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.tho...@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.tynd...@otago.ac.nz<mailto:joel.tynd...@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.tho...@gmail.com<mailto:jhon1.tho...@gmail.com>] Sent: Thursday, 26 March 2009 5:30 a.m. To: pymol-users@lists.sourceforge.net<mailto: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
