RE: [PyMOL] secondary structure and movie

[Warren L. D. <wa...@de...>]

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=3D1
mdo 2, dss state=3D2
mdo 3, dss state=3D3
mdo 4, dss state=3D4
mdo 5, dss state=3D5

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=3D%d"%a)

After which...
  =20
PyMOL>mdump
 Movie: General Purpose Commands:
    1: dss state=3D1
    2: dss state=3D2
    3: dss state=3D3

etc.

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154=20
Fax   (650)-593-4020

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Alan Wilter Sousa da Silva
> Sent: Friday, October 31, 2003 3:48 AM
> To: pym...@li...
> Subject: [PyMOL] secondary structure and movie
>=20
>=20
> Hi List!
>=20
> I did a polyalanine in helix ss.
> I tested:
> 1: dss (ok)
> 2: run stride_ss.py, stride2pymol (ok)
> 3: dssp (from rtools) (???)
>=20
> Case (1) differs a little bit from (2) in N term.
>=20
> Case (3) seems not to work. Or, maybe, I do not know how to=20
> use it. Tried via menu and via command dssp.  Got the same=20
> thing: two new objects=20
> (helix and sheet) that show nothing!
>=20
> In a crystallographic protein (HIV protease), (1) gave-me a=20
> better (and
> faster) result than (2).  (3) still gave-me nothing (except=20
> the ref to=20
> Dssp, which is properly installed in my box).
> I really want to see dssp working.
>=20
> Anyway, all that said, what I want to do is loading a=20
> multi-pdb file and see dss calculating different ss for each=20
> frame.  How could I do it?
>=20
> Cheers,
> -=20
> --------------------------
> Alan Wilter Sousa da Silva
> --------------------------
> B.Sc. - Dep. F=EDsica - UFPA
> M.Sc. - Dep. F=EDsica - PUC/RJ
> D.Sc. - IBCCF/UFRJ
> Bolsista Pesquisador LAC-INPE
> S=E3o Jos=E9 dos Campos (SP), Brasil
> www.lac.inpe.br/~alan
>=20
>=20
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