make one chain from two chains ID in PDB
Hello, I'm working with a PDB file, in this file, one protein peptide was recognized as two chains (B and C), I want to make it as one chain, so it will be easier to do some interface analysis and modeling. I guess I can open the file as WORD file and change all the C to B one by one, but it's too much work to edit it that way. May I get some help for this? Is there a easier way to do this? Many thanks, Jianbo
Dear Jianbo, You may want to try one of these PDB-editing web servers: <http://www.igs.cnrs-mrs.fr/Caspr2/magicPDB.cgi> <http://dicsoft2.physics.iisc.ernet.in/pdbgoodies/inputpage.html> Both make you choose the file before you can see the options, but can do several things, including changing chain ID and renumbering. I haven't tried exactly what you describe, but it is probably worth trying before using a text editor. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Mar 2, 2010, at 1:35 PM, Dong, Jianbo wrote:
Hello,
I'm working with a PDB file, in this file, one protein peptide was recognized as two chains (B and C), I want to make it as one chain, so it will be easier to do some interface analysis and modeling. I guess I can open the file as WORD file and change all the C to B one by one, but it's too much work to edit it that way.
May I get some help for this? Is there a easier way to do this?
Many thanks,
Jianbo
I forgot to mention that when you change chain ID, you usually also need to change the residue numbering so that residues will be uniquely specifiable. For example, if you have two residues both numbered 10 in chain B, it may be difficult to do something to only one or the other in Chimera. Those editing servers allow renumbering in addition to changing the chain ID. Elaine On Mar 2, 2010, at 2:12 PM, Elaine Meng wrote:
Dear Jianbo, You may want to try one of these PDB-editing web servers:
<http://www.igs.cnrs-mrs.fr/Caspr2/magicPDB.cgi>
<http://dicsoft2.physics.iisc.ernet.in/pdbgoodies/inputpage.html>
Both make you choose the file before you can see the options, but can do several things, including changing chain ID and renumbering. I haven't tried exactly what you describe, but it is probably worth trying before using a text editor.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 2, 2010, at 1:35 PM, Dong, Jianbo wrote:
Hello,
I'm working with a PDB file, in this file, one protein peptide was recognized as two chains (B and C), I want to make it as one chain, so it will be easier to do some interface analysis and modeling. I guess I can open the file as WORD file and change all the C to B one by one, but it's too much work to edit it that way.
May I get some help for this? Is there a easier way to do this?
Many thanks,
Jianbo
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Elaine, I think I got it now, by trying the first link. The residue numbering was not a problem, since although the peptide was made as two chains, the residues was numbered as one chain (chain B: 4-246, chain C:252-416). I simply changed C to B, and test it on PISA, it looks work. Thank you so much for the help! Jianbo -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Tue 3/2/2010 3:03 PM To: Dong, Jianbo Cc: Chimera BB Subject: Re: [Chimera-users] make one chain from two chains ID in PDB I forgot to mention that when you change chain ID, you usually also need to change the residue numbering so that residues will be uniquely specifiable. For example, if you have two residues both numbered 10 in chain B, it may be difficult to do something to only one or the other in Chimera. Those editing servers allow renumbering in addition to changing the chain ID. Elaine On Mar 2, 2010, at 2:12 PM, Elaine Meng wrote:
Dear Jianbo, You may want to try one of these PDB-editing web servers:
<http://www.igs.cnrs-mrs.fr/Caspr2/magicPDB.cgi>
<http://dicsoft2.physics.iisc.ernet.in/pdbgoodies/inputpage.html>
Both make you choose the file before you can see the options, but can do several things, including changing chain ID and renumbering. I haven't tried exactly what you describe, but it is probably worth trying before using a text editor.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 2, 2010, at 1:35 PM, Dong, Jianbo wrote:
Hello,
I'm working with a PDB file, in this file, one protein peptide was recognized as two chains (B and C), I want to make it as one chain, so it will be easier to do some interface analysis and modeling. I guess I can open the file as WORD file and change all the C to B one by one, but it's too much work to edit it that way.
May I get some help for this? Is there a easier way to do this?
Many thanks,
Jianbo
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi: On Tue, 2 Mar 2010, Elaine Meng wrote:
I forgot to mention that when you change chain ID, you usually also need to change the residue numbering so that residues will be uniquely specifiable. For example, if you have two residues both numbered 10 in chain B, it may be difficult to do something to only one or the other in Chimera. Those editing servers allow renumbering in addition to changing the chain ID. Elaine
Just a note: If two chains are given the same chain ID, it is not clear how everything will properly work out, even with renumbering. I would imagine that Chimera would see the last residue in the first original chain as the part of a backbone that joins it to the first residue in the second original chain. Would this unfortunate connection occur? Cheers, Forbes
On Mar 2, 2010, at 2:12 PM, Elaine Meng wrote:
Dear Jianbo, You may want to try one of these PDB-editing web servers:
<http://www.igs.cnrs-mrs.fr/Caspr2/magicPDB.cgi>
<http://dicsoft2.physics.iisc.ernet.in/pdbgoodies/inputpage.html>
Both make you choose the file before you can see the options, but can do several things, including changing chain ID and renumbering. I haven't tried exactly what you describe, but it is probably worth trying before using a text editor.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 2, 2010, at 1:35 PM, Dong, Jianbo wrote:
Hello,
I'm working with a PDB file, in this file, one protein peptide was recognized as two chains (B and C), I want to make it as one chain, so it will be easier to do some interface analysis and modeling. I guess I can open the file as WORD file and change all the C to B one by one, but it's too much work to edit it that way.
May I get some help for this? Is there a easier way to do this?
Many thanks,
Jianbo
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
On Mar 4, 2010, at 10:43 AM, Forbes J. Burkowski wrote:
Hi:
On Tue, 2 Mar 2010, Elaine Meng wrote:
I forgot to mention that when you change chain ID, you usually also need to change the residue numbering so that residues will be uniquely specifiable. For example, if you have two residues both numbered 10 in chain B, it may be difficult to do something to only one or the other in Chimera. Those editing servers allow renumbering in addition to changing the chain ID. Elaine
Just a note: If two chains are given the same chain ID, it is not clear how everything will properly work out, even with renumbering. I would imagine that Chimera would see the last residue in the first original chain as the part of a backbone that joins it to the first residue in the second original chain. Would this unfortunate connection occur?
Hi Forbes, Assuming that the TER card between the chains is retained, then no, Chimera will treat the two chains as completely separate entities despite the identical chain ID. This can be awkward in some interfaces that list chains since there will be two apparently- identical entries. If the TER card is removed then Chimera will treat them as one chain and will add a "missing structure" pseudobond connecting the last residue of one chain to the first residue of the other chain. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
participants (4)
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Dong, Jianbo -
Elaine Meng -
Eric Pettersen -
Forbes J. Burkowski