[PyMOL] Cartoon backbone nitrogens

2010-03-05 Thread J. Fleming
Hi all, Is there a good method to display backbone nitrogens while in cartoon mode? I tried using spheres on the backbone nitrogen positions but it doesn't look right. Sticks also looked strange as the transition from cartoon to sticks was broken. Perhaps there is a way to color just the cart

[PyMOL] Pymol and APBS

2010-04-15 Thread J. Fleming
Hi all, I've been trying to get APBS Tools and/or APBSTools2 running for a few weeks now on multiple linux systems (RedHat and Fedora). I've Installed MALOC and APBS Tools. I can start up Pymol through Phenix, load a .pqr generated from a PDB2PQR server, start APBS Tools, set the grid, but whe

[PyMOL] Rotation/Translation

2010-05-29 Thread J. Fleming
Hello, I've been using 'super' to align the C-alphas within one domain of two different models of the same protein while leaving the second domain to move freely. I can do this using: super (A and resid 1-100 and name ca), (B and resid 1-100 and name ca) What I would like to do is determine the