I like to add that PyMOL will only work as expected with upper and lower case chain identifiers if the "ignore_case" setting is off.
http://pymolwiki.org/index.php/Ignore_case Cheers, Thomas On 07 Jul 2015, at 11:59, Steve Darnell <darne...@dnastar.com> wrote: > 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 > (seehttp://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 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
