Re: [Chimera-users] building linker peptide
On May 21, 2008, at 1:29 AM, Fabian Glaser wrote:
Another question regarding this issue, I succeded to make a new bond and minimize it between two chains, A and B, in the same pdb. But this created apparently a problem with the residue numbering and Nterm recognition, since when I tried to add an additional linker to the chimera I created, I got the following error message:
"No MMTK name for atom "H" in standard residue ALA"
I suspect that this is related to the fact that I still have two chains, and Chimera does not identified the new bond, or something similar.
Is there a way to automatically rename the newly unified chains? Any suggetion will be highly appreciated.
Hi Fabian, There is no automatic way to change chain ID. Only the ugly manual text-editing way, sorry! I guess that the ATOM part of the file no longer agreed with the SEQRES part of the file. It might work to simply delete that atom, if it looks like it is extra. However, I would probably go back to a PDB file saved after you added all your linker residues and edit it to remove all the lines except the coordinates (the ATOM and HETATM lines), remove the chain IDs, and renumber all the residues. It is necessary to renumber the residues because there may be residues with the same number in the different chains, and now there would be no way to tell them apart (for example, two different residues numbered 10, which used to be residue 10 in A and residue 10 in B). Unfortunately you will lose the ability to use the "familiar" residue numbering within the second chain. I attached a fortran (f77) program to do this editing, but I realize you may not be able to use it depending on your computing environment. If you are on some unix-type computer you would just compile it with something like: f77 renum2.f -o renum Then execute it with renum It would ask for the names of the input and output PDB files and what residue number to start with. Then you would have to do the addh/addcharge/minimization stuff again, sorry. I think it would already have the bond you wanted, however. Maybe someone else can think of a more elegant approach. Best, Elaine -------- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
Just deleting the SEQRES records _might_ be good enough. Otherwise go with what Elaine wrote. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On May 21, 2008, at 9:59 AM, Elaine Meng wrote:
On May 21, 2008, at 1:29 AM, Fabian Glaser wrote:
Another question regarding this issue, I succeded to make a new bond and minimize it between two chains, A and B, in the same pdb. But this created apparently a problem with the residue numbering and Nterm recognition, since when I tried to add an additional linker to the chimera I created, I got the following error message:
"No MMTK name for atom "H" in standard residue ALA"
I suspect that this is related to the fact that I still have two chains, and Chimera does not identified the new bond, or something similar.
Is there a way to automatically rename the newly unified chains? Any suggetion will be highly appreciated.
Hi Fabian, There is no automatic way to change chain ID. Only the ugly manual text-editing way, sorry! I guess that the ATOM part of the file no longer agreed with the SEQRES part of the file.
It might work to simply delete that atom, if it looks like it is extra.
However, I would probably go back to a PDB file saved after you added all your linker residues and edit it to remove all the lines except the coordinates (the ATOM and HETATM lines), remove the chain IDs, and renumber all the residues. It is necessary to renumber the residues because there may be residues with the same number in the different chains, and now there would be no way to tell them apart (for example, two different residues numbered 10, which used to be residue 10 in A and residue 10 in B). Unfortunately you will lose the ability to use the "familiar" residue numbering within the second chain.
I attached a fortran (f77) program to do this editing, but I realize you may not be able to use it depending on your computing environment. If you are on some unix-type computer you would just compile it with something like:
f77 renum2.f -o renum
Then execute it with
renum
It would ask for the names of the input and output PDB files and what residue number to start with.
Then you would have to do the addh/addcharge/minimization stuff again, sorry. I think it would already have the bond you wanted, however.
Maybe someone else can think of a more elegant approach. Best, Elaine -------- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
<renum2.f>
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Dear Elaine and Eric, Elaine program worked beautifully, and it's in any case better to have a renumbered PDB, Thanks a lot!! Fabian Eric Pettersen said the following on 21/05/08 21:34:
Just deleting the SEQRES records _might_ be good enough. Otherwise go with what Elaine wrote.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
On May 21, 2008, at 9:59 AM, Elaine Meng wrote:
On May 21, 2008, at 1:29 AM, Fabian Glaser wrote:
Another question regarding this issue, I succeded to make a new bond and minimize it between two chains, A and B, in the same pdb. But this created apparently a problem with the residue numbering and Nterm recognition, since when I tried to add an additional linker to the chimera I created, I got the following error message:
"No MMTK name for atom "H" in standard residue ALA"
I suspect that this is related to the fact that I still have two chains, and Chimera does not identified the new bond, or something similar.
Is there a way to automatically rename the newly unified chains? Any suggetion will be highly appreciated.
Hi Fabian, There is no automatic way to change chain ID. Only the ugly manual text-editing way, sorry! I guess that the ATOM part of the file no longer agreed with the SEQRES part of the file.
It might work to simply delete that atom, if it looks like it is extra.
However, I would probably go back to a PDB file saved after you added all your linker residues and edit it to remove all the lines except the coordinates (the ATOM and HETATM lines), remove the chain IDs, and renumber all the residues. It is necessary to renumber the residues because there may be residues with the same number in the different chains, and now there would be no way to tell them apart (for example, two different residues numbered 10, which used to be residue 10 in A and residue 10 in B). Unfortunately you will lose the ability to use the "familiar" residue numbering within the second chain.
I attached a fortran (f77) program to do this editing, but I realize you may not be able to use it depending on your computing environment. If you are on some unix-type computer you would just compile it with something like:
f77 renum2.f -o renum
Then execute it with
renum
It would ask for the names of the input and output PDB files and what residue number to start with.
Then you would have to do the addh/addcharge/minimization stuff again, sorry. I think it would already have the bond you wanted, however.
Maybe someone else can think of a more elegant approach. Best, Elaine -------- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu> UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
<renum2.f>
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-- Fabian Glaser, PhD Bioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology Haifa 32000, ISRAEL Web: http://bku.technion.ac.il Email: fglaser@tx.technion.ac.il Tel: +972-(0)4-8293701 Cel: +972-(0)54-4772396
participants (3)
-
Elaine Meng -
Eric Pettersen -
Fabian Glaser