who can shed some light on that…. FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Oct 25, 2013, at 12:18 , Boaz Shaanan bshaa...@bgu.ac.il wrote: Hi, Referring to the Hb crystal that Bill Scott saw in the MRC crystal growing room (by now tho old one I guess), is that the one that was sitting in the largest part of the Pasteur pipette? I recall this one and I keep telling my students about it when they ask about crystal size limits. Cheers, Boaz הודעה מקורית מאת: simon.phill...@rc-harwell.ac.uk תאריך: אל: CCP4BB@JISCMAIL.AC.UK נושא: Re: [ccp4bb] largest protein crystal ever grown? Hi Derek, That brings back memories. I am pretty certain that is the myoglobin crystal that was already on Benno's shelf at Brookhaven when I went there in 1980 to collect my oxymyoglobin neutron data. It would the metmyoglobin crystal Benno got the early neutron data from. He just kept it on the shelf because there was, of course, no degradation in the beam and a crystal is a pretty stable way to store a protein. Whenever he wanted more data he took it off the shelf and put it back on the beamline. If Benno is reading this bulletin board I am sure he could tell us more. Simon Simon E.V. Phillips Director, Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email: susan.jo...@rc-harwell.ac.uk Direct email: simon.phill...@rc-harwell.ac.uk Tel: +44 (0)1235 567701 (direct) +44 (0)1235 567700 (sec) +44 (0)7884 436011 (mobile) www: www.rc-harwell.ac.uk -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Derek Logan Sent: 24 October 2013 19:08 To: ccp4bb Subject: Re: [ccp4bb] largest protein crystal ever grown? Hi, Last spring I visited the Protein Crystallography Station at Los Alamos. On a shelf, in a capillary in a serious exhibition-quality glass dome, was a crystal of myoglobin some 50 mm**3, if I remember correctly. I was told it had been made by Benno Schoenborn some decades earlier and had been exposed to most of the neutron sources in the world (radiation damage - forget about it!) Paul Langan or Zoë Fisher can correct me if I've exaggerated the size or age. Anyway, as I already lost the record several times over for having seen the biggest protein crystal ever, I can share with you the surprise and delight of having to centre the crystals using a telescope mounted on a tripod on the other side of the room. Apparently the magnification on the microscope on the diffractometer (visible in this photo, and maybe the giant crystal too? http://www.lanl.gov/_assets/php/flickrImage.php?photo_id=5033219363secret=291f519124) was too high, so any neutron-size crystals would filled the whole field of view even if they were not well-centered. FWIW, my crystals (somewhat optimistically 0.4 mm**3) didn't diffract neutrons even after a 24h exposure :-) Derek Derek Logan tel: +46 46 222
Re: [ccp4bb] RES: [ccp4bb] Identity of a Bacterial lipid
When USA budget is back :-\ you may give a try to : http://webbook.nist.gov/chemistry/ It helped me several times, very intuitive, I use just a formula for a search, it also accept a wild character for unknown number of atoms. FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Oct 3, 2013, at 16:33 , Andre Luis Berteli Ambrosio andre.ambro...@lnbio.cnpem.br wrote: Dear Michael, thank you for the prompt reply. The host was indeed E. coli. From what I have been reading I completely agree on the lack of biological support for such a molecule but still the map seems very convincing of the presence of cis bonds at such positions… Could such a conformation arise due to something other than unsaturations? We are working on isolating the lipid from the purified protein I will sure follow your suggestions on the additional characterization of this molecule, especially adding NMR analysis to it. Thanks also for referencing the literature. With kind regards, -Andre. De: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Em nome de R. M. Garavito Enviada em: quinta-feira, 3 de outubro de 2013 10:16 Para: CCP4BB@JISCMAIL.AC.UK Assunto: Re: [ccp4bb] Identity of a Bacterial lipid Dear Andre, It always impressive to see a near atomic resolution structure with a bound lipid. Congratulations. However, to identify what lipid you have requires a bit more analysis than just looking in databases. First, what is the bacterium you are using as the host? If it is E. coli, then the known lipids are very well characterized. Also, VERY FEW E. coli lipids have sites of unsaturation, and virtually polyunsaturated fatty acids (PUFAs) have one sp3 carbon in between the double bonds (arising from the mechanisms of biosynthesis). So your proposed structure doesn't seem right from a biological sense, which makes looking into databases unproductive. However, since you solved the structure, do your produce enough protein to isolate the putative lipid by simple TLC? With the help of a good lipid lab you should be able to tell what it with greater certainty. Try to get a copy of Techniques of Lipidology by Morris Kates from Elsevier. Although it is old school stuff, it will help you isolate enough for mass spec and NMR analysis. Good luck, Michael R. Michael Garavito, Ph.D. Professor of Biochemistry Molecular Biology 603 Wilson Rd., Rm. 513 Michigan State University East Lansing, MI 48824-1319 Office: (517) 355-9724 Lab: (517) 353-9125 FAX: (517) 353-9334Email: rmgarav...@gmail.com On Oct 3, 2013, at 8:42 AM, Andre Luis Berteli Ambrosio wrote: Dear colleagues, We have just determined the crystal structure (at 1.1 A max resolution) of a recombinant protein that crystallized in complex with a leftover bacterial lipid, the full identity of which we are currently struggling to identify. Please see attached (3 views of the molecule). The map strongly suggests an 18-carbon long polyunsaturated fatty acid, with 5 conjugated unsaturations (at positions 5, 7, 9, 11 and 13, all cis), covalently bound to some extra chemical group at is polar head. This extra group seems to be comprised of 4 (5?) atoms, though I am afraid cannot tell if it extends further into not-so-well-structured atoms. Myself and a student have spent the last two days searching on the web for possible matches for this ligand without any success. For instance, we have generated a SMILES formula for the aliphatic tail comprising the unsaturations and browsed for similar compounds at PubChem with different similarity cutoffs, but nothing seemed to resemble the complete molecule. We would appreciate if you could make any comments on the nature of this ligand or perhaps suggest your favorite computational tools. We will perform mass spec on it soon. Thank you beforehand. Andre LB Ambrosio, DSc Laboratório Nacional de Biociências - LNBio CNPEM, Brazil FA-density.png
Re: [ccp4bb] tricky mr problem
Taking Tfz of 14.3 I assume that you have used Phaser, and according to what authors say, it is most probably the solution. Maybe map is not yet good, but you can try to refine using modern approaches for refinement of low resolution structures which are recently implemented in Refmac and Phenix. Your map will look better after refinement, as model can move quite significant distance into better position. Phase extension into better resolution data is a method which is developed already the late 80's. So you are in… Good luck FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Sep 24, 2013, at 24:01 , RHYS GRINTER r.grinte...@research.gla.ac.uk wrote: Hi all, I have been attempting to find a MR solution for a low resolution data set (3.9A), with pretty poor merging stats of a 22 strand membrane beta barrel I'm working on. I've created a trimmed poly-alanine from a structure of 17% identity, that gives a solution with a Tfz of 14.3 with two molecules per asu (llg is around 900). I'm guessing this in a genuine solution, but the map is too poor to build into. Does anyone have any advice as to proceed from here? It may be just a case of needing better resolution data to work with, but would this indicate that Selenomet derivative crystals won't be needed for this structure? Cheers, Rhys
Re: [ccp4bb] ctruncate bug?
Intensity is subtraction: Inet=Iobs - Ibackground. Iobs and Ibackground can not be negative. Inet CAN be negative if background is higher than Iobs. We do not know how to model background scattering modulated my molecular transform and mechanical motion of the molecule, I recall we have called it TDS - thermal diffuse scattering. Many years ago Boaz Shaanan and JH were fascinated by it. If we would know how deal with TDS, we would go to much nicer structures some of us like and for sure to much lower R factors all of us love excluding maybe referees who will claim over refinement :-\ Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Jun 20, 2013, at 20:07 , Douglas Theobald dtheob...@brandeis.edu wrote: How can there be nothing wrong with something that is unphysical? Intensities cannot be negative. How could you measure a negative number of photons? You can only have a Gaussian distribution around I=0 if you are using an incorrect, unphysical statistical model. As I understand it, the physics predicts that intensities from diffraction should be gamma distributed (i.e., the square of a Gaussian variate), which makes sense as the gamma distribution assigns probability 0 to negative values. On Jun 20, 2013, at 1:00 PM, Bernard D Santarsiero b...@uic.edu wrote: There's absolutely nothing wrong with negative intensities. They are measurements of intensities that are near zero, and some will be negative, and others positive. The distribution around I=0 can still be Gaussian, and you have true esd's. With F's you used a derived esd since they can't be formally generated from the sigma's on I, and are very much undetermined for small intensities and small F's. Small molecule crystallographers routinely refine on F^2 and use all of the data, even if the F^2's are negative. Bernie On Jun 20, 2013, at 11:49 AM, Douglas Theobald wrote: Seems to me that the negative Is should be dealt with early on, in the integration step. Why exactly do integration programs report negative Is to begin with? On Jun 20, 2013, at 12:45 PM, Dom Bellini dom.bell...@diamond.ac.uk wrote: Wouldnt be possible to take advantage of negative Is to extrapolate/estimate the decay of scattering background (kind of Wilson plot of background scattering) to flat out the background and push all the Is to positive values? More of a question rather than a suggestion ... D From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ian Tickle Sent: 20 June 2013 17:34 To: ccp4bb Subject: Re: [ccp4bb] ctruncate bug? Yes higher R factors is the usual reason people don't like I-based refinement! Anyway, refining against Is doesn't solve the problem, it only postpones it: you still need the Fs for maps! (though errors in Fs may be less critical then). -- Ian On 20 June 2013 17:20, Dale Tronrud det...@uoxray.uoregon.edumailto:det...@uoxray.uoregon.edu wrote: If you are refining against F's you have to find some way to avoid calculating the square root of a negative number. That is why people have historically rejected negative I's and why Truncate and cTruncate were invented. When refining against I, the calculation of (Iobs - Icalc)^2 couldn't care less if Iobs happens to be negative. As for why people still refine against F... When I was distributing a refinement package it could refine against I but no one wanted to do that. The R values ended up higher, but they were looking at R values calculated from F's. Of course the F based R values are lower when you refine against F's, that means nothing. If we could get the PDB to report both the F and I based R values for all models maybe we could get a start toward moving to intensity refinement. Dale Tronrud On 06/20/2013 09:06 AM, Douglas Theobald wrote: Just trying to understand the basic issues here. How could refining directly against intensities solve the fundamental problem of negative intensity values? On Jun 20, 2013, at 11:34 AM, Bernhard Rupp hofkristall...@gmail.commailto:hofkristall...@gmail.com wrote: As a maybe better alternative, we should (once again) consider to refine against intensities (and I guess George Sheldrick would agree here). I have a simple question - what exactly, short of some sort of historic inertia (or memory lapse), is the reason NOT to refine against intensities? Best, BR -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt
Re: [ccp4bb] ctruncate bug?
Measurement worth not very much if simultaneously error of measurement is not considered. 10 counts intensity on the top of 1 counts background is close to nothing. 10 counts on the top of 1 count background is an excellent intensity. Simultaneously with diffraction several types of X-ray scattering events occurs such as: Scattering from the instrument parts can be regarded as one of the sources of systematic errors (apertures, beam-stops, peenholes) the should be eliminated or just disregarded Scattering from the air - more or less similar to latter but can be conveniently subtracted and will not produce much systematic errors Scattering from the water in crystal, sometime complicated by powder diffraction appearance Scattering from phonons of the crystalline lattice (TDS) These two are legitimate contributors to the negative net intensity which can be (see Andrew Lesley and Bernard Santasiero comments) negative. What is true value of Inet I do not know. I know that Inet can be properly measured according to accepted protocols and 101 of counting statistics in the nuclear physics. And a contribution of the negative intensity processed by FW or similar (maybe OZ and WM and others) into the quality of the structure and electron density map is MEASURABLE. It is documented already very long time ago: [10] Hirshfeld, F.L.; Rabinowich, D. Treating Weak Reflexions in Least-Squares Calculations. Acta Crystallogr. 1973, A29, 510–513. [11] Arnberg, L.; Hovmo¨ller, S.; Westman, S. On the Significance of ‘Non-Significant’ Reflexions. Acta Crystallogr. 1979, A35, 497–499 However these papers are related to small molecule structures. I personally do not think that protein crystals from point of view of diffraction physics are different from that from crystals of small molecules. Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Jun 20, 2013, at 20:59 , Douglas Theobald dtheob...@brandeis.edu wrote: On Jun 20, 2013, at 1:47 PM, Felix Frolow mbfro...@post.tau.ac.il wrote: Intensity is subtraction: Inet=Iobs - Ibackground. Iobs and Ibackground can not be negative. Inet CAN be negative if background is higher than Iobs. Just to reiterate, we know that the true value of Inet cannot be negative. Hence, the equation you quote is invalid and illogical --- it has no physical or statistical justification (except as an approximation for large Iobs and low Iback, when ironically background correction is unnecessary). That equation does not account for random statistical fluctuations (e.g., simple Poisson counting statistics of shot noise). We do not know how to model background scattering modulated my molecular transform and mechanical motion of the molecule, I recall we have called it TDS - thermal diffuse scattering. Many years ago Boaz Shaanan and JH were fascinated by it. If we would know how deal with TDS, we would go to much nicer structures some of us like and for sure to much lower R factors all of us love excluding maybe referees who will claim over refinement :-\ Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Jun 20, 2013, at 20:07 , Douglas Theobald dtheob...@brandeis.edu wrote: How can there be nothing wrong with something that is unphysical? Intensities cannot be negative. How could you measure a negative number of photons? You can only have a Gaussian distribution around I=0 if you are using an incorrect, unphysical statistical model. As I understand it, the physics predicts that intensities from diffraction should be gamma distributed (i.e., the square of a Gaussian variate), which makes sense as the gamma distribution assigns probability 0 to negative values. On Jun 20, 2013, at 1:00 PM, Bernard D Santarsiero b...@uic.edu wrote: There's absolutely nothing wrong with negative intensities. They are measurements of intensities that are near zero, and some will be negative, and others positive. The distribution around I=0 can still be Gaussian, and you have true esd's. With F's you used a derived esd since they can't be formally generated from the sigma's on I, and are very much undetermined for small intensities and small F's. Small molecule crystallographers routinely refine on F^2 and use all of the data, even if the F^2's are negative. Bernie On Jun 20, 2013, at 11:49 AM, Douglas Theobald wrote: Seems to me that the negative Is should be dealt with early on, in the integration
Re: [ccp4bb] Curious electron density associated with Asp sidechain
Call EBI, consider some kind of chemical modification. FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Apr 25, 2013, at 19:10 , Antony Oliver antony.oli...@sussex.ac.uk wrote: Dear CCP4 colleagues. I'm just finishing up a refinement, but am left with one little curio that I just can't seem to solve. One aspartic acid residue is associated with some extra, unexplained electron density. -- please see: http://i.imgur.com/vCYOqam.png Where, the Fo-Fc map is contoured at 3.78 rsmd in Coot. I have tried a number of different modelling scenarios, but as yet can't reach a wholly satisfactory conclusion; waters, alternate conformers, really don't seem to cut it. I though about some radiation-induced phenomena, but this data set was collected on a home-source, so I guess this is unlikely. So, I would really appreciate some ideas and suggestions. Hopefully it is blindingly obvious to someone. Random Thought: could it be PEGylation of the side-chain? Some other hopefully useful background information: * I'm sure it is/was an ASP, because the same protein (made from the same construct) has been used in previous crystallisations, and the resultant structures have clear, unambiguous electron density for the side chain. * the crystallization condition is PEG 200, with some Na/K phosphate at pH 5.8, and NaCl. The protein itself contains HEPES buffer. With many thanks, Tony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oli...@sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512
Re: [ccp4bb] CCP4 Update victim of own success
I would serve as a second in this duel, but I respect very much both engaged is this duel… Drop you pistols or swords ! :-) Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Apr 11, 2013, at 18:46 , eugene.krissi...@stfc.ac.uk wrote: That's really hard. Duel? Eugene On 11 Apr 2013, at 16:32, James Holton wrote: CCP4 has a GUI? -James Holton MAD Scientist On 4/11/2013 5:17 AM, eugene.krissi...@stfc.ac.uk wrote: Sorry that this was unclear. We assume that updater is used primarily from ccp4i, where nothing changed (and why it should be used from command line at all ?:)). The name was changed because it is reserved in Windows, which caused lots of troubles. Now it will stay as is. Eugene On 11 Apr 2013, at 05:16, James Stroud wrote: On Apr 10, 2013, at 9:30 PM, eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk eugene.krissi...@stfc.ac.ukmailto:eugene.krissi...@stfc.ac.uk wrote: No, it got renamed to ccp4um :) That should have been written in update descriptions, was it not? There was only one mention of ccp4um that I could find in all update descriptions that I found (6.3.0-020). I only figured out what information was trying to be communicated because of your message (see attachment). James um-what.png On 11 Apr 2013, at 03:54, James Stroud wrote: Hello All, I downloaded a crispy new version of CCP4 and ran update until the update update script disappeared. Is the reason that CCP4 has reached its final update? James -- Scanned by iCritical.
Re: [ccp4bb] 2Theta data set solving problem
Navin, You mean that you can not PROCESS your data set? What diffraction data processing program are you use? What is your source, goniostat, diffractometer, area detector? FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Apr 9, 2013, at 14:41 , navin narayanan navi...@gmail.com wrote: Hello everybody, We have a diffraction data set from home source with 2theta at 20deg. But we are not able to solve the data set using CCP4 suite. The software is picking up only the lower resolution data but not the higher resolution data points. Also we are not able to merge data two sets, one with 2theta at 0deg and the other with 2theta at 20deg. Is there anyway to solve the data. Any help will be truly appreciated. Thank you in advance. Navin V Narayanan
Re: [ccp4bb] High Rmerge and I/sigma values....?
