Dear Jhon,

 

You want to use the show sticks option. Using the sequence viewer, this will show your ligands etc. Select these by clicking on them in the sequence viewer then under selection pick show sticks. >From this point once you have displayed the selected residues it would be best to use the measurement wizard. You can turn off the actual distance using the label option. Pymol will only identify H-bonds you will have to identify the rest yourself.

 

I hope this helps. For further information look at the pymol wiki. It is also better to post these requests to the bulletin board so others cab see the results

 

Regards

 

Joel Tyndall, PhD

 

Senior Lecturer in Medicinal Chemistry

National School of Pharmacy

University of Otago

PO Box 56 Dunedin 9054

New Zealand

 

Pukenga

Te Kura Taiwhanga Putaiao

Te Whare Wananga o Otago

Pouaka Poutapeta 913 Otepoti 9054

Aotearoa

 

Ph / Waea +64 3 4797293

Fax / Waeawhakaahua +64 3 4797034

 

 


From: Jhon Thomas [mailto:jhon1.thomas@gmail.com]
Sent: Friday, 27 March 2009 8:20 p.m.
To: Joel Tyndall
Subject: Re: [PyMOL] depiction of ligands

 

Hi joel

Thanks for your reply...
I want to show my ligand (sulpahete) in my figure and its interaction with the selcted atoms of the selected residues (Hbonds, ionic etc). as well as i want to show the interaction (hbonds) with the selected atoms of the selected residues. shwing sphere wouldnot be a good way. i will appreciate your help.

Thank you

Thomas

On Thu, Mar 26, 2009 at 1:51 AM, Joel Tyndall <joel.tyndall@otago.ac.nz> wrote:

Hi there,

 

There are many ways to do this. You can also try Action>preset>ligands. This will show the ligands (hetatms) and their interactions. Unfortunately this doesn’t highlight metal ions everytime (unless it interacts with the ligands). You can usually view this using the sequence option. [show the sequence – S button bottom right, move the slider to the end of the protein (usually) and select the metal(s) show spheres of selection]

 

Hope this helps

 

J

 

_________________________________

Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand                   

http://www.researcherid.com/rid/C-2803-2008

Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea               +64 3 4797293
Fax / Waeawhakaahua     +64 3 4797034


From: Jhon Thomas [mailto:jhon1.thomas@gmail.com]
Sent: Thursday, 26 March 2009 5:30 a.m.
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] depiction of ligands

 

Hi all

I would like to know, how we can show the ligands in pymol. Although i can see the non-bonded atoms ( HOH) automatically, eacept other nonbonded atoms l;ike sulphate  and metal ions. I will appreciate the suggestions.

Thanks in advance

Thomas