VMD-L Mailing List

From: Trifan, Anda (atrifan2_at_illinois.edu)
Date: Sun Sep 25 2022 - 09:03:02 CDT

Are you also loading the psf when loading the pdb? Sometimes structures fail if psf is not loaded (first). Or the stride program may fail, you can see if this is the case in the vmd terminal window.

Best,

Anda

From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Vermaas, Josh <vermaasj_at_msu.edu>
Date: Saturday, September 24, 2022 at 1:47 PM
To: Nick Bayhi <bayhi_at_uchicago.edu>, vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Part of my molecule isn't rendering in New Cartoon
Hi Nick,

Does the selection for “protein” work? I’m betting that VMD doesn’t recognize your protein as protein, and so the protein-specific representations aren’t working.

-Josh

From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of Nick Bayhi <bayhi_at_uchicago.edu>
Date: Friday, September 23, 2022 at 7:09 PM
To: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: Part of my molecule isn't rendering in New Cartoon

Hello,

After running a simulation, portions of my molecule are invisible in cartoon representation mode (mostly beta strands). However, if I save a given frame and examine the .pdb file, it looks normal and it shows up as expected in Pymol. VMD can display those regions fine with Lines, Licorice, CPK, VDW, but not with Tube, Ribbon, Cartoon, or New Cartoon.

Does anyone have a suggestion about what could be going on here? This is true for various versions of VMD installed on multiple systems. I'm happy to share my files and some screenshots, or any other info that could be helpful or descriptive.

Thank you!
Nick 

--
Nick Bayhi
(971) 219-7408
Wei-Jen Tang Lab<https://urldefense.com/v3/__https:/voices.uchicago.edu/wtang-lab/__;!!DZ3fjg!6MhFY8bWskXQiXA1LrUPJtFissOggsAIcQK1yQk1ayAcuPWmGAtx2mM2ZKHCWngm_dLDVECqFvFKeRBvvnk$>
Biophysical Sciences
University of Chicago