To support James Holton, MAD Scientist From the very far past: In 60's we have estimated X-ray diffraction data by eyes, using strips of intensities made with propagating exposure factor increase of 2 (I guess in F it corresponds to sqrt(2)~=1.4). We have used to estimate our Weissenberg diffraction data 3 times (we used X-ray films). After 1 time, logbooks were locked in the deposit safe box by our advisers. The second round of estimation we recorded in a different logbook, and it was again locked in the safe deposit box. After 3 time we have punched (binary code) our data on cards, translated to ASCII, checked, corrected, and finally run averaging programs. Our best data were of about 30% Rmerge. However, as for the structure refinement (and maybe some flavours of structure determination) absolute error in a measurement of a single set of symmetry related reflections (precision) is much less important than relative error in measuring of other sets (accuracy), we were able to refine anisotropically small molecule structures to R=5%, because our data were not precise, but accurate. BTW some erroneous 'discoveries' in metalo-organic complexes with non-centrosymmetric space groups were made, based on our inability to measure anomalous signal (it is in the single set of symmetry related reflections), differences were averaged and absolute structure information was lost introducing artificial asymmetry of the coordination sphere. About 20 year later in H. D. Flack (1983). On Enantiomorph-Polarity Estimation, Acta Cryst A39: 876–881, all become clearly explained. To conclude : I am not impressed by very low Rmerge. Once ALL reflections were overexposed on XENTRONIX (which was the area detector with not very good dynamic range), as a result of running after low Rmerge without understanding procedures and instruments to measure diffraction, and Rmerge of 1% was seen, but data were useless. I am not depressed by diffraction data of very high (but correct) Rmerge of 13% with which a structure of important for us protein complex was swiftly solved by SAD (450 residues, 5 Se). The crystals were small; even 10 sec exposure produced relatively weak (but accurate) data. And long live a bending magnet that almost never burn down cryo-maintained crystals! All depends on circumstances My 2 cents... Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Mar 29, 2013, at 20:52 , James Holton jmhol...@lbl.gov wrote: Ahh. But what I'm saying is that Rmeas is not a replacement for Rmerge because Rmeas is _always_ lower than Rmerge. It is even less useful that a low-multiplicity Rmerge for evaluating the diffractometer. I fully realize that Rmeas does have the desirable property of being flatter with respect to multiplicity, but being equally too low for all multiplicity is not better than being too low for some multiplicities. IMHO. Yes, I know, we all like R statistics that are lower. Indeed, by using the mean absolute deviation |I-I|, Uli was able to come up with a definition of Rmerge that will always be lower than the RMS error (for infinite multiplicity and RMS 5% error you actually get Rmerge=3.99%). No doubt, this must have contributed to the acceptance of Rmerge at the time. But we can't just keep re-defining our metric of error every ~20 years so that the same crappy data keeps looking better and better. That's a slippery slope I'd rather not be on. I think it is important to remember what it is we are trying to measure, and to be honest and consistent about what the error bars really are. But that's just my opinion. I could be wrong. -James Holton MAD Scientist On Fri, Mar 29, 2013 at 10:28 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi James, you misquote me: I was saying that Rmeas should be replacing Rmerge, and I guess everything you say holds for Rmeas, too, but still it is a better statistical quantity than Rmerge. So please replace Rmerge with Rmeas. Best, Tim On 03/29/2013 06:08 PM, James Holton wrote: I must disagree with Tim on the statement Rmerge should not be published anymore. That would be a shame. Perhaps even a crime. When Uli Arndt introduced Rmerge he was in no way, shape or form proposing that it be used for resolution cutoffs, or anything else about the quality of the structure. He was, however, trying to define a good statistic to evaluate a diffractometer system, and Rmerge is still VERY useful for that! Any halfway decent modern detector/shutter/beam system should be able to measure reasonably strong spots to within 5% of their true
Re: [ccp4bb] Diffraction data with big rotation angle
Use HKL2000 Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Mar 13, 2013, at 22:12 , Niu Tou niutou2...@gmail.com wrote: Dear colleagues, We have some diffraction data from small peptide crystals, the shape of diffraction spots looks normal, and resolution is beyond 2A. The data were collected with 5 degree rotation per image. Later on we found it is hard to do index. Does anybody know some skills to figure this problem? Best wishes, Niu
Re: [ccp4bb] How to slow down crystallization? Need hep!
a. Go with phase diagram gradually changing concentrations of protein, precipitant, salt concentrations and pH. Find where you are going out of crystallisation. Define region for streak seeding. b. Screen for ratios of precipitant to protein from 1:9 to 9:1. Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Feb 25, 2013, at 18:02 , lei feng spartanfeng...@hotmail.com wrote: Hello everyone, I need your suggestion for slowing down crystallization for my protein my protein got hit in PEG/ION #5 ( 0.2 M MgCl2, 20% PEG 3350, pH 5.9), but it crystallize too fast. In 1 hr I can see tons of tiny needles. Can anyone give me some suggestion on how to slow down the process? I used lower conc. of potein, lower conc. of PEG ( 10%), it helped a little bit, giving me small rod crystal. but no improvement after that. Thank you very much for your suggestions
Re: [ccp4bb] Who invented PDB format?
On Jan 10, 2013, at 18:27 , Teri Arman teriar...@gmail.com wrote: Hi, I appreciate If anybody help me couple of things as follows. (a1) how multiple PDBs (of same or different space groups) can be brought into one frame of coordinates, when dealing with many PDBs? You mean that axes of inertia of the same molecule in the different structures(PDB's) - L,M,N are superimposed? You superimpose… :-) (a2) how does one get scatter plot? Scatter of what? :-0 (b) how easily can symmetry related units of original PDB (with description of which symmetry element has been used) be made when dealing with many PDBs . You have to explain better what are you meaning. :-\ Thank you, Teri Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608
Re: [ccp4bb] Who invented PDB format?
On Jan 11, 2013, at 03:47 , Teri Arman teriar...@gmail.com wrote: Dear Dr. Frolow Thank you for your mail. I stated again, and hope it is clear now. TA. On Fri, Jan 11, 2013 at 4:11 AM, Felix Frolow mbfro...@post.tau.ac.il wrote: On Jan 10, 2013, at 18:27 , Teri Arman teriar...@gmail.com wrote: Hi, I appreciate If anybody help me couple of things as follows. (a1) how multiple PDBs (of same or different space groups) can be brought into one frame of coordinates, when dealing with many PDBs? TA: Suppose we have a segment of structure (PDB). That segment carries different co-ordinates in different PDBs. How can that segment from hundreds of PDBs be converted so that we can see all converted segments in one frame/window I like to avoid superimposition of hundreds of times Most probably superposition or any other transformation could not be avoided. Properly written script will do it for you You mean that axes of inertia of the same molecule in the different structures(PDB's) - L,M,N are superimposed? You superimpose… :-) (a2) how does one get scatter plot? Scatter of what? :-0 TA: Suppose a surrounding neighbours of a segment as said above. (b) how easily can symmetry related units of original PDB (with description of which symmetry element has been used) be made when dealing with many PDBs . Knowing mathematical manipulation of a crystalline space (symmetry operations) one can write a script that will do it easy. You have to explain better what are you meaning. :-\ TA: Each PDB (X-ray structures) has its own space group. I like to generate symmetry related whole PDB or a segment of it in hundreds of PDBs of different space groups Again you will need to write or to get a script that will do it for you. Script (little or larger piece of software written using one of the shell syntaxes or by modern popular languages such as Python or JavaScript) may be written to expand each structure by symmetry producing set of coordinates of interacting molecules (you decide to what distance or to what neighbouring unit cells you wish to expand your structure, after that you teach your script to make multiple superposition of all to all (maybe difficult task) or one to one taking one of the structure as a master structure to which you superimpose others. After that you probably will which to clean this set of coordinates from expanded molecules that you do not need for your research. Again you can do it manually or writing script. . Thank you, Teri Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608
Re: [ccp4bb] About NCS and inhibitors
Why not? They can be mutually excluding! If one is in, the second can be. This phenomenon brakes a local symmetry. FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Jan 7, 2013, at 11:28 , Xiaopeng Hu huxp...@mail.sysu.edu.cn wrote: Dear All, We recently resolved an enzyme/inhibitor complex structure. The enzyme contains two NCS related active site and we did find extra density in both of them.However we observed that the two inhbitor moleculors are not NCS related, but partly overlaped if make a NCS moleculor. Has anyone else observed this before? Thanks for any help and suggestion! Best, Xiaopeng Hu
Re: [ccp4bb] About NCS and inhibitors
I apologise for typing blinbly: if one is in, the second can't be FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Jan 7, 2013, at 11:48 , Felix Frolow mbfro...@post.tau.ac.il wrote: Why not? They can be mutually excluding! If one is in, the second can be. This phenomenon brakes a local symmetry. FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Jan 7, 2013, at 11:28 , Xiaopeng Hu huxp...@mail.sysu.edu.cn wrote: Dear All, We recently resolved an enzyme/inhibitor complex structure. The enzyme contains two NCS related active site and we did find extra density in both of them.However we observed that the two inhbitor moleculors are not NCS related, but partly overlaped if make a NCS moleculor. Has anyone else observed this before? Thanks for any help and suggestion! Best, Xiaopeng Hu
Re: [ccp4bb] Who invented PDB format?
Well, for bioinformatitions the only benefit is that they can calculate distances without going into trigonometric functions. However, angles even in cartesian PDB system will require trigonometry. Fractional coordinates are more difficult, as even distance calculations require trigonometry and normalisation to cell dimensions :-\. This is all difference, no more. And what is nice, that mathematics takes care of all these complications. BTW, I have no problem with going back to fractional coordinates, anyhow all calculations during refinement are in fractional coordinates since BDLS or even Busing and Levy. Is it possible to convert PDB coordinate convention to fractional? : - ) FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 mathematic On Jan 6, 2013, at 10:57 , George Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: Chemical crystallographers have always used fractional coordinates, it makes it so much easier to handle symmetry, special positions etc. But if the PDB hadn't used orthogonal coordinates, bioinformatics might never have taken off. George On 01/06/2013 09:34 AM, Eleanor Dodson wrote: Some of us resisted using an orthogonal format for coordinates, arguing that the output from a crystal structure should refer to crystal axes. And since symmetry was a crystal property it was important that we could see it easily. The PDB format won out, but I still use coordconv a lot to turn back the orthogonalised PDB style to fractional coordinates - to see if this heavy atom solution is the same as that one, given an origin shift, etc etc. Eleanor On 4 Jan 2013, at 20:44, Soisson, Stephen M wrote: -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582
Re: [ccp4bb] Who invented PDB format?
Dear Ian, thank you for enlightening my ignorance! So George, maybe PDB coordinates will be accepted by chemical crystallographers? Doing this also them will develop something as nice as bioinformatics! :-) FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Jan 6, 2013, at 15:01 , Ian Tickle ianj...@gmail.com wrote: ... anyhow all calculations during refinement are in fractional coordinates ... Not necessarily: I can only speak for the RESTRAIN program for restrained refinement that I was involved in developing (the first use of TLS in macromolecular refinement), and at no point were co-ordinates converted to fractional or fractional co-ordinates ever used. All structure factor calculations (and of course the geometric restraints) were done with the original orthogonal co-ordinates read from the PDB file, using the classical structure factor equations (of course more modern programs use FFT for this). Essentially, you can express the phase factor as exp(2 pi i h.(Sr + t)) = exp(2 pi i (H.R + h.t)) where h is the index vector in integers as read from the MTZ file, r is the fractional co-ordinate vector (not needed in the calculation), S and t represent the real-space symmetry operator, H is the orthogonalised rotated reciprocal lattice vector (H~ = h~SB^-1), and R is the orthogonal co-ordinate vector (R = Br). I think this is the most efficient way of organising the calculation provided the outer loops are over symmetry operators and reflections (so H is calculated once) and the inner loop is over co-ordinates. Of course I accept that using FFT via the electron density is a much more efficient way but I think even then no conversion to fractional is necessary. Cheers -- Ian
Re: [ccp4bb] Who invented PDB format?
### ### ### ### CCP4 6.3: COORDCONVversion 6.3 : 17/09/08## ### User: mbfrolow Run date: 7/ 1/2013 Run time: 08:50:16 will help you FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Jan 7, 2013, at 07:48 , Teri Arman teriar...@gmail.com wrote: Fractional Coordiantes to Orthogonal Coordinates and Vice Versa Hi, I need help, how can I make coordiates of 100 of PDBs of different space groups to fractional coordiantes and vice versa. I do not find CCP4 do it? A program of fortran or C codes with possible suggestion may be helpful. Thank you. TA On Sun, Jan 6, 2013 at 2:27 PM, George Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: Chemical crystallographers have always used fractional coordinates, it makes it so much easier to handle symmetry, special positions etc. But if the PDB hadn't used orthogonal coordinates, bioinformatics might never have taken off. George On 01/06/2013 09:34 AM, Eleanor Dodson wrote: Some of us resisted using an orthogonal format for coordinates, arguing that the output from a crystal structure should refer to crystal axes. And since symmetry was a crystal property it was important that we could see it easily. The PDB format won out, but I still use coordconv a lot to turn back the orthogonalised PDB style to fractional coordinates - to see if this heavy atom solution is the same as that one, given an origin shift, etc etc. Eleanor On 4 Jan 2013, at 20:44, Soisson, Stephen M wrote: -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582
Re: [ccp4bb] SeCys usage for SAD
Dear Linda, If your molecule is not very big, your cell is not very big, you have an approach to modern in-house X-ray facility, your crystal diffract reasonably well ( :-\ ) you can try S phasing. If you will be able to measure accurate data, S anomalous phasing at 1.5417 Angstrom of Cu radiation may work like charm (it is usually a case in my hands). In addition, if it happened that you have also couple of Cl etc. it will support phasing even more. I prefer to test S-SAD cases with shelxC/D/E pipeline under HKL2MAP GUI. Happy holidays FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Dec 26, 2012, at 20:33 , Linda Olson lol...@mcw.edu wrote: Dear All, I have read a recent paper by Salgado et al about using non-auxotrophic E.coli to incorporate SeCys into recombinant protein for phasing purposes. Does anyone have a source for Selenocysteine? I have also seen a paper by Schaefer et al which uses nitric acid treated elemental Se for a sulfur surrogate to generate Se-labeled protein. Has anyone else tried this? My proteins are rich in Cys and tend to lack Met so the prospect of labeling cys is very attractive. Thanks, Linda Linda Olson, PhD Research Scientist II Dept Biochemistry Medical College of Wisconsin 8701 Watertown Plank Rd Milwaukee, WI 53226 phone: 414-955-8545 fax: 414-456-6510 _
Re: [ccp4bb] refining against weak data and Table I stats
James, thank you for taking time to write this nice essay. I only hope that your evaluation of possibility of cutting data to I/sigmaI = 3 is for EXHIBITION PURPOSE ONLY and not for the refinement or for the calculation of electron density maps. After all, what we see on the electron density maps is important and not any single number qualifiers :-) Do not believe in a single number qualifier, or, for that matter, in anything else! - Attributed to Vladimir Prelog by Jack Dunitz Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Dec 13, 2012, at 08:52 , James Holton jmhol...@lbl.gov wrote: I think CC* (derived from CC1/2) is an important step forward in how to decide where to cut off the data you give to your refinement program, but I don't think it is a good idea to re-define what we call the resolution of a structure. These do NOT have to be the same thing! Remember, what we crystallographers call resolution is actually about 3x the resolution a normal person would use. That is, for most types of imaging whether it be 2D (pictures of Mars) or 3D (such as electron density) the resolution is the minimum feature size you can reliably detect in the image. This definition of resolution makes intuitive sense, especially to non-crystallographers. It is also considerably less pessimistic than our current definition since the minimum observable feature size in an electron density map is about 1/3 of the d-spacing of the highest-angle spots. This is basically because the d-spacing is the period of a sine wave in space, but the minimum feature size is related to the full-width at half max of this same wave. So, all you have to do is change your definition of resolution and a 3.0 A structure becomes a 1.0 A structure! However, I think proposing this new way to define resolution in crystallography will be met with some resistance. Why? Because changing the meaning of resolution so drastically after ~100 years would be devastating to its usefulness in structure evaluation. I, for one, do not want to have to check the deposition date and see if the structure was solved before or after the end of the world (Dec 2012) before I can figure out whether or not I need to divide or multiply by 3 to get the real resolution of the structure. I don't think I'm alone in this. Now, calling what used to be a 1.6 A structure a 1.42 A structure (one way to interpret Karplus Diederichs 2012) is not quite as drastic a change as the one I flippantly propose above, but it is still a change, and there is a real danger of definition creep here. Most people these days seem to define the resolution limit of their data at the point where the merged I/sigma(I) drops below 2. However, using CC* = 0.5 would place the new resolution at the point where merged I/sigma(I) drops below 0.5. That's definitely going beyond what anyone would have called the resolution of the structure last year. So, which one is it? Is it a 1.6 A structure (refined using data out to 1.42 A), or is it actually a 1.42 A structure? Unfortunately, if you talk to a number of experienced crystallographers, they will each have a slightly different set of rules for defining the resolution limit that they learned from their thesis advisor, who, in turn, learned it from theirs, etc. Nearly all of these rule sets include some reference to Rmerge, but the acceptable Rmerge seems to vary from 30% to as much as 150%, depending on whom you talk to. However, despite this prevalence of Rmerge in our perception of resolution there does not seem to be a single publication anywhere in the literature that recommends the use of Rmerge to define the resolution limit. Several papers have been cited to that effect, but then if you go and read them they actually made no such claim. Mathematically, it is fairly easy to show that Rmerge is wildly unstable as the average intensity approaches zero, so how did we get stuck on it as a criterion for evaluating the outer resolution bin? I'm not really sure, but I think it must have happened around 1995. Before that, there are NO entries for Rmerge in the high-resolution bin in the PDB. Not one. Looking at papers from the pre-1995 era, you don't see it reported in table 1 either. What is more, ever since 1995, the average reported Rmerge in the high-resolution shell has been slowly rising by about 1.6 percentage points each year. Started around 20%, and now it is up to 50%. Seriously. Here is the graph: http://bl831.als.lbl.gov/~jamesh/pickup/outershell_Rmerge.png I think this could be yet another example of definition creep. For any given year, I imagine a high
Re: [ccp4bb] hkl2000 install
a. What operation system your notebook is running? b. There is no version of HKL2000 for Windows. c. Move to 17 laptop with larger resolution d. You will need special HKL2000 licence for the laptop FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 19, 2012, at 03:48 , 王瑞 wangrui...@gmail.com wrote: OK,thank you all of you. I have installed one copy of HKL2000 on our desktop computer. But for my notebook's low 1366*768 resolution, the HKL2000 can't work ! So what could I do to resolve it ? 2012/11/13 王瑞 wangrui...@gmail.com: Dear everyone: I have got the returned cr_info.dat to /usr/local/lib and /usr/local/hklint,when I typing HKL2000,it still display: dell@ubuntu:~$ HKL2000 ERROR: Not a valid HKL-2000 license: Licence info file (cr_info) not found Error code: -1 So could anyone can help me ? 2012/11/9 王瑞 wangrui...@gmail.com: Dear everyone: I'm sorry for a little off-topic! I want to install HKL2000 on ubuntu11.10 32bits, but it produces a file named info not cr_info after run the access_prod program.And when I put info to /usr/local/lib directory and typingHKL2000 in terminal, it display: root@ubuntu:/usr/local/bin# HKL2000 ERROR: Not a valid HKL-2000 license: Licence info file (cr_info) not found Error code: -1 So could anyone tell me how to do it ? Rui Wang
Re: [ccp4bb] diffraction protein or salt
Sorry to disappoint you. It is a diffraction pattern from crystals of salt. Spending some time it is possible to check of which :-\ FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 13, 2012, at 12:17 , George gkontopi...@vet.uth.gr wrote: Dear colleagues, There are some crystallographers with (much) more experience than me. I ‘ve attached few diffraction images which are not (in my opinion) typical salt but not typical protein either. Please let me know you suggestions. Is it worth investigating further those conditions or there are just salts crystals with large unit cell. Attached files: Crystal.jpg (Photo of crystal) dif_0.jpg (Diffraction 900 sec exposure/degree at 0 degrees) dif_90.jpg (Diffraction 900 sec exposure/degree at 90 degrees) dif_180.jpg (Diffraction 900 sec exposure/degree at 180 degrees) dif_270.jpg (Diffraction 900 sec exposure/degree at 270 degrees) protein: 3.3mg/ml in 20 mM TrisHCl pH 8, 150 mM NaCl, 5 mM DTT. Mother liquor: 28%Jefamine, 0,05mM Li2SO4, 10mM Tris pH 8.0 sitting drops, 1.2ul protein / 1.2ul mother liquor. Thanks in advance for your help, George Kontopidis From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von Delft Sent: Tuesday, November 13, 2012 8:56 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Reservoir buffer Acta Cryst. (2005). D61, 490-493[ doi:10.1107/S0907444905002726 ] Expanding screening space through the use of alternative reservoirs in vapor-diffusion experiments J. Newman Abstract: Setting up vapor-diffusion crystallization experiments against four different reservoir solutions showed that the reservoir solution may have a profound effect on the outcome of a crystallization experiment. This suggests that a facile way to increase crystallization space through screening is not to add more crystallization conditions to the process, but to set up the same conditions over different reservoirs. On 13/11/2012 06:03, Theresa Hsu wrote: Dear all In *initial screening* using vapor diffusion crystallization, does it matter whether the reservoir buffer is also the precipitant in the drop or just a high salt solution like 5 M NaCl? Thank you. Theresa Crystal.jpgdif_0.jpgdif_90.jpgdif_180.jpgdif_270.jpg
Re: [ccp4bb] diffraction protein or salt
