Alan,
Unfortunately, secondary structure is currently defined as an
atom rather than a coordinate property. Thus, in order to "animate"
secondary structure, you'll need to run dss automatically for each
state. For example:
mset 1 -5
mdo 1, dss state=1
mdo 2, dss state=2
mdo 3, dss state=3
mdo 4, dss state=4
mdo 5, dss state=5
Of course, Python can automate this:
from pymol import cmd
cmd.mset("1 -%d"%cmd.count_states())
for a in range(1,cmd.count_states()+1): \
cmd.mdo(a,"dss state=%d"%a)
After which...
PyMOL>mdump
Movie: General Purpose Commands:
1: dss state=1
2: dss state=2
3: dss state=3
etc.
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -----Original Message-----
> From: pymol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> Alan Wilter Sousa da Silva
> Sent: Friday, October 31, 2003 3:48 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] secondary structure and movie
>
>
> Hi List!
>
> I did a polyalanine in helix ss.
> I tested:
> 1: dss (ok)
> 2: run stride_ss.py, stride2pymol (ok)
> 3: dssp (from rtools) (???)
>
> Case (1) differs a little bit from (2) in N term.
>
> Case (3) seems not to work. Or, maybe, I do not know how to
> use it. Tried via menu and via command dssp. Got the same
> thing: two new objects
> (helix and sheet) that show nothing!
>
> In a crystallographic protein (HIV protease), (1) gave-me a
> better (and
> faster) result than (2). (3) still gave-me nothing (except
> the ref to
> Dssp, which is properly installed in my box).
> I really want to see dssp working.
>
> Anyway, all that said, what I want to do is loading a
> multi-pdb file and see dss calculating different ss for each
> frame. How could I do it?
>
> Cheers,
> -
> --------------------------
> Alan Wilter Sousa da Silva
> --------------------------
> B.Sc. - Dep. Física - UFPA
> M.Sc. - Dep. Física - PUC/RJ
> D.Sc. - IBCCF/UFRJ
> Bolsista Pesquisador LAC-INPE
> São José dos Campos (SP), Brasil
> www.lac.inpe.br/~alan
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: SF.net Giveback Program.
> Does SourceForge.net help you be more productive? Does it
> help you create better code? SHARE THE LOVE, and help us help
> YOU! Click Here: http://sourceforge.net/donate/
> _______________________________________________
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/p> ymol-users
>
