[ccp4bb] Refmac version
Dear users, I was using Refmac 5.5.0102 (ccp4- 6.1.2) for refining the structures, I was supposed to do one more roundof refinement with final model but unfortunately system crashed and i had to install the new version of ccp4 (6.2.0) which has refmac-5.6.0117. So my doubt here is - can I do the refinement of the final model with thisversion of refmac or do I need to complete with the older version itself?I however tried replacing the older version of refmac in place of new refmac. But the job failed while running(in the new interface) with an error message " ERROR: number of monomers 3000 /lib. limit/ Change parameter MAXMLIST in "lib_com.fh"Do i need to use the old interface itself or can i use the new interface to run old refmac binary? Kindly providesome suggestion.Thanking youWith RegardsKavya-- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
Re: [ccp4bb] Refmac version
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Kavya, I would trust the authors of such programs (ccp4-, phenix-, shelx-collection et al.) to only release new versions of their programs if they believe that version is an improvement over the previous version ;-) and generally use the latest version of their programs. You can get the latest version of refmac5 from Garib Murshudov's web site (http://www.ysbl.york.ac.uk/~garib/refmac/latest_refmac.html) and copy the binary into the binary directory of you ccp4-6.2.0 installation. When you run refmac, the header lists the program version so you can check that your environment picked up the correct version. Best wishes, Tim On 03/19/12 11:10, Kavyashree M wrote: Dear users, I was using Refmac 5.5.0102 (ccp4- 6.1.2) for refining the structures, I was supposed to do one more round of refinement with final model but unfortunately system crashed and i had to install the new version of ccp4 (6.2.0) which has refmac-5.6.0117. So my doubt here is - can I do the refinement of the final model with this version of refmac or do I need to complete with the older version itself? I however tried replacing the older version of refmac in place of new refmac. But the job failed while running (in the new interface) with an error message ERROR: number of monomers 3000 /lib. limit/ Change parameter MAXMLIST in lib_com.fh Do i need to use the old interface itself or can i use the new interface to run old refmac binary? Kindly provide some suggestion. Thanking you With Regards Kavya -- This message has been scanned for viruses and dangerous content by *MailScanner* http://www.mailscanner.info/, and is believed to be clean. - -- - -- 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/ iD8DBQFPZwtDUxlJ7aRr7hoRAnsvAKDfCCZHx2H5DwObakoBlpmCqEWmogCaAq1Z a7NBVsM5WHby6oRFxbuaTEQ= =CybB -END PGP SIGNATURE-
Re: [ccp4bb] Refmac version
Dear Kavya In principle you should be able to use newer version for old pdb file unless you have pdb v2 namings for DNA/RNA etc. New version of ccp4 has more dicitionary elements (1 or so). Older version was compiled for 3000. That is the reason why old version does not work with new dictionary. regards Garib On 19 Mar 2012, at 10:10, Kavyashree M wrote: Dear users, I was using Refmac 5.5.0102 (ccp4- 6.1.2) for refining the structures, I was supposed to do one more round of refinement with final model but unfortunately system crashed and i had to install the new version of ccp4 (6.2.0) which has refmac-5.6.0117. So my doubt here is - can I do the refinement of the final model with this version of refmac or do I need to complete with the older version itself? I however tried replacing the older version of refmac in place of new refmac. But the job failed while running (in the new interface) with an error message ERROR: number of monomers 3000 /lib. limit/ Change parameter MAXMLIST in lib_com.fh Do i need to use the old interface itself or can i use the new interface to run old refmac binary? Kindly provide some suggestion. Thanking you With Regards Kavya -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. Garib N Murshudov Structural Studies Division MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
[ccp4bb] PhD Studentship at the University of Cambridge: Chemical Probes of Protein-Protein Interactions
A 3.5 years PhD studentship is available from October 2012 in the group led by Dr Alessio Ciulli to design and develop novel small molecule chemical probes that target protein interfaces that recognise post-translational modifications of protein amino acids. This multi-disciplinary project will combine molecular/structural biology and biophysical studies of protein-protein complexes with small molecule drug design and organic synthesis. For a recent example of our approach see Buckley et al. *J. Am. Chem. Soc.*, *2012*, *134* (10), pp 4465–4468 ( http://pubs.acs.org/doi/abs/10.1021/ja209924v). Applicants should have (or expect to obtain) at least the equivalent of a UK II.1 honours degree (and preferably a Masters) in chemistry, biochemistry, chemical biology, structural biology or other relevant discipline. Applications from students with either a strong chemical or biological science background are encouraged, where the applicant is interested in learning the other discipline. The studentship will cover tuition fees and a maintenance grant for EU nationals who satisfy the eligibility requirements of the UK Research Councils. Owing to funding restrictions, the studentship is not available to non-EU nationals. Informal enquiries about the post can be sent to Dr Alessio Ciulli at ac...@cam.ac.uk Closing Date: 31 March 2012 Information on how to apply: http://www.jobs.cam.ac.uk/job/-14772/http://www.jobs.cam.ac.uk/job/-14591/ best wishes, Alessio