Ganesh!!! NO WAY !!! FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 13, 2012, at 12:40 , Ganesh Natrajan ganesh.natra...@ibs.fr wrote: Hi, First I'm sorry for my blank message earlier. Doesn't this depend on the oscillation angle? If those images were collected using 0 to 1° oscillations, I would assume he has a badly diffracting protein crystal. Ganesh Le 13/11/12 11:34, Tim Gruene a écrit : -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear George, the images don't look like a large cell to me: on the first image you can see spots from ice rings at about 4A and there are only very few spots inside that radius, all of which are at beyond 5A. I'd say there are traces of MgS04 or CaSO4, the Ca or Mg being left-overs from the expression media. Regards, Timd On 11/13/2012 11:17 AM, George wrote: Dear colleagues, There are some crystallographers with (much) more experience than me. I ‘ve attached few diffraction images which are not (in my opinion) typical salt but not typical protein either. Please let me know you suggestions. Is it worth investigating further those conditions or there are just salts crystals with large unit cell. Attached files: Crystal.jpg (Photo of crystal) dif_0.jpg (Diffraction 900 sec exposure/degree at 0 degrees) dif_90.jpg (Diffraction 900 sec exposure/degree at 90 degrees) dif_180.jpg (Diffraction 900 sec exposure/degree at 180 degrees) dif_270.jpg (Diffraction 900 sec exposure/degree at 270 degrees) protein: 3.3mg/ml in 20 mM TrisHCl pH 8, 150 mM NaCl, 5 mM DTT. Mother liquor: 28%Jefamine, 0,05mM Li2SO4, 10mM Tris pH 8.0 sitting drops, 1.2ul protein / 1.2ul mother liquor. Thanks in advance for your help, George Kontopidis From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von Delft Sent: Tuesday, November 13, 2012 8:56 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Reservoir buffer Acta Cryst. (2005). D61, 490-493[ doi:10.1107/S0907444905002726 http://dx.doi.org/10.1107/S0907444905002726 ] Expanding screening space through the use of alternative reservoirs in vapor-diffusion experiments J. Newman http://scripts.iucr.org/cgi-bin/citedin?search_on=nameauthor_name=Newman,%20J. Abstract: Setting up vapor-diffusion crystallization experiments against four different reservoir solutions showed that the reservoir solution may have a profound effect on the outcome of a crystallization experiment. This suggests that a facile way to increase crystallization space through screening is not to add more crystallization conditions to the process, but to set up the same conditions over different reservoirs. On 13/11/2012 06:03, Theresa Hsu wrote: Dear all In *initial screening* using vapor diffusion crystallization, does it matter whether the reservoir buffer is also the precipitant in the drop or just a high salt solution like 5 M NaCl? Thank you. Theresa - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQoiIZUxlJ7aRr7hoRAlOtAKD9vm5OgG/GH/SMXv4LwTybKnlU3gCghuVH dFhZk5C5gK3fjVG1z00+jzw= =VN4A -END PGP SIGNATURE-
Re: [ccp4bb] hkl2000 install
cr_info can be in several places ~/ (user home directory) working directory /usr/local/lib ( This is the place where I keep it as it is a consensus location for cr_info) about /usr/local/hklint I am not sure, but if you say so, you probably know :-) FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 13, 2012, at 18:12 , Dmitry Rodionov d.rodio...@gmail.com wrote: I believe cr_info should go in /usr/local/hklint along with site files. It does not have to be executable but must be readable by all. (chmod a+r cr_info) Regards, Dmitry Rodionov On 2012-11-13, at 12:33 AM, 王瑞 wrote: Dear everyone: I have got the returned cr_info.dat to /usr/local/lib and /usr/local/hklint,when I typing HKL2000,it still display: dell@ubuntu:~$ HKL2000 ERROR: Not a valid HKL-2000 license: Licence info file (cr_info) not found Error code: -1 So could anyone can help me ? 2012/11/9 王瑞 wangrui...@gmail.com: Dear everyone: I'm sorry for a little off-topic! I want to install HKL2000 on ubuntu11.10 32bits, but it produces a file named info not cr_info after run the access_prod program.And when I put info to /usr/local/lib directory and typingHKL2000 in terminal, it display: root@ubuntu:/usr/local/bin# HKL2000 ERROR: Not a valid HKL-2000 license: Licence info file (cr_info) not found Error code: -1 So could anyone tell me how to do it ? Rui Wang
Re: [ccp4bb] Glass Capillaries
Light glasses such as borosilicate. Can be purchased from Hampton research. FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 12, 2012, at 18:13 , Michael Roberts mrobert...@talktalk.net wrote: Dear All, I would be interested to learn of other crystallographers' experience in their use of glass capillaries for protein crystal growth and X-ray diffraction clarity. There are many types of glass available - quartz, soda glass, borosilicate, etc. Are there specific types which people prefer for best results overall? Best wishes, Michael Roberts
Re: [ccp4bb] Glass Capillaries
Traditional crystallography is difficult to practice, unless you know mathematics, physics, chemistry, computing etc….. :-) If one need to make science with room temperature diffraction, there is know substitution to old type glass capillaries that can be properly sealed :-\ FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 12, 2012, at 19:00 , Nian Huang huangn...@gmail.com wrote: Hi Michael, I would recommend an alternative http://www.mitegen.com/products/micrort/micrort.shtml Traditional capillary is a pain to handle, unless you have a rock sized crystal. Good luck, Nian Huang On Mon, Nov 12, 2012 at 11:13 AM, Michael Roberts mrobert...@talktalk.net wrote: Dear All, I would be interested to learn of other crystallographers' experience in their use of glass capillaries for protein crystal growth and X-ray diffraction clarity. There are many types of glass available - quartz, soda glass, borosilicate, etc. Are there specific types which people prefer for best results overall? Best wishes, Michael Roberts
Re: [ccp4bb] Glass Capillaries
I apologise for typing in dark. That is why know substitute no :-\ Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 12, 2012, at 19:05 , Felix Frolow mbfro...@post.tau.ac.il wrote: Traditional crystallography is difficult to practice, unless you know mathematics, physics, chemistry, computing etc….. :-) If one need to make science with room temperature diffraction, there is know substitution to old type glass capillaries that can be properly sealed :-\ FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 12, 2012, at 19:00 , Nian Huang huangn...@gmail.com wrote: Hi Michael, I would recommend an alternative http://www.mitegen.com/products/micrort/micrort.shtml Traditional capillary is a pain to handle, unless you have a rock sized crystal. Good luck, Nian Huang On Mon, Nov 12, 2012 at 11:13 AM, Michael Roberts mrobert...@talktalk.net wrote: Dear All, I would be interested to learn of other crystallographers' experience in their use of glass capillaries for protein crystal growth and X-ray diffraction clarity. There are many types of glass available - quartz, soda glass, borosilicate, etc. Are there specific types which people prefer for best results overall? Best wishes, Michael Roberts
Re: [ccp4bb] hkl2000 install
It should be called cr_info you have to : sudo chmod +x cr_info in the directory were it is, I think it should be executable try to activate HKL2000 first of all from there : cd /usr/local/lib HKL2000 FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 13, 2012, at 07:33 , 王瑞 wangrui...@gmail.com wrote: Dear everyone: I have got the returned cr_info.dat to /usr/local/lib and /usr/local/hklint,when I typing HKL2000,it still display: dell@ubuntu:~$ HKL2000 ERROR: Not a valid HKL-2000 license: Licence info file (cr_info) not found Error code: -1 So could anyone can help me ? 2012/11/9 王瑞 wangrui...@gmail.com: Dear everyone: I'm sorry for a little off-topic! I want to install HKL2000 on ubuntu11.10 32bits, but it produces a file named info not cr_info after run the access_prod program.And when I put info to /usr/local/lib directory and typingHKL2000 in terminal, it display: root@ubuntu:/usr/local/bin# HKL2000 ERROR: Not a valid HKL-2000 license: Licence info file (cr_info) not found Error code: -1 So could anyone tell me how to do it ? Rui Wang
Re: [ccp4bb] Reservoir buffer
You should and can try, but I guess 5 M NaCl will dry your drop quite fast, unless in your drop NaCl concentration is ~2,5 M :-) That is why first mixture of well and protein solution is 1:1 v/v. Other variations such as 1:9, 9:1 etc sometimes help. Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 13, 2012, at 08:03 , Theresa Hsu theresah...@live.com wrote: Dear all In *initial screening* using vapor diffusion crystallization, does it matter whether the reservoir buffer is also the precipitant in the drop or just a high salt solution like 5 M NaCl? Thank you. Theresa
Re: [ccp4bb] hkl2000 install
info is send to HKL.com to get cr_info if you have a legal version FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 9, 2012, at 12:37 , 王瑞 wangrui...@gmail.com wrote: Dear everyone: I'm sorry for a little off-topic! I want to install HKL2000 on ubuntu11.10 32bits, but it produces a file named info not cr_info after run the access_prod program.And when I put info to /usr/local/lib directory and typingHKL2000 in terminal, it display: root@ubuntu:/usr/local/bin# HKL2000 ERROR: Not a valid HKL-2000 license: Licence info file (cr_info) not found Error code: -1 So could anyone tell me how to do it ? Rui Wang
Re: [ccp4bb] low-resolution and zinc
What program do you use for refinement? FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 9, 2012, at 20:09 , SD Y ccp4...@hotmail.com wrote: Dear All, Thanks for all the suggestions on low resolution, SG and Zn and I learned a lot. I am not done yet. I am trying model co-ordinated ZN+2. I got lot of help from Prof. Roger Rowlett. Also an excellent protocol is available at http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Model+Refinement. Protocol seems to be very straight forward. I am not getting the result I wanted. 1. When ever I generate cif file, its not writing any for ZN-SG links at all. 2. After refmac refinement it only draw in LINK for His-ZN. Please see the images https://www.dropbox.com/s/7sl01pcdmxxcu2z/ZN-cpoordination-1.png https://www.dropbox.com/s/cxlp2m2stbple02/ZN-cpoordination-2.png 3. I get this His-Zn link without using .cif file, so what stage do I use this .cif file? 4. Though cysteines were placed around 2.2 - 2.5 A from ZN, its not writing LINK in PDB. I only see LINKR ZNZN H 1 SG CYS A 83ZN-CYS I dont know what is missing, I also attached the log file which generated the ZN-His coordination. Any help is highly appreciated. Thanks SDY Date: Thu, 8 Nov 2012 14:36:59 +0200 From: mbfro...@post.tau.ac.il Subject: Re: [ccp4bb] low-resolution and zinc To: CCP4BB@JISCMAIL.AC.UK The experiment should be very problematic if I can't determine point group on the base of the symmetry merging statistics. Watch CHI2 :-) Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 8, 2012, at 14:29 , herman.schreu...@sanofi.com wrote: Then we agree. I got confused because you mentionedspace group and not point group in your phrase about PHASER and MOLREP and was afraid others might have gotten confused as well. Also, in case of twinning or almost crystallographic non-crystallographic symmetry, determining the point group on the basis of processing statistics alone can be inconclusive or even misleading. If I recall correctly, there has recently been a thread about this in the bulletin board. Herman 74_refmac5_1.log
Re: [ccp4bb] low-resolution and zinc
I do not see with what you do not agree in what was written (maybe not very carefully). One determine space group looking on systematic absences, this I know. Space groups P41 - P43 ( I do not go to more general discussion for the sake of argument) are not distinguishable and one have to try molecular replacement in both. Most probably the correct space group will give a sensible solution and wrong one will not. I was talking about distinguishing between point groups P4 and P422. I hope you grew that they CAN be distinguished on the level prior to molecular replacement? And I hope that you agree that starting refinement of demanding project at relatively low resolution such as 3.4 Angstrom it is advisable to characterise space group, twinning status etc.? If you agree also to that, with what you do not agree? FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 8, 2012, at 12:20 , herman.schreu...@sanofi.com wrote: Dear Dr. Frolow, I do not agree. In the absence of heavy atom/anomalous data, the only way to distinguish e.g. between P41 and P43 is with molecular replacement. On could do it automatically, like is implemented in modern programs, or run MR in different space groups manually, but one has to test the various possibilities. Herman From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Felix Frolow Sent: Thursday, November 08, 2012 10:36 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] low-resolution and zinc Yogi, I was not mentioning MY book, it is not written yet :-) Zn an Ca are different element. Zn is transition element 24'th most abundant on earth, and Ca is alkaline element 5 most abundant on earth. But in the case of affinity to very strong binding site they behave similarly - they are picked by the molecule from the surrounding even if they are present in very low concentrations. Beeng in your position I will stop refinement and will take time to define space group properly. Difference P43 and P43212 (forget about screw axes - the point groups are important - P4 or P422) MUST be visible during data processing. If you did not inherited your data from the source going back in time and collected them (data) by yourself, difference between merging your data in P4 or P422 will be VERY visible. If the difference between them is negligible ( Rmerge factors say 0.04 in one case and 0.05 in another) you have space group P422 (or merohedral twinning in P4, I can't think clearly in this time of the day if such twinning is possible). If your space group is P4 and you try to merge it in space group P422, your Rmerge will be 0.4 -0.5. Generally, elegant practice of crystallography does not require determination of the space group using PHASER or MOLREP :-\ These facilities were inserted into molecular replacement programs for younger generation who come to protein crystallography with 0 (zero) of mathematics and physics and are surrounded by similar flock. In the moment you will know what your space group is and you will know if the twinning is present, you can concentrate only on refinement. In your case (3.4 Angstrom resolution) you will find DEN extremely useful. FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 8, 2012, at 05:27 , SD Y ccp4...@hotmail.com wrote: Dear Prof. Frolow, Our library has that book and I will look read it. I will also look in to your book too. I haven't been able to differentiate between P43 and P43 21 2, all refining results in similar numbers. P43 is slightly better with R work/Rfree is 30.5/37%. But its stuck there. I have built everything except Zn co-ordination. I will read your chapters to learn about SG. I understand that Zn is same as Ca as you are suggesting. I will also follow the other suggestion you have made regarding Anomolous signal. I sincerely appreciate your time and help which I was very much in need of. Thanks Yogi From: mbfro...@post.tau.ac.il Subject: Re: [ccp4bb] low-resolution and zinc Date: Wed, 7 Nov 2012 23:35:35 +0200 To: ccp4...@hotmail.com It is THE BOOK published in 1976! There is a chapter about determination of a space group (actually speaking enantiomeric space groups such as P3121 or P3112). But it can be expanded to anything, as in Blandell (and mine) times we have used to take so called presses ion phortographs from which the space groups where easily and swiftly
Re: [ccp4bb] low-resolution and zinc
The experiment should be very problematic if I can't determine point group on the base of the symmetry merging statistics. Watch CHI2 :-) Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 8, 2012, at 14:29 , herman.schreu...@sanofi.com wrote: Then we agree. I got confused because you mentionedspace group and not point group in your phrase about PHASER and MOLREP and was afraid others might have gotten confused as well. Also, in case of twinning or almost crystallographic non-crystallographic symmetry, determining the point group on the basis of processing statistics alone can be inconclusive or even misleading. If I recall correctly, there has recently been a thread about this in the bulletin board. Herman From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Felix Frolow Sent: Thursday, November 08, 2012 1:14 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] low-resolution and zinc I do not see with what you do not agree in what was written (maybe not very carefully). One determine space group looking on systematic absences, this I know. Space groups P41 - P43 ( I do not go to more general discussion for the sake of argument) are not distinguishable and one have to try molecular replacement in both. Most probably the correct space group will give a sensible solution and wrong one will not. I was talking about distinguishing between point groups P4 and P422. I hope you grew that they CAN be distinguished on the level prior to molecular replacement? And I hope that you agree that starting refinement of demanding project at relatively low resolution such as 3.4 Angstrom it is advisable to characterise space group, twinning status etc.? If you agree also to that, with what you do not agree? FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 8, 2012, at 12:20 , herman.schreu...@sanofi.com wrote: Dear Dr. Frolow, I do not agree. In the absence of heavy atom/anomalous data, the only way to distinguish e.g. between P41 and P43 is with molecular replacement. On could do it automatically, like is implemented in modern programs, or run MR in different space groups manually, but one has to test the various possibilities. Herman From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Felix Frolow Sent: Thursday, November 08, 2012 10:36 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] low-resolution and zinc Yogi, I was not mentioning MY book, it is not written yet :-) Zn an Ca are different element. Zn is transition element 24'th most abundant on earth, and Ca is alkaline element 5 most abundant on earth. But in the case of affinity to very strong binding site they behave similarly - they are picked by the molecule from the surrounding even if they are present in very low concentrations. Beeng in your position I will stop refinement and will take time to define space group properly. Difference P43 and P43212 (forget about screw axes - the point groups are important - P4 or P422) MUST be visible during data processing. If you did not inherited your data from the source going back in time and collected them (data) by yourself, difference between merging your data in P4 or P422 will be VERY visible. If the difference between them is negligible ( Rmerge factors say 0.04 in one case and 0.05 in another) you have space group P422 (or merohedral twinning in P4, I can't think clearly in this time of the day if such twinning is possible). If your space group is P4 and you try to merge it in space group P422, your Rmerge will be 0.4 -0.5. Generally, elegant practice of crystallography does not require determination of the space group using PHASER or MOLREP :-\ These facilities were inserted into molecular replacement programs for younger generation who come to protein crystallography with 0 (zero) of mathematics and physics and are surrounded by similar flock. In the moment you will know what your space group is and you will know if the twinning is present, you can concentrate only on refinement. In your case (3.4 Angstrom resolution) you will find DEN extremely useful. FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640
Re: [ccp4bb] low-resolution and zinc
As far as sigma level is concerned, and if I remember that you are working at 3.4 angstrom resolution - this 6 sigma is VERY STRONG. I am sure it is a metal atom. But you can re-process your data preserving anomalous signal and calcule anomalous map easily done in PHENIX, less so in CCP4 and then displaying anomalous map as a difference map in COOT you MUST see strong peak on this map in the heavy atom location. Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 7, 2012, at 20:13 , SD Y ccp4...@hotmail.com wrote: Dear Prof. Frolow, During sample development I have not used anything related to Zn but could be from traces of contamination from Tris, NaCl, DTT, EDTA, LiSO4, HEPES and other salt which were part of auto induction media. I am trying to search the refence in google. Are you refering to the Book published in 1976 titled protein crystallography, if not could you please kindly direct me to right reference. I sincerely appreciate your time and suggestion. Warm reagrds, SDY From: mbfro...@post.tau.ac.il Subject: Re: [ccp4bb] low-resolution and zinc Date: Wed, 7 Nov 2012 19:35:21 +0200 To: ccp4...@hotmail.com Zn is always there as anything else. If you have high affinity binding site, it will be filled with Zn (or similar) on the various stages of your sample development. BTW use old BlandellJohnson popular in my time (70-90's) approach - in the correct space group the peak hight of this heavy atom will be the highest comparing to other space groups FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 7, 2012, at 19:29 , SD Y ccp4...@hotmail.com wrote: Dear all, I have a related question to the one I have posted low resolution and SG, on which I am still working based on the suggestions I have got. The model I have used, has Zn co-ordinated well in tetrahydral fashion by 3 cys and 1 His residues. They have add Zn in to their experiment. In my 3.4 A structure (I am still working on right SG), initial maps show very strong positive density (sigma=6.5) at the place of Zn ( https://www.dropbox.com/s/4jd6gdor87ab9lj/Zn-coordination.png). I have not used Zn in my experiment. I could only suspect Tryptone and yeast extract which I used to make media. I would like to know how likely this positive density belongs to Zn? How to reason the presence of Zn when its not been used? Is there is any way to confirm if its Zn. If this is not Zn, what else could it be? Any thing I could try to rule out or in Zn or other ions. I appreciate your help and suggestions. Sincerely, SDY
Re: [ccp4bb] low-resolution and zinc
Well, galvanised iron is an old story of Zn in insuline… :-\ Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 7, 2012, at 23:58 , Katherine Sippel katherine.sip...@gmail.com wrote: As a follow up to Roger's statement if you are doing any sort of analytical metal analysis be careful with the controls (metal-free water/acid washed glassware). Also most AC/heating systems include galvanized steel in the duct work that spits out Zn like crazy and can screw up your measurements. If you have access to a neurotically OCD analytical chemist to assist I'd suggest plying them with coffee and complements. Cheers, Katherine On Wed, Nov 7, 2012 at 3:41 PM, Felix Frolow mbfro...@post.tau.ac.il wrote: As far as sigma level is concerned, and if I remember that you are working at 3.4 angstrom resolution - this 6 sigma is VERY STRONG. I am sure it is a metal atom. But you can re-process your data preserving anomalous signal and calcule anomalous map easily done in PHENIX, less so in CCP4 and then displaying anomalous map as a difference map in COOT you MUST see strong peak on this map in the heavy atom location. Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 7, 2012, at 20:13 , SD Y ccp4...@hotmail.com wrote: Dear Prof. Frolow, During sample development I have not used anything related to Zn but could be from traces of contamination from Tris, NaCl, DTT, EDTA, LiSO4, HEPES and other salt which were part of auto induction media. I am trying to search the refence in google. Are you refering to the Book published in 1976 titled protein crystallography, if not could you please kindly direct me to right reference. I sincerely appreciate your time and suggestion. Warm reagrds, SDY From: mbfro...@post.tau.ac.il Subject: Re: [ccp4bb] low-resolution and zinc Date: Wed, 7 Nov 2012 19:35:21 +0200 To: ccp4...@hotmail.com Zn is always there as anything else. If you have high affinity binding site, it will be filled with Zn (or similar) on the various stages of your sample development. BTW use old BlandellJohnson popular in my time (70-90's) approach - in the correct space group the peak hight of this heavy atom will be the highest comparing to other space groups FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 7, 2012, at 19:29 , SD Y ccp4...@hotmail.com wrote: Dear all, I have a related question to the one I have posted low resolution and SG, on which I am still working based on the suggestions I have got. The model I have used, has Zn co-ordinated well in tetrahydral fashion by 3 cys and 1 His residues. They have add Zn in to their experiment. In my 3.4 A structure (I am still working on right SG), initial maps show very strong positive density (sigma=6.5) at the place of Zn ( https://www.dropbox.com/s/4jd6gdor87ab9lj/Zn-coordination.png). I have not used Zn in my experiment. I could only suspect Tryptone and yeast extract which I used to make media. I would like to know how likely this positive density belongs to Zn? How to reason the presence of Zn when its not been used? Is there is any way to confirm if its Zn. If this is not Zn, what else could it be? Any thing I could try to rule out or in Zn or other ions. I appreciate your help and suggestions. Sincerely, SDY
Re: [ccp4bb] What to put on Custom Declaration for shipped samples?
