Re: [ccp4bb] Placing an EM map in a large P1 box
Hi Larry, here is how I'd do it: mapmask MAPIN your.map MAPOUT padded.map EOF SYMMETRY 1 XYZLIM CELL PAD 0.0 END EOF Good luck with it! Ciao Pietro -- Pietro Roversi Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3ER, England UK Tel. 0044-1865-275385
[ccp4bb] too good R/Rfree with resolve
Dear CCP4bb readers, this is my problem: I solved a structure by MR: the solution was easily found (molrep, phaser and balbes found always the same one), density looked generally reasonable (however in several places it was dubious) but R/Rfree were stuck at 42/47%. Then I tried some density modifications, resolve worked spectacularly the density became wonderful and several parts which were not in the model appeared. So I finished to build the model and everything looked good. The problem is now for a structure at 2.8 Å resolution I have R/Rfree of 8/9.5% respectively, which is clearly too good. Checking refmac log file it looked to me that refmac uses all the reflections in the .mtz file (that is as many reflections as before the resolve run). Ideas? thanks Stefano ps this is my last refmac: 2 mol in the AU, no NCS used, weighting term 0.01, no tls. NcycRfactRfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.0943 0.1051 0.937102149.5673.2 0.0070 0.298 1.202 0.546 0.077 1 0.0910 0.1024 0.940101442.5642.4 0.0058 0.252 1.091 0.481 0.073 2 0.0898 0.1019 0.940101221.5634.0 0.0055 0.238 1.061 0.461 0.072 3 0.0891 0.1016 0.941101080.5628.8 0.0052 0.226 1.045 0.451 0.072 4 0.0884 0.1011 0.942100947.5622.7 0.0050 0.217 1.033 0.445 0.071 5 0.0877 0.1006 0.942100824.5617.0 0.0049 0.211 1.024 0.440 0.071 6 0.0872 0.1001 0.943100708.5611.4 0.0047 0.205 1.016 0.436 0.070 7 0.0866 0.0997 0.943100593.5606.5 0.0047 0.202 1.008 0.432 0.070 8 0.0861 0.0992 0.944100483.5601.5 0.0046 0.199 1.002 0.429 0.069 9 0.0857 0.0989 0.944100391.5597.5 0.0045 0.196 0.996 0.426 0.069 10 0.0852 0.0985 0.944100313.5593.5 0.0045 0.193 0.990 0.423 0.068 _ Explore the seven wonders of the world http://search.msn.com/results.aspx?q=7+wonders+worldmkt=en-USform=QBRE
Re: [ccp4bb] MolRep of coiled coils
Sorry - I should have added that, yes, there are 2 identical peptide chains that should be parallel coiled-coil. Any advice gratefully received. Ed -Original Message- From: cockburn [mailto:[EMAIL PROTECTED] Sent: Fri 3/28/2008 1:35 PM To: Thomas Edwards Subject: Re: [ccp4bb] MolRep of coiled coils Hi Thomas, Does your coiled-coil consist of two polypeptide chains, and are their sequences identical? Do you expect it to be a parallel or anti-parallel coiled-coil? Yours Joe Thomas Edwards a écrit : Dear BB, I am attempting molecular replacement with a 2.8A data set from crystals of a coiled coil of about 150 residues. Probably p21212 but maybe p2221. So far, Phaser, MolRep, Amore, Mr Bump, have not provided a good solution as judged by Z-scores, CCs, Rfactors, and whether there is any density outside the model (there should be - I'm using a slightly shorter model to search with). One possible problem is that the coiled coil may not be straight. It may have a slight curve to it. I have used models from the PDB that are straight or slightly curved, so far with no success. I have tried a few different resolution cutoffs too. I have tried single helix chains or dimeric coiled coils. Is there anything special about MR with coiled coils? Can anybody provide any tips/hints on MR with coiled coils?? Thanks Ed
Re: [ccp4bb] MolRep of coiled coils
My short experience with coiled-coil is that molecular replacement can be difficult for classical software (due to the very anysotropic shape of the protein). In our case (a short parallel dimeric coiled-coil), molecular replacement trials using AMoRe or MOLREP were unsuccessful. We solved the structure using EPMR (evolutionary search molecular replacement software). http://www.msg.ucsf.edu/local/programs/epmr/epmr.html Michel.
