Re: [ccp4bb] Problem with Rfactor
Dear Sudarshan, I have the feeling the your R factor after Molrep is really high because the program has failed to produce a correct/not-partial solution, which could be due to many things, but usually the main problem is how good your search model is. The difference in spacegroups is not a problem as in MR the model will be rotated and translated inside the new cell. The number of molecules that you need to search for is a tricky question. You need to make some educated guesses with help from analysis of, for example, crystal solvent content (e.g., Matthews program from CCP4) and/or self-rotation maps (Molrep or Polarrfn programs, also available from CCP4 suite). If you have never before used molecular replacement, however, I would advise that you get some help/guidance from some more experienced colleague/friend in the Department, since you may encounter quite a few more other problems that would perhaps be a bit too long to go through by email. Some of these problems could also be probably self-solved by looking at some tutorials on Molecular replacements. Best wishes, D From: Sudarshan Murthy [mailto:sudarshan.murthy...@gmail.com] Sent: 29 April 2014 05:11 To: ccp4bb Subject: [ccp4bb] Problem with Rfactor Dear All, I am very new to the field of crystallography, I have a few questions which are very basic and getting input from this forum would help me a lot. Firstly I am trying to solve a structure using MR Molrep. In the result the Rfactors are really high how do I reduce the same?? ..When I tried with Phaser I didnt get any solution at all.. Will der be a problem with the space group?? like the model is in monoclinic and the data which I have is processed in hexagonal. Secondly while using hexagonal space group should I search for only one monomer in Molrep?? These are very basic questions if anybody could help me out with this , I would be very happy for the same. Sudarshan .N. Murthy Crystallography Division Bangalore
Re: [ccp4bb] Confusion about space group nomenclature
Hi Fellows, I have bugged now the ultimate authorities including Howard Flack (of Flack parameter fame), and alas, there is no official descriptive adjective for these 65 Söhnke space groups. Chiral is definitely wrong, and so is enantiomorphic, although 22 of the nameless form 11 enantiomorphic pairs. Thou shallst not use those descriptors for SGs, only for structures. So the contest for a proper descriptive adjective is still open. Best, BR PS: Otherwise it is a bit like saying 'You know, that thing, the one where you see stuff moving and it is not black and white' instead of simply 'color TV' - almost as old as space groups
Re: [ccp4bb] Problem with Rfactor
We need more information. First if the pointgroup is hexagonal are you searching al likely SPACEgroup - eg PG P6, SGs might P6 P61 P62P63 P64 P65.. There is a GUI option to do this for both MOLREP Phaser. You can guess the likely no of molecules using matthews In the GUI - that is in the MOL REp task - option analyse. Eleanor On 29 April 2014 10:21, Dom Bellini dom.bell...@diamond.ac.uk wrote: Dear Sudarshan, I have the feeling the your R factor after Molrep is really high because the program has failed to produce a correct/not-partial solution, which could be due to many things, but usually the main problem is how good your search model is. The difference in spacegroups is not a problem as in MR the model will be rotated and translated inside the new cell. The number of molecules that you need to search for is a tricky question. You need to make some educated guesses with help from analysis of, for example, crystal solvent content (e.g., Matthews program from CCP4) and/or self-rotation maps (Molrep or Polarrfn programs, also available from CCP4 suite). If you have never before used molecular replacement, however, I would advise that you get some help/guidance from some more experienced colleague/friend in the Department, since you may encounter quite a few more other problems that would perhaps be a bit too long to go through by email. Some of these problems could also be probably self-solved by looking at some tutorials on Molecular replacements. Best wishes, D From: Sudarshan Murthy [mailto:sudarshan.murthy...@gmail.com] Sent: 29 April 2014 05:11 To: ccp4bb Subject: [ccp4bb] Problem with Rfactor Dear All, I am very new to the field of crystallography, I have a few questions which are very basic and getting input from this forum would help me a lot. Firstly I am trying to solve a structure using MR Molrep. In the result the Rfactors are really high how do I reduce the same?? ..When I tried with Phaser I didnt get any solution at all.. Will der be a problem with the space group?? like the model is in monoclinic and the data which I have is processed in hexagonal. Secondly while using hexagonal space group should I search for only one monomer in Molrep?? These are very basic questions if anybody could help me out with this , I would be very happy for the same. Sudarshan .N. Murthy Crystallography Division Bangalore
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 the
Re: [ccp4bb] error in starting imosflm
Hi Felix
You're very trusting! Bugs in new versions of software are not unknown!