[ccp4bb] Trying to cut the resolution of the datasets
hello everyone, I am new in this bulletin board. I would like to know on how to cut my resolution in my datasets that have been processed/produced in diamond light source. In my processed directory, I found there are 3 files (free.mtz, scaled.sca and unmerged.sca). May I know which one can be used to cut my data that was diffracted to 1.5A? Cheers regards Abd Ghani The University of Sheffield
Re: [ccp4bb] Trying to cut the resolution of the datasets
Qs 1) Why do you want to limit your data? Most applications allow you to only use a specified sub-set - see GUI tasks for resolution limits. In general you may want to run moleculer replacement or exptl phasing at a limited resolution, but for refinenement or phase extension it is good to use the whole range.. Eleanor On Mar 19 2012, Abd Ghani Abd Aziz wrote: hello everyone, I am new in this bulletin board. I would like to know on how to cut my resolution in my datasets that have been processed/produced in diamond light source. In my processed directory, I found there are 3 files (free.mtz, scaled.sca and unmerged.sca). May I know which one can be used to cut my data that was diffracted to 1.5A? Cheers regards Abd Ghani The University of Sheffield -- Professor Eleanor Dodson YSNL, Dept of Chemistry University of York Heslington YO10 5YW tel: 00 44 1904 328259 Fax: 00 44 1904 328266
Re: [ccp4bb] Trying to cut the resolution of the datasets
... presuming of course the automated software got this resolution limit right. If for whatever reason you would like to cut the limit mtzutils will do this nicely: mtzutils hklin blah_free.mtz hklout blah_lower.mtz eof resolution 1.8 eof (say) - I am sure there are other ways within the suite to do this. Best wishes, Graeme On 19 March 2012 14:21, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Qs 1) Why do you want to limit your data? Most applications allow you to only use a specified sub-set - see GUI tasks for resolution limits. In general you may want to run moleculer replacement or exptl phasing at a limited resolution, but for refinenement or phase extension it is good to use the whole range.. Eleanor On Mar 19 2012, Abd Ghani Abd Aziz wrote: hello everyone, I am new in this bulletin board. I would like to know on how to cut my resolution in my datasets that have been processed/produced in diamond light source. In my processed directory, I found there are 3 files (free.mtz, scaled.sca and unmerged.sca). May I know which one can be used to cut my data that was diffracted to 1.5A? Cheers regards Abd Ghani The University of Sheffield -- Professor Eleanor Dodson YSNL, Dept of Chemistry University of York Heslington YO10 5YW tel: 00 44 1904 328259 Fax: 00 44 1904 328266
Re: [ccp4bb] Trying to cut the resolution of the datasets
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Abd Ghani, The method described by Graeme is how the resolution can be delimited artificially. If you want to get the best from your data, determine the resolution limit of your data e.g. with pointless (I/sigI 2.0 is a good marker) and reprocess the data to that limit. If you integrate the whole detector area and the outer parts contain only noise, the noise has a negative effect on the real data. Tim On 03/19/12 15:25, Graeme Winter wrote: ... presuming of course the automated software got this resolution limit right. If for whatever reason you would like to cut the limit mtzutils will do this nicely: mtzutils hklin blah_free.mtz hklout blah_lower.mtz eof resolution 1.8 eof (say) - I am sure there are other ways within the suite to do this. Best wishes, Graeme On 19 March 2012 14:21, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Qs 1) Why do you want to limit your data? Most applications allow you to only use a specified sub-set - see GUI tasks for resolution limits. In general you may want to run moleculer replacement or exptl phasing at a limited resolution, but for refinenement or phase extension it is good to use the whole range.. Eleanor On Mar 19 2012, Abd Ghani Abd Aziz wrote: hello everyone, I am new in this bulletin board. I would like to know on how to cut my resolution in my datasets that have been processed/produced in diamond light source. In my processed directory, I found there are 3 files (free.mtz, scaled.sca and unmerged.sca). May I know which one can be used to cut my data that was diffracted to 1.5A? Cheers regards Abd Ghani The University of Sheffield -- Professor Eleanor Dodson YSNL, Dept of Chemistry University of York Heslington YO10 5YW tel: 00 44 1904 328259 Fax: 00 44 1904 328266 - -- - -- 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/ iD8DBQFPZ0MfUxlJ7aRr7hoRAgysAKDwEYp5QK8l1ggcjNWeGDqfHHfMnQCfRVrZ 9kR9Pkg0bkZsHFQDSsI5QFU= =mn05 -END PGP SIGNATURE-