[ccp4bb] Model ensemble for x-ray crystallography
Some time ago I've heard about the idea of proposing an ensemble of models (as in NMR), instead of a single model for x-ray crystallography structures. If I remember correctly, this idea has been published somewhere. Can anyone tell me what article is that? Lucas Abra sua conta no Yahoo! Mail, o único sem limite de espaço para armazenamento! http://br.mail.yahoo.com/
Re: [ccp4bb] Model ensemble for x-ray crystallography
On Fri, March 28, 2008 10:13 am, Lucas Bleicher wrote: Some time ago I've heard about the idea of proposing an ensemble of models (as in NMR), instead of a single model for x-ray crystallography structures. If I remember correctly, this idea has been published somewhere. Can anyone tell me what article is that? Lucas Abra sua conta no Yahoo! Mail, o único sem limite de espaço para armazenamento! http://br.mail.yahoo.com/ The earliest I recall hearing about this from was W. F. van Gunsteren, where he used an ensemble average of ten chains instead of a a single atom chain with anisotropic Gaussian displacement parameters. Check out: P. Gros, M. Fujinaga, B. W. Dijkstra, K. H. Kalk, and W. G. J. Hol, Acta Cryst., B45, 488-499 (1989) Bernie
Re: [ccp4bb] Model ensemble for x-ray crystallography
Didn't that trick very successfully lower the R-factors of the completely wrong models that led to the Great Pentaretraction? Unless you have stunningly high resolution, beware. Phoebe At 10:13 AM 3/28/2008, you wrote: Some time ago I've heard about the idea of proposing an ensemble of models (as in NMR), instead of a single model for x-ray crystallography structures. If I remember correctly, this idea has been published somewhere. Can anyone tell me what article is that? Lucas Abra sua conta no Yahoo! Mail, o único sem limite de espaço para armazenamento! http://br.mail.yahoo.com/ --- Phoebe A. Rice Assoc. Prof., Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 fax 773 702 0439 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 RNA is really nifty DNA is over fifty We have put them both in one book Please do take a really good look http://www.rsc.org/shop/books/2008/9780854042722.asp
Re: [ccp4bb] Model ensemble for x-ray crystallography
have fun ... http://mordred.bioc.cam.ac.uk/~nick/files/Furnham-Structure-2006.pdf http://mordred.bioc.cam.ac.uk/~nick/files/Furnham-NSMB-2006.pdf M.A. DePristo, P.I.W. de Bakker, T.L. Blundell (2004) Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography. Structure (Camb). 12:831-838 and many more just google for RAPPER modelling server cheers Stefan -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Behalf Of Lucas Bleicher Sent: 28 March 2008 15:13 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Model ensemble for x-ray crystallography Some time ago I've heard about the idea of proposing an ensemble of models (as in NMR), instead of a single model for x-ray crystallography structures. If I remember correctly, this idea has been published somewhere. Can anyone tell me what article is that? Lucas Abra sua conta no Yahoo! Mail, o único sem limite de espaço para armazenamento! http://br.mail.yahoo.com/
Re: [ccp4bb] Model ensemble for x-ray crystallography
Hi, This idea was rejuvenated recently in the follg. work from 2007. I believe the article you are looking for is: Ensemble refinement of protein crystal structures: validation and application. Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr. Structure. 2007 Sep;15(9):1040-52. Regards, Debanu. -Original Message- From: CCP4 bulletin board on behalf of Lucas Bleicher Sent: Fri 3/28/2008 8:13 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Model ensemble for x-ray crystallography Some time ago I've heard about the idea of proposing an ensemble of models (as in NMR), instead of a single model for x-ray crystallography structures. If I remember correctly, this idea has been published somewhere. Can anyone tell me what article is that? Lucas Abra sua conta no Yahoo! Mail, o único sem limite de espaço para armazenamento! http://br.mail.yahoo.com/
Re: [ccp4bb] Model ensemble for x-ray crystallography
At 10:13 AM 3/28/2008, Lucas Bleicher wrote : Some time ago I've heard about the idea of proposing an ensemble of models (as in NMR), instead of a single model for x-ray crystallography structures. If I remember correctly, this idea has been published somewhere. Can anyone tell me what article is that? jmb 301 1237-1256, 2000 analyzes the disorder in calmodulin that considers such a treatment along with other models of disorder. http://www.ncbi.nlm.nih.gov/pubmed/10966818 -bryan
[ccp4bb] program to draw 2D image of a peptide
Does anyone know of a program, different from Ligplot, that can draw 2D image of peptides out a pdb file? It would be a plus if it can establish and draw contacts between this peptide and the neighbors residues. thanks in advance for any input. Sandra
Re: [ccp4bb] Model ensemble for x-ray crystallography