The bug may not manifest itself in a program crash (though it makes life
easier if it does), rather it may simply give different numerical results
that you may not spot for some after. This is why CCP4 distributes test
data (in $CEXAM) for users to test the software (though the examples there
are hardly comprehensive). Most major software packages (e.g. LAPACK)
provide comprehensive test suites that test all possible ways in which the
software may be used so you can verify that the new version at least gives
the same results as the distributor's test suite (this also checks whether
there are machine dependencies). So I need to run tests on the new version
compare with results from the old one before I release it to users, for
which I obviously need access to both versions. Also the man pages are
missing from the new version: I just find it quicker easier to type 'man
fft' or whatever than to fire up the browser.
Cheers
-- Ian
On 29 April 2014 11:23, Felix Frolow mbfro...@post.tau.ac.il wrote:
Hi Tim,
What can be a reason to work with an obsolete version of CCP4?
I remember reading somewhere that 6.3.0 version is obsolete.
FF
Dr Felix Frolow
Professor of Structural Biology and Biotechnology, Department of
Molecular Microbiology and Biotechnology
Tel Aviv University 69978, Israel
Acta Crystallographica F, co-editor
e-mail: mbfro...@post.tau.ac.il
Tel: ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608
On Apr 28, 2014, at 19:01 , Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Sreetama, dear Ian,
I avoid sourcing both version 6.3 and 6.4 in the same terminal. If I
need to work with 6.3 I modify my .bashrc from 6.4 to 6.3 and then
open a new terminal to make sure everything refers to v6.3 and vice versa.
Best,
Tim
On 04/28/2014 04:51 PM, Ian Tickle wrote:
Harry,
I've run into this problem before with other programs when I switch
between v6.3 v6.4. I think the problem is this code in
ccp4.setup-sh:
if [ `expr :${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
[ccp4bb] project and literature organization software (laboratory information management software)
Dear all, I am looking for a software solution to organize many pieces of information 1.) Results from (bio)chemical experiments, such as spectral data, pictures. 2.) Project ideas, milestones, etc. 3.) Literature, including tags, short comments, etc. For example, for a certain project I would like to collect information about experiments conducted, then link this to literature/literature experiments and to project outlines. All this should be accessible for multiple users on different OS. I have briefly looked into PiMS (too much crystallography oriented), Contor ELN (only on Safari on Mac?), Labguru (nice, but not too flexible and mostly for biosciences) and Confluence (nice wiki, but so far no real literature plugin). I know that this sounds maybe a little bit like something called in German a 'eierlegende Wollmilchsau' http://en.wiktionary.org/wiki/eierlegende_Wollmilchsau But I would be happy to hear about what software people (and labs) have tried, liked/disliked and ideally the reasons. (I am aware that there was a similar query https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg24657.html, but this was more than 2 years ago) Thanks a lot! Best wishes, Tobias. -- ___ Dr. Tobias Beck ETH Zurich Laboratory of Organic Chemistry Vladimir-Prelog-Weg 3, HCI F 322 8093 Zurich, Switzerland phone: +41 44 632 68 65 fax:+41 44 632 14 86 web: http://www.protein.ethz.ch/people/tobias ___
[ccp4bb] AW: [ccp4bb] Problem with Rfactor
Dear Sudarshan, There are quite a few point to consider in MR: -How good is your model? At 50% sequence identity with your protein, it is probably ok, around 25% sequence identity it may or may not work. If your protein is of the same protein family with a similar biological function it is probably ok. -How many protein monomers should I expect? Proteins have in general between 25 and 75% solvent, so e.g. with the Matthews program one can estimate how many molecules might be in the asymmetric unit. Conversely, if your search model contains more than one molecule in the asymmetric unit, you have to delete the additional copies, otherwise many MR programs will fail. -If your search model has low homology, you may want to trim away surface loops which are missing or likely different in your protein. You may also want to change side chains that are different to Ala, so they won’t cause problems. -Space group: As Eleanor pointed out, there are many hexagonal space groups and you have to try them all. -Important: before you continue, check that both the mtz file and the pdb file you continue with have the correct space group, found by the MR program. Other wise, you have to reset the space group, e.g. with cad or pdbset. -A high Rfactor just after MR may not be a problem, probably quite a few residues have to be mutated from the search sequence to your sequence and many loops may need rebuilding too. Important is that you recognize some of your residues in the electron density maps. -The thing to do is to rebuild your model and run a few rounds of refinement. If the Rfactors do not go down, you have a problem, but otherwise you can just continue. Good luck! Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Sudarshan Murthy Gesendet: Dienstag, 29. April 2014 06:11 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Problem with Rfactor Dear All, I am very new to the field of crystallography, I have a few questions which are very basic and getting input from this forum would help me a lot. Firstly I am trying to solve a structure using MR Molrep. In the result the Rfactors are really high how do I reduce the same?? ..When I tried with Phaser I didnt get any solution at all.. Will der be a problem with the space group?? like the model is in monoclinic and the data which I have is processed in hexagonal. Secondly while using hexagonal space group should I search for only one monomer in Molrep?? These are very basic questions if anybody could help me out with this , I would be very happy for the same. Sudarshan .N. Murthy Crystallography Division Bangalore
Re: [ccp4bb] error in starting imosflm
On Mon, Apr 28, 2014 at 03:51:57PM +0100, 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}: : .*:${dir}:` -eq 0 ]; then
We can remove this condition if it does more harm than good.