Jim, dottore... Starting back traveling to synchrotrons in the beginning of 80 I say, do not volunteer information, more magic words you say, more papers you fetch, more faxes you send in advance more they will torture you. You do not need custom declaration anywhere (at least in Europe), in states I would drive We have send a fax with a full description of Polaroid 3000ASA in 1992 in Heathrow, and they ( security, I was ready to take them apart) burn these sensitive films on the purpose by X-rays on our way to Photon Factory. Many years after that in 2008, one of these people (I have very good memory) again in Heathrow told me - you have two choices - either irradiation or invasive check, and we will not be gentle. I choose irradiation. I will met him next time in a bar or a pub and will take very nice care of him :-) DO NOT VOLUNTEER INFORMATION, IT WILL BE AGAINST YOU…. If it is written non-infectious, they will read infectious, you will write non-hazardous - they will read hazardous, you will say lysozyme - they will read anthrax…. And the most terrible thing for you will be if they will apply frontal check, not selection which you may snick, but total check. Just go forward, take another person with you, takes doubles, go to different check-in points, system is working sporadically, increase your chance by multiplication FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 6, 2012, at 22:25 , Jim Pflugrath jim.pflugr...@rigaku.com wrote: I was asked by our shipping folks what we should put on the Customs Declaration so that samples that we ship or that are shipped to us (in dewars, styrofoam boxes, and/or padded envelopes) would not be held up in Customs. I had them put: Scientific samples of less than 1 mg of non-infectious, non-hazardous protein. No health hazard. but it has been so long that I have had to do so. I suppose I could name the exact protein, (e.g. hen egg white lysozyme), but maybe that is not a good idea. What wording do folks put on these forms nowadays? What works? Do I need to put the buffer components? Thanks for responses. Jim
Re: [ccp4bb] Weird electron density on the two-fold axis
As only small part of the molecules is shown and it appears to be in poly-alanine representation, more interesting thing may happened apart of numerical instabilities of Fourier transform. These can be mutually exclusive conformations that brake local symmetry but preserve overall symmetry. The alts penetrate forbidden region of the symmetry, but only from one molecule. I have seen such things. BTW what program was used to calculate maps? FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 5, 2012, at 12:22 , Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Shutong Xu, one often finds artefacts on special positions. As far as I understand, these are numerical 'instabilities' or artefacts rather than of chemical origin. Best, Tim On 11/05/2012 10:50 AM, Crystal Xu wrote: Dear all, I am now determining a structure at 2.2 A resolution. The space group is C2, and there is only one molecular in an ASU. During the refinement, some weird electron density appears right on the two-fold axis. Does anyone have any idea what could this be? Thanks a lot. Best regards Shutong Xu - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQl5NkUxlJ7aRr7hoRAkUtAKC/6mrt5LdcG9bjZm3rN6UfDzpotQCg7B20 WknHYPcUECMxk//k9zKjiqE= =WCPn -END PGP SIGNATURE-
Re: [ccp4bb] Professor Dame Louise Johnson
As a devoted reader of the Protein Crystallography - the first and only comprehensive manual of the protein crystallography, I express my deep sorrow on the departure from us of DBE Commander, Professor Louise Johnson. May her soul rest in peace. In full honor, Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Oct 2, 2012, at 20:45 , Laurie Betts wrote: What a great lady to have inspired so many, and to remind us how welcoming the field of X-ray crystallography has been in general for women because of people like Dr. Johnson, Dorothy Hodgkin, and Rosalind Franklin, and many others. On Tue, Oct 2, 2012 at 12:03 PM, Gloria Borgstahl gborgst...@gmail.com wrote: This indeed is sad news for today. I just wanted to note that Professor Johnson's early papers on time-resolved crystallography truly inspired me to continue in crystallography, influenced my decision for my first postdoctoral position and to push the limits. I still have the carefully highlighted photocopies (yes used a photocopier and a real bound journal in gradual school) in my filing cabinet next to my office. My condolences to those close to her and her family. Gloria On Tue, Oct 2, 2012 at 6:40 AM, elizabeth.d...@diamond.ac.uk wrote: It is with great sadness that I would like to inform the crystallographic community of the death of one of the great pioneers of the field, Professor Dame Louise Johnson. Those of us who had the privilege to work alongside her benefitted greatly from her vision for extending technique and instrumentation such that increasingly complex problems could be successfully solved and found her quiet determination to succeed inspirational. Dr. Liz Duke Diamond Light Source Harwell Science and Innovation Campus Chilton, Didcot Oxon OX11 0DE UK Tel. +44 (0) 1235 778057 Mob. +44 (0)7920 138148 -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
Re: [ccp4bb] CCP4 Update
EXCELLENT !!! Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Sep 6, 2012, at 19:00 , eugene.krissi...@stfc.ac.uk wrote: Dear CCP4 Users, Following the release of ccp4 6.3.0, CCP4 core team sets up an update mechanism for moderate modifications of Suite's components between the releases. It is expected that updates will be essential for CCP4 maintenance and will make patch releases less frequent or even redundant, while delivering bug fixes and new features much more efficiently than before. Please take a moment to install CCP4 update functionality as described below. While update mechanism will be integrated in all future CCP4 releases, it needs to be installed manually in CCP4 6.3.0. When installed, the updater checks for new updates automatically, and issues a message when new updates are available. After that, updates can be installed in a few mouse clicks. If, for some reason, you find a particular update undesirable, it can be removed with auto-reverting your CCP4 setup to the pre-update state. Note that the update mechanism cannot be used with CCP4 versions lower than 6.3.0, therefore, please upgrade to the latest CCP4 release if you have not done it so far. For upgrade, proceed to CCP4 download pages at http://www.ccp4.ac.uk/download/ . Detail update installation instructions are given in http://www.ccp4.ac.uk/download/update_manual.html The document may seem to be lengthy, however, installation should not take more than a few minutes: 1) download update client (archived) using an appropriate link in the above manual 2) unpack the archive into the top of CCP4 directory ( C:/CCP4/6.3/ in Windows, ccp4-6.3.0/ in Linux/Mac OSX) 3) run the update client (update.exe/update/Update.app) _from CCP4 directory_ by double-clicking on it in your file browser 4) install 1st update 5) (re-)start ccp4i, and see new Manage Updates button in the bottom-right corner of ccp4i window. If this does not work for you for any reason, please (re-)read update manual for details. If that does not help as well, please write to us. Thank you for using CCP4, Eugene Krissinel. -- Scanned by iCritical.
Re: [ccp4bb] relative intensity of ice rings
It is better to spent time learning how to collect without ice… :-) FF Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Jun 27, 2012, at 21:00 , JORGE IULEK wrote: I thank for the references and the comprehensive discussion from Dr. Holton. Also, for the reference indicated by Dr. Berry. I think I will get what I am looking for, now I need to process all this information. Partially answering Dr. Holton, my aim is to have a side guide for improving parameters to process images with ice diffraction rings. In general, the idea is to exclude the minimum area from the detector, but large enough to avoid bad regions. In this, ice ring widths have a role, so, besides the amount of ice, exposure time and beam intensity, relative diffraction intensities contribute, and this way one could decide better what the best width might be for each individual ring. Sure, looking at the images are the base here, but it is interesting to be seconded by the ring expected positions and relative intensities. Yours, Jorge On Tuesday 26 June 2012 09:16 PM, James Holton wrote: I think an appropriate reference is Bragg (1921) http://dx.doi.org/10.1088/1478-7814/34/1/322 who compared various possible crystal structures to the relative strength of the reflections from ice powder measured by Dennison (1921) http://dx.doi.org/10.1103/PhysRev.17.20. However, as Bragg noted Dennison's intensities don't agree all that well with those you would expect from what we now know is the structure of hexagonal ice (Ih). It is possible that Dennison's preparation (plunge-cooling pure water in a capillary) actually created some cubic ice (ice Ic) along with his hexagonal ice (ice Ih). The high intensity he saw for the middle line of the triplet we normally see for true hexagonal ice is consistent with this. Cubic ice is actually more commonly seen in MX diffraction patterns than hexagonal ice (in my experience). However, you do have to be very careful about what you mean by intensity. Are you talking about photons/pixel? Photons/spot? Photons integrated over a powder_ring? All these will be different relative numbers. I'm not sure if they knew about Lorentz factors yet in 1921 There is no mention of correcting for them in either paper. Anyway, if you are after the true hexagonal ice ring intensities, I would advise taking the following PDB file: CRYST14.5114.5117.346 90.00 90.00 120.00 P 63/m m c SCALE1 0.221680 0.127987 -0.00 -0.0 SCALE2 -0.00 0.255974 -0.000.0 SCALE3 0.00 -0.00 0.136129 -0.0 ATOM 1 O WAT A 1 0.000 2.604 0.457 1.00 0.00 O ANISOU1 O WAT A 1 603630172302 0 0 O ATOM 2 H WAT A 1 0.000 2.604 1.308 0.50 0.00 H ANISOU2 H WAT A 1 510510 56255 0 0 H ATOM 3 H WAT A 1 0.000 3.432 0.148 0.50 0.00 H ANISOU3 H WAT A 1 487361163185199 95 H Calculate structure factors from it, add up F2 of same-resolution indicies and plot them out that way. remember, the square of a structure factor is proportional to the integrated intensity of a single-crystal spot, which is not the same thing as a powder ring intensity. The relationship was described most recently by Norby (1997) http://dx.doi.org/10.1107/S0021889896009995 Which I paraphrase as: for a flat detector, the average intensity of a pixel in a powder ring is given by: Ipix = k*p*sum(F2)*omega/sin(theta)/sin(2*theta) where Ipix is the recorded value of one pixel, 'k is a resolution-independent scale factor, p is the polarization factor (see Holton Frankel 2010), F is the structure factor of an hkl index that falls on the ring (there can be more than one, hence the sum), omega is the solid angle subtended by the pixel and theta is the Bragg angle. For the above PDB, I get: d sum(F2) 3.907 121 3.673 156 3.449 111 2.676 88.5 2.255 111 2.075 153 1.953 62.9 1.922 84.2 1.888 62.5 1.836 4.33 1.725 47.8 1.662 1.84 1.527 96.7 1.477 42.8 1.448 39.5 1.375 78.9 1.370 34.6 HTH, -James Holton MAD Scientist On Tue, Jun 26, 2012 at 2:34 PM, Edward A. Berryber...@upstate.edu wrote: Maybe figure 4 in Viatcheslav Berejnov et al. Vitrification of aqueous solutions J. Appl. Cryst. (2006). 39, 244–251 ? JORGE IULEK wrote: Hi, all, I thought I could easily find a reference to comment upon the relative intensity of rings
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
Anomalous signal even with room temperature capillary data was measurable on diffractometers and early area detectors. However there were misspellings in software packages such as sending anomalous phase 90deg into the wrong direction in one of them or others. After in-house editing, anomalous signal contributed significantly. It was also very instrumental in discovering mis-setings in formats of area detectors. We have used a method as appeared in Tom Blundell and Louise Johnson unrivaled book Protein Crystallography ( I own one!) by checking the peaks of the second derivatives with the phases of the first derivative with the contribution of correct or inverted anomalous signal contribution to get correct detector format or space group or else. I still have a logbook that keep records of getting out correct Xentronics format. So no fiction, just errors… Physics works!!! FF Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Jun 6, 2012, at 18:02 , Dyda wrote: I suspect that pure MIR (without anomalous) was always a fiction. I doubt that anyone has ever used it. Heavy atoms always give an anomalous signal Phil I suspect that there was a time when the anomalous signal in data sets was fictional. Before the invent of flash freezing, systematic errors due to decay and the need of scaling together many derivative data sets collected on multiple crystals could render weak anomalous signal useless. Therefore MIR was needed. Also, current hardware/software produces much better reduced data, so weak signals can become useful. Fred [32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred ***[m
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
Bijvoet - 1949 ! FF Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Jun 6, 2012, at 18:28 , Jacob Keller wrote: I think some have used anomalous signals since the 1930s-40s, e.g., Bijvoet! JPK On Wed, Jun 6, 2012 at 10:23 AM, Ronald E Stenkamp stenk...@u.washington.edu wrote: There were a number of labs using anomalous dispersion for phasing 40 years ago. The theory for using it dates from the 60s. And careful experimental technique allowed the structure solution of several proteins before 1980 using what would be labeled now as SIRAS. Ron On Wed, 6 Jun 2012, Dyda wrote: I suspect that pure MIR (without anomalous) was always a fiction. I doubt that anyone has ever used it. Heavy atoms always give an anomalous signal Phil I suspect that there was a time when the anomalous signal in data sets was fictional. Before the invent of flash freezing, systematic errors due to decay and the need of scaling together many derivative data sets collected on multiple crystals could render weak anomalous signal useless. Therefore MIR was needed. Also, current hardware/software produces much better reduced data, so weak signals can become useful. Fred [32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred *** [m -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] P21221 to P21212 conversion
HKL or most probably SCALEPACK know nothing above point group if you do not tell it. But even in GUI one can use hkl matrix with the needed transformation matrix :-\ What is nice about it that it will never let you to change the handedness of the data, so anomalous signal is safe… FF Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On May 7, 2012, at 23:48 , Jacob Keller wrote: Is it true that HKL adopts the naming convention of putting the screw axes first and then naming abc if possible, whereas CCP4 just makes the cell abc? E.g., would HKL ever output by default a p22121 dataset, or would it automatically be p21212? JPK On Mon, May 7, 2012 at 3:33 PM, Ethan Merritt merr...@u.washington.edu wrote: On Monday, May 07, 2012 01:09:25 pm Shya Biswas wrote: Hi all, I was wondering if anyone knows how to convert the P21221 to P21212 spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I got a correct MR solution in P21221 spacegroup. Shya: Scaling is done in a point group, not a space group. The point group P222 contains both space groups P2(1)22(1) and P2(1)2(1)2, so your original scaling is correct in either case. It is not clear from your query which of two things happened: 1) The MR solution kept the same a, b, and c axis assignments but made a different call on whether each axis did or did not correspond to a 2(1) screw. In this case you don't need to do anything to your files. Just make sure that you keep the new space group as you go forward into refinement. 2) The MR solution kept the orginal screw-axis identifications but permuted the axes to the standard setting (non-screw axis is labelled c). In this case you will need to construct a file containing the permuted indices. For example, the reflection originally labeled (h=1 k=2 l=3) is now (h=3 k=1 l=2). There are several programs that can help you do this, including the HKL2000 GUI. But you do not need to go back into HKL if you don't want to. You could, for example, use the ccp4i GUI to select - Reflection Data Utilities - Reindex Reflections Define Transformation Matrix by entering reflection transformation h=l k=h l=k Ethan I have a script file that runs with scalepack but was wondering if there is an easier way to do it with HKL2000 gui mode. thanks, Shya -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742 -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] P21221 to P21212 conversion
Forget to tell that all is done in the menu Macros : - ( FF Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On May 7, 2012, at 23:48 , Jacob Keller wrote: Is it true that HKL adopts the naming convention of putting the screw axes first and then naming abc if possible, whereas CCP4 just makes the cell abc? E.g., would HKL ever output by default a p22121 dataset, or would it automatically be p21212? JPK On Mon, May 7, 2012 at 3:33 PM, Ethan Merritt merr...@u.washington.edu wrote: On Monday, May 07, 2012 01:09:25 pm Shya Biswas wrote: Hi all, I was wondering if anyone knows how to convert the P21221 to P21212 spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I got a correct MR solution in P21221 spacegroup. Shya: Scaling is done in a point group, not a space group. The point group P222 contains both space groups P2(1)22(1) and P2(1)2(1)2, so your original scaling is correct in either case. It is not clear from your query which of two things happened: 1) The MR solution kept the same a, b, and c axis assignments but made a different call on whether each axis did or did not correspond to a 2(1) screw. In this case you don't need to do anything to your files. Just make sure that you keep the new space group as you go forward into refinement. 2) The MR solution kept the orginal screw-axis identifications but permuted the axes to the standard setting (non-screw axis is labelled c). In this case you will need to construct a file containing the permuted indices. For example, the reflection originally labeled (h=1 k=2 l=3) is now (h=3 k=1 l=2). There are several programs that can help you do this, including the HKL2000 GUI. But you do not need to go back into HKL if you don't want to. You could, for example, use the ccp4i GUI to select - Reflection Data Utilities - Reindex Reflections Define Transformation Matrix by entering reflection transformation h=l k=h l=k Ethan I have a script file that runs with scalepack but was wondering if there is an easier way to do it with HKL2000 gui mode. thanks, Shya -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742 -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] P21221 to P21212 conversion
If one make a proper transformation :-/ and supply a correct space group, absent reflections will be printed in the end of scale.log Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On May 8, 2012, at 24:00 , Phil Jeffrey wrote: The program that does the indexing in HKL is Denzo. Denzo doesn't care about the space group. It cares about the point group (cf. Ethan's point) and the cell dimensions, because it integrates the data without regard to the symmetry expressed in the intensities - however it does take notice of the restrictions placed on cell dimensions by point groups. Denzo therefore picks primitive orthorhombic cells in abc. Scalepack scales the integrated data but does not reindex the data if you tell it the space group is P22121. Therefore unit cell choice in HKL is by default driven by cell edge size. Scalepack has the ability to reindex the data, for those of us that like to work in P21212 rather than P22121. On Mon, May 7, 2012 at 3:33 PM, Ethan Merritt Scaling is done in a point group, not a space group. My quibble with this statement is that the output reflection data from Scalepack differs depending on what space group you tell it, since systematic absences along h00, 0k0 and 00l in P2x2x2x are not written out. The number of reflections affected is quite small, of course. Phil Jeffrey Princeton On 5/7/12 4:48 PM, Jacob Keller wrote: Is it true that HKL adopts the naming convention of putting the screw axes first and then naming abc if possible, whereas CCP4 just makes the cell abc? E.g., would HKL ever output by default a p22121 dataset, or would it automatically be p21212? JPK On Mon, May 7, 2012 at 3:33 PM, Ethan Merritt merr...@u.washington.edu mailto:merr...@u.washington.edu wrote: On Monday, May 07, 2012 01:09:25 pm Shya Biswas wrote: Hi all, I was wondering if anyone knows how to convert the P21221 to P21212 spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I got a correct MR solution in P21221 spacegroup. Shya: Scaling is done in a point group, not a space group. The point group P222 contains both space groups P2(1)22(1) and P2(1)2(1)2, so your original scaling is correct in either case. It is not clear from your query which of two things happened: 1) The MR solution kept the same a, b, and c axis assignments but made a different call on whether each axis did or did not correspond to a 2(1) screw. In this case you don't need to do anything to your files. Just make sure that you keep the new space group as you go forward into refinement. 2) The MR solution kept the orginal screw-axis identifications but permuted the axes to the standard setting (non-screw axis is labelled c). In this case you will need to construct a file containing the permuted indices. For example, the reflection originally labeled (h=1 k=2 l=3) is now (h=3 k=1 l=2). There are several programs that can help you do this, including the HKL2000 GUI. But you do not need to go back into HKL if you don't want to. You could, for example, use the ccp4i GUI to select - Reflection Data Utilities - Reindex Reflections Define Transformation Matrix by entering reflection transformation h=l k=h l=k Ethan I have a script file that runs with scalepack but was wondering if there is an easier way to do it with HKL2000 gui mode. thanks, Shya -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742 -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu mailto:j-kell...@northwestern.edu ***
