[gmx-users] Secondary structure not visible after converting from .gro to .pdb

Christopher Neale chris.neale at alum.utoronto.ca
Thu May 29 05:58:14 CEST 2014

Sounds reasonable now. If 10 molecules are all listed as part of the same chain (PDB format) then maybe Pymol will stop rendering after the first "chain". So either script changing the chain info or find some other way to have them listed as different chains in the .pdb or (perhaps) just use a .gro -- if pymol will work with this -- since AFAIK a .gro file does not list chains so Pymol may be forced to figure things out on its own.

At this point, it does really seem like a Pymol issue, so I agree with previous posters that you will get the most useful help on a Pymol mailing list.

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of bharat gupta <bharat.85.monu at gmail.com>
Sent: 28 May 2014 21:24
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Secondary structure not visible after converting       from .gro to .pdb


I energy minimized a protein consisting 10 chains using gromacs. When I
converted the structure of the protein from gro format to pdb format to
visualize in Pymol, it shows only one chain in ribbon form and rest of the
chains are not shown ... How to rectify this error ??

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