[ccp4bb] Accuracy of the position of coordinates
Dear CCP4 user, I have a set of pdb coordinates and I would like to know the accuracy (error) of the position of the coordinates. I understand that this is dependent on the variation of Rfree with respect to resolution. I would appreciate it if you can help me with this, like what is the appropriate program to use. Thank you so much. Best regards, Joe Yap
Re: [ccp4bb] Estimation of coordinate errors
By the way, I used this one recently: http://zhang.bioinformatics.ku.edu/TM-score/ It computes a lot of scores: TM-score, MaxSub-score, GDT-TS-score and GDT-HA-score. All of this with a single Fortran file (so nothing more needed except a Fortran compiler), I was impressed. Regards, F. Pavel Afonine wrote: Hi Joe, do you want to calculate rms deviations between two sets of coordinates that are originating from two PDB files? If my guess is correct, then you can get this number using the command below: phenix.superpose_pdbs file1.pdb file2.pdb which will superpose two sets of coordinates and print RMS deviations before and after superposition, like this: RMSD between fixed and moving atoms (start): 0.575 RMSD between fixed and moving atoms (final): 0.563 Is this is what you want? Good luck! Pavel. On 8/2/10 9:59 PM, Joe Yap wrote: Dear CCP4 users, I have two sets of coordinates that are of similar structure and I would like to know is there a program I can use to calculate the coordinate errors between these two sets of coordinates? I would appreciate it if you can help me with this. Thank you so much. Best regards, Joe Yap
Re: [ccp4bb] R-Rfree vs resolution
Dear Bei, Pavel's statistic can be completed by the analysis of the most frequent values (modes) versus resolution. When the resolution is plotted in the LOG-scale, these most frequent values are practically linear functions giving their easy interpolation / extrapolation as mode(R) = 0.091*ln(resolution) + 0.134 mode(Rfree-R) = 0.024*ln(resolution) + 0.020 More detail can be found in Urzhumtsev, Afonine Adams (2009) Acta Cryst., D65, 1283-1291. Best regards, Sacha phenix.r_factor_statistics gives: Histogram of Rwork for models in PDB at resolution 0.6-99.0 A: On 8/2/10 9:24 PM, joybeiyang wrote: Dear all, I remember that there used to be a post about the R-Rfree statistics vs different resolution, but can not find it now, could anybody shed a light on me? Thank you very much in advance! Best, Bei 2010-08-03 -- joybeiyang
Re: [ccp4bb] Accuracy of the position of coordinates
I would like to know the accuracy (error) of the position of the coordinates This is provided by the output of the refinement software. An example (CNS-refined structure, from the pdb header, there is an input file called xtal_pdbsubmission.inp REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT(A) : 0.36 REMARK 3 ESD FROM SIGMAA (A) : 0.45 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT(A) : 0.49 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.60 Another example, from Phenix: REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.41 A third example, from Refmac: REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE(A): 0.356 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.279 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.282 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.096 Can't provide you with an example for Buster because I requested the software last year and I do not know what happened to that request. The coordinate errors are estimated using statistical methods. Relevant papers to read are those of Randy Read and of Vittorio Luzzatti (and probably of others), Luzzatti V. (1952), Acta Cryst. 5, 802-810; Read, R.J. (1986), Acta Cryst. A42, 140-149. There are probably papers by the Russian school (Lunin and others) but I can't locate them right now... Fred.
Re: [ccp4bb] Accuracy of the position of coordinates
Received from John Helliwell and thus forwarded to the bb - why should you miss important information? Original Message Subject:Re: [ccp4bb] Accuracy of the position of coordinates Date: Tue, 3 Aug 2010 09:08:30 +0100 From: John R Helliwell jrhelliw...@gmail.com To: Vellieux Frederic frederic.velli...@ibs.fr References: 4c57c841.2080...@ibs.fr Dear Fred, I think the Cruickshank Diffraction Precision Index and its specific reformulation by David Blow are a better estimate of overall coordinate errors. These two papers are in Acta D. Greetings, John On Tue, Aug 3, 2010 at 8:41 AM, Vellieux Frederic frederic.velli...@ibs.fr mailto:frederic.velli...@ibs.fr wrote: I would like to know the accuracy (error) of the position of the coordinates This is provided by the output of the refinement software. An example (CNS-refined structure, from the pdb header, there is an input file called xtal_pdbsubmission.inp REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT(A) : 0.36 REMARK 3 ESD FROM SIGMAA (A) : 0.45 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT(A) : 0.49 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.60 Another example, from Phenix: REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.41 A third example, from Refmac: REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE(A): 0.356 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.279 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.282 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.096 Can't provide you with an example for Buster because I requested the software last year and I do not know what happened to that request. The coordinate errors are estimated using statistical methods. Relevant papers to read are those of Randy Read and of Vittorio Luzzatti (and probably of others), Luzzatti V. (1952), Acta Cryst. 5, 802-810; Read, R.J. (1986), Acta Cryst. A42, 140-149. There are probably papers by the Russian school (Lunin and others) but I can't locate them right now... Fred. -- Professor John R Helliwell DSc
Re: [ccp4bb] R-Rfree vs resolution
Bei You can do various statistics, including R-Rfree + resolution from the PDBeStatistics pages from this link http://www.ebi.ac.uk/pdbe-as/pdbestatistics/PDBeStatistics.jsp Specifically you can do the following for your query, but there are many other combinations you can try. Xtal : Rdiff from the Experiment drop down and resolution for the second parameter drop down. [show Distribution] will then produce a dynamic rotatable graph that can be selected to determine subsets. Regards Tom Oldfield PDBe Dear all, I remember that there used to be a post about the R-Rfree statistics vs different resolution, but can not find it now, could anybody shed a light on me? Thank you very much in advance! Best, Bei 2010-08-03 joybeiyang
[ccp4bb] Extremely long c-axis...reasonable?