PDB entries 1LYZ, 2LYZ, 3LYZ, 4LYZ, 5LYZ, 6LYZ all have the same reference: Diamond, R. (1974) Real-space refinement of the structure of hen egg-white lysozyme. J.Mol.Biol. 82: 371-391 I believe they are independent refinements using the same experimental data. I do not have access to the journal so I cannot verify this. Frances = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** [EMAIL PROTECTED] *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = On Fri, 28 Mar 2008, Santarsiero, Bernard D. wrote: On Fri, March 28, 2008 10:13 am, Lucas Bleicher wrote: Some time ago I've heard about the idea of proposing an ensemble of models (as in NMR), instead of a single model for x-ray crystallography structures. If I remember correctly, this idea has been published somewhere. Can anyone tell me what article is that? Lucas Abra sua conta no Yahoo! Mail, o único sem limite de espaço para armazenamento! http://br.mail.yahoo.com/ The earliest I recall hearing about this from was W. F. van Gunsteren, where he used an ensemble average of ten chains instead of a a single atom chain with anisotropic Gaussian displacement parameters. Check out: P. Gros, M. Fujinaga, B. W. Dijkstra, K. H. Kalk, and W. G. J. Hol, Acta Cryst., B45, 488-499 (1989) Bernie
[ccp4bb] problem with Coot and ccp4mg
Dear all, I recently installed CCP4 suite on a DELL workstation running Red Hat Enterprise Linux 5. CCP4 seems to be working fine, however, Coot and ccp4mg fail to open. This is what I get when I try to run Coot: current_exe_dir is /usr/local/ccp4/ccp4-6.0.2/Coot-0.3.3/bin COOT_PREFIX is /usr/local/ccp4/ccp4-6.0.2/Coot-0.3.3 /usr/local/ccp4/ccp4-6.0.2/Coot-0.3.3/bin/coot-real: error while loading shared libraries: libXmu.so.6: cannot open shared object file: No such file or directory coot-exe: /usr/local/ccp4/ccp4-6.0.2/Coot-0.3.3/bin/coot-real core: #f No core file found. No debugging I get something similar when I try to run ccp4mg, it also complains about libXmu.so.6. libXmu.so.6 is in /usr/lib64/. I tried to create symbolic links at various places, like /usr/lib/ and lib/ of coot and ccp4mg, still could not get rid of the problem. Is it the problem because of 64-bit system? How can I overcome it? Thanks in advance, Best regards, Uma. -- Uma Katre, Department of Chemistry Biochemistry, Auburn University, Auburn, AL, USA. - Never miss a thing. Make Yahoo your homepage.
Re: [ccp4bb] MolRep of coiled coils
Hi Thomas, MR of coiled coils can be quite tricky including considerations of being curved, etc. If conventional MR is failing (assuming you have tried different kinds of parameter and search model tweaks, you can also play around with the search thresholds in phaser), you may try the following: If you have multiple copies in the asu, you may try to find the orientation of the NCS axis. If you think that the molecules may be aligned along a particular direction, you can then generate a list of rotation search angles manually in fine increments (couple of degrees) and then force a translation search around all these rotation angles and then follow it up with a packing function search. This is like a brute force rotation/translation search across all rotation angles. Therefore identification of the ncs axis/molecular orientation will provide some search time advantage. You can do this in PHASER. Check out the manual to run stand alone scripts for these steps. Although different from the above, the follg. reference may provide useful reading: Gonzalez L Jr, Brown RA, Richardson D, Alber T. Crystal structures of a single coiled-coil peptide in two oligomeric states reveal the basis for structural polymorphism. Nat Struct Biol. 1996 Dec;3(12):1002-9. Also check tropomysin structure MR attempts from Carolyn Cohen's group. Regards, Debanu. -- Debanu Das, Structure Determination Core, Joint Center for Structural Genomics. Stanford Synchrotron Radiation Laboratory, Menlo Park, CA. -Original Message- From: CCP4 bulletin board on behalf of Thomas Edwards Sent: Fri 3/28/2008 5:57 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] MolRep of coiled coils Dear BB, I am attempting molecular replacement with a 2.8A data set from crystals of a coiled coil of about 150 residues. Probably p21212 but maybe p2221. So far, Phaser, MolRep, Amore, Mr Bump, have not provided a good solution as judged by Z-scores, CCs, Rfactors, and whether there is any density outside the model (there should be - I'm using a slightly shorter model to search with). One possible problem is that the coiled coil may not be straight. It may have a slight curve to it. I have used models from the PDB that are straight or slightly curved, so far with no success. I have tried a few different resolution cutoffs too. I have tried single helix chains or dimeric coiled coils. Is there anything special about MR with coiled coils? Can anybody provide any tips/hints on MR with coiled coils?? Thanks Ed
[ccp4bb] Abstract submission deadline
