Re: [PyMOL] Pymol visualization problem

2013-01-08 Thread Martin Hediger
Hi Abida Is it possible that you have multiple states in your PDB file? Try clicking the arrow in the bottom right corner of PyMOL and see if you can display the other protein. If so, you probably need to delete the MODEL and END from your PDB file. Then all should appear at once. Martin

Re: [PyMOL] DNA measurement help require by sculptor

2013-01-08 Thread Thomas Holder
Hi Briony, this sounds like a very cool project! Regarding question 1: If your PDB DNA model is long enough, you can use cafit_orientation from the psico module (a PyMOL extension) to draw the axis. It determines the axis by least-square linear fit on the backbone atoms. This requires a recent

Re: [PyMOL] Pymol visualization problem

2013-01-08 Thread Abida Siddiqa
Thomas and Martin I have tried both suggestions. Still it did not work out.RegardsAbida From: abida_sidd...@hotmail.com To: pymol-users@lists.sourceforge.net Subject: Pymol visualization problem Date: Tue, 8 Jan 2013 10:12:46 +0500 Hello, I have docked one protein named 'L1'( 450 amino

Re: [PyMOL] Pymol visualization problem

2013-01-08 Thread Thomas Holder
Hi Abida, thanks for the PDB file that you sent me off-list. It is a naming conflict, you have more than one chain A which have overlapping residue numbers and even IDs. You can still load them like this: PyMOL set retain_order PyMOL load complex.1.pdb PyMOL as cartoon I also suggest to fix

[PyMOL] Problem Opening Session File

2013-01-08 Thread Mike Feldkamp
I created a session file with Pymol Version 1.5.0.4 that I am unable to open up on my laptop which is running 1.2r5pre. I am able to see the first state but all of the other remaining states are lost. I haven't had opening session files with saved states in the past so I do not suspect it is

Re: [PyMOL] Problem Opening Session File

2013-01-08 Thread Pete Meyer
The handling of density maps changed with (I believe) version 1.5 - earlier versions would just load the map as given, later ones appear to try to do symmetry expansion (even if the map isn't covering the ASU). I've seen this result in a similar error message when loading session files (with

[PyMOL] DNA ligand presentation in PyMOL

2013-01-08 Thread amna khan
Hi, I have a model of DNA-Ligand, defualt both ligand and DNA are represented as sticks i make DNA as cartoon and ligand as stick, this is general presentation DNA molecule has internal HBONDS too.. how can i see the hbonds made between just ligand and DNA, ??? how can i show just