From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 23 2018 - 11:12:12 CST

This is a very old script, but I think it should still work.
It will let you use the secondary structure from the PDB rather
than using the assignment made by STRIDE:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/vmd_use_pdb_ss/

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jan 23, 2018 at 12:01:48PM -0500, CPMAS Chen wrote:
> 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 <[1]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
> [2]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!* *
> > On Sun, Jan 21, 2018 at 10:43 PM, Murpholino Peligro
> > <[1][3]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][4]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!* *
> > Best Regards,
> > Charles
> > --
> >
> > ***************************************************
> >
> > Charles Chen
> >
> > Research Instructor
> >
> > University of Pittsburgh School of Medicine
> >
> > Department of Anesthesiology
> >
> > ******************************************************
> >
> > _______________________________________________
> > phenixbb mailing list
> > [3][5]phenixbb_at_phenix-online.org
> > [4][6]http://phenix-online.org/mailman/listinfo/phenixbb
> > Unsubscribe: [5][7]phenixbb-leave_at_phenix-online.org
> >
> > --
> >
> > ***************************************************
> >
> > Charles Chen
> >
> > Research Instructor
> >
> > University of Pittsburgh School of Medicine
> >
> > Department of Anesthesiology
> >
> > ******************************************************
> >
> > References
> >
> > Visible links
> > 1. mailto:[8]murpholinox_at_gmail.com
> > 2. mailto:[9]cpmasmit_at_gmail.com
> > 3. mailto:[10]phenixbb_at_phenix-online.org
> > 4. [11]http://phenix-online.org/mailman/listinfo/phenixbb
> > 5. mailto:[12]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
> [13]http://www.ks.uiuc.edu/~johns/ Phone:
> [14]217-244-3349
> [15]http://www.ks.uiuc.edu/Research/vmd/
>
> --
>
> ***************************************************
>
> Charles Chen
>
> Research Instructor
>
> University of Pittsburgh School of Medicine
>
> Department of Anesthesiology
>
> ******************************************************
>
> References
>
> Visible links
> 1. mailto:johns_at_ks.uiuc.edu
> 2. mailto:vmd_at_ks.uiuc.edu
> 3. mailto:murpholinox_at_gmail.com
> 4. mailto:cpmasmit_at_gmail.com
> 5. mailto:phenixbb_at_phenix-online.org
> 6. http://phenix-online.org/mailman/listinfo/phenixbb
> 7. mailto:phenixbb-leave_at_phenix-online.org
> 8. mailto:murpholinox_at_gmail.com
> 9. mailto:cpmasmit_at_gmail.com
> 10. mailto:phenixbb_at_phenix-online.org
> 11. http://phenix-online.org/mailman/listinfo/phenixbb
> 12. mailto:phenixbb-leave_at_phenix-online.org
> 13. http://www.ks.uiuc.edu/~johns/
> 14. file:///tmp/tel:217-244-3349
> 15. http://www.ks.uiuc.edu/Research/vmd/

-- 
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/