Dear Colleagues, This is a friendly reminder that the abstract submission deadline for IUCr Congress in Osaka, Japan is March 31st. One of the many interesting sessions is entitled Recent progress in synchrotron data collection (Session number is MS65). This session will cover new developments in hardware, software and techniques for synchrotron data collection. Abstracts are welcome addressing wide range of techniques and complementarity of multiple methods. For more information and details please visit home page of the Congress at http://www.iucr2008.jp/ Looking forward to seeing your abstracts and to meeting you in Osaka. Regards, Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT, Bld. 436, D007 Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]
Re: [ccp4bb] Model ensemble for x-ray crystallography
Something to think about in using ensembles for refinement: Even in ultra high resolution crystal structures, usually only a single conformation for MC (maybe dual in some places) is seen and maybe 2-3 conformations for many SCs. Occupancies of these SCs can be adjusted during refinement with even the lowest occupany ones ending up with something like 0.1-0.2 occ. In that case, what extra knowledge is gained by modeling 5 or more ensembles other that possibly some lowering of R/Rf (which in itself may be justifiable since lower R/Rf == higher model accuracy). -Debanu. -Original Message- From: CCP4 bulletin board on behalf of Bryan W. Lepore Sent: Fri 3/28/2008 8:57 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Model ensemble for x-ray crystallography At 10:13 AM 3/28/2008, Lucas Bleicher wrote : Some time ago I've heard about the idea of proposing an ensemble of models (as in NMR), instead of a single model for x-ray crystallography structures. If I remember correctly, this idea has been published somewhere. Can anyone tell me what article is that? jmb 301 1237-1256, 2000 analyzes the disorder in calmodulin that considers such a treatment along with other models of disorder. http://www.ncbi.nlm.nih.gov/pubmed/10966818 -bryan
Re: [ccp4bb] Model ensemble for x-ray crystallography
Have a look at this: Acta Cryst. (2007). D63, 597-610 Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models T. C. Terwilliger, R. W. Grosse-Kunstleve, P. V. Afonine, P. D. Adams, N. W. Moriarty, P. Zwart, R. J. Read, D. Turk and L.-W. Hung Pavel. On 3/28/2008 8:57 AM, Bryan W. Lepore wrote: At 10:13 AM 3/28/2008, Lucas Bleicher wrote : Some time ago I've heard about the idea of proposing an ensemble of models (as in NMR), instead of a single model for x-ray crystallography structures. If I remember correctly, this idea has been published somewhere. Can anyone tell me what article is that? jmb 301 1237-1256, 2000 analyzes the disorder in calmodulin that considers such a treatment along with other models of disorder. http://www.ncbi.nlm.nih.gov/pubmed/10966818 -bryan
Re: [ccp4bb] program to draw 2D image of a peptide
I have a perl script to do this. It creates a pymol script and runs pymol to generate the view you are looking for. Thanks Abhinav Stanford Synchrotron Radiation Laboratory Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926-2992 Fax: (650) 926-3292 -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Sandra Dias Sent: Friday, March 28, 2008 9:15 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] program to draw 2D image of a peptide Does anyone know of a program, different from Ligplot, that can draw 2D image of peptides out a pdb file? It would be a plus if it can establish and draw contacts between this peptide and the neighbors residues. thanks in advance for any input. Sandra lig_contact Description: lig_contact
[ccp4bb] 3D structure based alignment
Hello, I´m having a problem that I would like to know if someone could help me. I want to do a 3D structure based alignment of my protein with another one. The problem is that my protein has 2 domains, and the structure that I want to superimpose just have one. I can do the structure superimposition by hand, but I´m not being able to do the sequence alignment based on the 3D structure, because the program that I´m using (SSM) starts to superimpose the sequence of my second domain in the beginning of the sequence of my reference model (exactly the same thing that it does with the sequence of the first domain). Do you know if there is any program where I can do this. Thanks in advance, Tânia Oliveira, PhD Student Membrane Protein Crystallography and Microbial Biochemistry Laboratory - ITQB-UNL
Re: [ccp4bb] program to draw 2D image of a peptide
I want to draw a picture of the contact of a 22-mer peptide with a protein in a 2-D perspective. Would be basically be what Ligplot does, however I don`t like the output of this program. I know that using programs like ChemDraw I can do it manually but decide to see if anyone knew about a program that could at least project a 3-D pdb file of a peptide into a 2-D image. As already posted MIFit is an option but it seems that only does it for individual residues. Sandra At 01:15 PM 3/28/2008, you wrote: just out of curiosity, why ? A. On 28 Mar 2008, at 17:15, Sandra Dias wrote: Does anyone know of a program, different from Ligplot, that can draw 2D image of peptides out a pdb file? It would be a plus if it can establish and draw contacts between this peptide and the neighbors residues. thanks in advance for any input. Sandra