Re: [ccp4bb] Trying to cut the resolution of the datasets
Hi Tim, That's interesting. When I looked at this (and I would say I looked reasonably carefully) I found it only made a difference in the scaling - integrating across the whole area was fine. However, I would expect to see a difference, and likely an improvement, in scaling only the data you want. It would also give you sensible merging statistics which you'll probably want when you come to publish or deposit. Abd Ghani: if you'd like to rerun the processing at Diamond to a chosen resolution limit I will be happy to send some instructions. That's probably a good idea. Best wishes, Graeme On 19 March 2012 14:31, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Abd Ghani, The method described by Graeme is how the resolution can be delimited artificially. If you want to get the best from your data, determine the resolution limit of your data e.g. with pointless (I/sigI 2.0 is a good marker) and reprocess the data to that limit. If you integrate the whole detector area and the outer parts contain only noise, the noise has a negative effect on the real data. Tim On 03/19/12 15:25, Graeme Winter wrote: ... presuming of course the automated software got this resolution limit right. If for whatever reason you would like to cut the limit mtzutils will do this nicely: mtzutils hklin blah_free.mtz hklout blah_lower.mtz eof resolution 1.8 eof (say) - I am sure there are other ways within the suite to do this. Best wishes, Graeme On 19 March 2012 14:21, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Qs 1) Why do you want to limit your data? Most applications allow you to only use a specified sub-set - see GUI tasks for resolution limits. In general you may want to run moleculer replacement or exptl phasing at a limited resolution, but for refinenement or phase extension it is good to use the whole range.. Eleanor On Mar 19 2012, Abd Ghani Abd Aziz wrote: hello everyone, I am new in this bulletin board. I would like to know on how to cut my resolution in my datasets that have been processed/produced in diamond light source. In my processed directory, I found there are 3 files (free.mtz, scaled.sca and unmerged.sca). May I know which one can be used to cut my data that was diffracted to 1.5A? Cheers regards Abd Ghani The University of Sheffield -- Professor Eleanor Dodson YSNL, Dept of Chemistry University of York Heslington YO10 5YW tel: 00 44 1904 328259 Fax: 00 44 1904 328266 - -- - -- 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/ iD8DBQFPZ0MfUxlJ7aRr7hoRAgysAKDwEYp5QK8l1ggcjNWeGDqfHHfMnQCfRVrZ 9kR9Pkg0bkZsHFQDSsI5QFU= =mn05 -END PGP SIGNATURE-
[ccp4bb] Refining Against Reflections?
Dear Crystallographers, it occurred to me that most datasets, at least certainly since the advent of synchrotrons, have probably some degree of radiation damage, if not some huge degree thereof. Therefore, I was thinking an exposure-dependent parameter might be introduced into the atomic models, as an exposure-dependent occupancy of sorts. However, this would require refinement programs to use individual observations as data rather than combined reflections, effectively integrating scaling into refinement. Is there any talk of doing this? I think the hardware could reasonably handle this now? And, besides the question of radiation damage, isn't it perhaps reasonable to integrate scaling into refinement now anyway, since the constraints of hardware are so much lower? Jacob -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
[ccp4bb] unstable refinement error in SHELXL
Hi all, I was using SHELXL for the refinement of a small peptide molecule (6-7 residues), and it was working for the first round. But then it gave me an error message. I don't know what's going on and have you had the same problems? Can you give me some suggestions? *For more information*: I was using coot to read in .fcf and .res file, and after model building, coot can generate an .ins file. I was using this .ins file and the original .hkl for the next round of SHELXL, except I added one line ANIS in the .ins file: DEFS 0.02 0.1 0.01 0.04 CGLS 10 -1 SHEL 10 0.1 FMAP 2 PLAN 200 2.3 LIST 6 WPDB 2 *ANIS* I checked the working .ins and not-working (generated from coot) .ins files, 1)* the working .ins* (generated from .res file at the very beginning) has: WGHT0.10 SWAT1.3527622.1931 FVAR 2.6206 0.5 0.5 0.5 0.5 2) *the not-workind(generated from coot) .ins* has: WGHT 0.1 FVAR 1.0 *The refinement is shown as follows:* Read instructions and data ** Warning: unusual EXTI or SWAT parameter ** ** Warning:8 bad CHIV instructions ignored ** Data:6342 unique, 0 suppressed R(int) = 