Re: [PyMOL] Ligand Surface Representation

[Nicholas N. <no...@uk...>]

can you get a surface for the protein-ligand complex? =20



cheers,
nick


-----Original Message-----
From: Simon Holton <sim...@em...>
To: "Andrew Colasanti" <aco...@gm...>
Date: Thu, 2 Nov 2006 15:36:55 +0100
Subject: Re: [PyMOL] Ligand Surface Representation

Maybe it wasn't clear from my original email, but I did try making a =20
new object for the ligand and one for the 'empty' protein, but this =20
doesn't help :-(

Simon




On Nov 2, 2006, at 3:19 PM, Andrew Colasanti wrote:

> Did you create a new object for the ligand?  Try creating 2 objects,
> one for ligand and one for protein w/o ligand.
>
> Andrew
>
>
> On 11/2/06, Simon Holton <sim...@em...> wrote:
>> Hi Folks,
>>
>>         I'm trying to generate a surface for a ligand which is =20
>> part of a
>> ligand-protein complex.  I realise this is the other way around to
>> normal, but somehow when I select the ligand in pymol and then 'show
>> surface, ligand', absolutely nothing happens.  No error, but no
>> surface.  The same happens if I just open a pdb file describing the
>> ligand alone.  Other representations work, but the problem is not PDB
>> specific.  I'm using the macpymol X11 hybrid (0.98)
>>
>>         Any suggestions?
>>
>> Cheers
>>
>>         SImon
>>
>> ---------------------------------------------------------------------=20
>> ----
>> Using Tomcat but need to do more? Need to support web services, =20
>> security?
>> Get stuff done quickly with pre-integrated technology to make your =20
>> job easier
>> Download IBM WebSphere Application Server v.1.0.1 based on Apache =20
>> Geronimo
>> http://sel.as-us.falkag.net/sel?=20
>> cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=3D121642
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>
> ----------------------------------------------------------------------=20
> ---
> Using Tomcat but need to do more? Need to support web services, =20
> security?
> Get stuff done quickly with pre-integrated technology to make your =20
> job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache =20
> Geronimo
> http://sel.as-us.falkag.net/sel?=20
> cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users


-------------------------------------------------------------------------
Using Tomcat but need to do more? Need to support web services, security?
Get stuff done quickly with pre-integrated technology to make your job easi=
er
Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=3D1=
21642
_______________________________________________
PyMOL-users mailing list
PyM...@li...
https://lists.sourceforge.net/lists/listinfo/pymol-users


________________________________________

Nicholas Noinaj
University of Kentucky College of Medicine
Department of Molecular and Cellular Biochemistry
The Center for Structural Biology
Biomedical Biological Sciences Research Building, Rm 236
741 S. Limestone
Lexington, Ky 40536
Lab:  859-323-8183
Cell:  859-893-4789
Home:  859-228-0978
no...@uk...
noinaj.com