Re: [ccp4bb] very informative - Trends in Data Fabrication
Or as tensor, see classic: ANISOTROPIC SCALING OF 3-DIMENSIONAL INTENSITY DATA Author(s): SHAKKED, Z (SHAKKED, Z) Source: ACTA CRYSTALLOGRAPHICA SECTION A Volume: 39 Issue: MAY Pages: 278-279 DOI: 10.1107/S0108767383000665 Published: 1983 I guess this or similar is implemented in shelxl. Look also in : J. F. Nye Physical Properties of Crystals: Their Representation by Tensors and Matrices Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Apr 9, 2012, at 21:02 , Pavel Afonine wrote: Hi Alex, It is not clear to me how to report the resolution of data when it is 3A in one direction, 3.5A in another and 5A in the third. can't be easier I guess: just switch from characterizing data sets with one single number (which is suboptimal, at least, as Phil pointed out earlier) and show statistics by resolution instead. For example, R-factors, data completeness, Fobs shown in resolution bins are obviously much more informative metrics then a single number. If you want to be even more sophisticated, you can. See for example: A program to analyze the distributions of unmeasured reflections J. Appl. Cryst. (2011). 44, 865-872 L. Urzhumtseva and A. Urzhumtsev Pavel
Re: [ccp4bb] Always Modelling Anomalous Signal
On Jan 10, 2012, at 22:00 , Jacob Keller wrote: Dear Crystallographers, it seems to me that on a certain level we are always throwing away (sort of) about half of our data when we merge Bijvoet pairs--why Who We ? shouldn't we keep them separate, since we know that they should be a little bit different, especially in light of the higher multiplicities which are more common now? Shouldn't modelling them give better R-values, and wouldn't it just be more true? I guess a sort of proof for this is that sulfurs are almost always detectable on anomalous As a matter of protocol, for the last 25 years I keep anomalous signal in my data for refinement, does not matter what ignorant annotators say. I do it for several reasons, one of them is matter of principle. difference maps, implying that we are actually measuring those differences accurately enough to see them (I don't think these things The problem is sometimes to deposit the data, which were used for the refinement. Developers refuse to add the redundant information into the deposition file, annotators refuse to accept the data file without averaged value for F or I, directors keep silent. Be strong Jacob... can arise from model bias, as anomalous differences are not modeled.) At least maybe at the final steps of refinement...? JPK -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608
Re: [ccp4bb] 1.95A, different phases, maps look the same, R/Rfree 22/24, wrong space group? - No alternative origin
Napoleao, It is so called alternative origins play a game with you. You do not change your structure by shifting 1/2 translation (or even combination of these translations) into directions of the main axes of your unit cell. Structure factors after this operation stay the same, however phases change systematically, producing however the same map features. Would I be a begin crystallographer now, I would read a bit more old fashioned books on crystallography such as probably Jensen and Stout… FF Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 20, 2011, at 07:42 , Napoleão Valadares wrote: Hello, I'm observing a very strange phenomena (at least to me, I'm a beginner). It is related to symmetry (I think). I got a data set at 1.95A (I/Sigma 3.5, R-Factor and R-meas 35% in the last shell) and a partially refined solution with R/Rfree 22/24, 166 aminoacids observed and around 30 solvent molecules. I'll call this Solution-1. The refinement was smooth, the densities were very clearly asking for the correct missing side chains and the map looks good. The space group I'm using is P212121, pointless and XDS agree with that (but me and pointless both have a long history of being wrong about space groups). Phenix.xtriage says there's no twinning. I took Solution-1 and used it as a template in a molecular replacement in the same space group (P212121) using the same mtz as the one used to refine the template. I got a different (not superposed in space) solution (called Solution-2, scores by Phaser RFZ=24.2 TFZ=33.0 PAK=0 LLG=1413 LLG=1899) that was readily refined in Phenix to R/Rfree 24/26 without any solvent molecule. - The solutions are not superposed in space, although they are near-identical and can be superposed yielding a C-alpha rmd =0.001. - Both structures present VERY similar density maps. The maps are not superposed in space, but when you run the chain in one map in Coot and do the same in the other it they the present exactly the same features. It is impossible to ignore their similarities. - Both structures and maps present the same origin and unit cell. - If I add to Solution-2 the equivalent solvent molecules of Solution-1 (I did this by superposing Solution-1 to Solution-2 then copy/pasting the solvent molecules), the R/Rfree become 22/24. This is a clear indication that the solutions are related. - I can't find any MR solutions using the same template and space groups P222, P2221 and P21212. How two different sets of phases can yield maps with the same features? What is happening, wrong space group? I have a feeling my lack of experience is the problem. Thank you. Regards, Napo
Re: [ccp4bb] Can I combine selenoMet data and MR model to solve the phase problem?
Could DANO/SIGDANO be included to REFMAC output mtz automatically? I find it very useful on the various stages of refinement to observe anomalous map. Last time I was trying, I failed, probably due to GUI'sh addiction and abandonning line editor. Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 16, 2011, at 13:57 , Eleanor Dodson wrote: Yes - one solution is to use the MR phases to do a anom diff map to position the Se sites. You need to a) run CAD to combine the DANO/ SIGDANO columns from your data with the refmac output b) use the fft utility to do a DANO map with PHIC and FOM and run a peak search. Ideally you should find whacking peaks related to your previous Se sites (may be different origin, and symmetry equivalent. If that is so, then use phistats (Reflection utility ) to move the Se phases to the MR ones and you can do several things then. I often just check the MR solution against the exptl phases first - correct obvious errors, delete wrong residues etc) Then do some refinement using phases and you will get out combined phases from REFMAC.. Or use the SIRAS option #or Eleanor On 11/16/2011 06:23 AM, Frederic VELLIEUX wrote: Hi, This hasn't been mentioned by the people who have answered so far so here we go: your molecular replacement solution and your SeMet solution to the phase problem are not necessarily using the same origin. There is a ccp4 program (is it phistats ? and there may be other programs around) that can deal with this. Fred. Message du 15/11/11 22:56 De : Feng Guo A : CCP4BB@JISCMAIL.AC.UK Copie à : Objet : [ccp4bb] Can I combine selenoMet data and MR model to solve the phase problem? Hi, there, Maybe someone asked this question before, but I couldn't find it in the archive. We use the native data to do molecular replacement before, but only part of the model fit the density. After collect a new set of selenoMet data, we try to use it to solve the phase, it solve some of the phase problem other than the MR, but still not complete. Is there anyway that I can somehow combine the two phases together? Thank you. Best, Feng
Re: [ccp4bb] Archiving Images for PDB Depositions
God bess the symmetry, we are saved from the over-interpreting symmetry (except probably of very exotic cases) by the very high Rsym factors around 40% 50% if the symmetry is wrong. Even wild rejection of outliers, cannot reform acceptable Rmerge. In my personal repository, 1QZV is a manifest of that. In 4.4 angstrom resolution, wrong interpretation of 90.2 angle monoclinic angle as 90 degrees orthorhombic supported by two molecules in the monoclinic asymmetric was corrected in the middle of the first data collection. Habitual on-fly processing of the data (integration and repetitive scaling after every several frames with HKL) detected that about half-through the data R factor in orthorhombic space group jumped to 40% from about 7%. Reindexing solved the problem on the spot. I still keep the raw data. Needless to say that before about a decade we would make precession photographs (I still own precession camera) and would not make such a mistake. Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 3, 2011, at 21:42, Clemens Vonrhein wrote: Hi James, scary ... I was just looking at exactly the same thing (P21 with beta~90), using the same tool (POINTLESS). Currently I'm going through the structures for which images can be found ... I haven't gone far through that list yet (in fact actually only the first one), but this first case should indeed be in a higher spacegroup (P 2 21 21). As you say (and that's what Graeme looks for): finding 'over-merged' datasets can be a bit more tricky ... once the damage is done. I have the hunch that it might happen even more often though: we tend to look for the highest symmetry that still gives a good indexing score, right? Otherwise we would all go for P1 ... Some other interesting groups for under-merging: * orthorhombic with a==b or a==c or b==c (maybe tetragonal?) * trigonal (P 3 etc) when it should be P 6 * monoclinic with beta==120 A few cases for each of those too ... all easy to check in ftp://ftp.wwpdb.org/pub/pdb/derived_data/index/crystal.idx and then (if structure factors are deposited) running POINTLESS on it (great program Phil!). Cheers Clemens On Thu, Nov 03, 2011 at 12:00:33PM -0700, James Holton wrote: I tried looking for such evil symmetry problem examples some time ago, only to find that primitive monoclinic with a 90-degree beta angle is much more rare than one might think by looking at the PDB. About 1/3 of them are in the wrong space group. Indeed, there are at least 366 PDB entries that claim P2-ish, but POINTLESS thinks the space group of the deposited data is higher (PG222, C2, P6, etc.). Now, POINTLESS can be fooled by twinned data, but at least 286 of these entries do not mention twinning. Of these, 40 explicitly list NCS operators (not sure if the others used NCS?), and 35 of those were both solved by molecular replacement an explicitly say the free-R set was picked at random. These are: Now, I'm sure there is an explanation for each and every one of these. But in the hands of a novice, such cases could easily result in a completely wrong structure giving a perfectly reasonable Rfree. This would happen if you started with, say, a wrong MR solution, but picked your random Rfree set in PG2 and then applied NCS. Then each of your free hkls would actually be NCS-restrained to be the same as a member of the working set. However, I'm sure everyone who reads the CCP4BB already knew that. Perhaps because a discerning peer-reviewer, PDB annotator or some clever feature in our modern bullet-proof crystallographic software caught such a mistake for them. (Ahem) Of course, what Graeme is asking for is the opposite of this: data that would appear as nearly PG222, but was actually lower symmetry. Unfortunately, there is no way to identify such cases from deposited Fs alone, as they will have been overmerged. In fact, I did once see a talk where someone managed to hammer an NCS 7-fold into a crystallographic 2-fold by doing some aggressive outlier rejection in scaling. Can't remember if that ever got published... -James Holton MAD Scientist On 11/2/2011 1:33 AM, Graeme Winter wrote: Hi Ed, Ok, I'll bite: I would be very interested to see any data sets which initially were thought to be e.g. PG222 and scale OK ish with that but turn out in hindsight to be say PG2. Trying to automatically spot this or at least warn inside xia2 would be really handy. Any pseudosymmetric examples interesting. Also any which are pseudocentred - index OK in C2 (say) but should really be P2 (with the same cell) as the missing reflections are in fact present but are just rather weaker due to NCS. I have one example of each from the JCSG but more would be great, especially in cases where
Re: [ccp4bb] Archiving Images for PDB Depositions
Clemens, In the past, we have used TRACER (free domain) for higher symmetry or we interpreted manually Niggly values :-) TRACER is gone long time ago. Niggly values are not displayed anymore, so we trust auto indexing of DENZO which, assuming all experimental parameters are properly set ( we do this by using a standard crystal such as lysozyme) is extremely sensitive in defining Bravais system. I have no experience with POINTLESS, but assume that it is also doing an excellent work. FF Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 3, 2011, at 22:27 , Clemens Vonrhein wrote: On Thu, Nov 03, 2011 at 04:13:44PM -0400, Bryan Lepore wrote: not sure I follow this thread, but this table might be interesting : http://journals.iucr.org/d/issues/2010/05/00/dz5193/dz5193sup1.pdf from: Detection and correction of underassigned rotational symmetry prior to structure deposition B. K. Poon, R. W. Grosse-Kunstleve, P. H. Zwart and N. K. Sauter Acta Cryst. (2010). D66, 503-513[ doi:10.1107/S0907444910001502 ] Oh yes, that is relevant and very interesting. As far as I understand it, the detection of higher symmetry is based on the atomic coordinates and not structure factors though (please correct me if I'm wrong here). At least some of the cases for which the deposited structure factors strongly suggest a higher symmetry don't seem to be detected using that papers approach (I can't find them listed in the supplemental). Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
Re: [ccp4bb] IUCr committees, depositing images
I could not agree less. There is constant development of the software for refinement that allow to do things that were not possible or were not necessary in the past such as intelligent refinement of occupancies of mutually exclusive sites, entities and conformations. I frequently remeasure lysozyme crystals. I use them as a test system for the beam lines, new detectors, novel software developments, refinement improvement etc. Sometimes I am collecting data in quite different wavelength than of existing structures. And what about diffraction data from a chemically modified lysozyme molecule? They are good data that show evolution of the beam line stations if they are keeper in historical order. To store them all, or not to store at all… Storage of the diffraction data is not a drinking club with muscle-bound selectors outside :-) Felix Frolow Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Oct 18, 2011, at 12:52 , Chris Morris wrote: Some crystals are hard to make, so storing all the data the best way to get reproducibility. On the other hand, no one needs more images of lysozyme. So using the same standard for every deposition doesn't sound right. The discussion should be held on the basis of overall cost to the research budget - not on the assumption that some costs can be externalised. It is too easy to say you should store the images, in case I want to reprocess them sometime. IT isn't free, nor is it always cheaper than the associated experimental work. The key comparison is: Cost of growing new crystals + cost of beam line time With: Cost of storing images * probability of processing them again At present, detectors are improving more quickly than processing software. Sample preparation methods are also improving. These forces both press downward the probability that a particular image will ever be reprocessed. regards, Chris Chris Morris chris.mor...@stfc.ac.uk Tel: +44 (0)1925 603689 Fax: +44 (0)1925 603634 Mobile: 07921-717915 Skype: chrishgmorris http://pims.structuralbiology.eu/ http://www.citeulike.org/blog/chrishmorris Daresbury Lab, Daresbury, Warrington, UK, WA4 4AD
Re: [ccp4bb] IUCr committees, depositing images
Sure they will There is no irony in what I say FF Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Oct 18, 2011, at 20:01 , Phoebe Rice wrote: One more consideration: Since organization is not one of my greatest talents, I would be absolutely delighted if a databank took over the burden of archiving my raw data for me. Phoebe = Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp Original message Date: Tue, 18 Oct 2011 18:17:14 +0100 From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK (on behalf of Gerard Bricogne g...@globalphasing.com) Subject: Re: [ccp4bb] IUCr committees, depositing images To: CCP4BB@JISCMAIL.AC.UK Dear Enrico, Frank and colleagues, I am glad to have suggested that everyone's views on this issue should be aired out on this BB rather than sent off-list to an IUCr committee member: this is much more interactive and thought-provoking. There would seem to be clear biases in some of the positions - for instance, the statement that we overvalue individual structures and that there is value only in their ensemble has to be seen to be coming from someone in a structural genomics centre ;-) . However, as Wladek pointed out, when an investigator's project is crucially dependent on a result embodied in a deposited structure, it would be of the greatest value to that investigator to be able to double-check how reliable some features of that structure (especially its ligands) actually are. On the other hand Enrico, as a specialist of crystallisation and modelling, sees value only in improving those contributors to the task of structure determination. This is forgetting (1) an essential capability of crystallography: that, through experimental phasing, it can show you what a protein looks like even if you have never seen nor modelled one before, through the wondrous process of producing model-free electron-density maps; and (2) an essential aspect of the task of structure determination: that it doesn't aim at producing a model with perfect geometry, but one that best explains the measured data and neither under- nor over-interprets them (I realise, though, that Enrico's statement Data just introduces experimental errors into what would otherwise be a perfect structure is likely to be tongue-in-cheek ...). When it comes to making explicit the advantages of archiving at least the raw images that yielded the data against which a deposited PDB entry was refined, many good reasons have been given, but I feel that (1) there is an over-emphasis on the preservation of diffuse scattering that has a tendency to give this archiving a nuance of blue-skies research and thus to detract from its practical urgency; time will come for diffuse scattering to be fully appreciated, but at the moment its mention acts as a bit of a distraction, if not a turn-off in this context for people who not not love it already; (2) as far as I see it, the highest future benefit of having archived raw images will result from being able to reprocess datasets from samples containing multiple lattices (non-merohedral twinning). Numerous structures are determined and refined against data obtained by integrating only the spots from the major lattice, without rejecting those that are corrupted by overlap by a spot from a minor lattice. This leads to systematic errors in these data that may only be incompletely taken out by outlier rejection at the merging stage, and will create noise or confusing residual features in difference maps, if not false features in the main map and therefore its interpretation by the model. In my opinion it will be the development of methods for dealing with overlapped lattices and for the proper treatment of such data in scaling and refinement (as is already possible with small molecules) that will bring about the major possibility of substantially improving deposited results by reprocessing the raw images co-deposited with them; (3) there is also the more immediate possibility of better removing ice rings, or ligand powder rings, from images, than by having to throw away certain thin shells of merged data in the structure factor file. I see the case for raw image deposition as absolutely compelling, especially in view of the auto-catalytic process through which their availability will speed up the development of precisely the new methods and software to extract better data from them
Re: [ccp4bb] IUCr committees, depositing images