0. R(sigma) = 0.0615 Systematic absence violations:0Bad equivalents:0 wR2 = 0.4370 before cycle 1 for 6058 data and 1690 / 1690 parameters GooF = S = 4.279; Restrained GooF = 5.862 for 2243 restraints Max. shift = 0.259 A for O_1131bMax. dU =-0.409 for O_1131b at 06:08:24 wR2 = 0.7365 before cycle 2 for 6058 data and 1690 / 1690 parameters GooF = S =12.229; Restrained GooF = 12.221 for 2243 restraints Max. shift = 0.175 A for O_2131aMax. dU =-0.157 for O_5017at 06:08:25 ** REFINEMENT UNSTABLE ** The other peptide dataset also has similar problem: I was using coot-SHELXL, model building - refinement cycle *successfully for the first 3 rounds*, but then, it gave me an error message: Read instructions and data ** Warning: unusual EXTI or SWAT parameter ** ** Warning: no match for1 atoms in CONN ** ** CANNOT RESOLVE ISOR .. O LAST ** I checked the working .ins and not-working .ins files (both generated from coot this case), 1) the *working .ins*: WGHT0.10 SWAT1.2889323.0398 FVAR 2.6472 0.5 0.5 2) the* not-working .ins*: WGHT0.10 SWAT1.3447083.0452 FVAR 2.731 0.54231 0.5409 I was really confused, since I was using coot for model building for other datasets, and the .ins file generated from coot is good for SHELXL, but it didn't work all the time, eg. it work for the first few rounds, then there is a problem. Can you give me some suggestions about what I should do to get the SHELXL running again? Thanks, Lu
Re: [ccp4bb] unstable refinement error in SHELXL
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Lu Yu, your wR2 in the first log-extract seems very high (43%) - it might simply be that you model is still not good enough to refine the data anisotropically. Does it work if you refine the model isotropically? If so, improve the model as much as possible before going anisotropically. You might also want to include more reflections - with SHEL 10 0.1 you leave out all data with d10A which might be quite a few important reflections. It is difficult to go into more detail without knowing the exact content of the output (lst-files), especially in the second case where the listing file tells you that something is wrong with the 'ISOR'-command. Regards, Tim On 03/19/12 17:00, Lu Yu wrote: Hi all, I was using SHELXL for the refinement of a small peptide molecule (6-7 residues), and it was working for the first round. But then it gave me an error message. I don't know what's going on and have you had the same problems? Can you give me some suggestions? *For more information*: I was using coot to read in .fcf and .res file, and after model building, coot can generate an .ins file. I was using this .ins file and the original .hkl for the next round of SHELXL, except I added one line ANIS in the .ins file: DEFS 0.02 0.1 0.01 0.04 CGLS 10 -1 SHEL 10 0.1 FMAP 2 PLAN 200 2.3 LIST 6 WPDB 2 *ANIS* I checked the working .ins and not-working (generated from coot) .ins files, 1)* the working .ins* (generated from .res file at the very beginning) has: WGHT0.10 SWAT1.3527622.1931 FVAR 2.6206 0.5 0.5 0.5 0.5 2) *the not-workind(generated from coot) .ins* has: WGHT 0.1 FVAR 1.0 *The refinement is shown as follows:* Read instructions and data ** Warning: unusual EXTI or SWAT parameter ** ** Warning:8 bad CHIV instructions ignored ** Data:6342 unique, 0 suppressed R(int) = 0. R(sigma) = 0.0615 Systematic absence violations:0Bad equivalents:0 wR2 = 0.4370 before cycle 1 for 6058 data and 1690 / 1690 parameters GooF = S = 4.279; Restrained GooF = 5.862 for 2243 restraints Max. shift = 0.259 A for O_1131bMax. dU =-0.409 for O_1131b at 06:08:24 wR2 = 0.7365 before cycle 2 for 6058 data and 1690 / 1690 parameters GooF = S =12.229; Restrained GooF = 12.221 for 2243 restraints Max. shift = 0.175 A for O_2131aMax. dU =-0.157 for O_5017at 06:08:25 ** REFINEMENT UNSTABLE ** The other peptide dataset also has similar problem: I was using coot-SHELXL, model building - refinement cycle *successfully for the first 3 rounds*, but then, it gave me an error message: Read instructions and data ** Warning: unusual EXTI or SWAT parameter ** ** Warning: no match for1 atoms in CONN ** ** CANNOT RESOLVE ISOR .. O LAST ** I checked the working .ins and not-working .ins files (both generated from coot this case), 1) the *working .ins*: WGHT0.10 SWAT1.2889323.0398 FVAR 2.6472 0.5 0.5 2) the* not-working .ins*: WGHT0.10 SWAT1.3447083.0452 FVAR 2.731 0.54231 0.5409 I was really confused, since I was using coot for model building for other datasets, and the .ins file generated from coot is good for SHELXL, but it didn't work all the time, eg. it work for the first few rounds, then there is a problem. Can you give me some suggestions about what I should do to get the SHELXL running again? Thanks, Lu - -- - -- 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/ iD8DBQFPZ1pBUxlJ7aRr7hoRAvZRAJ9TKlJLQjho67GGxZAyHIcioDcnrwCeIYjy 4rL0aiefine9z1LcQ3SSGno= =aoDC -END PGP SIGNATURE-
Re: [ccp4bb] unstable refinement error in SHELXL
