Hi everyone,
First, thank you Tom for redirecting me.
I am trying to split a long single chain which is contained in a PDB file into several shorter chains, each to be contained in individual PDB files. I have tried Chimera (save as) and PDBEditor.jar software to do that but each approach messes the format somehow and I cannot use it in Chimera later (visualization suffers). Could you recommend me a way to do this splitting properly such that the PDB format is not messed up in the resultant 6 AAA domains and I can use the files further in Chimera. The file is attached if of any use.
Thank you in advance and I do appreciate your help.
Sincerely, Milen Raytchev
On Nov 30, 2011, at 6:16 AM, Milen Raytchev wrote:
Hi everyone,
First, thank you Tom for redirecting me.
I am trying to split a long single chain which is contained in a PDB file into several shorter chains, each to be contained in individual PDB files. I have tried Chimera (save as) and PDBEditor.jar software to do that but each approach messes the format somehow and I cannot use it in Chimera later (visualization suffers). Could you recommend me a way to do this splitting properly such that the PDB format is not messed up in the resultant 6 AAA domains and I can use the files further in Chimera. The file is attached if of any use.
Hi Milen, This seems to be pretty straightforward. Maybe I'm missing something? Anyway, open the structure in Chimera and using whatever means you are comfortable with, select each part you want separately saved in turn. After selecting each, save that part in a file with File->Save PDB... and turning on the "Save selected atoms only" option. One possible way to select parts is to bring up the sequence viewer (Favorites->Sequence) and drag the mouse across the residues you want to select. If you need to change the chain IDs, you could then open your saved files and use the Change Chain IDs tool (in the Structure Editing category, and only in the 1.6 daily build) to change them. If this is what you're already doing perhaps you could describe the problems you're having in a little more detail? The files I saved using the approach above looked fine when I opened them again in Chimera.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
Hi,
pdb files are text files so a text editor (cut and copy in a new file the region of interest) is a solution to the problem.
Ciao, Marco
Eric Pettersen pett@cgl.ucsf.edu ha scritto:
On Nov 30, 2011, at 6:16 AM, Milen Raytchev wrote:
Hi everyone,
First, thank you Tom for redirecting me.
I am trying to split a long single chain which is contained in a PDB file into several shorter chains, each to be contained in individual PDB files. I have tried Chimera (save as) and PDBEditor.jar software to do that but each approach messes the format somehow and I cannot use it in Chimera later (visualization suffers). Could you recommend me a way to do this splitting properly such that the PDB format is not messed up in the resultant 6 AAA domains and I can use the files further in Chimera. The file is attached if of any use.
Hi Milen, This seems to be pretty straightforward. Maybe I'm missing something? Anyway, open the structure in Chimera and using whatever means you are comfortable with, select each part you want separately saved in turn. After selecting each, save that part in a file with File->Save PDB... and turning on the "Save selected atoms only" option. One possible way to select parts is to bring up the sequence viewer (Favorites->Sequence) and drag the mouse across the residues you want to select. If you need to change the chain IDs, you could then open your saved files and use the Change Chain IDs tool (in the Structure Editing category, and only in the 1.6 daily build) to change them. If this is what you're already doing perhaps you could describe the problems you're having in a little more detail? The files I saved using the approach above looked fine when I opened them again in Chimera.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dr.Marco Sette, Ph.D.
Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it e-mail: m77it@yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328
www.rete29aprile.it
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participants (3)
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Eric Pettersen -
Milen Raytchev -
sette＠uniroma2.it