Marcin
--
This e-mail and any attachments may contain confidential, copyright and or
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Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments
are free from viruses and we cannot accept liability for any damage which you
may sustain as a result of software viruses which may be transmitted in or with
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and
Wales with its registered office at Diamond House, Harwell Science and
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
Re: [ccp4bb] error in starting imosflm
Hi Marcin
It was obviously added originally because there was a limit to the length
of the PATH variable (presumably there still is), so repeated invocations
of setup scripts could take you over the limit. Ideally the script should
remove old versions from the PATH, not just prepend the new one, but
there's no easy way to make that completely general. David's
CCP4Dispatchers script would seem to offer the best solution.
So I would leave it as it is, the cure may be worse than the disease!
Thanks
-- Ian
On 29 April 2014 12:47, Marcin Wojdyr marcin.woj...@diamond.ac.uk wrote:
On Mon, Apr 28, 2014 at 03:51:57PM +0100, Ian Tickle wrote:
Harry,
I've run into this problem before with other programs when I switch
between
v6.3 v6.4. I think the problem is this code in ccp4.setup-sh:
if [ `expr :${PATH}: : .*:${dir}:` -eq 0 ]; then
We can remove this condition if it does more harm than good.
Marcin
--
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] error in starting imosflm
Hi Ian,
Improving the CCP4 tests is a priority. We (the core team) have a project
looking into that. If developers have their own tests for components of the
suite that have not made it into the distribution, then we'd be happy to
collect them for the new test set.
Best wishes
-- David
On 29 April 2014 11:59, Ian Tickle ianj...@gmail.com wrote:
Hi Felix
You're very trusting! Bugs in new versions of software are not unknown!
The bug may not manifest itself in a program crash (though it makes life
easier if it does), rather it may simply give different numerical results
that you may not spot for some after. This is why CCP4 distributes test
data (in $CEXAM) for users to test the software (though the examples there
are hardly comprehensive). Most major software packages (e.g. LAPACK)
provide comprehensive test suites that test all possible ways in which the
software may be used so you can verify that the new version at least gives
the same results as the distributor's test suite (this also checks whether
there are machine dependencies). So I need to run tests on the new version
compare with results from the old one before I release it to users, for
which I obviously need access to both versions. Also the man pages are
missing from the new version: I just find it quicker easier to type 'man
fft' or whatever than to fire up the browser.
Cheers
-- Ian
On 29 April 2014 11:23, Felix Frolow mbfro...@post.tau.ac.il wrote:
Hi Tim,
What can be a reason to work with an obsolete version of CCP4?
I remember reading somewhere that 6.3.0 version is obsolete.
FF
Dr Felix Frolow
Professor of Structural Biology and Biotechnology, Department of
Molecular Microbiology and Biotechnology
Tel Aviv University 69978, Israel
Acta Crystallographica F, co-editor
e-mail: mbfro...@post.tau.ac.il
Tel: ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608
On Apr 28, 2014, at 19:01 , Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Sreetama, dear Ian,
I avoid sourcing both version 6.3 and 6.4 in the same terminal. If I
need to work with 6.3 I modify my .bashrc from 6.4 to 6.3 and then
open a new terminal to make sure everything refers to v6.3 and vice versa.