Dear Lu Yu, SHELXL is usually very stable so there must be an error in your .ins file, but it is difficult fo us to guess what it is without seeing the full file. A common error that can cause such instability is caused by a long-standing bug in Coot, which sets some occupancies in the .ins file to 1.0 (meaning that they can be refined freely starting at 1.0) rather than the usual 11.0 (which means that they should be fixed at 1.0; you can add 10 to a parameter to fix it). Another possibility is that Coot has not understood a 'free variable' that has been used for e.g. occupancy refinement. The small molecule people use other graphical GUIs for SHELXL (shelXle, WinGX, Olex2, System-S, XSEED, Oscail, XSHELL etc.) that make far fewer mistakes. The .ins files written by Coot should always be checked carefully and if necessary edited before running SHELXL. Best wishes, George On 03/19/2012 05:00 PM, Lu Yu wrote: Hi all, I was using SHELXL for the refinement of a small peptide molecule (6-7 residues), and it was working for the first round. But then it gave me an error message. I don't know what's going on and have you had the same problems? Can you give me some suggestions? _For more information_: I was using coot to read in .fcf and .res file, and after model building, coot can generate an .ins file. I was using this .ins file and the original .hkl for the next round of SHELXL, except I added one line ANIS in the .ins file: DEFS 0.02 0.1 0.01 0.04 CGLS 10 -1 SHEL 10 0.1 FMAP 2 PLAN 200 2.3 LIST 6 WPDB 2 *ANIS* I checked the working .ins and not-working (generated from coot) .ins files, 1)*the working .ins* (generated from .res file at the very beginning) has: WGHT0.10 SWAT1.3527622.1931 FVAR 2.6206 0.5 0.5 0.5 0.5 2) *the not-workind(generated from coot) .ins* has: WGHT 0.1 FVAR 1.0 *The refinement is shown as follows:* Read instructions and data ** Warning: unusual EXTI or SWAT parameter ** ** Warning:8 bad CHIV instructions ignored ** Data:6342 unique, 0 suppressed R(int) = 0. R(sigma) = 0.0615 Systematic absence violations:0Bad equivalents:0 wR2 = 0.4370 before cycle 1 for 6058 data and 1690 / 1690 parameters GooF = S = 4.279; Restrained GooF = 5.862 for 2243 restraints Max. shift = 0.259 A for O_1131bMax. dU =-0.409 for O_1131b at 06:08:24 wR2 = 0.7365 before cycle 2 for 6058 data and 1690 / 1690 parameters GooF = S =12.229; Restrained GooF = 12.221 for 2243 restraints Max. shift = 0.175 A for O_2131aMax. dU =-0.157 for O_5017at 06:08:25 ** REFINEMENT UNSTABLE ** The other peptide dataset also has similar problem: I was using coot-SHELXL, model building - refinement cycle *successfully for the first 3 rounds*, but then, it gave me an error message: Read instructions and data ** Warning: unusual EXTI or SWAT parameter ** ** Warning: no match for1 atoms in CONN ** ** CANNOT RESOLVE ISOR .. O LAST ** I checked the working .ins and not-working .ins files (both generated from coot this case), 1) the *working .ins*: WGHT0.10 SWAT1.2889323.0398 FVAR 2.6472 0.5 0.5 2) the*not-working .ins*: WGHT0.10 SWAT1.3447083.0452 FVAR 2.731 0.54231 0.5409 I was really confused, since I was using coot for model building for other datasets, and the .ins file generated from coot is good for SHELXL, but it didn't work all the time, eg. it work for the first few rounds, then there is a problem. Can you give me some suggestions about what I should do to get the SHELXL running again? Thanks, Lu -- 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] Refining Against Reflections?
As you observe, radiation damage is local, but the effect is - to different extent - on all Fs i.e. global (all atoms and their damage contribute to each hkl). So one would need additional local parameters (reducing N/P) if you want to address it as such, your use of occupancy is an example (even if you have a reflection-specific decay, somehow a realistic underlying atomic model would be desirable, and just changing occ might not be ideal)..So is the question then 'Could a reflection-specific time dependent decay factor translate into any useful atom-specific model parameter? BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller Sent: Monday, March 19, 2012 7:46 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Refining Against Reflections? Dear Crystallographers, it occurred to me that most datasets, at least certainly since the advent of synchrotrons, have probably some degree of radiation damage, if not some huge degree thereof. Therefore, I was thinking an exposure-dependent parameter might be introduced into the atomic models, as an exposure-dependent occupancy of sorts. However, this would require refinement programs to use individual observations as data rather than combined reflections, effectively integrating scaling into refinement. Is there any talk of doing this? I think the hardware could reasonably handle this now? And, besides the question of radiation damage, isn't it perhaps reasonable to integrate scaling into refinement now anyway, since the constraints of hardware are so much lower? Jacob -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Refining Against Reflections?
