pymol-users

[PyMOL] secondary structure and movie

[Alan W. S. da S. <al...@la...>]

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=
=20
(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=20
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,
-=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

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
> -------------------------------------------------------
> This SF.net email is sponsored by: SF.net Giveback Program.=20
> 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/=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...=20
> https://lists.sourceforge.net/lists/listinfo/p> ymol-users
>=20

RE: [PyMOL] secondary structure and movie

[Alan W. S. da S. <al...@la...>]

Thank you very much Dr. DeLano.

However

mdo 1, dss state=3D1 gave errors, but=20

mdo 1: dss state=3D1

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,
>=20
> =09Unfortunately, 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:
>=20
> 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
>=20
> Of course, Python can automate this:
>=20
> 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)
>=20
> After which...
>   =20
> PyMOL>mdump
>  Movie: General Purpose Commands:
>     1: dss state=3D1
>     2: dss state=3D2
>     3: dss state=3D3
>=20
> etc.
>=20
> Cheers,
> Warren
>=20
>=20
> --
> mailto:wa...@de...
> Warren L. DeLano, Ph.D.
> Principal Scientist
> DeLano Scientific LLC
> Voice (650)-346-1154=20
> Fax   (650)-593-4020
>=20
> > -----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
> > -------------------------------------------------------
> > This SF.net email is sponsored by: SF.net Giveback Program.=20
> > 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/=20
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...=20
> > https://lists.sourceforge.net/lists/listinfo/p> ymol-users
> >=20
>=20
>=20

--=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