Re: [PyMOL] protein cartoon/floating sidechains/ligands

[Tsjerk Wassenaar]

Hey,

In addition, you may also want to

set cartoon_smooth_loops,0

in order to have your loops nice and wiggly, attaching to your side-chains.

Cheers,

Tsjerk

On 3/6/07, Andreas Forster  wrote:

Hey Gary,

in order to have sidechains be attached to your cartoon representation, the
cartoons must not be smoothened.
set cartoon_flat_sheets, off
will do that.  Be warned that your sheets will look like the ocean beyond
the reef of Tunnels beach.

To get just a sidechain, type
show sticks, selection and not (n. ca,c,n and not pro/n)

or use the jiffy I wrote for this task:
http://sourceforge.net/mailarchive/message.php?msg_id=37303291

You don't have to duplicate anything for what you want to do (show protein
cartoon and sidechains and ligand spheres), you just have to define your
selections properly.  You might want to duplicate objects (I usually do.) in
order to color more flexibly.

To display all atoms
show spheres, all

To hide them from the GUI, click on the objects in the list.

Hope that helps.


Andreas



On 3/6/07, Gary Laco  wrote:
>
>
>
>
> Hi,
>
> I have read the manual on how to have a cartoon representation of a
protein and have one or more sidechains visible "and" connected to the
ribbon (versus floating in space, see pg 39 manual).  But I can not get that
to happen following the instructions (using GUI or command line).  Also, how
do you get just the sidechain to be visible and not the backbone N and O?
Can not find a way to select just one atom to turn them off, always get the
whole residue using the GUI.
>
>
>
> My goal is to have a cartoon representation of a protein with several
connected sidechains visible with a ligand in the active site in spheres
(CPK).  It seems to me that I need to duplicate the structure and use the
cartoon representation for the backbone/sidechains on molecule 1 and spheres
for the ligand on molecule 2, is this necessary or is there another way?
And is there a way to display all the residues/atoms in a structure and turn
them on/off in the GUI?
>
> Thank you for your help,
>
> Gary
>
>
>
> Gary S. Laco, Ph.D.
>
> Assistant Professor of Biochemistry
>
> Lake Erie College of Osteopathic Medicine-Bradenton
>
> 5000 Lakewood Ranch Blvd.
>
> Bradenton, FL 34211
>
>
>
> Office:  941-782-5666
>
> Fax:   941-782-5729
>
> E-mail:  gl...@lecom.edu
>


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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

[PyMOL] cyclic structures

[jkulpiii]

 This question has appeared a few times in the mailing list yet I could not 
find any answer (maybe I missed it).
 
 http://sourceforge.net/mailarchive/message.php?msg_id=10556819
 http://sourceforge.net/mailarchive/message.php?msg_id=36990895
 
 Basically, in cyclic structures there is a discontinuity at the last residue 
to the first residue when displaying the cartoon representation. How do we make 
a cyclic cartoon representation?
 
 Cheers, 
 John Kulp
 NRL 

Check Out the new free AIM(R) Mail -- 2 GB of storage and industry-leading spam 
and email virus protection.

Re: [PyMOL] cyclic structures

[DeLano Scientific]

Unfortunately, this is not something PyMOL can do at present, and we were
not able to come up with a workaround previously.
 
In short, the code needs to be modified at a fundamental level, but the
cartoon generator in PyMOL is about as bad as it gets: deeply nested code,
1-2 letter variables names, fragile pointers, and almost all of it in one
massive ~2,000 line C subroutine.  RepCartoon.c is one of those skeleton
demons in the closet that must eventually be challenged but will not be
easily defeated...apologies.

  _  

From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of
jkulp...@netscape.net
Sent: Wednesday, March 07, 2007 11:33 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] cyclic structures


This question has appeared a few times in the mailing list yet I could not
find any answer (maybe I missed it).

http://sourceforge.net/mailarchive/message.php?msg_id=10556819
http://sourceforge.net/mailarchive/message.php?msg_id=36990895

Basically, in cyclic structures there is a discontinuity at the last residue
to the first residue when displaying the cartoon representation.  How do we
make a cyclic cartoon representation?

Cheers, 
John Kulp
NRL
  _  

 
 Check Out the new free AIM(R)
Mail -- 2 GB of storage and industry-leading spam and email virus
protection.