Re: [ccp4bb] 3D structure based alignment
Hallo Tânia, you can try 'Rapido' by R. Mosca and T. Schneider at EMBL Hamburg. It is available as a web application under: http://webapps.embl-hamburg.de/rapido/ Best wishes, Gerrit Langer. Tânia Oliveira wrote: Hello, I´m having a problem that I would like to know if someone could help me. I want to do a 3D structure based alignment of my protein with another one. The problem is that my protein has 2 domains, and the structure that I want to superimpose just have one. I can do the structure superimposition by hand, but I´m not being able to do the sequence alignment based on the 3D structure, because the program that I´m using (SSM) starts to superimpose the sequence of my second domain in the beginning of the sequence of my reference model (exactly the same thing that it does with the sequence of the first domain). Do you know if there is any program where I can do this. Thanks in advance, Tânia Oliveira, PhD Student Membrane Protein Crystallography and Microbial Biochemistry Laboratory - ITQB-UNL
Re: [ccp4bb] 3D structure based alignment
Hi, You can use Chimera to do the work . Good Luck! liu Tânia Oliveira wrote: Hello, I´m having a problem that I would like to know if someone could help me. I want to do a 3D structure based alignment of my protein with another one. The problem is that my protein has 2 domains, and the structure that I want to superimpose just have one. I can do the structure superimposition by hand, but I´m not being able to do the sequence alignment based on the 3D structure, because the program that I´m using (SSM) starts to superimpose the sequence of my second domain in the beginning of the sequence of my reference model (exactly the same thing that it does with the sequence of the first domain). Do you know if there is any program where I can do this. Thanks in advance, *Tânia Oliveira*, /PhD Student/ *Membrane Protein Crystallography and Microbial Biochemistry Laboratory - ITQB-UNL*
Re: [ccp4bb] MolRep of coiled coils
MR on CCs is generally a pain. The problem is that sliding any CC along its own supertwist (say by one heptad) will give you a solution that lines up very well with the right model. There are a lot of solutions of this type, so you basically have a multitude of models that are all okay and the right one is not that much better than any of them. Hence, the Z-score is low. This problem gets even worse if your CC crystallizes end-to-end with another copy of itself (CCs like to do that). I'd be willing to bet that you actually already have the right solution. Take the best one from your favorite program and start refining it. Do rigid body first and keep re-applying rigid-body refinement until the model stops moving. This is important. Don't just stop when the Rcryst flattens out. Let the MODEL settle down. Then break the CC in half. Rigid-body each half until they stop moving. Keep sub-dividing like this. Eventually, you will be refining individual heptads from each chain. This is a poor-man's way to do rubber body refinement which should let you refine a bent CC. rubber body refinement in general lets you make much bigger leaps in coordinate space than all-atom refinement. Using this methodology, I was once able to solve an antiparallel trimer CC using a parallel trimer as the starting model. (the reversed chain was apparent in the refined map, but not in the starting map). It can also be useful to start with idealized coiled-coil models. The PDB does not always contain what you want. I wrote a little jiffy program for generating an idealized coiled-coil in PDB format here: http://bl831.als.lbl.gov/~jamesh/scripts/supertwist.awk The top of this file (text) contains instructions on how to use it. The idealized CC MR method proved useful in solving this structure: R. Howard et. al. Neuron 53(5), 663-75. and the methodology is described in that paper. Using idealized models allows you to scan over the various superhelical parameters and then plot the Z-score, CC, or whatever you like vs the parameter. Once you have optimized each parameter, you can do a multi-dimensional MR meta-search over a small range of all the parameters. -James Holton MAD Scientist Thomas Edwards wrote: Dear BB, I am attempting molecular replacement with a 2.8A data set from crystals of a coiled coil of about 150 residues. Probably p21212 but maybe p2221. So far, Phaser, MolRep, Amore, Mr Bump, have not provided a good solution as judged by Z-scores, CCs, Rfactors, and whether there is any density outside the model (there should be - I'm using a slightly shorter model to search with). One possible problem is that the coiled coil may not be straight. It may have a slight curve to it. I have used models from the PDB that are straight or slightly curved, so far with no success. I have tried a few different resolution cutoffs too. I have tried single helix chains or dimeric coiled coils. Is there anything special about MR with coiled coils? Can anybody provide any tips/hints on MR with coiled coils?? Thanks Ed
