Thank you very much Dr. DeLano.
However
mdo 1, dss state=1 gave errors, but
mdo 1: dss state=1
Worked fine. It is a bug? If so, manual need to be also updated.
I'm using 0.92. Gonna update to 0.93.
Cheers,
On Fri, 31 Oct 2003, Warren L. DeLano wrote:
> 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:[email protected]
> Warren L. DeLano, Ph.D.
> Principal Scientist
> DeLano Scientific LLC
> Voice (650)-346-1154
> Fax (650)-593-4020
>
> > -----Original Message-----
> > From: [email protected]
> > [mailto:[email protected]] On Behalf Of
> > Alan Wilter Sousa da Silva
> > Sent: Friday, October 31, 2003 3:48 AM
> > To: [email protected]
> > 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
> >
> >
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>
>
--
--------------------------
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