Best,
Tim
On 04/28/2014 04:51 PM, Ian Tickle wrote:
Harry,
I've run into this problem before with other programs when I switch
between v6.3 v6.4. I think the problem is this code in
ccp4.setup-sh:
if [ `expr :${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
[ccp4bb] PhD in Structural Biology of membrane proteins
Dear All, A 4-year BBSRC DTP PhD (1 year MRes and 3 year PhD) position is available in my lab jointy supervised with Dr Ed Tate (Department of Chemistry) at Imperial College London. The project involves structure based inhibitor design for multi-drug bacterial membrane transporters. The PhD will focus on the design of novel inhibitors and their structural determination in complex with the membrane protein by X-ray crystallography. We are looking for an outstanding biochemistry or chemistry graduate with a strong interest in structural biology and structure-guided inhibitor design, and in research at the life science/chemistry interface. The position is fully funded and funding is available to UK/home students. More details on the project and how to apply: http://www.findaphd.com/search/ProjectDetails.aspx?PJID=54634 Best, Kostas Dr. Konstantinos Beis Lecturer Imperial College London Membrane Protein Lab Research Complex at Harwell Harwell Oxford Didcot Oxfordshire OX11 0FA UK tel: 01235567809 url: http://www3.imperial.ac.uk/people/konstantinos.beis
[ccp4bb] Postdoc position available
The Helmholtz Zentrum Berlin für Materialien und Energie, the Max-Delbrück-Center for Molecular Medicine Berlin, the Freie Universität Berlin, the Humboldt Universität zu Berlin and the Leibniz-Institute for Molecular Pharmacology jointly operate three experimental stations for bio-macromolecular crystallography within the Joint Berlin MX-Laboratory cooperation at BESSY II, one of the world's most modern synchrotron radiation sources for VUV and soft X-rays. The Macromolecular Structure and Interaction Group of the Max-Delbrück-Center is seeking a Post Doctoral Research Assistant to conduct research on various structural biology / biochemistry projects of the MDC Macromolecular Structure and Interaction Group (headed by Prof. Dr. Udo Heinemann, https://www.mdc-berlin.de/1154162/de/research/research_teams/macromolecular_structure_and_interaction). According to research interests and qualifications, the candidate may also participate in instrumental and/or computational projects of the HZB-MX group. The successful candidate will also be involved in the operation of the BESSY II bio-macromolecular crystallography beamlines (headed by Dr. Uwe Müller Dr. Manfred S. Weiss, http://www.helmholtz-berlin.de/bessy-mx) and will take part in graduate student education. Initially, a two-year contract will be offered to the successful candidate with the possibility for an extension. The salary will be based on German federal TvÖD. The position is available immediately, and applications will be considered until the position is filled. The MDC is an equal-opportunity employer committed to excellence through diversity. Applications of women are explicitly encouraged. Applicants should hold a Ph.D. in the biological, chemical or physical sciences and have a background in bio-macromolecular crystallography, biochemistry or computational sciences. The position also requires the documented ability to conduct independent research as well as excellent communication and interpersonal skills. Please send applications (CV, list of publications, in one combined .pdf-file) in electronic form, with the Code MDC-MX-2014/1 to: Dr. Uwe Müller (u...@helmholtz-berlin.demailto:u...@helmholtz-berlin.de) -- Dr. Manfred. S. Weiss Helmholtz-Zentrum Berlin für Materialien und Energie Macromolecular Crystallography (HZB-MX) Albert-Einstein-Str. 15 D-12489 Berlin GERMANY Fon: +49-30-806213149 Fax: +49-30-806214975 Web: http://www.helmholtz-berlin.de/bessy-mx Email: mswe...@helmholtz-berlin.demailto:mswe...@helmholtz-berlin.de Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de
Re: [ccp4bb] Confusion about space group nomenclature
Response to off-board mail: How about [calling them] non-centro-symmetric space groups, as I often tell my students? Almost, but not exact enough. The 65 are only a subset of non-centrosymmetric space groups: Not all enantiogenic (not elements of the 65-set) space groups are centrosymmetric. Simplest example Pm. According to above definition Pm (and many more lacking a center of inversion) would be a ok space group for chiral motifs. (when a space group has the 'center at ' annotation in the Tables, it has a coi and is a centrosymmetric space group). This implies that there are actually three types of crystal structures (cf. Flack): (a) chiral (non-centrosymmetric) crystal structures (b) centrosymmetric crystal structures (c) achiral non-centrosymmetric crystal structures And just as a reminder, the substructure inversion for 3 members of the 65 is not about the origin (0,0,0): I41, I4122, F4132 are their own enantiomorph, so for them there is no enantiomorphic pair (eg. I41 and I43), in fact no separate space group I43 is even necessary - look at the SG diagram #80 - both, 41 and 43 axes appear in the same SG. (2005 Erice paper of George explains more) Enough yet? Cheers, BR
