[PyMOL] protein cartoon/floating sidechains/ligands

[Gary Laco]

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: [phone]

E-mail: <mailto:***@lecom.edu> ***@lecom.edu

[Andreas Forster]

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

Post by Gary Laco
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: [phone]

[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

Post by Andreas Forster
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)
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

Post by Gary Laco
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.

Post by Gary Laco
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?

Post by Gary Laco
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: [phone]

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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: [phone]
F: [phone]