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.Â
> Now I get it.Â
> 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,
> Â 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,
> Â John Stone
> Â [2]vmd_at_ks.uiuc.edu
> On Mon, Jan 22, 2018 at 04:58:44PM -0500, CPMAS Chen wrote:
> >Â Â I did.
> >Â Â I tried it on VMD-1.9.2, the same result. My colleague had
> VMD-1.9.3, the
> >Â Â same result. Do not have a clue why.
> >Â Â Thanks!Ä* Ä*
> >Â Â On Sun, Jan 21, 2018 at 10:43 PM, Murpholino Peligro
> >Â Â <[1][3]murpholinox_at_gmail.com> wrote:
> >
> >Â Â Â Have you tried with a stable version of VMD?
> >Â Â Â 2018-01-21 9:04 GMT-06:00 CPMAS Chen
> <[2][4]cpmasmit_at_gmail.com>:
> >
> >Â Â Â Â Hi, Phenix users,
> >Â Â Â Â This may be a little off-topic. I have posted this in VMD
> users mail
> >Â Â Â Â list. I want to try here too to see if anyone experienced
> similar
> >Â Â Â Â issue.
> >Â Â Â Â VMD and pymol gave different presentation on the secondary
> structure
> >Â Â Â Â of a protein.
> >Â Â Â Â During phenix.refinement, I added secondary structure
> restraints and
> >Â Â Â Â correctly labelled all helices and sheets. However, VMD
> does not
> >Â Â Â Â correctly present the secondary structure in
> cartoon/new-cartoon
> >Â Â Â Â presentation.
> >Â Â Â Â A little more detail.
> >Â Â Â Â In VMD-1.9.4a12, after I loaded the pdb, I chose new
> cartoon to
> >Â Â Â Â present the secondary structure. All chains are presented
> as random
> >Â Â Â Â coil, the same as tube representation. However, pymol
> correctly shows
> >Â Â Â Â the secondary structure of the same pdb file in cartoon
> >Â Â Â Â representation.
> >Â Â Â Â Has anyone encountered similar situation? what would be the
> fix?
> >Â Â Â Â Thanks!Ä* Ä*
> >Â Â Â Â Best Regards,
> >Â Â Â Â Charles
> >Â Â Â Â --
> >
> >Â Â Â Â ***************************************************
> >
> >Â Â Â Â Charles Chen
> >
> >Â Â Â Â Research Instructor
> >
> >Â Â Â Â University of Pittsburgh School of Medicine
> >
> >Â Â Â Â Department of Anesthesiology
> >
> >Â Â Â Â ******************************************************
> >
> >Â Â Â Â _______________________________________________
> >Â Â Â Â phenixbb mailing list
> >Â Â Â Â [3][5]phenixbb_at_phenix-online.org
> >Â Â Â Â [4][6]http://phenix-online.org/mailman/listinfo/phenixbb
> >Â Â Â Â Unsubscribe: [5][7]phenixbb-leave_at_phenix-online.org
> >
> >Â Â --
> >
> >Â Â ***************************************************
> >
> >Â Â Charles Chen
> >
> >Â Â Research Instructor
> >
> >Â Â University of Pittsburgh School of Medicine
> >
> >Â Â Department of Anesthesiology
> >
> >Â Â ******************************************************
> >
> > References
> >
> >Â Â Visible links
> >Â Â 1. mailto:[8]murpholinox_at_gmail.com
> >Â Â 2. mailto:[9]cpmasmit_at_gmail.com
> >Â Â 3. mailto:[10]phenixbb_at_phenix-online.org
> >Â Â 4. [11]http://phenix-online.org/mailman/listinfo/phenixbb
> >Â Â 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/Â Â Â Â Â Â 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/