Re: [ccp4bb] Confusion about space group nomenclature
Bernhard The term enantiomorphic pair is used consistently in ITC-A to mean one of the 11 pairs of what you previously called chiral space groups. PersonalIy I would never use the term chiral in this context even though it is synonymous with enantiomorphic (I would reserved chiral for single objects like hands, screws, mollusc shells and molecules - actually pretty well everything in Nature is chiral, natural achiral objects are in the minority). You say Thou shalt not use those descriptors for SGs, only for structures but enantiomorphic in the sense above is being used in ITC-A exactly to describe a SG, so on which tablet of stone is this commandment inscribed? Certainly not in ITC. Also on my CCP4 web page that I referred to earlier I used enantiomorphic to describe a structure (or to be precise a crystal), not a SG (43 enantiomorphic SGs are not enantiomorphic if it refers to the SG). I accept that nowhere does ITC use enantiomorphic in the way I'm using it but you wanted a suitable descriptor and I don't see any alternative candidates. As you said the only distinction ITC makes is between centrosymmetric and non-centrosymmetric (presumably having centrosymmetry leads to great simplication of the structure-factor equations in that you only have to worry about 2 alternative values for the phase), but that's not the description you're seeking for the reasons you gave. The only apparent inconsistency here is that the same adjective is being used to describe two different things. But is that really an inconsistency? Can't I use black to describe both crows and blackboards? Cheers -- Ian On 29 April 2014 10:32, Bernhard Rupp hofkristall...@gmail.com wrote: Hi Fellows, I have bugged now the ultimate authorities including Howard Flack (of Flack parameter fame), and alas, there is no official descriptive adjective for these 65 Söhnke space groups. Chiral is definitely wrong, and so is enantiomorphic, although 22 of the nameless form 11 enantiomorphic pairs. Thou shallst not use those descriptors for SGs, only for structures. So the contest for a proper descriptive adjective is still open. Best, BR PS: Otherwise it is a bit like saying 'You know, that thing, the one where you see stuff moving and it is not black and white' instead of simply 'color TV' - almost as old as space groups
Re: [ccp4bb] project and literature organization software (laboratory information management software)
Dear Tobias, My group uses a web based content management system called drupal to manage inventory, orders and are now setting it up to manage data. Drupal has a SQL server to manage different types of information and it is normally utilized to build websites, but you can also use it as a database only. To do this, you make different tables (drupal calls them content types) for your results project ideas, literature or whatever else you want to manage. Since the database is relational you can setup fields that lookup information from other content types or you can just put in a hyperlink since it is also a webpage. You can attach an unlimited number of files, but we usually put in links to the files that are stored on our server. Happy to talk in more detail if you want to contact me offline. David Blum Bioexpression and Fermentation Facility University of Georgia b...@uga.edu bff.uga.edu On Tue, Apr 29, 2014 at 7:21 AM, Tobias Beck tobiasb...@gmail.com wrote: Dear all, I am looking for a software solution to organize many pieces of information 1.) Results from (bio)chemical experiments, such as spectral data, pictures. 2.) Project ideas, milestones, etc. 3.) Literature, including tags, short comments, etc. For example, for a certain project I would like to collect information about experiments conducted, then link this to literature/literature experiments and to project outlines. All this should be accessible for multiple users on different OS. I have briefly looked into PiMS (too much crystallography oriented), Contor ELN (only on Safari on Mac?), Labguru (nice, but not too flexible and mostly for biosciences) and Confluence (nice wiki, but so far no real literature plugin). I know that this sounds maybe a little bit like something called in German a 'eierlegende Wollmilchsau' http://en.wiktionary.org/wiki/eierlegende_Wollmilchsau But I would be happy to hear about what software people (and labs) have tried, liked/disliked and ideally the reasons. (I am aware that there was a similar query https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg24657.html, but this was more than 2 years ago) Thanks a lot! Best wishes, Tobias. -- ___ Dr. Tobias Beck ETH Zurich Laboratory of Organic Chemistry Vladimir-Prelog-Weg 3, HCI F 322 8093 Zurich, Switzerland phone: +41 44 632 68 65 fax:+41 44 632 14 86 web: http://www.protein.ethz.ch/people/tobias ___
