Hi Yeping -

I followed  Jared's instruction and then show surface, but the surface is still an incomplete plane, unlike what I wish as in the sample.

You will probably have to create new objects for those individual residues to show their surfaces in whole.  Otherwise, you only get the portion of the whole object’s surface belonging to each residue.  Use the `create` command to duplicate a selection as a new object.

create peptide_surface_residues, chain P and resi 3+5
create protein_surface_residues, chain A and resi 97+114+116+156
show surface, *_surface_residues

There is also `extract`, which does the same thing, but removes the selection from the original object.  That’s good for separating out ligands.

And I have another question:

I show a residue in a helix of cartoon representation as sticks, and give it a color different from the cartoons of the helix, but the new color extented to the helix. How chould I prevent this happening? cartoon_discrete_colors seems doesn't work. 


You picked the wrong cartoon color setting.  :)

`cartoon_discrete_colors` controls where and how the color changes if two residues are colored differently in a cartoon.  When set to 1 (or `on`), the color changes abruptly between two residues.  When 0 (or `off`), there is a smooth gradient between the two colors.


To change the color of the cartoon for a selection, use the `cartoon_color` setting:

set cartoon_color, blue, resi 1-100

Hope that helps.

Cheers,
Jared


Dear Yeping,
you should check Jared's reponse to your message.
I think he gave you all the hints you need.
:)
Gian


Guess I missed one.  :)

On 7/11/14 8:27 AM, sunyeping wrote:
>
> 发送时间:2014年7月10日(星期四) 21:20
> 收件人:pymol-users <pymol-users@lists.sourceforge.net>
> 主 题:Re: [PyMOL] what is the pymol representation in this figure?
>
> It should be a solid surface with transparency on,
> if I'm not getting it wrong.
>
> Dear Gianluca,
>
> Thank you for the response, but how to set the side chain of the
> selected residues as solid surface? I used the command
>
> show surface, sele
>
> but the surface appears not like the sample figure in which there seems
> to be a 3D volume around the sticks representations of the side chains,
> instead, the surface shown is just a plane aside the sticks
> representation. So what is the proper way to obtain the effects in the
> sample figure?
>
> Best Regards.
>
> Yeping
>
> On 7/10/14 12:40 PM, sunyeping wrote:
> > Dear all,
> >
> > Could anyone tell me how the figure attached to the following web site
> > or the attach file is drawn? In What pymol repersentation of the
> > residues is shown?
> >
> > http://cashero.lingw.net/
> >
> > Yeping Sun
> >
> >
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > Open source business process management suite built on Java and Eclipse
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> >
> >
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>
>
> --
> Gianluca Santoni,
> Dynamop Group
> Institut de Biologie Structurale
> 6 rue Jules Horowitz
> 38027 Grenoble Cedex 1
> France
> _________________________________________________________
> Please avoid sending me Word or PowerPoint attachments.
> See http://www.gnu.org/philosophy/no-word-attachments.html
>
> ------------------------------------------------------------------------------
> Open source business process management suite built on Java and Eclipse
> Turn processes into business applications with Bonita BPM Community Edition
> Quickly connect people, data, and systems into organized workflows
> Winner of BOSSIE, CODIE, OW2 and Gartner awards
> http://p.sf.net/sfu/Bonitasoft
> _______________________________________________
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--
Gianluca Santoni,
Dynamop Group
Institut de Biologie Structurale
6 rue Jules Horowitz
38027 Grenoble Cedex 1
France
_________________________________________________________
Please avoid sending me Word or PowerPoint attachments.
See http://www.gnu.org/philosophy/no-word-attachments.html

------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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