I was thinking actually the dose-dependent-occupancy would really be a tau in an exponential decay function for each atom, and they could be fitted by how well they account for the changes in intensities (these should actually not always be decreases, which is the problem for correcting radiation damage at the scaling stage without iterating with models/refinement). I guess accurate typical values would be needed to start with, similar to the routinely-used geometry parameters. Actually, perhaps it would just be better to assume book values initially at least, and then fit the dose rate, since this is probably not known so accurately, then refine the individual tau's, especially for heavy atoms. This of course would also have great implications for the ability to phase using radiation damage to heavy atoms (RIP)--there would have to be something like a Patterson map mixed somehow with the exponentials, which would show sites with the shortest half-lives. JPK On Mon, Mar 19, 2012 at 12:00 PM, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com wrote: As you observe, radiation damage is local, but the effect is - to different extent - on all Fs i.e. global (all atoms and their damage contribute to each hkl). So one would need additional local parameters (reducing N/P) if you want to address it as such, your use of occupancy is an example (even if you have a reflection-specific decay, somehow a realistic underlying atomic model would be desirable, and just changing occ might not be ideal)….So is the question then ‘Could a reflection-specific time dependent decay factor translate into any useful atom-specific model parameter? ** ** BR ** ** *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Jacob Keller *Sent:* Monday, March 19, 2012 7:46 AM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] Refining Against Reflections? ** ** Dear Crystallographers, ** ** it occurred to me that most datasets, at least certainly since the advent of synchrotrons, have probably some degree of radiation damage, if not some huge degree thereof. Therefore, I was thinking an exposure-dependent parameter might be introduced into the atomic models, as an exposure-dependent occupancy of sorts. However, this would require refinement programs to use individual observations as data rather than combined reflections, effectively integrating scaling into refinement. Is there any talk of doing this? I think the hardware could reasonably handle this now? ** ** And, besides the question of radiation damage, isn't it perhaps reasonable to integrate scaling into refinement now anyway, since the constraints of hardware are so much lower? ** ** Jacob ** ** -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
[ccp4bb] Announcing a Web Server for the Grade ligand restraints generator.
Dear all, The generation of reliable restraints for novel small-molecule ligands in macromolecular complexes is of great importance for both ligand placement into density maps and subsequent refinement. This has led us to develop Grade, a ligand restraint generator whose main source of restraint information is the Cambridge Structural Database (CSD) of small-molecule crystal structures, queried using the MOGUL program developed by the CCDC. Where small-molecule information is lacking, Grade uses quantum chemical procedures to obtain the restraint values. Grade was released to academic users as part of the BUSTER package in July 2011 and has proved popular. However, a problem for numerous academic users has been that, in order to get the best restraints from Grade, a CSD system licence is necessary to make use of MOGUL. Although many institutions already have CSD site licences, and otherwise licences are available at a reasonable cost, this has prevented the use of Grade by small groups and occasional users. To provide easy access to Grade, the CCDC has kindly agreed that we can provide a public Web server that includes the use of MOGUL in its invocation of Grade. The first version of the server is now available, free of charge, at http://grade.globalphasing.org We hope this server will prove useful to academic users. We will be very grateful for any feedback you might be able to provide about this server, so that we can keep improving it to meet the needs of the community. Please send us your feedback and comments at buster-deve...@globalphasing.com rather than write to a specific developer. With best wishes, The Global Phasing developers: Gerard Bricogne, Claus Flensburg, Peter Keller, Wlodek Paciorek, Andrew Sharff, Oliver Smart, Clemens Vonrhein and Thomas Womack.