Re: [ccp4bb] project and literature organization software (laboratory information management software)
Hi Tobias, There is Quartzy, which is free. https://www.quartzy.com I am not sure it covers all of your desired functionalities. Best regards, Florian On Apr 29, 2014, at 7:21 AM, Tobias Beck tobiasb...@gmail.com wrote: Dear all, I am looking for a software solution to organize many pieces of information 1.) Results from (bio)chemical experiments, such as spectral data, pictures. 2.) Project ideas, milestones, etc. 3.) Literature, including tags, short comments, etc. For example, for a certain project I would like to collect information about experiments conducted, then link this to literature/literature experiments and to project outlines. All this should be accessible for multiple users on different OS. I have briefly looked into PiMS (too much crystallography oriented), Contor ELN (only on Safari on Mac?), Labguru (nice, but not too flexible and mostly for biosciences) and Confluence (nice wiki, but so far no real literature plugin). I know that this sounds maybe a little bit like something called in German a 'eierlegende Wollmilchsau' http://en.wiktionary.org/wiki/eierlegende_Wollmilchsau But I would be happy to hear about what software people (and labs) have tried, liked/disliked and ideally the reasons. (I am aware that there was a similar query https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg24657.html, but this was more than 2 years ago) Thanks a lot! Best wishes, Tobias. -- ___ Dr. Tobias Beck ETH Zurich Laboratory of Organic Chemistry Vladimir-Prelog-Weg 3, HCI F 322 8093 Zurich, Switzerland phone: +41 44 632 68 65 fax:+41 44 632 14 86 web: http://www.protein.ethz.ch/people/tobias ___ --- Florian Schmitzberger, PhD Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, Seeley G. Mudd 127 Boston, MA 02115, USA Tel: 001 617 432 5601
[ccp4bb] Position for X-ray crystallographer available
Dear colleagues: We have a position available for an X-ray crystallographer. The job description follows. If you have any questions, please feel free to contact me. Investigator III, Structural and Biophysical Chemistry About Novartis Institutes for Biomedical Research: At Novartis Institutes for BioMedical Research (NIBR), the global research organization of Novartis, we are committed to discovering innovative medicines to cure disease and improve human health. We aim to hire the best trained scientists from academia, biotechnology and pharmaceuticals and we cultivate an environment for drug discovery science where innovation is rewarded. It is ultimately the talent of the individuals we recruit that determines our success and our state-of-the-art technologies and resources that enable individuals to realize this success. NIBR has sites in Cambridge, Massachusetts; Emeryville, California; Basel, Switzerland; Horsham, UK; and Shanghai, China. Our Infectious Diseases research is headquartered in Emeryville, California under the global leadership of Don Ganem, M.D., one of the world's leading virologists and infectious disease specialists About Structural and Biophysical Chemistry Group: The NIBR Emeryville Structural and Biophysical Chemistry group is responsible for actively pursuing the structures of macromolecular drug targets either as apo-proteins or in complex with lead compounds to help guide structure-based drug design, and actively participates in the drug discovery process. The group also provides biophysics and solutions studies support for drug discovery projects. Position Description: The qualified candidate will use his/her scientific expertise to aid in structure-based drug design efforts. Specifically, this individual will determine high-resolution, three-dimensional structures of macromolecular drug targets (typically proteins), including crystallization and structure solution of medically important structures and target-ligand complexes. This individual will interact with computational chemists and medicinal chemists to design new scaffolds and improve lead compounds. Additionally, this individual will provide biophysical support for fragment based drug discovery efforts and other biophysical studies. Please apply at http://www.novartis.com/careers/job-search/#keyword=140884BR . referencing job ID 140884BR . You must apply on-line to be considered. Qualifications: The ideal candidate will have - * An M.S. degree and 7 or more years of work experience or a Ph.D. and 3-6 years of postdoctoral and/or work experience. Degrees in Biochemistry, Chemistry, or Molecular Biophysics are acceptable. * Strong experience in protein biochemistry, protein crystallization, crystallographic methods, structure solution, structure refinement and molecular modeling. Pharmaceutical industry