Re: [Chimera-users] Two-letter ID of polypeptide in Chimera
Hi Pu Qian, PDB format only has one column for chain ID, so if you put in a 2-character chain ID it is no longer the correct format. Chimera only reads and understands the correct PDB format, not modified formats (except “pqr”), so I believe you would need to convert to mmCIF. See PDB format documentation, chain ID is column 22 only: <http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#A...> Please use the address chimera-users@cgl.ucsf.edu (CC’d here) for Chimera questions unless you are including private data. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 16, 2019, at 3:29 AM, Pu Qian <p.qian@sheffield.ac.uk> wrote:
Hi Meng anf Tom,
I used two-letter (for example, AA, AB etc.) to ID polypeptide in DPB file. The protein can be displayed using chimera, however, chains of ID, name of ligands cannot be recognised by the chimera. Is there any way I can see them in the Chimera, or I have to convert it to .cif first?
Best regards
Pu Qian
To elaborate a little on this, column 21 in an ATOM record is unassigned and Chimera conscripts that column to allow for 4-character residue names rather then 2-character chain IDs (the former were more far common a million years ago when Chimera was originally designed). So knowing that that column is part of the residue name may help you work around some things. For instance PDB residue name LIG in chain AB will be treated by Chimera as residue name LIGA in chain B (so, an atom spec of :LIGA.B rather than :LIG.AB). —Eric Eric Pettersen UCSF Computer Graphics Lab
On Apr 16, 2019, at 7:43 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Pu Qian, PDB format only has one column for chain ID, so if you put in a 2-character chain ID it is no longer the correct format. Chimera only reads and understands the correct PDB format, not modified formats (except “pqr”), so I believe you would need to convert to mmCIF.
See PDB format documentation, chain ID is column 22 only: <http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#A...>
Please use the address chimera-users@cgl.ucsf.edu (CC’d here) for Chimera questions unless you are including private data. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 16, 2019, at 3:29 AM, Pu Qian <p.qian@sheffield.ac.uk> wrote:
Hi Meng anf Tom,
I used two-letter (for example, AA, AB etc.) to ID polypeptide in DPB file. The protein can be displayed using chimera, however, chains of ID, name of ligands cannot be recognised by the chimera. Is there any way I can see them in the Chimera, or I have to convert it to .cif first?
Best regards
Pu Qian
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participants (2)
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Elaine Meng -
Eric Pettersen