Re: [PyMOL] Setting transparency for CGOs

2005-08-16 Thread tanrikul
Michael, thanks for your reply, this works fine for me. However, I thought there is a nicer solution on setting the transparency for cgo's after creation. Regards, Yusuf -- Yusuf Tanrikulu Bioinformatics Diploma Student Department of Biosciences Johann-Wolfgang-Goethe Univerity Frankfurt Siesm

[PyMOL] Measuring dihedrals

2005-08-16 Thread Christopher Bond
Hi All, I'm trying to measure the dihedral angle between 4 unrelated atoms, the alpha carbons from for disparate residues. Can I do this with Get_dihedral or is this command only good for backbone phi, psi measurements? If it is possible could someone send me an example as I can't get the

[PyMOL] display problem (slab?)

2005-08-16 Thread Marc Vogt
Hi all For some reason I am now having a strange problem when I use pymol to display molecules. It acts sort of like it is in slab mode where some of the molecule fades into nothingness. However, when I spin the molecule, the same regions remain invisible. If it were a true slab effect, the reg

Subject: [PyMOL] display problem (slab?)

2005-08-16 Thread Michelle Gill
Hi Marc, I think I've come across the same problem when looking at your molecule as a cartoon, sphere, or surface. It seems to be related to two transparency settings within pymol. Maybe it's a bug?? Search for my name on the list. The only two replies I have ever posted pertain to this. A

[PyMOL] Ca-only and surfaces

2005-08-16 Thread Bronwyn Carlisle
Hi, A couple of things: a) I've just installed the latest MacPymol (after having a major crash and having to re-install EVERYTHING), and my middle mouse button doesn't seem to work. I can't move things around on the screen. The other buttons work fine, and the middle one scrolls OK, so I