experience is a plus, as is experience in membrane protein crystallography and experience in developing biologics. * Significant experience in the use of biophysics (SPR, ITC, DSC, NMR, etc.) to support biological research and drug discovery projects. Experience in supporting fragment-based drug discovery is a plus. * Excellent verbal and written communication skills and the ability to work in large, multidisciplinary project teams. The Novartis Group of Companies are Equal Opportunity Employers and take pride in maintaining a diverse environment. Our policies are not to discriminate in recruitment, hiring, training, promotion or other employment practices for reasons of race, color, religion, gender, national origin, age, sexual orientation, marital or veteran status, disability, or any other legally protected status. Dirksen Bussiere, Ph.D., M.B.A. Director, Structural and Biophysical Chemistry Novartis Insts. for BioMedical Research 4560 Horton Street, M/S 4.6 Emeryville, CA 94608-2916 USA Phone+1 510923-2114 Fax +1 5106559910 dirksen.bussi...@novartis.commailto:dirksen.bussi...@novartis.com www.novartis.comhttp://www.novartis.com/
[ccp4bb] CASP 11: Call for targets to assess the state of the art in protein structure modeling
Summary: CASP is soliciting target proteins for structure prediction - specifically proteins with new folds, membrane proteins, disordered proteins, oligomers, complexes, and multi-domain proteins. Call for targets: = As many of you know, CASP (Critical Assessment of Structure Prediction) has been assessing the state of the art in modeling protein structure from sequence since 1994, running a community experiment once every two years. In these experiments, information on soon to be solved structures is collected from the experimental community, and the sequence data are passed to the structure modeling community so that blind predictions of structure can be collected and assessed (1). Over that period CASP has seen enormous progress in the quality of modeled structures (2), but many problems remain. CASP is only possible because of the generous participation of the experimental community in providing the modeling targets (3). The prediction season for the next full biannual experiment, CASP 11, begins May 1, and so we are now asking for your help in reaching our goal of releasing at least varied 100 targets in a the three-month period. We need all sorts of targets, spanning the categories below: 1. (More than ever) novel folds and membrane protein targets. Even with the extended collection season provided by CASP ROLL, there will be still a shortage. There are some interesting methods developments for ab initio modeling, and it is important to be able to decisively evaluate their effectiveness. 2. Oligomers, complexes, and multi-domain proteins: This round, CASP has entered collaboration with CAPRI for specifically assessing the accuracy of predictions of protein-interactions and relative domain orientation. 3. Targets containing significant amounts of disordered structure, so as to test the ability of methods to identify these regions. We are especially interested in targets where disorder has been directly characterized experimentally, e.g. by NMR. 4. A diversity of comparative modeling targets. Cases where there is fairly high sequence identity (30-50%) between the target structure and an available template are valuable for testing the degree to which model accuracy can approach that of experiment, particularly in functionally critical regions. Cases with lower sequence identity to template, right down to undetectable, are valuable for testing the ability of the methods to detect remote homologs, to overcome challenging alignment difficulties, to make use of multiple templates, and to build regions of the structure not obviously available from a template. 5. Some targets will also be used to test methods of structure refinement. In these cases, the best model received for a target will be released to the refinement community, who will subsequently submit new models. This too is an area where there have been some exciting developments in the last year, so we are hoping for significant progress. Refinement targets are selected based on the nature of the errors in the initial models. Because of the extended process, these targets need to be available for longer before release of the experimental structure. Procedure = For those of you who have not provided targets to CASP before, the procedure is simple. There are three ways to submit targets: (1) Go the target submission web page and fill in the easy form; (2) When you submit your co-ordinates to the PDB, tick the 'CASP HOLD' box, automatically setting up a target entry; (3) Send an email the prediction center with details. If you have queries, there is very experienced prediction center staff to deal with them. The key thing is timing: We need a window of at least four weeks between receiving information