[ccp4bb] generate Hendrickson Lattman coefficients
Dear all, I would like to generate HL coefficients to an mtz file I get from Phaser after Molecular replacement. Does anyone know how to? also, does anyone know how to within Phenix? Best Almu -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
[ccp4bb] Large conformational change upon phosphorylation
Dear all, I am looking for proteins which undergo large conformational changes (more than 5 A RMSD) upon phosphorylation. A reference to structures or biochemical/biophysical experiments on such proteins will be very helpful. Thanking you -- Debayan Dey
[ccp4bb] Phaser segmentation fault (core dump)
Hello Everyone, I'm trying to using Phaser to perform molecular replacement, however each time I run my input script Phaser ends with a segmentation fault. Here is the error phaser0.inp: line 29: 1414 Segmentation fault (core dumped) phaser EOF My input script can be found here: https://gist.github.com/anonymous/2b474f501e1ad694be47 If anyone can provide any input I would be greatly appreciative. Best, Parker
Re: [ccp4bb] generate Hendrickson Lattman coefficients
Hi Almudena, also, does anyone know how to within Phenix? that's the tool that should do it: http://www.phenix-online.org/documentation/reciprocal_space_arrays.htm Note there is a corresponding utility in the GUI (if I recall correctly under Reflection tools). Pavel
Re: [ccp4bb] generate Hendrickson Lattman coefficients
Thanks a lot!!! I also managed with ccp4/reflection data utilities/convert FoM to/from HL Best wishes Almudena 2014-03-24 15:22 GMT+01:00 Pavel Afonine pafon...@gmail.com: Hi Almudena, also, does anyone know how to within Phenix? that's the tool that should do it: http://www.phenix-online.org/documentation/reciprocal_space_arrays.htm Note there is a corresponding utility in the GUI (if I recall correctly under Reflection tools). Pavel -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
[ccp4bb] Announcement: EMBO Practical Course on Protein Expression, Purification and Characterization (PEPC9)
Dear all, we are pleased to announce that applications are open for the EMBO Practical Course Protein expression, purification and characterization/crystallization (PEPC9), which will be held at EMBL Hamburg from the 8th of September until the 16th of September 2014. This is an extensive hands-on course with practicals in cloning, expression (E. coli Baculo virus), purification (with and without tags) and characterization (CD, thermofluor, light scattering and crystallization). The course is aimed at PhD students and postdoctoral students who want to improve their protein production skills to be able to structurally characterize their proteins. Speakers include: Imre Berger, EMBL Grenoble (MultiBac system) Huseyin Besir, EMBL Heidelberg (Cloning) Louise Bird, OPPF, Oxford University (E. coli expression) Opher Gileadi, SGC, Oxford University (Purification optimization) Martin Halberg, Karolinksa Institutet (Thermofluor and other optimization techniques) Michael Marr, Brandeis University (CSH course on protein purification) David Hacker, EPFL Lausanne (Mammalian cell expression) Alex McPherson, University of California (protein crystallization) Preben Morth, University of Oslo (membrane protein production crystallization) Joanne Nettleship, University of Oxford (E. coli expression) Janet Newman, CSIRO (Crystal optimization) Dmitri Svergun, EMBL Hamburg (SAXS) Participants are encouraged to bring their own sample to the course for cloning and expression in E. coli and baculo-virus, high-throughput crystallization, and biophysical characterization. A more extensive characterization of samples is possible under the auspices of Biostruct-X: http://www.biostruct-x.eu/content/apply-funding For more information, please visit our website: http://events.embo.org/14-pepc/ or contact us by email: pe...@t-online.de Best regards, Rob Meijers, , Annabel Parret, Stephane Boivin Christian Loew EMBL Hamburg Notkestrasse 85 D-22603, Hamburg, Germany
Re: [ccp4bb] pairwise CCano - SUMMARY
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear all,
I received three responses to my Email, those two you saw on the BB
and one from Clemens Vonrhein who pointed me at the program
'check_indexing' from the AutoBuster Suite.
I tried both pointless and check_indexing, and both work equally fine.
I did not try Pierre Legrand's solution because I already had two, but
I am convinced it works equally well.
Pointless has the advantage of doing all combinations automatically,
check_indexing has the advantage of the more concise output. Since
check_indexing only relates all input file to the first one, I applied
the following bash-script to get all pairwise combinations, which
repeatedly pops the first mtz-file from the stack until there are only
two left:
#-- 8 snip --
mtzs=(1.mtz \
2.mtz \
3.mtz
)
while (( ${#mtzs[*]} 1 )); do
check_indexing -v ${mtzs[*]}
mtzs=(${mtzs[@]:1})
done
#-snap 8 -
The list of mtz-files can surely be expanded (I used the script with
14 entries).
