VMD-L Mailing List

From: Robert Campbell (rlc_at_k2.med.jhmi.edu)
Date: Fri Aug 23 2002 - 12:13:44 CDT

Hi Mark,

On 2002-08-23 16:18 you wrote:
>
> I just started to play a little bit with VMD 1.8a21 (SGI 64-bit). So far
> I couldn't find out how I can change the secondary structure elements
> detected by VMD (or Stride). Is there an easy way to do this? In the
> mail archive I saw a VMDTECH report dated back to 1997. Is this still
> this only way?
> When I type "structure top {resid 383 to 390} helix" in the vmd console
> it always complains: invalid command name "structure".
>

There is a script in the script repository that allows you to use the
secondary structure from a PDB file if it is defined there.

http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/vmd_use_pdb_ss/

but I found what I would consider a bug in it. It didn't reset all atoms
to be of type "coil" before defining those that it found to be helix
or sheet, thus there could be remnants of what stride had initially
calculated if you had all ready tried stride. So I added a couple of
lines between lines 48 and 49:

    set sel_all [atomselect $molid "all"]
    $sel_all set structure coil

I then made a new version of it to read the stride output. So you can
manually run stride (stride -o file.pdb > file.stride), edit the output
of it and then read it back in with this script (attached here). So you
"source" this script, that I called vmd_use_stride_ss and then it writes
to the terminal window:

   "In order to apply the new secondary structure information, do:"
   "apply_stride_ss <mol_id> <stride_info_filename>"
   " mol_id can be 'top' or the number next to the file name in"
   " the list of files that you have read in"

I hope this helps.

Cheers,
Robert 

-- 
Robert L. Campbell, Ph.D.               http://biophysics.med.jhmi.edu/rlc
rlc_at_k2.med.jhmi.edu                                    phone: 410-614-6313
Research Specialist/X-ray Facility Manager
HHMI/Dept. of Biophysics & Biophysical Chem., The Johns Hopkins University
    PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2