Re: [ccp4bb] unusual bond lengths in PRODRG cif file (Grade Web Server)
On Tue, 10 Jan 2012, Stephen Graham wrote: On 10 January 2012 09:50, John Liebeschuetz j...@ccdc.cam.ac.uk wrote: ...available to anyone who has access to the Cambridge Structural Database System How many academic labs will bother / can afford to buy a CCSD license just to check the geometry of small molecule ligands, especially when they need to do so them only once every blue moon? The ability for the PDB to check a ligand against the CCSD upon deposition would be great. The ability to generate the restraint definition for free via the web before deposition is better: that's why people use PRODRG! Stephen Stephen, We had anticipated your request and got permission from the CCDC to provide a public Web server that would include the use of MOGUL in its invocation of Grade. The Grade Web Server has been publicly launched today, so for ligand restraint definitions that are (partly) based on CSD small molecule structures try using: http://grade.globalphasing.org Regards, Oliver | Dr Oliver Smart | | Global Phasing Ltd., Cambridge UK | | http://www.globalphasing.com/people/osmart/ |
Re: [ccp4bb] unusual bond lengths in PRODRG cif file
On Mon, 9 Jan 2012, Soisson, Stephen M wrote: I will second Ian's recommendation for GRADE from the Global Phasing group. GRADE overcomes nearly all of the shortcomings we have encountered with other approaches for ligand dictionary generation. Steve, Thanks to you and to Ian Tickle for the positive comments about grade. We have just launched the Grade Web Server so it should be now be much easier for academic and occasional users to generate ligand restraints with it. http://grade.globalphasing.org Regards, Oliver | Dr Oliver Smart | | Global Phasing Ltd., Cambridge UK | | http://www.globalphasing.com/people/osmart/ |
[ccp4bb] microseeding
Dear All, I have few papers in hand which explain me about microseeding, matrix microseeding, and cross seeding.I have also read few earlier threads and some more literature in google.Using Phoenix robot, I did a matrix micro-seeding and matrix cross seeding. I have few hits with this.In 96 well I used 100+100+50 nL and 200+200+50 nl (protein+screen+seed) in separate expts.I have hard time to plan to translate this 96 sitting drop well plate to 24 well plate to refine the conditions to get better crystals. only 1-2 hits are small crystals and they are tiny. I wonder in 24 well plate, if I should do-1) for Example 500+500+50nl (I am sure I cant add less that 500 nL precisely)2) to a drop of 500+500 nL do microseeding/streaking with a hair I appreciate if you could advise and share some practical ways to further my experiment. Thanks in advanceRegards,Rajesh
Re: [ccp4bb] microseeding
Scaling up 100nl drops is problematic. What I understand is that it is not only the different equilibration conditions, but primarily the amount of protein that gets absorbed on the surface is relatively higher for small drops. There were some empirical formula for scaling up (i.e. how much you need to increase the protein concentration, but I am afraid you would have to re-screen anyway. On Mon, 2012-03-19 at 15:31 -0500, Rajesh kumar wrote: Dear All, I have few papers in hand which explain me about microseeding, matrix microseeding, and cross seeding. I have also read few earlier threads and some more literature in google. Using Phoenix robot, I did a matrix micro-seeding and matrix cross seeding. I have few hits with this. In 96 well I used 100+100+50 nL and 200+200+50 nl (protein+screen +seed) in separate expts. I have hard time to plan to translate this 96 sitting drop well plate to 24 well plate to refine the conditions to get better crystals. only 1-2 hits are small crystals and they are tiny. I wonder in 24 well plate, if I should do- 1) for Example 500+500+50nl (I am sure I cant add less that 500 nL precisely) 2) to a drop of 500+500 nL do microseeding/streaking with a hair I appreciate if you could advise and share some practical ways to further my experiment. Thanks in advance Regards, Rajesh -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse /
[ccp4bb] Position available
Research Associate position Protein Characterization and Crystallization Facility, University of Saskatchewan, Saskatoon The newly established Protein Characterization and Crystallization Facility at the College of Medicine, University of Saskatchewan is seeking a candidate with expertise in various biophysical methods of protein characterization to aid the users in designing their experiments, provide assistance in running the experiments and help in interpreting the results. The instrumentation will include surface plasmon resonance, isothermal calorimetry, circular dichroism, dynamic light scattering, visible, UV and fluorescent spectroscopy, and FPLC instruments for a variety of chromatographic applications. The emphasis of the research will be on protein-protein and protein-small molecule interactions. Medium-throughput experiments will utilize a liquid handling robot. The successful candidate will be expected to participate in collaborative research with the faculty of the College of Medicine and other researchers on the U of S campus and will have an opportunity to pursue his/her own research program. The laboratory will be located in the new wing of the Health Sciences Building on the U of S campus. Close interaction with other facilities such as Mass Spectrometry Facility and Saskatchewan Structural Sciences Centre are expected. The candidate should have a PhD in biochemistry, enzymology or a related discipline and several year of experience in protein characterization. Good communication skills and a team spirit are essential. The position is initially for a 3-year period with possibility for a permanent appointment. The salary will be commensurate with experience. The University of Saskatchewan places a strong emphasis on research and is a home for 20,000 students. Saskatoon is a rapidly growing city, within the province that is in a strong economic position. The University campus is one of the most beautiful campuses not only in Canada but in North America. The student life is vibrant, with variety of activities on and off the campus (http://explore.usask.ca/campuslife/). Contact information: Mirek Cygler Professor, Department of Biochemistry, University of Saskatchewan and Adjunct Professor, Department of Biochemistry, McGill University, 107 Wiggins Road, Saskatoon, SK S7N 5E5 Canada E-mail : miroslaw.cyg...@usask.ca Phone : (306) 996-4361