Hi everybody, indexing of recently collected data gave me unit cell parameters of a=b= 88 and an extremely long c-axis of 652 A. My question is, if the value of the c-axis can be reasonable? Or am I wrong with the SG? I know that length doesn't count, but does anybody has a longer one? Is there a function in the pdb to look for the length of axes? Thanks, Christian Helmholtz-Zentrum f?r Infektionsforschung GmbH | Inhoffenstra?e 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: MinDir'in B?rbel Brumme-Bothe, Bundesministerium f?r Bildung und Forschung Stellvertreter: MinDirig Heiko Gevers, Nieders?chsisches Ministerium f?r Wissenschaft und Kultur Gesch?ftsf?hrung: Prof. Dr. J?rgen Wehland; Ulf Richter, MBA Gesellschaft mit beschr?nkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477
Re: [ccp4bb] Extremely long c-axis...reasonable?
Totally reasonable, yes. (But when it's that wrong, you easily get it wrong, too.) It's probably P6122 or P4122. Be careful to mount your crystals so you can rotate around the long axis, otherwise you'll never get non-overlapping data. phx On 03/08/2010 12:45, Christian Strube wrote: Hi everybody, indexing of recently collected data gave me unit cell parameters of a=b= 88 and an extremely long c-axis of 652 A. My question is, if the value of the c-axis can be reasonable? Or am I wrong with the SG? I know that length doesn't count, but does anybody has a longer one? Is there a function in the pdb to look for the length of axes? Thanks, Christian Helmholtz-Zentrum f?r Infektionsforschung GmbH | Inhoffenstra?e 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: MinDir'in B?rbel Brumme-Bothe, Bundesministerium f?r Bildung und Forschung Stellvertreter: MinDirig Heiko Gevers, Nieders?chsisches Ministerium f?r Wissenschaft und Kultur Gesch?ftsf?hrung: Prof. Dr. J?rgen Wehland; Ulf Richter, MBA Gesellschaft mit beschr?nkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477
[ccp4bb] Phenix Autobuild
Hi everybody, I have a problem with Phenix autobuild. I want to input sequence file together with the pdb and mtz that I got from molecular replacement. But I have no idea which types of sequence files its required. if anybody please help me out. thanks === Md. Munan Shaik Department of Chemical Biology University of Padova via G. Colombo 03 Padova 35131, Italy
[ccp4bb] molecule name from pdb id and chain identifier
Hi, Sorry for the off topic question! I'm looking at Dali search results and find the molecule names are not always the same as the ones for the chain identifier from the pdb entry (maybe the molecule names are always of chain A of the entries???). I'm wondering if there is a way/tool to extract the proper molecule names of the corresponding chains for the dali hits giving multiple hits at the same time. So far I've found only Uniprot ID mapping that might be useful but it doesn't allow using chain id's. My googling skills have failed me. So any help would be very much appreciated. Many thanks. Kind regards, Sid.
Re: [ccp4bb] Phenix Autobuild
use fasta my_amazing_protein THISMESSAGESHOULDHAVEBEENSENTTOTHEPHENIXBB ;-) Preben On 03/08/2010, at 14.19, Md. Munan Shaik wrote: Hi everybody, I have a problem with Phenix autobuild. I want to input sequence file together with the pdb and mtz that I got from molecular replacement. But I have no idea which types of sequence files its required. if anybody please help me out. thanks === Md. Munan Shaik Department of Chemical Biology University of Padova via G. Colombo 03 Padova 35131, Italy Jens Preben Morth, Ph.D Aarhus University Department of Molecular Biology Gustav Wieds Vej 10 C DK - 8000 Aarhus C Tel. +45 8942 5257, Fax. +45 8612 3178 j...@mb.au.dk website: http://person.au.dk/en/j...@mb.au.dk
Re: [ccp4bb] Extremely long c-axis...reasonable?
