VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jan 22 2018 - 16:03:48 CST

Hi,
  VMD uses STRIDE to compute secondary structure assignments.
Other programs like PyMol simply read the secondary structure assginment
in a PDB (I think we've got example scripts for that in VMD also in the
script library), however that approach doesn't work in the general case
for molecular dynamics simulations, which is what VMD was intended for.
There are few cases where STRIDE will either fail to compute a secondary
structure, and it sounds like yours is one such case. Do you get errors
in your VMD text console at the point when it prints STRIDE citation
information?

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jan 22, 2018 at 04:58:44PM -0500, CPMAS Chen wrote:
> I did.
> I tried it on VMD-1.9.2, the same result. My colleague had VMD-1.9.3, the
> same result. Do not have a clue why.
> Thanks! Â
> On Sun, Jan 21, 2018 at 10:43 PM, Murpholino Peligro
> <[1]murpholinox_at_gmail.com> wrote:
>
> Have you tried with a stable version of VMD?
> 2018-01-21 9:04 GMT-06:00 CPMAS Chen <[2]cpmasmit_at_gmail.com>:
>
> Hi, Phenix users,
> This may be a little off-topic. I have posted this in VMD users mail
> list. I want to try here too to see if anyone experienced similar
> issue.
> VMD and pymol gave different presentation on the secondary structure
> of a protein.
> During phenix.refinement, I added secondary structure restraints and
> correctly labelled all helices and sheets. However, VMD does not
> correctly present the secondary structure in cartoon/new-cartoon
> presentation.
> A little more detail.
> In VMD-1.9.4a12, after I loaded the pdb, I chose new cartoon to
> present the secondary structure. All chains are presented as random
> coil, the same as tube representation. However, pymol correctly shows
> the secondary structure of the same pdb file in cartoon
> representation.
> Has anyone encountered similar situation? what would be the fix?
> Thanks! Â
> Best Regards,
> Charles
> --
>
> ***************************************************
>
> Charles Chen
>
> Research Instructor
>
> University of Pittsburgh School of Medicine
>
> Department of Anesthesiology
>
> ******************************************************
>
> _______________________________________________
> phenixbb mailing list
> [3]phenixbb_at_phenix-online.org
> [4]http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: [5]phenixbb-leave_at_phenix-online.org
>
> --
>
> ***************************************************
>
> Charles Chen
>
> Research Instructor
>
> University of Pittsburgh School of Medicine
>
> Department of Anesthesiology
>
> ******************************************************
>
> References
>
> Visible links
> 1. mailto:murpholinox_at_gmail.com
> 2. mailto:cpmasmit_at_gmail.com
> 3. mailto:phenixbb_at_phenix-online.org
> 4. http://phenix-online.org/mailman/listinfo/phenixbb
> 5. mailto:phenixbb-leave_at_phenix-online.org 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/