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
------------------------------------------------------------------------------
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
------------------------------------------------------------------------------
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