In my particular case pointless had another important advantage which
gave me a great crystallographic lesson:
The beta-angles of all these mtz-files (spacegroup C2) vary by less
than 0.1 degree about 90degrees. While check_indexing takes all the
crystallographic reindexing possibilities into account, pointless also
realised that in this particular case, the crystallographic convention
of beta90 degrees would render some of the data sets incompatible
with others and therefore reindexed them to beta90degrees. I was
reminded the molecules don't attend lectures in crystallography and
may therefore not obey conventions. In case of a single data set this
is surely no problem, but in this case it was.
Of course XDS would have picked the correct indexing with beta89
degrees if only I had provided the same REFERENCE_DATA_SET to all data
sets, but I did not here, and I had to see the reindexing operator in
the form [-h -k l] from pointless in order to realise what was going on.
Thanks a lot for all three suggestions
Tim
On 03/14/2014 11:14 AM, Phil Evans wrote:
If you assigns them to different datasets in Pointless, then
Aimless will give you the cross-dataset correlations. By default it
will scale them to together first, but you can skip that if you
want
It might not scale well to a large number of files (OK up to about
10 I guess)
Phil
On 14 Mar 2014, at 09:33, Tim Gruene t...@shelx.uni-ac.gwdg.de
wrote:
Dear all,
I am looking for a tool that prints (and preferably plots, e.g. as
postscript) the pairwise anomalous CC vs. resolution for several
input HKL-files. xprep does this, but it is interactive and
requires a fair bit of typing. Since I have a large number of
HKL-files from XDS, I would like to script that and then flip
through the pages of the postscript-plots.
I looked into pointless but could not find even a table.
Since there recently were some publications one the use of many
files for phasing, I though such a tool should exist!?
Best, Tim
- --
- --
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 Icedove - http://www.enigmail.net/
iD8DBQFTMG2dUxlJ7aRr7hoRAiHUAJ9meTS1Fgc/xYQ2mdOoViVuB7Y8pgCdErms
cVnEfiLoM5SJXxbr+srO9PU=
=NybG
-END PGP SIGNATURE-
[ccp4bb] small molecule crystallography
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 -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London
Re: [ccp4bb] small molecule crystallography
Hi Andreas - My two cents, from having tried this a couple of times on small molecule crystals that crossed my path: - You can get an answer using only standard macromolecular crystallography programs. It may not be up to the standards of the small molecule community, but that's probably not what your student needs. - Denzo can handle small molecule diffraction - the key is to collect enough spots on each image. Use big oscillation ranges (10-20 degrees) and push the detector in as far as possible, with 2theta offset as well. - Use very short exposure times to avoid overloads. I also turned my generator down to minimum power. If your optics permit it, you might also slit down the beam. - Even with small molecules, crystal quality is important. Make sure you have good-looking diffraction - no streaky spots, multiple lattices, etc. The great thing about small molecule crystals is that you can always break off small pieces if the big chunk isn't clean enough - you have diffraction intensity to spare! - If your molecule of interest is chiral, you won't have to worry about the centric space groups that protein crystallographers never think about. If it's not (or there's a chance of a racemic mixture), then you should probably process in P1 and use Pointless to tell you the space group. - You can use SHELXS for direct methods structure determination if you're able to collect high enough resolution data. I believe this should work with 1.2 A data, and it ought to work well with 1.0 A or better. I found these webpages useful in helping me interpret the SHELX output: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Solve_a_small-molecule_structure http://shelx.uni-ac.gwdg.de/tutorial/english/shelxs.htm - If you have a heavy atom (iodine, iron, etc.) in the small molecule, you can probably get a phasing solution by SAD even with Cu Kalpha. You could probably even solve it by looking at the Patterson maps! Good luck! If it works, I think you'll be done in an afternoon. If it doesn't work, I'm not sure how to troubleshoot things. - Matt On 3/24/14 2:04 PM, 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 -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374
Re: [ccp4bb] small molecule crystallography
