Hi Yeping,
Just to clarify on Jose’s comment. The valid chain identifiers for the PDB
format are [A-Za-z0-9], which allows up to 62 identifiers. This should be
sufficient for your current usage. I agree with Jose, mmCIF format is the
currently recommended format.
~Steve
From: Jose Manuel Duarte [mailto:jose.dua...@psi.ch]
Sent: Monday, July 06, 2015 10:01 AM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] How to name overfull chains in PDB file?
Hi Yeping
The limitation to 1 character chain-identifiers is indeed one of the
limitations of the PDB format. There are tricks to extend it a bit: using
digits or using case-sensitive chain identifiers, but in the end you will
always hit a limitation.
This problem with the PDB format is already known for many years, that's why
the PDB has introduced a new file format called mmCIF. With the new mmCIF
format the limitations imposed by the PDB format are gone, for instance you can
use any number of characters for the chain identifier. In fact since December
2014 the PDB is producing some large structures in mmCIF format only (see
http://www.rcsb.org/pdb/static.do?p=general_information/whats_new.jsp?b=1412)
PyMOL already has very good support to read mmCIF format, so I'd definitely
recommend using it.
Hope this helps
Jose
On 06.07.2015 13:45, sunyeping wrote:
Dear all,
I now have some problems in naming the chains in PDB files. If a PDB file
contains more than 26 chains, say, 40 chains, I can name the first 26 chains
with the letters "A" to "Z", but how should I name the rest 14 chains？ It seems
that they can not be named with repeated letters which have been used because
this cause abnormality in display function in pymol. And identifier like "A1",
"A2", etc, can not be used either because there is only one colum (colum 22)
for the chain ID in PDB file format. So what is the proper way to name the
chains for this circumstance? Thanks in advance.
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences
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