Thread: RE: [PyMOL] automated H-bond computation & visualization in pyMOL?

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RE: [PyMOL] automated H-bond computation & visualization in pyMOL?

From: Warren D. <wa...@de...> - 2005-10-17 20:16:30

Michael

d/l a recent build http://delsci.com/beta

and use the "find"->"polar contacts" option under the objects Action "A"
menu in the viewer window.

Cheers,
Warren


--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Michael Weber
> Sent: Monday, October 17, 2005 5:03 AM
> To: pym...@li...
> Subject: [PyMOL] automated H-bond computation & visualization=20
> in pyMOL?
>=20
> Hello everybody,
> I am new to PyMOL and I have a short question: In pyMOL - is=20
> it possible to automatically compute and visualize H-bonds in=20
> .PDB files as it is e.g. possible in SWISS-PDB-VIEWER? Maybe=20
> there is a pyMOL script for this purpose? I need such a=20
> function for my work with catalytically active RNA molecules=20
> (e.g. PDB # 2A2E, 2A64, 1NBS, 1U9S). Would be nice if someone=20
> could help me with this problem...
> =20
> All the best & thanks in advance,
> Michael.
>=20

RE: [PyMOL] automated H-bond computation & visualization in pyMOL?

From: Warren D. <wa...@de...> - 2005-10-18 13:59:22

Yes,

dist name, sele1, sele2, mode=3D2

eg.

load $TUT/1hvp.pdb

dist name, solvent, protein, mode=3D2

Cheers,
Warren


--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Marc Bruning
> Sent: Tuesday, October 18, 2005 5:03 AM
> To: pym...@li...
> Cc: Warren DeLano; Michael Weber
> Subject: Re: [PyMOL] automated H-bond computation &=20
> visualization in pyMOL?
>=20
> hello,
>=20
> is this feature accessible from the command line as well?
>=20
> cheers,
> marc
>=20
> On Monday 17 October 2005 22:16, Warren DeLano wrote:
> > Michael
> >
> > d/l a recent build http://delsci.com/beta
> >
> > and use the "find"->"polar contacts" option under the=20
> objects Action "A"
> > menu in the viewer window.
> >
> > Cheers,
> > Warren
> >
> >
> > --
> > Warren L. DeLano, Ph.D.
> > Principal Scientist
> >
> > . DeLano Scientific LLC
> > . 400 Oyster Point Blvd., Suite 213
> > . South San Francisco, CA 94080 USA
> > . Biz:(650)-872-0942  Tech:(650)-872-0834 . Fax:(650)-872-0273 =20
> > Cell:(650)-346-1154 . mailto:wa...@de...
> >
> > > -----Original Message-----
> > > From: pym...@li...
> > > [mailto:pym...@li...] On Behalf Of=20
> > > Michael Weber
> > > Sent: Monday, October 17, 2005 5:03 AM
> > > To: pym...@li...
> > > Subject: [PyMOL] automated H-bond computation & visualization in=20
> > > pyMOL?
> > >
> > > Hello everybody,
> > > I am new to PyMOL and I have a short question: In pyMOL - is it=20
> > > possible to automatically compute and visualize H-bonds in .PDB=20
> > > files as it is e.g. possible in SWISS-PDB-VIEWER? Maybe=20
> there is a=20
> > > pyMOL script for this purpose? I need such a function for my work=20
> > > with catalytically active RNA molecules (e.g. PDB # 2A2E, 2A64,=20
> > > 1NBS, 1U9S). Would be nice if someone could help me with this=20
> > > problem...
> > >
> > > All the best & thanks in advance,
> > > Michael.
> >
> > -------------------------------------------------------
> > This SF.Net email is sponsored by:
> > Power Architecture Resource Center: Free content, downloads,=20
> > discussions, and more. http://solutions.newsforge.com/ibmarch.tmpl
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by:
> Power Architecture Resource Center: Free content, downloads,=20
> discussions, and more. http://solutions.newsforge.com/ibmarch.tmpl
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

Re: [PyMOL] automated H-bond computation & visualization in pyMOL?