Andreas, What is your setup? We have a Cu Anode with an R-Axis IV, and just due to the geometry, the maximum resolution we can collect is around 1.4A. That won't do for small molecules. I think if your resolution is worse than something like 0.85A alarm bells start going off. If you can collect to higher resolution, you can process with XDS and read the XDS_ASCII.HKL (unmerged data) into xprep and run the output through shelxs/l. Olex2 is also pretty helpful for visualization and building. Cheers, Jens On Mon, 2014-03-24 at 18:04 +, 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
Re: [ccp4bb] small molecule crystallography
Dear Andreas, It's a closely guarded secret that the data collection for small molecules is not that different from that for macromolecular crystallography. (Otherwise there's the risk that more macromolecular folks might get hooked to the addictive charm of the small-molecule world!) Just mount the crystals (various oils typically work) and test them for diffraction. Usual tests: easily indexable, Bravais lattice, Laue group, integration stats? It helps if the compound is stable (which seems to be the case here?). Switch on the liquid nitrogen stream on the diffractometer, as usual. You may need to go down with the wattage, especially for a large crystal like you describe, and if a heavy metal is present. Try to measure data to at least 0.83 A if you can (requirement for Acta Cryst.; should be doable even on a Cu source), though that is not necessarily required for structure solution (better than 1.1 A should be fine for that). Programs after integration, through refinement: This is a matter of personal choice. There are many excellent software packages. Here's a list that does not claim to be exhaustive (in alphabetical order), as I hardly know all of the possibilities (others should be able to add to this list): CRYSTALS, D. Watkin group, Oxford: http://www.xtl.ox.ac.uk/crystals.1.html JANA, V. Petricek group, Prague: http://www-xray.fzu.cz/jana/jana.html SADABS, XPREP, SHELXT/SHELXS, SHELXL, G. Sheldrick, Goettingen: http://shelx.uni-ac.gwdg.de/SHELX/ SIR, C. Giacovazzo group, Bari: http://www.ic.cnr.it/icnew/site/index.php SUPERFLIP, L. Palatinus, Prague: http://superflip.fzu.cz/. For visualization, you could use ShelXle or Olex2 (on an occasion or two, I've even used Coot!). For validation, you would need PLATON and CHECKCIF, http://checkcif.iucr.org/. A disadvantage of small molecule crystallography is that structure solution now typically takes only a few seconds. So no time for coffee there! Wish you lots of fun nevertheless. Best regards, Navdeep --- On Mon, Mar 24, 2014 at 06:04:25PM +, 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 --- Navdeep Sidhu Departments of Structural Chemistry Pediatrics II University of Goettingen Office Address: Institute of Inorganic Chemistry Tammannstrasse 4 37077 Goettingen Germany Email: nsi...@shelx.uni-ac.gwdg.de Phone: +49 551 39 33059 Fax: +49 551 39 22582 Homepage: http://shelx.uni-ac.gwdg.de/~nsidhu/crystals_in_flatland.html ---
Re: [ccp4bb] small molecule crystallography
Dear Andreas, if you find a single crystal, you can use your favourite program for data collection, none of them should have problems with small molecule data. Since data integration only takes the Laue group into account, the space group make no problems, since also the Laue group of a protein crystal contains an inversion centre (cf. Friedel's Law). Make sure, however, that you do not merge your data upon scaling, especially not the Bijvoet pairs, so that you can determine the absolute structure later on. If your crystal is cracked, you can often get away with assuming it is still a single crystal - I recently published a structure where the diffraction images looked more like powder than a single crystal. If you cannot find a single crystal you may want to try the latest mosflm, of course, which can integrate several lattices. Once you collected the data you may want to continue with the programs available for small molecule crystals. Obviously I am biased here. From a physicist's point of view, i.e. within an error bar of about 10%, all crystal structures ever were refined with shelxl, and this is for many good reasons - one being that for publication the cif-file (not mmCIF!!) has to pass Ton Spek's program Platon ;-) For a standard structure determination you might even get away with not fully understanding shelxl by using Christian Huebschle's GUI shelXle. ShelXle is particularly handy for renaming the atoms and for assigning the element types in case you have to. You can also use Coot - there used to be a few issues, but it is getting tougher and tougher to find a shelxl-related bugs in coot, and Paul fixes any reports often faster than I can install the next version ;-) You can find the programs including tutorials required for solving and refining on the SHELX web site. Cheers, Tim On 03/24/2014 07:04 PM, 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 signature.asc Description: OpenPGP digital signature
[ccp4bb] rotating a map with maprot.
