VMD-L Mailing List

From: CPMAS Chen (cpmasmit_at_gmail.com)
Date: Tue Jan 23 2018 - 11:01:48 CST

Thanks, John.

Now I get it.

Is there a way to manipulate STRIDE result in VMD? No error msg about
STRIDE.

The secondary structure might be just a little off as they are correctly
shown in pymol.

Charles

On Mon, Jan 22, 2018 at 5:03 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> 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!Ā Ā
> > 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!Ā Ā
> > Best Regards,
> > Charles
> > --
> >
> > ***************************************************
> >
> > Charles Chen
> >
> > Research Instructor
> >
> > University of Pittsburgh School of Medicine
> >
> > Department of Anesthesiology
> >
> > ******************************************************
> >
> > _______________________________________________
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> >
> > --
> >
> > ***************************************************
> >
> > 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/
> 

-- 
***************************************************
Charles Chen
Research Instructor
University of Pittsburgh School of Medicine
Department of Anesthesiology
******************************************************