On the deposition of raw data: Committees, wherever you are! I guess that abstaining from storing the raw diffraction data in the form of frames is not very wise whatever its size is. I regret that for some PDB entries I do not have diffraction data (needless to say that authors do not submitted even structure factors). I maintain a bit more than 1.2 T diffraction data starting from 2001 and all is nicely resides on two small WD pocket disks (needless to say that I have several copies of the data). Generally I have all data I ever collected going back to beginning of 80's, but I am to lazy to reform DAT tapes. Sure, running Pilatus for an olympic record, we will go home with several T of data after 24 h (will we?). But this is an abuse of the system. The final goal is the structure determination, and there are much less good crystals everywhere in one year that one Pilatus could collect in one week. But to decide fast if the crystal diffraction data from Pilatus is good for storage or even for measurement whatever the speed of data collection is, good data processing software is needed. I personnaly think that there is only one, the one. Anyhow, I think if the author wish to publish his structure, and it is important, and I am a reviewer, and it is going to prestigious journal, I will reprocess his data and will check his way to the final crystal structure solution from the beginning. It is as in mathematics. If someone claim that he solved a long-staing problem from the past, he will not go away from his envious colleagues, who will drop everything and will sit and check, until they will find a mistake. What a pleasure!!! And if there are no mistakes - chapeau !!! FF Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Oct 16, 2011, at 20:38 , Frank von Delft wrote: On the deposition of raw data: I recommend to the committee that before it convenes again, every member should go collect some data on a beamline with a Pilatus detector [feel free to join us at Diamond]. Because by the probable time any recommendations actually emerge, most beamlines will have one of those (or similar), we'll be generating more data than the LHC, and users will be happy just to have it integrated, never mind worry about its fate. That's not an endorsement, btw, just an observation/prediction. phx. On 14/10/2011 23:56, Thomas C. Terwilliger wrote: For those who have strong opinions on what data should be deposited... The IUCR is just starting a serious discussion of this subject. Two committees, the Data Deposition Working Group, led by John Helliwell, and the Commission on Biological Macromolecules (chaired by Xiao-Dong Su) are working on this. Two key issues are (1) feasibility and importance of deposition of raw images and (2) deposition of sufficient information to fully reproduce the crystallographic analysis. I am on both committees and would be happy to hear your ideas (off-list). I am sure the other members of the committees would welcome your thoughts as well. -Tom T Tom Terwilliger terwilli...@lanl.gov This is a follow up (or a digression) to James comparing test set to missing reflections. I also heard this issue mentioned before but was always too lazy to actually pursue it. So. The role of the test set is to prevent overfitting. Let's say I have the final model and I monitored the Rfree every step of the way and can conclude that there is no overfitting. Should I do the final refinement against complete dataset? IMCO, I absolutely should. The test set reflections contain information, and the final model is actually biased towards the working set. Refining using all the data can only improve the accuracy of the model, if only slightly. The second question is practical. Let's say I want to deposit the results of the refinement against the full dataset as my final model. Should I not report the Rfree and instead insert a remark explaining the situation? If I report the Rfree prior to the test set removal, it is certain that every validation tool will report a mismatch. It does not seem that the PDB has a mechanism to deal with this. Cheers, Ed. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
Re: [ccp4bb] should the final model be refined against full datset
Recently we (I mean WE - community) frequently refine structures around 1 Angstrom resolution. This is not what for the Rfree was invented. It was invented to go away with 3.0-2.8 Angstrom data in times when people did not possess facilities good enough to look on the electron density maps…. We finish (WE - I again mean - community) the refinement of our structures too early. Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Oct 14, 2011, at 22:35 , Nat Echols wrote: On Fri, Oct 14, 2011 at 1:20 PM, Quyen Hoang qqho...@gmail.com wrote: Sorry, I don't quite understand your reasoning for how the structure is rendered useless if one refined it with all data. Useless was too strong a word (it's Friday, sorry). I guess simulated annealing can address the model-bias issue, but I'm not totally convinced that this solves the problem. And not every crystallographer will run SA every time he/she solves an isomorphous structure, so there's a real danger of misleading future users of the PDB file. The reported R-free, of course, is still meaningless in the context of the deposited model. Would your argument also apply to all the structures that were refined before R-free existed? Technically, yes - but how many proteins are there whose only representatives in the PDB were refined this way? I suspect very few; in most cases, a more recent model should be available. -Nat
Re: [ccp4bb] Denzo/HKL2000 for Pilatus 6M detector
Why not to ask The Lord of Rings? FF Quoting Petr Leiman petr.lei...@epfl.ch: Dear all, What is the status of Denzo/HKL2000 availability/support for the Pilatus 6M detector? Thank you, Petr Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica D, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-(0)-3640-8723 Cel: ++972-0547-459-608 Fax: ++972-(0)-3640-9407
Re: [ccp4bb] Y-Chi2 running out of chart
What is your cold stream - phi axis relative and absolute orientation? FF Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Jun 22, 2011, at 19:22 , bie gao wrote: Dear Colleagues, I'm collecting a dataset on our recently repaired Rigaku home source. Crystal diffracts to 2.2A. Indexing seems to be all fine. However, during integration, I realize Y-Chi2 is increasing constantly (from 2 to 4.5, almost linear) within 60 degree collection, whereas X-Chi2 stays the same. An image is attached. There are still another 60 degree to go. Although the prediction fits the images well so far, I'm afraid the Y-Chi2 will eventually run out of the chart. My question is could it be related to any hardware malfunctioning, i.e., goniometer, image plates, etc, which may be a side effect of the recent major repair? Or what else it can be? Thanks, Bing Chi1.gif
Re: [ccp4bb] off-topic: Synchrotron look alike
I still keep a bill of SGI Indigo memory extension from 64 Mb to 128Mb - $ 12,000 from Kingston in 1994 Friends, do not be niggards, life is much nicer today. Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Jun 9, 2011, at 19:52 , William Scott wrote: Yeah, I know what you mean. That Zalman 3D LCD monitor put me back almost $300, and the mac mini I hooked it to, nearly another $600. My SGIs only cost $12K each in 1998. On Jun 9, 2011, at 9:43 AM, Mayer, Mark (NIH/NICHD) [E] wrote: The sad thing is, although Macs are great crystallography platforms, stereo is hard at best, ridiculously expensive compared to Linux systems, and still requires the use of CRTs which have not been manufactured for years ...
Re: [ccp4bb] Script / program to change chain ID 's in symmetry mates - MOLEMAN
MOLEMAN from the Uppsala Software Factory by Gerard Kleywegt of course It is easy as to say Do it! FF Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Apr 8, 2011, at 14:17 , krishan wrote: Dear CCP4BB members, We are using a script written in python to generate symmetry mates for a given pdb file using PYMOL. After generating symmetry mates we want to combine all the symmetry molecules in a single PDB file with all the chains having unique chain IDs. Since all the symmetry mates have same chain ID's I was wondering if some one knows a script that can give unique chain ID for each symmetry mate. We are interested in script because that dataset that we are handling is large. I thank you all in advance for your help. Best, Krishan
Re: [ccp4bb] Solidarity with Japan
Hassan, dear friend I was afraid to suggest what Soichi Wakatsuki is asking for in his comprehensive letter - beam time to accommodate protein crystallographers from Japan- not to sound patronizing. But after his explicit request we have to act into this direction. ESRF have to announce the program of help with the beam time. I am sure that our community (ESRF users) will support the initiative. FF Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Mar 15, 2011, at 10:18 , hassan belrhali wrote: Dear Colleagues would you agree that we express our solidarity with our Japanese friends in those very dark times via this scientific forum? Is there any individual or global initiative we could initiate to help? Warmest thoughts from France, Hassan Belrhali EMBL Grenoble France
Re: [ccp4bb] I/sigmaI of 3.0 rule- do not underestimate gels
Well BR, do not underestimate complexity of running a gel! There are even more harsh referees comments on gel appearance and quality than comments on cutting data based on R,RF and sigmaI :-) Especially when one is trying to penetrate into prestigious journals... Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Mar 3, 2011, at 18:38 , Bernhard Rupp (Hofkristallrat a.D.) wrote: related to what I feel is recent revival of the significance of the R-values because it's so handy to have one single number to judge a highly complex nonlinear multivariate barely determined regularized problem! Just as easy as running a gel! Best BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ed Pozharski Sent: Thursday, March 03, 2011 8:19 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] I/sigmaI of 3.0 rule On Thu, 2011-03-03 at 08:08 -0700, Bart Hazes wrote: I don't know what has caused this wave of high I/Sigma threshold use but here are some ideas It may also be related to what I feel is recent revival of the significance of the R-values in general. Lower resolution cutoffs in this context improve the R-values, which is (incorrectly) perceived as model improvement. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] AW: [ccp4bb] bruker smart and mosflm
Tying customers to formats with unbreakable, softwares and secret tricks is seldom productive. Customers suspect that something really wrong with the machines is hiding behind that. It is not clear if it is legal. After all, academic customers pay money taken from public and transferred to granting agencies. It means that public support unbreakable format codings, softwares and secret tricks... The question is what for? - for unbreakable format codings, softwares and secret tricks? It puts a lot of noise into the system which is already noisy and people start to prefer open codes... There is another option: maybe these are still XENTRONIX formats that were about 18 or 8 altogether if elders remember properly? Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 9, 2010, at 15:30 , Stefan Gerhardt wrote: I'd have to say, in general the easiest thing to do when confronted with Mosflm issues is to get in touch with the authors and ask them. We are all very friendly, approachable people who will do our best to help! I cannot agree more with this... Many thanks with all your help provided so far... (more needed surely soon :) ) Cheers Stefan
Re: [ccp4bb] Strange spots - In book of John Helliwell
I have seen such features myself from time to time on diffraction pictures recorded on X-ray films in the far past and was explaining them by the presence of electron diffraction as they resemble electron diffraction patterns. Source of focused electron beam during X-ray diffraction experiment is a different story. I have no explanation for that. BTW1 when we started to use area detectors, these features disappeared. However features David Goldstone showing us is something else. We never have seen such things before. I would try to take a similar picture on X-ray film. But maybe why to bother?. Unfortunately to be a genius of X-ray diffraction physics in the present MX world will fast convert a person to homeless. My question to John Goldstone: Is it intermittent, of for certain crystal/station/detector you always get that? BTW2 I feel in contemptuous reaction of the community deep discontent of all of us.What? even diffraction physics we do not understand in depth? Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Oct 29, 2010, at 23:23 , Charles W. Carter, Jr wrote: Hi Gérard, I actually bought John's book some time ago and can provide page 321 (attached). I think perhaps John is exaggerating his case, although as I have frequently made similarly inflated claims, I am sympathetic. Here is the pdf file. If it does not go through the CCP4 filters, I would be happy to send it to the first few who request it. Charlie p321.PDF On Oct 29, 2010, at 11:03 PM, Gerard Bricogne wrote: Dear Liz, You will be disappointed. I went immediately to that link, but page 321 is not available as part of the Googlebook sample, which jumps directly from page 320 to page 325. With best wishes, Gerard. -- On Fri, Oct 29, 2010 at 09:13:27PM +0100, elizabeth.d...@diamond.ac.uk wrote: There is always hope!!! Seriously though, I have never seen anything like this before! I am watching this thread with interest to see what others suggest. THanks Also thanks should go specifically to Julian Nomme who took the trouble to send us all the Helliwell book link. Liz From: CCP4 bulletin board on behalf of Sanishvili, Ruslan Sent: Fri 29/10/2010 21:08 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Strange spots C'mon now! Everybody knows that frogs in real space become handsome princes in the reciprocal one... N. Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Jacob Keller Sent: Friday, October 29, 2010 3:00 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Strange spots Yes, but the question is what in real space gives rise to reciprocal-space frog spawn? (Frogs, I guess?) - Original Message - From: Marcus Winter mailto:marcus.win...@agilent.com To: CCP4BB@JISCMAIL.AC.UK Sent: Friday, October 29, 2010 2:56 PM Subject: Re: [ccp4bb] Strange spots Dear David, Further to the previous learned responses, surely, this is just frog spawn ? My apologies: it is a Friday evening, after all... Marcus Winter. -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of David Goldstone Sent: 29 October 2010 17:08 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Strange spots Dear All, Does anyone have any insight into what the circles around the spots might be? cheers Dave -- David Goldstone, PhD National Institute for Medical Research Molecular Structure The Ridgeway Mill Hill London NW7 1AA *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Strange spots
Fig from John (I have a copy of his book in the office and will see it only tomorrow) due to better quality makes it clear (at least for me) that we see the similar effect shown by David Goldstone. Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Oct 30, 2010, at 10:16 , John R Helliwell wrote: Dear Colleagues, Here is scan of a portion of Fig 8.1b, including a zoom in, as per my earlier email. This was recorded on photographic film, which hopefully removes the worry about whether Dave's detector was malfunctioning, and secondly, being Laue, a simple X-ray optic set up (I have to check if it included a focussing X-ray mirror or not). Even if there is no sure explanation of such halo features, although I did declare 'defects in the crystal' as a possibility, we know in this case that these features were radiation sensitive. Best wishes, John On Fri, Oct 29, 2010 at 5:08 PM, David Goldstone david.goldst...@nimr.mrc.ac.uk wrote: Dear All, Does anyone have any insight into what the circles around the spots might be? cheers Dave -- David Goldstone, PhD National Institute for Medical Research Molecular Structure The Ridgeway Mill Hill London NW7 1AA -- Professor John R Helliwell DSc diffuse spots 3.jpgdiffuse spots 2 .jpg
Re: [ccp4bb] Deposition of riding H- Are they or are they not? Additional experiments are needed
Well , maybe they are there (hydrogens), maybe they are not (also depends on location). They, or something else also boils sometimes. I also understand from some other publications such as doi:10.1107/S090904509002192 (cyclosporine) that hydrogen abstraction is irreversible. Is it supported my Mass Spectroscopy post mortem in the case of cyclosporine and aldose reductase? Just what left from the irradiated crystals - molecules with or without hydrogens can be checked in mass-spectrometer. BTW, part of my early life I practiced small molecule X-ray crystallography, which is by definition ultra-high resolution. When we wished to know in critical cases were hydrogens are and if they are, we exchanged them with deuterium in large crystals and performed neutron diffraction. One major advantage of neutron diffraction over X-ray diffraction is that the latter is rather insensitive to the presence of hydrogen (H) in a structure, whereas the nuclei 1H and 2H (i.e. Deuterium, D) are strong scatterers for neutrons. This means that the position of deuterium in a crystal structure and its thermal motions can be determined far more precisely with neutrons Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Sep 16, 2010, at 15:45 , Sanishvili, Ruslan wrote: Hi Pavel, Note that in the ultra-high resolution structure of aldose reductase http://www.ncbi.nlm.nih.gov/pubmed/15146478 we didn't see all (or most) hydrogens. So, the converse question one could ask is why we didn't see all of them? Was it only because of higher B-factors or because some of them were stripped during data collection? Note that in my original message I said they are, in most cases, still assumed. Ultra-high resolution structures are exactly what I meant under few cases when some of the positions are not assumed, so thanks for pointing that out. It's not all or nothing - some hydrogens will be stripped and some won't. But since we don't know which ones are gone, depositing the coordinates of all of them may be misleading. It can be particularly dangerous for structure-based functional interpretations because several publications suggest that active sites are one of the first ones to suffer from radiation damage. And aren't the functional interpretations the ultimate goal of protein structures? Cheers, N. From: Pavel Afonine [mailto:pafon...@lbl.gov] Sent: Wed 9/15/2010 5:56 PM To: Sanishvili, Ruslan Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Deposition of riding H Hi Nukri, thanks for the paper (I haven't read the paper yet), I definitely missed this one! Interesting though, if we assume that they get stripped off during data collection, how you could see so many hydrogen atoms in Fo-Fc residual maps for Aldose Reductase structure at 0.66A? B. Guillot, C. Jelsch, N. Muzet, C. Lecomte, E. Howard, B. Chevrier, A. Mitschler, A. Podjarny, A. Cousson, R. Sanishvili A. Joachimiak (2000). Multipolar refinement of aldose reductase at subatomic resolution. Acta Cryst. A56, s199. E. I. Howard, R. Cachau, A. Mitschler, P. Barth, B. Chevrier, V. Lamour, A. Joachimiak, R. Sanishvili, M. Van Zandt, D. Moras A. Podjarny (2000). Crystallization of Aldose Reductase leading to Single Wavelength (0.66 Å) and MAD (0.9 Å) subatomic resolution studies. Acta Cryst. A56, s57. A. D. Podjarny, A. Mitschler, I. Hazemann, T. Petrova, F. Ruiz, E. Howard, C. Darmanin, R. Chung, T. R. Schneider, R. Sanishvili, C. Schulze-Briesse, T. Tomizaki, M. Van Zandt, M. Oka, A. Joachimiak O. El-Kabbani (2005). Inhibitor binding to aldose reductase studied at subatomic resolution. Acta Cryst. A61, c122. Pavel. On 9/15/10 3:34 PM, Sanishvili, Ruslan wrote: Hi All, I have not read all messages in the trace so my apologies if somebody already pointed out what I have to say. There is lot of talk about how this or that software treats the riding hydrogens. What to do with the fact that however these hydrogens are treated in calculations, they are, in most cases, still assumed? Meents et al http://scripts.iucr.org/cgi-bin/paper?xh0004 showed that proteins are stripped of hydrogens during X-ray data collection. So, IMHO it is a good argument against depositing the H coordinates in PDB. Cheers, N. Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of George M. Sheldrick Sent: Wednesday, September 15, 2010 5:14 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb
Re: [ccp4bb] Deposition of riding H
Pavel, Shelxl is working in correct coordinates - fractional... Many things are easier in fractional coordinates. Are you sure that Phenix does not go orthogonal - fractional - orthogonal in internal calculations? When fixing of parameter is made in fractional coordinates it does not produce confusion. Shelxl also make fractional - orthogonal (AKA PDB) which is also correct. Constrain is not transferred there. BTW Shelxl knows symmetry very well and will constrain atoms that occupying symmetry elements. Shortly Shelxl knows crystallography best. When you will see number of lines in Shelxl Fortran code ( do not kill Fortran to early) you will be surprised. There are not so many of them. No graphical user interface yet, but COOT is of great help. Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Sep 15, 2010, at 19:11 , Pavel Afonine wrote: Hi Tim, The pdbe.org, for example allows to upload auxiliary files and in my opinion the uploading of the final .ins-file (not the .res-file!) should be made mandatory in the case of shelxl refinement. Since coot has now become utterly convenient even for shelxl refinement, there is no reason one should not deposit the .ins-file ([flame] and the PDB-file probably for legacy reasons [/flame]). I was always wondering but never had a good occasion to ask (my Shelxl knowledge is limited and may be outdated so I apology in advance if my questions are too dummy; also I realize that I'm asking a non-CCP4 question on CCP4bb for which I apology again): - how .ins file encodes the information about NCS groups used in refinement (atom selection for NCS groups, restraint weights for different groups, etc? - how .ins file encodes the information about TLS (again, atom selections for TLS groups, TLS matrices, etc)? Related, does it have a concept of having TLS and other components to the total atomic displacement parameter (ADP)? - If I recall it correctly, to fix (=not refine) a certain parameter (say occupancy or B-factor) in Shelxl you need to add a number 10 to it. Is it true? IMHO, this might lead to confusion if such a file gets deposited to PDB. All the best! Pavel.
