Hi Phenix users, I am wondering if phenix or other program provide superimposing pdb files as best as possible(!) I used Superpose in CCP4 but only worked for same sequence of pdb files. So my first question is how I can superimpose more than two different pdb files that are homologues (including water or not). Of course you can do similar thing in coot or pymol, but I wonder if we have better ways to do this kind of job. Secondly, if things working, to do better superimposition, is it possible to input core domain residues information vs. flexible residues information while superimposing. Thirdly, if I have 10 different structures, is there any way to superimpose into such as a calculated average structure of them and fit others into this averaged structure for better comparison? As always, thanks in advance, Young-Jin
I will refer you to a discussion we recently had on the CCP4BB on the same
topic:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1002&L=CCP4BB&F=&S=&P=209060
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1002&L=CCP4BB&F=&S=&P=209060My
personal favorite is Profit (
http://www.bioinf.org.uk/software/profit/index.html).
On Thu, Apr 8, 2010 at 11:19 AM, Young-Jin Cho
Hi Phenix users, I am wondering if phenix or other program provide superimposing pdb files as best as possible(!) I used Superpose in CCP4 but only worked for same sequence of pdb files.
So my first question is how I can superimpose more than two different pdb files that are homologues (including water or not). Of course you can do similar thing in coot or pymol, but I wonder if we have better ways to do this kind of job. Secondly, if things working, to do better superimposition, is it possible to input core domain residues information vs. flexible residues information while superimposing. Thirdly, if I have 10 different structures, is there any way to superimpose into such as a calculated average structure of them and fit others into this averaged structure for better comparison?
As always, thanks in advance,
Young-Jin
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-- Jim Fairman, Ph D. Post-Doctoral Fellow National Institutes of Health - NIDDK Cell: 1-865-748-8672 Lab: 1-301-594-9229 E-mail: [email protected] [email protected]
Hi Young-Jin, yes, you can do it in PHENIX: phenix.superpose_pdbs [pdb_file_fixed] [pdb_file_moving] [parameter_file] More details: http://www.phenix-online.org/documentation/superpose_pdbs.htm Regarding your 3rd question: I'm not sure how you define an average structure. You need to define it first, then find out how to obtain it, and then you will be able to use the above tool Let me know if you have questions. Pavel. On 4/8/10 8:19 AM, Young-Jin Cho wrote:
Hi Phenix users, I am wondering if phenix or other program provide superimposing pdb files as best as possible(!) I used Superpose in CCP4 but only worked for same sequence of pdb files.
So my first question is how I can superimpose more than two different pdb files that are homologues (including water or not). Of course you can do similar thing in coot or pymol, but I wonder if we have better ways to do this kind of job. Secondly, if things working, to do better superimposition, is it possible to input core domain residues information vs. flexible residues information while superimposing. Thirdly, if I have 10 different structures, is there any way to superimpose into such as a calculated average structure of them and fit others into this averaged structure for better comparison?
As always, thanks in advance,
Young-Jin
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stamp will help the user calculate an "average structure". stamp is
from Geoff Barton's group. stamp is old. jalview is the new stamp.
I think stamp is still available.
HTH
-bryan
On Apr 8, 2010, at 11:36, Pavel Afonine
'm not sure how you define an average structure. You need to define it first, then find out how to obtain it, and then you will be able to use the above tool
Hi, Does PHENIX can keep fix the backbone of a selected part in one chain during refinement using phenix.refine? If yes, can someone tell me the command line promt. I want to fix the backbone(N, CA, C, O) of a long helix ( 62 to 157 of chain A and also of chain B) during refinement. I have two similar helices in chain A and chain B. I am also using NCS. Thank you in advance Raja
Hi Raja,
Does PHENIX can keep fix the backbone of a selected part in one chain during refinement using phenix.refine?
you can exclude from refinement any selected part of your structure (SA is exception).
If yes, can someone tell me the command line promt.
phenix.refine model.pdb data.mtz refine.sites.individual="not (chain A and resseq 20:50 and backbone)" More atom selection syntax examples: http://www.phenix-online.org/documentation/refinement.htm#anch82 Pavel.
A quick remark: in the example below the atoms in "chain A and resseq 20:50 and backbone" will not move but they will participate in calculations of the restraints, including NCS. Use NCS groups definition to exclude these atoms from NCS. Pavel. On 4/8/10 4:16 PM, Pavel Afonine wrote:
Hi Raja,
Does PHENIX can keep fix the backbone of a selected part in one chain during refinement using phenix.refine?
you can exclude from refinement any selected part of your structure (SA is exception).
If yes, can someone tell me the command line promt.
phenix.refine model.pdb data.mtz refine.sites.individual="not (chain A and resseq 20:50 and backbone)"
More atom selection syntax examples:
http://www.phenix-online.org/documentation/refinement.htm#anch82
Pavel.
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Hi Pavel,
Many thanks for the example. This will certainly be helpful.
Raja
----- Original Message -----
From: Pavel Afonine
A quick remark:
in the example below the atoms in "chain A and resseq 20:50 and backbone" will not move but they will participate in calculations of the restraints, including NCS. Use NCS groups definition to exclude these atoms from NCS.
Pavel.
On 4/8/10 4:16 PM, Pavel Afonine wrote:
Hi Raja,
Does PHENIX can keep fix the backbone of a selected part in one chain during refinement using phenix.refine?
you can exclude from refinement any selected part of your structure (SA is exception).
If yes, can someone tell me the command line promt.
phenix.refine model.pdb data.mtz refine.sites.individual="not (chain A and resseq 20:50 and backbone)"
More atom selection syntax examples:
http://www.phenix-online.org/documentation/refinement.htm#anch82
Pavel.
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Hi Young-Jin, my personal favourite for superpositions is theseus3d (http://www.theseus3d.org/). It is Maximum Likelihood based and lets you do all the things you want, including the 'averaged structure' calculation. HTH, Jonathan Ghent University Op 08/04/10 17:19, Young-Jin Cho schreef:
Hi Phenix users, I am wondering if phenix or other program provide superimposing pdb files as best as possible(!) I used Superpose in CCP4 but only worked for same sequence of pdb files.
So my first question is how I can superimpose more than two different pdb files that are homologues (including water or not). Of course you can do similar thing in coot or pymol, but I wonder if we have better ways to do this kind of job. Secondly, if things working, to do better superimposition, is it possible to input core domain residues information vs. flexible residues information while superimposing. Thirdly, if I have 10 different structures, is there any way to superimpose into such as a calculated average structure of them and fit others into this averaged structure for better comparison?
As always, thanks in advance,
Young-Jin
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participants (6)
-
Bryan Lepore -
Jim Fairman -
Jonathan Elegheert -
Pavel Afonine -
Raja Dey -
Young-Jin Cho