Re: [ccp4bb] Trying to cut the resolution of the datasets
Hi Graeme, That's interesting. When I looked at this (and I would say I looked reasonably carefully) I found it only made a difference in the scaling - integrating across the whole area was fine. However, I would expect to see a difference, and likely an improvement, in scaling only the data you want. It would also give you sensible merging statistics which you'll probably want when you come to publish or deposit. I've seen low-resolution datasets where the resolution cutoff had a fairly significant impact on integration - usually in cell or orientation refinement. This seemed to make sense, as trying to use large numbers of spots that weren't really there (and so had essentially undetermined positions) tended to lead to instabilities in refinement. What resolution ranges were you looking at? Pete Abd Ghani: if you'd like to rerun the processing at Diamond to a chosen resolution limit I will be happy to send some instructions. That's probably a good idea. Best wishes, Graeme On 19 March 2012 14:31, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Abd Ghani, The method described by Graeme is how the resolution can be delimited artificially. If you want to get the best from your data, determine the resolution limit of your data e.g. with pointless (I/sigI 2.0 is a good marker) and reprocess the data to that limit. If you integrate the whole detector area and the outer parts contain only noise, the noise has a negative effect on the real data. Tim On 03/19/12 15:25, Graeme Winter wrote: ... presuming of course the automated software got this resolution limit right. If for whatever reason you would like to cut the limit mtzutils will do this nicely: mtzutils hklin blah_free.mtz hklout blah_lower.mtz eof resolution 1.8 eof (say) - I am sure there are other ways within the suite to do this. Best wishes, Graeme On 19 March 2012 14:21, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Qs 1) Why do you want to limit your data? Most applications allow you to only use a specified sub-set - see GUI tasks for resolution limits. In general you may want to run moleculer replacement or exptl phasing at a limited resolution, but for refinenement or phase extension it is good to use the whole range.. Eleanor On Mar 19 2012, Abd Ghani Abd Aziz wrote: hello everyone, I am new in this bulletin board. I would like to know on how to cut my resolution in my datasets that have been processed/produced in diamond light source. In my processed directory, I found there are 3 files (free.mtz, scaled.sca and unmerged.sca). May I know which one can be used to cut my data that was diffracted to 1.5A? Cheers regards Abd Ghani The University of Sheffield -- Professor Eleanor Dodson YSNL, Dept of Chemistry University of York Heslington YO10 5YW tel: 00 44 1904 328259 Fax: 00 44 1904 328266 - -- - -- 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/ iD8DBQFPZ0MfUxlJ7aRr7hoRAgysAKDwEYp5QK8l1ggcjNWeGDqfHHfMnQCfRVrZ 9kR9Pkg0bkZsHFQDSsI5QFU= =mn05 -END PGP SIGNATURE-
Re: [ccp4bb] microseeding
Rajesh If you set up the volumes you suggest you will probably get precipitation. This is counterintuitive until you realize that (as Ed says) you will be losing a lot of protein with those small drops. When you scale up the surface area to volume ratio is lower, so a smaller proportion of the protein is lost. Therefore you go *up* on the phase diagram and get precipitant or very small crystals. Normally halving the amount of protein for the hits from 200 nl drops works (suggesting that half the protein is lost from such small drops). Try say 500+1000+500 (don't reduce the volume of seed stock because the solution that you suspended the crystals in may be important). Or dilute the protein and use 1000+1000+500. For the hits from the 450 nl drops you could reduce or dilute the protein by say 25.%. Or make plenty of seed-stock and try seeding into a random screen again with larger drops, say 1.5+1+0.5 ul Those tiny crystals should be good for seeding, don't worry about that (provided they are protein of course). Streak seeding may work but bear in mind that roughly a third of the precipitant comes from the seed stock in your 250 nl drops. You can add the seed stock with a syringe and needle if you don't have suitable robot ;) Experience and data-mining suggests that reducing the salt precipitant (in high-salt drops) or salt additive (in PEG drops) by around 50% may be helpful too when scaling up - I'm not sure why this works. Good luck Patrick For the hits in the 250 nl drops you are probably losing On 19 March 2012 20:31, Rajesh kumar ccp4...@hotmail.com wrote: Dear All, I have few papers in hand which explain me about microseeding, matrix microseeding, and cross seeding. I have also read few earlier threads and some more literature in google. Using Phoenix robot, I did a matrix micro-seeding and matrix cross seeding. I have few hits with this. In 96 well I used 100+100+50 nL and 200+200+50 nl (protein+screen+seed) in separate expts. I have hard time to plan to translate this 96 sitting drop well plate to 24 well plate to refine the conditions to get better crystals. only 1-2 hits are small crystals and they are tiny. I wonder in 24 well plate, if I should do- 1) for Example 500+500+50nl (I am sure I cant add less that 500 nL precisely) 2) to a drop of 500+500 nL do microseeding/streaking with a hair I appreciate if you could advise and share some practical ways to further my experiment. Thanks in advance Regards, Rajesh -- patr...@douglas.co.ukDouglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36
[ccp4bb] structure refinement and analysis work
Dear All, Do you need some help for structure refinement or structure analysis? I will be very happy to work for you, while I am looking for next position. To me, solving structure is a puzzle game and for fun. Regards, Kevin Jin
