From: Bennion, Brian (Bennion1_at_llnl.gov)
Date: Mon Nov 19 2012 - 17:30:19 CST

Could it be that stride gives and error if the selection is too big? There is a limit of 10000 hbonds. Not sure how the other viewers calculate the cartoons.

brian

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From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of Larry Guy [gglarry0_at_gmail.com]
Sent: Monday, November 19, 2012 2:00 PM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: VMD can't display new PDB secondary structure properly (pyMol, jMol can)

Hi all,

I hope that somebody here can help me solve a mystery regarding a newly released pdb 4G7O. Chain C of this protein can't be visualized using the ribbons or cartoon representations. Some smaller sections of chain C that I have removed and put in to a new pdb files show up fine in new cartoon representation. pyMol, jMol and other visualization software packages handle this structure with no problems, displaying all of chain C.

What could be happening in VMD that would cause this kind of problem in the cartoon representation of chain C?

Thanks in advance for your help!