From: Marc B. <br...@mp...> - 2005-10-18 09:06:28

hello,

is this feature accessible from the command line as well?

cheers,
marc

On Monday 17 October 2005 22:16, Warren DeLano wrote:
> Michael
>
> d/l a recent build http://delsci.com/beta
>
> and use the "find"->"polar contacts" option under the objects Action "A"
> menu in the viewer window.
>
> Cheers,
> Warren
>
>
> --
> Warren L. DeLano, Ph.D.
> Principal Scientist
>
> . DeLano Scientific LLC
> . 400 Oyster Point Blvd., Suite 213
> . South San Francisco, CA 94080 USA
> . Biz:(650)-872-0942  Tech:(650)-872-0834
> . Fax:(650)-872-0273  Cell:(650)-346-1154
> . mailto:wa...@de...
>
> > -----Original Message-----
> > From: pym...@li...
> > [mailto:pym...@li...] On Behalf Of
> > Michael Weber
> > Sent: Monday, October 17, 2005 5:03 AM
> > To: pym...@li...
> > Subject: [PyMOL] automated H-bond computation & visualization
> > in pyMOL?
> >
> > Hello everybody,
> > I am new to PyMOL and I have a short question: In pyMOL - is
> > it possible to automatically compute and visualize H-bonds in
> > .PDB files as it is e.g. possible in SWISS-PDB-VIEWER? Maybe
> > there is a pyMOL script for this purpose? I need such a
> > function for my work with catalytically active RNA molecules
> > (e.g. PDB # 2A2E, 2A64, 1NBS, 1U9S). Would be nice if someone
> > could help me with this problem...
> >
> > All the best & thanks in advance,
> > Michael.
>
> -------------------------------------------------------
> This SF.Net email is sponsored by:
> Power Architecture Resource Center: Free content, downloads, discussions,
> and more. http://solutions.newsforge.com/ibmarch.tmpl
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Re: [PyMOL] automated H-bond computation & visualization in pyMOL?

From: Michael W. <we...@st...> - 2005-10-18 10:01:12

Hi Warren,
thanks a lot for the quick & useful information concerning H-bond 
visualization.

All the best,
Michael.

----- Original Message ----- 
> On Monday 17 October 2005 22:16, Warren DeLano wrote:
>> Michael
>>
>> d/l a recent build http://delsci.com/beta
>>
>> and use the "find"->"polar contacts" option under the objects Action "A"
>> menu in the viewer window.
>>
>> Cheers,
>> Warren
>>
>>
>> --
>> Warren L. DeLano, Ph.D.
>> Principal Scientist
>>
>> . DeLano Scientific LLC
>> . 400 Oyster Point Blvd., Suite 213
>> . South San Francisco, CA 94080 USA
>> . Biz:(650)-872-0942  Tech:(650)-872-0834
>> . Fax:(650)-872-0273  Cell:(650)-346-1154
>> . mailto:wa...@de...
>>
>> > -----Original Message-----
>> > From: pym...@li...
>> > [mailto:pym...@li...] On Behalf Of
>> > Michael Weber
>> > Sent: Monday, October 17, 2005 5:03 AM
>> > To: pym...@li...
>> > Subject: [PyMOL] automated H-bond computation & visualization
>> > in pyMOL?
>> >
>> > Hello everybody,
>> > I am new to PyMOL and I have a short question: In pyMOL - is
>> > it possible to automatically compute and visualize H-bonds in
>> > .PDB files as it is e.g. possible in SWISS-PDB-VIEWER? Maybe
>> > there is a pyMOL script for this purpose? I need such a
>> > function for my work with catalytically active RNA molecules
>> > (e.g. PDB # 2A2E, 2A64, 1NBS, 1U9S). Would be nice if someone
>> > could help me with this problem...
>> >
>> > All the best & thanks in advance,
>> > Michael.