Hi Christian - As a number of others have pointed out, this unit cell is unusual, but not impossible. It is, in fact, possible to search the PDB for unit cell parameters. From the home page, choose Advanced Search; on the search page, choose X-ray cell dimensions from the dropdown list of query types. Performing this search finds 12 structures in the PDB with c axis 600 A and a and b axes 100 A. Two of these are fiber diffraction molecular envelopes, but the other 10 are well-refined crystal structures at reasonable resolutions. So it can be done! - Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems, a wholly owned subsidiary of Eli Lilly Company 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Christian Strube Sent: Tuesday, August 03, 2010 7:46 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Extremely long c-axis...reasonable? Hi everybody, indexing of recently collected data gave me unit cell parameters of a=b= 88 and an extremely long c-axis of 652 A. My question is, if the value of the c-axis can be reasonable? Or am I wrong with the SG? I know that length doesn't count, but does anybody has a longer one? Is there a function in the pdb to look for the length of axes? Thanks, Christian Helmholtz-Zentrum f?r Infektionsforschung GmbH | Inhoffenstra?e 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: MinDir'in B?rbel Brumme-Bothe, Bundesministerium f?r Bildung und Forschung Stellvertreter: MinDirig Heiko Gevers, Nieders?chsisches Ministerium f?r Wissenschaft und Kultur Gesch?ftsf?hrung: Prof. Dr. J?rgen Wehland; Ulf Richter, MBA Gesellschaft mit beschr?nkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.
Re: [ccp4bb] Extremely long c-axis...reasonable?
There's no theoretical reason it can't be that long. BUT it is possible, especially for problematic diffraction patterns (e.g. from a badly-diffracting, cracked crystal) for the software to pick some wacky value in its attempt to fit spots that don't really all belong in the same pattern. You should be able to tell by looking at the images - are there rows of spots regularly spaced 1/652 A apart? Phoebe Original message Date: Tue, 3 Aug 2010 10:27:34 -0400 From: Matthew Franklin matthew.frank...@imclone.com Subject: Re: [ccp4bb] Extremely long c-axis...reasonable? To: CCP4BB@JISCMAIL.AC.UK Hi Christian - As a number of others have pointed out, this unit cell is unusual, but not impossible. It is, in fact, possible to search the PDB for unit cell parameters. From the home page, choose Advanced Search; on the search page, choose X-ray cell dimensions from the dropdown list of query types. Performing this search finds 12 structures in the PDB with c axis 600 A and a and b axes 100 A. Two of these are fiber diffraction molecular envelopes, but the other 10 are well-refined crystal structures at reasonable resolutions. So it can be done! - Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems, a wholly owned subsidiary of Eli Lilly Company 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Christian Strube Sent: Tuesday, August 03, 2010 7:46 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Extremely long c-axis...reasonable? Hi everybody, indexing of recently collected data gave me unit cell parameters of a=b= 88 and an extremely long c-axis of 652 A. My question is, if the value of the c-axis can be reasonable? Or am I wrong with the SG? I know that length doesn't count, but does anybody has a longer one? Is there a function in the pdb to look for the length of axes? Thanks, Christian Helmholtz-Zentrum f?r Infektionsforschung GmbH | Inhoffenstra?e 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: MinDir'in B?rbel Brumme- Bothe, Bundesministerium f?r Bildung und Forschung Stellvertreter: MinDirig Heiko Gevers, Nieders?chsisches Ministerium f?r Wissenschaft und Kultur Gesch?ftsf?hrung: Prof. Dr. J?rgen Wehland; Ulf Richter, MBA Gesellschaft mit beschr?nkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you. Phoebe A. Rice Assoc. Prof., Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 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] Fab:Peptide complex crystallization
Hi All, I want thank everyone who replied to my request on Fab:peptide crystallization. I received wonderful advice from all of you and it was very helpful in that I did get some beautiful crystals in my screens! Whether or not there is peptide bound is another matter..:). In case anyone of you are interested I prepared my Fab:peptide complex as follows: I first dissolved my peptide in 100% DMSO at a stock concentration of 100mg/mL (this peptide a very high solubility in DMSO!). I added enough peptide to my protein to give me a 10:1 peptide:protein molar ratio and a final DMSO concentration of ~2%. I did not see any precipitate after addition of peptide to protein nor after subsequent centrifugation This was a promising observation in that when I did a mock set up of peptide in the same volume of the same buffer as protein but without protein I saw very visible precipitate after addition of peptide. This suggested to me that a significant portion of peptide bound to the protein and reducing free peptide to a reasonable concentration so as to remain in solution possibly?I used this protein:peptide mixture to set up screens and of course the rest is history. Thanks again everyone! Christine
[ccp4bb] CCP4-omit crashes for large system
Hi there, I was using the CCP4-omit to generate the omit maps. However, for 2 input mtz files with exactly the same colume labels but different system size, for the small system, it works, but for the large systems, it ended up with: ./omit: line 9: 8510 Segmentation fault I am not sure whether this is a memory issue, and I appreciate for any hints about how to fix it. Thanks! Hailiang
[ccp4bb] Two cells, one crystal
Hi all, I work on a protein that has two know space groups at the same condition. One is P21 with 1 molecule in the ASU (small cell) and the other is P21 with 2 molecules in the ASU (large cell with pseudo-translational symmetry and is a giant pain in the butt to deal with). I was shooting a crystal today and the first image was the large cell, as it is a large crystal and I was feeling lazy so I just translated the crystal in the beam and collected another image and it was the small cell. I looked around but there doesn't seem to be any literature covering this topic. Is this a common phenomenon or should I be intrigued? Thanks in advance for the help, Katherine --