about a target and the release of your experimental structure. A longer window - up to eight weeks - is often useful, for example so that a target can be used to test refinement methods, but is not essential (note that using the PDB target submission route automatically selects eight weeks). We don't need your experimental structure in advance of its release by the PDB, provided that will happen by the end of August. Please consult the target submission page for more details: http://www.predictioncenter.org/casp11/targets_submission.cgi There are already many prediction teams signed for CASP 11, and so any targets provided will receive plenty of attention. If you have a suitable target now, we are ready to receive it. If new targets come up before mid of July, we would also love to have them. (After July, we will continue with CASP ROLL for novel folds, disordered proteins, and membrane proteins). So please get in touch whenever a suitable opportunity arises, and help improve modeling methods. Thanks, CASP organizing committee John Moult, IBBR, University of Maryland, USA Anna Tramontano, University of Rome, Italy Krzysztof Fidelis, University of California,
[ccp4bb] shelxCDE in ccp4i
Hi, I have shelx programs installed on my computer but only shelxs shows as active on the ccp4i interface. How to activate shelxCDE? Thanks, Mirek
Re: [ccp4bb] Confusion about space group nomenclature
Dear Bernhard (and others), I was looking for catchy combinations of chiral or enantio and Latin or Greek words for support or allow -- until I realized there is already a name for this very concept, used widely in chemistry: I think the precise and correct term applicable to the 65 should be pro-chiral spacegroups. They are not chiral by themselves, but addition of something /allows/ for the creation of a chiral object (i.e. the crystal). Cheers, Jens On Tue, 2014-04-29 at 16:12 +0200, Bernhard Rupp wrote: Response to off-board mail: How about [calling them] non-centro-symmetric space groups, as I often tell my students? Almost, but not exact enough. The 65 are only a subset of non-centrosymmetric space groups: Not all enantiogenic (not elements of the 65-set) space groups are centrosymmetric. Simplest example Pm. According to above definition Pm (and many more lacking a center of inversion) would be a ok space group for chiral motifs. (when a space group has the 'center at ' annotation in the Tables, it has a coi and is a centrosymmetric space group). This implies that there are actually three types of crystal structures (cf. Flack): (a) chiral (non-centrosymmetric) crystal structures (b) centrosymmetric crystal structures (c) achiral non-centrosymmetric crystal structures And just as a reminder, the substructure inversion for 3 members of the 65 is not about the origin (0,0,0): I41, I4122, F4132 are their own enantiomorph, so for them there is no enantiomorphic pair (eg. I41 and I43), in fact no separate space group I43 is even necessary - look at the SG diagram #80 - both, 41 and 43 axes appear in the same SG. (2005 Erice paper of George explains more) Enough yet? Cheers, BR
Re: [ccp4bb] Confusion about space group nomenclature
actually, I'll have to amend that: Dear Bernhard (and others), I was looking for catchy combinations of chiral or enantio and Latin or Greek words for support or allow -- until I realized there is already a name for this very concept, used widely in chemistry: I think the precise and correct term applicable to the 65 should be the 22 chiral (aka 11 enantiomorphic paris) and the 43 pro-chiral spacegroups. They are not chiral by themselves, but addition of something /allows/ for the creation of a chiral object (i.e. the crystal). Cheers, Jens On Tue, 2014-04-29 at 16:12 +0200, Bernhard Rupp wrote: Response to off-board mail: How about [calling them] non-centro-symmetric space groups, as I often tell my students? Almost, but not exact enough. The 65 are only a subset of non-centrosymmetric space groups: Not all enantiogenic (not elements of the 65-set) space groups are centrosymmetric. Simplest example Pm. According to above definition Pm (and many more lacking a center of inversion) would be a ok space group for chiral motifs. (when a space group has the 'center at ' annotation in the Tables, it has a coi and is a centrosymmetric space group). This implies that there are actually three types of crystal structures (cf. Flack): (a) chiral (non-centrosymmetric) crystal structures (b) centrosymmetric crystal structures (c) achiral non-centrosymmetric crystal structures And just as a reminder, the substructure inversion for 3 members of the 65 is not about the origin (0,0,0): I41, I4122, F4132 are their own enantiomorph, so for them there is no enantiomorphic pair (eg. I41 and I43), in fact no separate space group I43 is even necessary - look at the SG diagram #80 - both, 41 and 43 axes appear in the same SG. (2005 Erice paper of George explains more) Enough yet? Cheers, BR