Re: [ccp4bb] Why appear the grid on the low resolution areas
Xingliangzhang These are Kikuchi lines that usually are observed in the electron diffraction from thick specimen. For X-ray they are called Kossel lines. Well, if you are so called high throughput structural biologist, you can forget about that, It is hard core diffraction physics. But if you think you have to know what it is - explore more the web. Copied from: Kikuchi lines pair up to form bands in electron diffraction from single crystal specimens, there to serve as roads in orientation-space for microscopists not sure what they are looking at. Intransmission electron microscopes, they are easily seen in diffraction from regions of the specimen thick enough for multiple scattering[1]. Unlike diffraction spots, which blink on and off as one tilts the crystal, Kikuchi bands mark orientation space with well-defined intersections (called zones or poles) as well as paths connecting one intersection to the next. Experimental and theoretical maps of Kikuchi band geometry, as well as their direct-space analogs e.g. bend contours, electron channeling patterns, and fringe visibility maps are increasingly useful tools in electron microscopy of crystalline and nanocrystalline materials[2]. Because each Kikuchi line is associated with Bragg diffraction from one side of a single set of lattice planes, these lines can be labeled with the same Miller or reciprocal-lattice indices that are used to identify individual diffraction spots. Kikuchi band intersections, or zones, on the other hand are indexed with direct-lattice indices i.e. indices which represent integer multiples of the lattice basis vectors a, b and c. Kikuchi lines are formed in diffraction patterns by diffusely scattered electrons, e.g. as a result of thermal atom vibrations[3]. The main features of their geometry can be deduced from a simple elastic mechanism proposed in 1928 by Kikuchi[4], although the dynamical theory of diffuse inelastic scattering is needed to understand them quantitatively[5]. In X-ray scattering these lines are referred to as Kossel lines [6]. See also in a dissertation by Eric Sutter The Theory of Kossel Lines http://adsabs.harvard.edu/abs/2000PhDT...109S Or in http://scripts.iucr.org/cgi-bin/paper?S0021889805024660 Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Sep 14, 2010, at 08:59 , Mark J van Raaij wrote: Interesting! it appears to be some kind of secondary order...I hope someone wise/experienced can shed more light on this. the diffraction spots appear to fall consistently in the middle of the hexagonal(ish) grid lines, so it must be some partial order effect related to the unit cell. do you also see this with data collected from an unfrozen crystal? if so, it is a crystal property. you also appear to have quite strong solvent/ice rings, in any case I would optimise the cryo-protection/freezing procedure. Mark Quoting xingliang zhang xingliangche...@gmail.com: Dear everyone, Recently,we collected data of a native protein crystal on synchrotron in Shanghai. When we did with the original data with HKL2000, we found an unconversant phenomenon ,just as the picture in the enclosure, there were some grid indicated by arrows appearing on the low resolution areas.The crytal grew in 20%PEG3000,100mMTris-Cl,200mM Ca(OAc)2 ,and the cryo-protectant is 20% sucrose mixed with well buffer?Who can tell me the reasons it appear the grid ?because of the sucrose? I'll appreciated for any explains and suggestion. Best wishes xingliangzhang -- Best wishes! xingliangcheung,PhD,candidate Protein crystallography Lab ,College of biological sciences ,China agricultural university. No. 2 yuanmingyuan west road HaidianDistrict, Beijing, 100193 Tel:01062814122, E-mail:xingliangche...@gmail.com e-mail%3axingliangche...@gmail.com
Re: [ccp4bb] About SAD phasing
Yes! Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Aug 30, 2010, at 21:32 , Jane Bailey wrote: Hi, All I would like to ask whether is it possible to allocate the Se site and obtain the phase by just using the SAD data set (no native dataset used)? Thanks, Qing
Re: [ccp4bb] Heavy atom sites?- Only them?
The present generation of high throughput structural biologists stays on the intellectual shoulders of the giants of crystallography from past days (modifying GOOGLE). In the military jargon, in the constant wars with the structures, situation described in this exchanges is called encounter. To know all this - is as to know how to calculate without computers. Or to have Mentates to navigate in space without computer technology which is presently prohibited after attempts of computers to take over (citing Dune). Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Aug 20, 2010, at 19:42 , Clemens Vonrhein wrote: Dear Eleanor at al, On Fri, Aug 20, 2010 at 05:20:05PM +0100, Eleanor Dodson wrote: There is quite a lot of background to these Qs in a variwty of text books, and something on this website. http://www.ccp4.ac.uk/dist/html/pxmaths/index.html Nice page :-) When changing hand you need to consider whether this also involves a change of spacgroup; eg P32 instead of P31 It always does involve a change to the enantiomorph. One only ever needs to check two solutions: * if you started with your dataset in P31 you will have to check (X,Y,Z) P31 and (-X,-Y,-Z) P32 and never: (-X,-Y,-Z) P31 * if you started with P32 just check (X,Y,Z) P32 and (-X,-Y,-Z) P31 and never: (-X,-Y,-Z) P32 It helps to process data always in the same enantiomorph spacegroup (since the extinction rules are identical): e.g. sticking with P61 and P62 at the beginning and never go into P65 and P64 for a start (only after phasing or MR points to that spacegroup). Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
Re: [ccp4bb] detection of anomalous signal using HKL2000
Quoting Phil Evans p...@mrc-lmb.cam.ac.uk: Can anyone explain what Zbyszek Otwinowski means by Chi squared? If I understand properly, CHI**2 value as used in Scalepack is: SUM(I-Ij)**2/SUMsigma(I)**2 (I have to use formula editor to write it properly, but the idea is clear) and is useful in exhibiting and detection of systematic errors. Intuitively this value will be close to 1.0 if only counting statistics contribute to errors in measurements of I. Drawing CHI**2 distribution as a function of various values such as frame number, shell of resolution, intensity of reflection etc. may show very interesting things related to the status of systematic errors during data collection. In the case of absence of systematic errors and radiation decay and in presence of a stable X-ray beam these distributions will be featureless and their value will be dependent on a counting statistics, quality of a detector and absorption of a crystal mainly. Systematic errors of various sources change these distributions in a sensible way. Despite the fact that it is impossible to correct systematic errors, understanding of CHI**2 distributions lead to better understanding of the experiment and in most cases these systematic errors can be eliminated leading to a perfect data shaped mostly by a counting statistics. CHI**2 distributions a la Otwinowsky - Minor (or else, I also do not know if Zbyszek Otwinovsky developed it by himself or adopted from earlier sources),is as used in Scalepack an instrument of a great power. FF Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica D, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 I can't find a definition in any of his papers (though I may have missed it). Is there a reference? It doesn't seem obviously related to the chi squared distribution (In probability theory and statistics, the chi-square distribution (also chi-squared orχ²-distribution) with k degrees of freedom is the distribution of a sum of the squares of k independent standard normal random variables. http://en.wikipedia.org/wiki/Chi-square_distribution) Phil On 29 Jun 2010, at 21:14, Felix Frolow wrote: Graphical information from Scalepack as used in HKL2000 is of unprecedented help to detect anomalous signal. Anomalous detection for S anomalous data using CHI**2 and Rfactor statistics for reflections with averaged and separated Bijvoet pairs is attached. It is very well described in HKL2000 manual. There is nothing special about data collection (strategy was used) and measurement was relatively fast (4 h on MicroMax007 and RaxisIV++). BTW Rfactor is 1.9% with separated Bijvoet reflections and 2.6% with averaged BTW James Holton website calculate for this case 0.078 crystal Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica D, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 Quoting Bernhard Rupp b...@ruppweb.org: I second the hkl2map/SHELXCDE approach. Two complete examples explaining how to do this for MAD and S-SAD cases are in my book. I wish to emphasize the importance of a) running enough trials b) careful selection of resolution cutoffs c) look at the solution distribution d) play with SHELXE parameters. The hkl2map graphs are enormously helpful for this purpose. BR -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Tim Gruene Sent: Tuesday, June 29, 2010 2:29 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] measure of anamolous signal Dear Murugan, you can use the program hkl2map from Thomas Schneider, available at http://webapps.embl-hamburg.de/hkl2map/ It's a graphical interface to the programs shelx c/d/e which are available from http://shelx.uni-ac.gwdg.de/SHELX/index.html With SAD data you want to look at the d/sigma line at the end of the shelxc output. Where that drops below about 1.3 is approximately where your anomalous signal ends. You might get slightly improved statistics with xprep instead of shelxc, but xprep is not free and you have to get a copy from Bruker-AXS. Tim On Tue, Jun 29, 2010 at 02:35:29PM +0530, Vandu Murugan wrote: Dear all, I have collected a 2.7 angstrom home source data with Cu-Kalpha source for a protein with 6 cysteines, with a multiplicity of around 23. I need to know, is there any significant anamolous signal present in the data set, since there is no good model for my protein. Can any one tell, which program to run, and what parameter to see? Thanks in advance. cheers, Murugan -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077
Re: [ccp4bb] Converting cif-files into pdb-files / reading cif -files into coot
Hi Fred Well, it is ironic that after acquiring ability to determine a protein structure some times in a few minutes we are still failed my format conversions like 30 years ago :-( Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica D, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972 3640 8723 Fax: ++972 3640 9407 Cellular: ++972 547 459 608 On Jun 1, 2010, at 16:30 , Vellieux Frederic wrote: Hi Christian, Had exactly the same problem (converting an mmCIF file into a PDB). I located and installed CIFTr . The version I have running here is ciftr-v2.053 . I am afraid I can't remember exactly where I downloaded it from. I think it one of the PDB associated files. Fred. Christian Engel wrote: Dear All, I am looking for a ccp4 program that reads in cif-files and converts them into pdb-files, including the CRYST1 card. Can anybody suggest a solution? I didn't find any in ccp4i, e.g. the coordinate utilities. I also tried COOT to read in cif-files (downloaded from the pdb server). For one example it crashed, for others it doesn't colour the bonds properly if Bonds (Colour by Atom) is chosen but shows all bonds in one colour. Is that a known feature? If I save these coordinates in pdb-format and try to read it back, I get an ERROR saying: Wrong ASCII format of an integer. Thanks for any suggestions Christian Engel */Mit freundlichen Grüßen / Best regards / Cordialement/* Dr. Christian Engel Sanofi-Aventis Deutschland GmbH RD CAS Structural Biology FFM Industriepark Hoechst Bldg. G877, Room 020 D-65926 Frankfurt am Main t: +49 69 305 12946 f: +49 69 305 80169 w:_www.sanofi-aventis.de_ 125 Jahre Arzneimittel aus Deutschland von sanofi-aventis * Sanofi-Aventis Deutschland GmbH · Sitz der Gesellschaft: Frankfurt am Main · Handelsregister: Frankfurt am Main, Abt. B Nr. 40661 Vorsitzender des Aufsichtsrats: Hanspeter Spek - Geschäftsführer: Dr. Martin Siewert (Vorsitzender), Ulf Bialojahn, Dr. Matthias Braun, Peter Guenter, Prof. Dr. Dr. Werner Kramer, Dr. Klaus Menken, Dr. Heinz Riederer *
Re: [ccp4bb] X-Ray films
You are absolutely right, it was not a student but an elderly scholar, probably professor of crystallography in one of the London colleges or Universities. Maybe Imperial (so we can also trace this person). Anthony Burgess, the author, probably projected someone he knew into the book. In the movie there is a scene of Alex's gang beating an elderly scholar, but the list of books that were in his possession is not there. I think it is still counts. I whatched the film after I have reading the book, and knew that crystallography book is there. ;--) Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica D, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972 3640 8723 Fax: ++972 3640 9407 Cellular: ++972 547 459 608 On Apr 16, 2010, at 11:33 , Philip Leonard wrote: I have a vague recollection of a student carrying books about crystallography getting beaten up at the start of Clockwork Orange. This might only be in the book though... This opens a whole new can of worms! How many films would contain references to crystallography if only the screenwriter hadn't decide to omit the reference in favour of something else more fun. Phil. -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of harry powell Sent: Thursday, April 15, 2010 5:16 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] X-Ray films Hi Not a question about films for recording X-rays on, but a question about films about X-rays, Crystallography and related subjects! I was wondering what ccp4bbers favourite movies involving real science, especially crystallography might be? If they're from Hollywood, though, I'd guess it should be favorite... I'm a little tired, but the only one I can think of at the moment is actually based on results from fibre diffraction - Life Story, with Jeff Goldblum. There must be others, though. Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH -- DISCLAIMER: This e-mail and any attachments are confidential. They may contain privileged information and are intended for the named addressee(s) only. If you are not the named addressee do not disseminate, distribute, copy or retain this e-mail, or any part of it, in any manner. Please notify the sender immediately if you have received this e-mail by mistake and delete it from your system. The sender does not accept any liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. Unless expressly stated, opinions in this e-mail are those of the individual sender, and not of Galapagos NV or any of its subsidiaries including BioFocus. Galapagos NV and its subsidiaries including BioFocus reserve the right to monitor all e-mail communications through its network. Although this e-mail has been scanned for all known viruses, the sender does not guarantee that this message is virus-free and disclaims any liability for viruses that may be transmitted with this message.
Re: [ccp4bb] X-Ray films and BOOKS
I would also suggest CP Snow, The search, written in 1934 Very crystallographic, very touching, probably inspired by CP Snow friend JD Bernal This is about our life, friends... FF Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica D, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972 3640 8723 Fax: ++972 3640 9407 Cellular: ++972 547 459 608 On Apr 16, 2010, at 21:38 , James Holton wrote: Well, I have to admit that that whole R32 vs H32 thing bugs me too ... James Stroud wrote: On Apr 16, 2010, at 5:15 AM, Judith Murray-Rust wrote: The list of books is here. http://kubrickmovies.hostei.com/aconovel.html Dim and Pete doing a tug-of-war with /The Rhombohedral System/. The starry prof type began to creech: 'But those are not mine, those are the property of the municipality, this is sheer wantonness and vandal work,' or some such slovos. And he tried to sort of wrest the books back off of us, which was like pathetic. 'You deserve to be taught a lesson, brother,' I said, 'that you do.' This crystal book I had was very tough-bound and hard to razrez to bits, being real starry and made in days when things were made to last like, but I managed to rip the pages up and chuck them in handfuls of like snowflakes, though big, all over this creeching old veck, and then the others did the same with theirs, old Dim just dancing about like the clown he was.