Hi all, I'm having a difficult time rotating a map from crystal A to crystal B. I obtained the transformation matrices from lsqkab. Specifically, the Crowther (Euler) Alpha beta gamma angles and the orthogonal A translation vector from superpose I supplied directly to maprot. However, the rotated map does not overlay with the target structure at all. Any ideas? Thanks!, F Here are the log files : lsqkab: ROTATION MATRIX: -0.40473 0.58092 0.70621 -0.18898 0.70248 -0.68616 -0.89469 -0.41117 -0.17453 TRANSLATION VECTOR IN AS -4.9859926.07288 -22.20167 TRANSLATION VECTOR IN fractions of cell edge 0.130.402062 -0.100921 ROTATION MATRIX -0.405 0.581 0.706 -0.189 0.702-0.686 -0.895-0.411-0.175 PATTERSON SPHERICAL POLARS OMEGA PHI CHI OMEGA TO AXIS ZOPHI FROM AXIS XO TO AXIS YO WHEN BETA=0 CAN ONLY DEFINE ALPHA + GAMMA . WHEN BETA = 180 CAN ONLY DEFINE GAMMA - ALPHA. trace 0.1232092 not 10- dc(1),dc(2),dc(3),chk 0.1529777 0.8905933 -0.4283007 1.00 CROWTHER (Euler) ALPHA BETA GAMMA135.82501 -100.05162 155.31825 SPHERICAL POLARS OMEGA PHI CHI115.3598680.25346 116.00163 DIRECTION COSINES OF ROTATION AXIS 0.15298 0.89059-0.42830 maprot script: MODE FROM SYMMETRY WORK 5 XYZLIM -32 57 -21 30 -15 41 GRID WORK 100 48 60 CELL WORK 105.9580 49.9510 62.6330 90. 114.7000 90. AVERAGE ROTATE EULER 135.82501 -100.05162 155.31825 TRANS -4.98599 26.07288 -22.20167
Re: [ccp4bb] small molecule crystallography
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 -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
[ccp4bb] Error in ccp4lib?
I am reading an external file, which contains phases and ABCDs in the space group P43212. My file has an asymmetric unit with k= h. Since CCP4 uses a different asymmetric unit with h=k, this requires phase and ABCD coefficients transformation. The transformation seems to be correct for reflections with initial h not equal to zero, but gives wrong result for 0 k l reflections. Zbyszek Otwinowski Zbyszek Otwinowski UT Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, TX 75390-8816 (214) 645 6385 (phone) (214) 645 6353 (fax) zbys...@work.swmed.edu
Re: [ccp4bb] Error in ccp4lib?
You don't say how you are doing the transformation? I would simply input the file to cad cad hklin1 thisfile.mtz hklout newfile.mtz labi file 1 allin end I think (and hope) that the data and phases will be converted correctly to the CCP4 asymmetric unit. Eleanor On 25 Mar 2014, at 09:16, Zbyszek Otwinowski wrote: I am reading an external file, which contains phases and ABCDs in the space group P43212. My file has an asymmetric unit with k= h. Since CCP4 uses a different asymmetric unit with h=k, this requires phase and ABCD coefficients transformation. The transformation seems to be correct for reflections with initial h not equal to zero, but gives wrong result for 0 k l reflections. Zbyszek Otwinowski Zbyszek Otwinowski UT Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, TX 75390-8816 (214) 645 6385 (phone) (214) 645 6353 (fax) zbys...@work.swmed.edu
Re: [ccp4bb] Error in ccp4lib?
Centrosymmetric reflections typically have C=0 and D=0, although non-zero values should not matter, as they do not modify phase probabilities for centrosymmetric reflections. Somehow, entering non-zero values for C and D for centrosymmetric reflection creates strange results during transformation of phase. Definitively a bug in ccp4lib, however only triggered by non-standard input. In practice, probably does not matter much. On 03/24/2014 06:11 PM, Eleanor Dodson wrote: You don't say how you are doing the transformation? I would simply input the file to cad cad hklin1 thisfile.mtz hklout newfile.mtz labi file 1 allin end I think (and hope) that the data and phases will be converted correctly to the CCP4 asymmetric unit. Eleanor On 25 Mar 2014, at 09:16, Zbyszek Otwinowski wrote: I am reading an external file, which contains phases and ABCDs in the space group P43212. My file has an asymmetric unit with k= h. Since CCP4 uses a different asymmetric unit with h=k, this requires phase and ABCD coefficients transformation. The transformation seems to be correct for reflections with initial h not equal to zero, but gives wrong result for 0 k l reflections. Zbyszek Otwinowski Zbyszek Otwinowski UT Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, TX 75390-8816 (214) 645 6385 (phone) (214) 645 6353 (fax) zbys...@work.swmed.edu -- Zbyszek Otwinowski UT Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, TX 75390-8816 (214) 645 6385 (phone) (214) 645 6353 (fax) zbys...@work.swmed.edu