[ccp4bb] Phasing statistics now and once
Well, Frank, your membranous by their science (not very frequently) colleagues will say - first of all look on the properly calculated electron density maps first of all - good map will be manifested by continuity, shape, accordance to the secondary structure elements etc. For us/them (membranous colleagues) evolution of many one-number qualifiers such as PP and FOM (very important), Rcullis (less important) during phasing progress was/is absolutely necessary parameters to observe to guide phase development . Values of the standard deviations of differences between heavy atom and protein phases are important to judge the validity of the phases, they should be ideally 51.96 and 90 (in degrees) for non-centric and centric reflections respectively (Maybe Eleanor will remind us a source of these numbers). They correlate with linear and exponential parts of the scale factors. These values are calculated and printed by MLPHARE, which recently is forgotten, ignored and even despised by many newcomers. BTW MLPHARE was one of the first phasing program that properly calculated FOM (usually low) and not overestimated , ready to please crystallographer (usually high) FOM, accompanying non-interpratable electron density map. Many excellent phasing parameters are also supplied by SHARP, a vintage brand tool for the manual development of phases in extremely difficult cases. Rumors also claim the superiority of phasing and reported phasing statistics in HKL3000. To conclude: For automatique protein structure solutions cases - who cares about one number qualifiers? Good auto-tracing algorithms will never trace wrong structure. It you get your structure from ARP/wARP it is most probably correct. However, for cases that usually go to the most prestigious journals (reciprocality of resolution - impact factor can be observed frequently), the demand for several well defined parameters that will properly describe overall quality of phasing should be revived to bring back from dusty pages of complementary materials concise, but full description back into the main pages. And if there is no place for that according to the publishers policies, publish in journals such as Acta Crystallographica, that provide such place. When authors claim experimental structure solution - ALL experimental data used for phasing, such as heavy atom derivative data sets with anomalous signal in them, complete MAD and SAD data, heavy atom coordinates etc. that will give ability TO RE-SOLVE the structure MUST BE deposited in PDB or elsewhere. Who knows, maybe by availability of the data, decorations even higher than publication in prestigious journals will be shaken and snapped off from the gleaming uniforms of the royal hussars, or even will not be given in the first place, to clean the protein crystallography from the reappearing stench of forgery, intentional or not - alike. Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972 3640 8723 Fax: ++972 3640 9407 Cellular: ++972 547 459 608 On Apr 12, 2010, at 14:24 , Frank von Delft wrote: I fully agree, for high quality data. What though if the data are not impeccable and the structure necessarily ropey? E.g. 4A phases and anisotropic diffraction. By what metrics do we then judge the results? (I don't know the answer, btw, but our membranous colleagues surely spend quite a bit of time with that question...) phx. On 12/04/2010 12:10, Anastassis Perrakis wrote: Hi - A year or so ago, I have asked as a referee somebody to provide for a paper the statistics for their heavy atom derivative dataset, and for the phasing statistics. For some good reasons, they were unable to do that, and they (politely) asked me 'what would it change if you knew these, isn't the structure we present impeccable?'. Well, I think they were right. Their structure was surely correct, surely high quality. After that incident and giving it some thought, I fail to see why should one report e.g. PP or Rcullis, or why will I care what they were if the structure has a convincing Rfree and is properly validated. If someone wants to cheat at the end of the day, its easy to provide two numbers, but its hard to provide a good validated model that agrees with the data. (and, yes, you can also make up the data, but we have been there, haven't we?!?) So, my question to that referee, likely being a ccp4bb aficionado that is reading this email, or to anyone else really, is: What would it help to judge the quality of the structure or the paper if you know PP, Rcullis and FOM? Best - A. PS Especially since you used SHELXE for phasing these statistics are utterly irrelevant, and possibly you could advice
Re: [ccp4bb] anomalous difference fourier maps, or how to keep chastity of CCP4BB
I guess Phenix people are just trying to help. After all they are not selling us Zinger sewing machines (zin...@sewing CO, my apology) nor they are trying to push us Kirby (http://www.consumeraffairs.com/in_home/kirby.htm, no apology) vacuum cleaners using naive chastity of CCP4BB site. They are a bunch of young dynamic people, all of them excellent crystallographers, who are participate in evolution of the alternative tool for crystallographic calculations with already possess visible nice features. They trespass borders of CCP4BB quite frequently, but for that they don't have to be prosecuted. However CCP4BB subscribers can start discussion about implementation of chastity belt (see Wiki site http://en.wikipedia.org/wiki/Chastity_belt for explanation of chastity belt metaphor) for prevention of CCP4BB abuse. Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972 3640 8723 Fax: ++972 3640 9407 Cellular: ++972 547 459 608 On Feb 19, 2010, at 16:04 , Gerard Bricogne wrote: Dear all, This is a remark I have wanted to make for a long time but managed so far to repress. However, this case is absolutely clear: Ivan was not asking for general advice on how to carry out a general task, but how to perform a specific task with the CCP4 software. In response we get (surprise, surprise, ...) another instance of the relentless touting for Phenix on the CCP4BB, which has long been an expected (or tolerated?) feature of this BB. Contributions from Phenix developers are of course much appreciated when questions are about general crystallographic matters where their expertise and experience is valuable; but when people ask specifically how to do something with CCP4 programs, could they please not be grabbed by the sleeve and enticed to buy their sweets from the shop next door? In this case, for instance, Ivan thanks guys (plural) for the answers he got (All of your suggestions were great). Perhaps one of those was a CCP4-based answer, but if so it has not even been communicated to the rest of the CCP4BB subscribers - so not only is this touting in bad taste after a while: it even interferes with the sharing of expertise in using the CCP4 software, which after all must be one of the main missions of this BB. I have long wondered whether anyone on the CCP4 side been assigned the task of answering every question to the Phenix BB by describing how to do it with CCP4 programs ... . With best wishes, Gerard. -- On Thu, Feb 18, 2010 at 03:53:02PM -0800, Pavel Afonine wrote: Hi Ivan, two ways (at least) to do it in PHENIX: - phenix.refine always computes anomalous difference Fourier map (provided that your input data file contains Fobs(+) and Fobs(-)). The command below will do it: phenix.refine model.pdb data.mtz strategy=none main.number_of_macro_cycles=0 output.prefix=maps_only - you can use phenix.maps that is a general tool to compute a broad variety of maps. Type phenix.maps from the command line for usage instructions. You need to have the latest development (or one of) PHENIX nightly build for this. All this is available from the GUI too. Pavel. On 2/18/10 3:34 PM, xaravich ivan wrote: Hello, I wanted to make an anomalous difference fourier map of a structure with zinc bound to it. However I have not been successful in making the map and I would really appreciate your help if anyone could suggest me where I am going wrong. I solved this zinc bound structure, by molecular replacement from a calcium bound structure (1.4 angstrom) that I solved. I want to show that the zinc binds to the identical site by the anomalous difference fourier map. I am using CCP4i and the steps that I have been taking are, (names of the files are arbitrary) 1) generating structure factors and phases from the solved coordinates by SFALL Input files zinc bound pdb original zinc .mtz data from synchrotron output file sfall.mtz 2)merging the sfall.mtz containing the PHICalc and FCalc columns with the original synchrotron .mtz file containing DANO and SIGDANO by running CAD. input files sfall.mtz and zinc synchrtron .mtz output file CAD.mtz 3) Running FFT to make anomalous map, selecting labels from CAD.mtz as input files. There is an output map file but nothing in it. all the values are 0 and the map is not recognized by coot. There is no error message in the log file. I must be missing something or doing something wrong/stupid. Thanks, Ivan -- === * * * Gerard Bricogne g
Re: [ccp4bb] where I have been going wrong in crystallization?
If respect is concerned, try to stop a blow of a sharp samurai sword with a sharp word. I myself have no problems whatsoever with the Rigaku recipes. And yes, I have stopped, at leas once, a blow of samurai sword with my bare hands. Since than I paint pictures with my left foot. BTW In ALL my crystallization attempts I ALWAYS use double distilled (rectified) water. However there is, I must admit, a fume of triple distilled Jameson around (almost always). All this is not written in the Rigaku recipe but is very important. Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica D, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972 3640 8723 Fax: ++972 3640 9407 Cellular: ++972 547 459 608 On Dec 21, 2009, at 23:02 , mjvdwo...@netscape.net wrote: I was going to comment that I have learned the following: respect does not mean the same thing in all places in the world. Some time back I had a protein here that I thought needed extra respect and I had learned from a Rigaku employee how to do this - I bowed very very deeply in front of the protein before handling it. But it still did not crystallize. So when I complained to the Rigaku employee about the recipe, he asked with appropriate hesitation in his voice: are you saying that you only bowed ONCE? In defense of the original poster, I think the recipe on the Rigaku web site is entirely correct, but it does not specify how to pay proper respect. This was self-evident to the person who wrote down the recipe, but as we all know, what it obvious to one person, is not obvious to the next - especially in such difficult things like respect. Good recipes are indispensable and should be explicit about such important ingredients. Mark -Original Message- From: Mark J. van Raaij mark.vanra...@usc.es To: CCP4BB@JISCMAIL.AC.UK Sent: Mon, Dec 21, 2009 12:18 pm Subject: Re: [ccp4bb] where I have been going wrong in crystallization? - I think the original poster was only calling attention to the fact that some proteins want to be treated respectfully in order to crystallise (and the fact that Rigaku Japan realises this). I find that indeed the case. Other proteins, however, prefer the attitude I don't know why I am setting up these drops, this protein is too crappy to crystallise, i.e. a challenge. Lysozyme, on the other hand, even crystallises under conditions of complete indifference. At least I find that every student in a practical course can get nice crystals of lysozyme, and a majority of these drops have been set up under conditions of complete indifference...maybe lysozyme is not a protein after all, but a salt: lysozyme-chloride / LyCl7 ? Mark PS the detailed protocols and experiences are useful though. Quoting Jeffrey Wilson wil...@ucmail.uc.edu: I was recently testing out the 30% PEGMME 5k, 0.1M NaOAc pH 4.5, 1M NaCl method mentioned in a Hampton Research catalog and attributed to Enrico Stura. I see that he has also just commented on this thread. I found that at 80mg/ml, batch with 1.5ul:1.5ul protein to precipitant ratio, lysozyme crystallized in about 1 hour. Jumping that up to 150mg/ml allowed for crystallization in minutes. Hanging drop behaved similarly. I was using lysozyme from Sigma. Jeff Jeffrey Wilson, Ph.D. University of Cincinnati College of Medicine Molecular Genetics Department 231 Albert Sabin Way MSB 3109A Cincinnati, OH 45267-0524 (513) 558-1360 On Dec 21, 2009, at 11:12 AM, MARTYN SYMMONS wrote: Dear All checking out the Lysozyme crystallization methods on the web I liked the Rigaku Instructions that I found: (http://www.rigaku.com/protein/crystallization.html) ...create a drop of 3ul lysozyme solution, and 3 ul of well solution, respectfully, for a total drop size of 6ul... So perhaps sometimes I am just not respectful enough to deserve crystals ? good wishes to all regards, Martyn --- Martyn Symmons MRC-MBU Cambridge UK 'Chan fhiosrach mur feòraich.' Gaelic proverb - Nothing asked, nothing learned.
Re: [ccp4bb] fake images and R-Rfree values
I must add something... ID14-2 beam line in our hands produced during first decade of 2000's data sets that for structures at about 1.8 - 1.6 Angstrom constantly leaded to a very good R - Rfree (in the range of 12 %-18%) As an example see PDB entry 1Y9A. If will be needed I will supply diffraction data for several structures. Such quality produces problems as a referee accused us by over-fitting Rfree whatever it means. He also new what is a theoretical difference of R-Rfree in any resolution? During our discussions recently with Dr Alexander Popov, responsible for the ESRF ID23-1 beam line on this matter Dr Popov suggest that it is because the X-ray beam on this station is very large. I also think that its is largely parallel, old quality of the synchrotron lines. Maybe other people who noticed similar thing may add more. BTW final data set scaling statistics (SCALEPAK) is shown: Shell Lower Upper Average Average Norm. Linear Square limitAngstrom I errorstat. Chi**2 R- facR-fac 20.00 3.79 7081.7 258.9 136.6 1.172 0.029 0.031 3.79 3.01 3894.0 157.2 95.2 1.2780.038 0.040 3.01 2.63 1514.9 97.1 64.8 0.9560.056 0.140 2.63 2.39 938.8 75.4 57.5 0.9760.074 0.080 2.39 2.22 717.1 74.5 59.5 0.9250.093 0.100 2.22 2.09 534.2 71.6 62.2 0.9470.122 0.116 2.09 1.99 398.6 70.6 65.1 0.9150.164 0.169 1.99 1.90 258.1 69.1 66.3 0.957 0.256 0.299 All reflections 1875.3 108.175.5 1.018 0.051 0.046 Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica D, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972 3640 8723 Fax: ++972 3640 9407 Cellular: ++972 547 459 608 On Mar 20, 2009, at 2:29 PM, James Holton wrote: Yes, Harry, indeed there is a program for simulating diffraction patterns. You can get a development snapshot of it here: http://bl831.als.lbl.gov/~jamesh/mlfsom/development_snapshot.tar.gz MLFSOM (mosflm in reverse) is not the only program of its kind in existence and I don't think it is a good idea to keep the fact that they exist a secret in any way. In fact, MLFSOM has been extremely instructive in establishing how important different sources of error are to the structure determination process, and where the threshold of solvability is in real-world units. I am writing this up now and I have given several talks about it recently but it has always puzzled me that noone has EVER asked me if there is some way to identify as fake the images that come from MLFSOM. The answer to this question is: Yes, there are several. Moving on... When it comes to Garib's original question of do we need the images, I am definitely of the opinion that the answer to this question is yes. In fact, I would like to ask Garib and everyone else if they can answer the question: Why is Rcryst/Rfree from almost every protein crystal structure on the order of 20% when the intensities are generally measured to better than 5%? What are we missing? Small molecule structures are unpublishable with Rcryst Rsym because this means that the presented model does not explain the observations to within experimental error. I will tell you for nothing that if you feed fake data from MLFSOM into Elves and ARP/ wARP, you will get back an Rcryst/Rfree that is roughly equal to Rsym (~5-6%), so this means that none of the sources of error I have included in MLFSOM: photon-counting noise, shutter jitter, beam flicker, sample vibration, diffuse scatter, absorption effects, funny spot shapes, radiation damage, detector read-out and calibration noise. None of these sources of error are big enough to explain the R-factor gap in macromolecular crystallography. So, if you don't know what it is we are missing, how can you be sure it is not in the image data? -James Holton MAD Scientist harry powell wrote: Hi I've heard of a tool from the Golden State which could (potentially) be used
Re: [ccp4bb] 3ftt and gremlins
Pavel, I have a problem with the number of reflections for refinement PHENIX report a. I have almost complete data for the data set - 48071 reflections. I keep always anomalous pairs separated. PHENIX reports (using phenix.model_vs_data.log) 94475 reflections (reasonable, taking into account 98% data and possible mismatch in anomalous pairs). I assume that (+) and (-) are separated in this case. b. Problems come when depositing data to PDB using their tools. They do not accept ( I think) anomalous separated data and complain about number of reflections that is not consistent between reflections file and PDB file header. c. What happened in the extreme cases? Let us say that for anisotropic data I have 78% of completeness. The anomalous data is separated. Will PHENIX use during refinement complete set of reflections ( for various density maps calculation) or it will use only WHAT IS THERE IN THE INPUT FILE? Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica D, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972 3640 8723 Fax: ++972 3640 9407 Cellular: ++972 547 459 608 On Mar 12, 2009, at 8:27 PM, Pavel Afonine wrote: Hi Dale, 1) There is a need for additional validation of structure factor depositions. PHENIX has tools for this: 1) phenix.cif_as_mtz will convert the PDB data file with diffrcation data into MTZ file. It automatically will figure out if the data are X-ray: Iobs or Fobs, or Neutron Fobs or Iobs. 2) The next step will be running phenix.model_vs_data that will take the MTZ from from above and the corresponding PDB file and give a complete statistics, that you can immediately compare with the published value. Note, phenix.model_vs_data can handle: - twinned data; - neutron data; - all unknown ligands dictionaries are generated internally; - PDB files with multiple models (with multiple MODEL records). I run it every month or two, and so I have a nice list of interesting cases. The database of all converted to MTZ data files is used internally by PHENIX developers for various developments etc... In fact, this was used in POLYGON validation tool: Acta Cryst. (2009). D65, 297-300 Pavel.
Re: [ccp4bb] 3ftt and gremlins
My personal experience is ( I frequently re-refine structures I cite if all the data for that exist in PDB) that PDB possesses a significant number of artifacts unsupported by reality but by the wild imagination only. These artifacts are originated from the modest, good and excellent laboratories alike. They are maybe not as sounding as tracing the protein main-chain in reverse mode, but sometimes they support quite significant and sounding conclusions. I myself suffered frequently on a stage of structure validations by PDB due to the wrong treatment of the anisotropic thermal parameters and erroneous Rfactor calculationsdue to that during structure factors validation. I think this problem is resolved now or at least I am not bothered by annotators anymore for that matter. Personally I dot believe that by fingerposting events of miss- interpretations and errors that are difficult to catch will help to resolve the situation. Peer-reviewing of the data that enter the PDB is unrealistic. Automatic re-refinement of the all PDB content which is in the tune with modern high-throughput of everything approaches will not solve the problem either. It will produce a bit better refinement statistics in the best cases. Nothing can change human eye interpretation of the electron density until AI problem will be solved. Responsibility for the correct interpretation of the structure is of these who publish it and of these who cite it. To resume I only wonder, why to fingerpost to 3ftt direction, why now, why in public and why so emotional ? Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica D, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972 3640 8723 Fax: ++972 3640 9407 Cellular: ++972 547 459 608
Re: [ccp4bb] Structural biology inside the cell
Dear Mark Stay calm Buzz-words come and very frequently do not stay, they go away with the artifacts they advocate... Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica D, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972 3640 8723 Fax: ++972 3640 9407 Cellular: ++972 547 459 608 On Mar 12, 2009, at 6:14 PM, Mark J. van Raaij wrote: Dear All, a News Views article in Nature 458, pages 37-38 of 5 March 2009 (link below) states: The development of structural biology WAS historically based on the principle of divide and conquer — individual proteins were purified to homogeneity and their atomic structures were solved in vitro by using either X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. This approach WAS tremendously successful, and led to the creation of a protein-structure databank that currently contains more than 50,000 structures. I find the past tense here too much... Greetings, Mark Mark J. van Raaij Dpto de Bioquímica, Facultad de Farmacia Universidad de Santiago 15782 Santiago de Compostela Spain http://web.usc.es/~vanraaij/ http://www.nature.com/nature/journal/v458/n7234/full/458037a.html Structural biology: Inside the living cell
Re: [ccp4bb] Arp/warp space group P 21 2
Among very many other great things Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica D, co-editor e-mail: [EMAIL PROTECTED] Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: On Jun 10, 2008, at 9:40 PM, George M. Sheldrick wrote: SHELX has been able to handle P 21 2 21 and other such space groups without any problems for the last 38 years! George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Tue, 10 Jun 2008, Garib Murshudov wrote: I think in refmac it has already been fixed (since October or so). refmac 5.4 and later version should handle all available space groups with their various disguises. Garib On 10 Jun 2008, at 16:11, Clemens Grimm wrote: seems to be a 'non-standard' setting. Refmac also has problems with this spacegroup, reindexing to P21 21 2 fixed the problem for me. Clemens Quoting PhilEvans [EMAIL PROTECTED]: Is there a reason why Arp/warp doesn't like space group P 21 2 21? Phil
