[PyMOL] abalone

2010-06-02 Thread mohan raj
hi all: i have came across the sowftware abalone for molecular simulations, where they have mentioned we can do simulations of proetin molecule by stating specific force fields and at specified temperature. could i create mutations in pymol and open the same file in abalone?? how useful

Re: [PyMOL] pymol dies when minimizing

2010-06-02 Thread Maia Cherney
I had once a problem with pymol that itr would not open from a terminal window. After a long battle with it, the problem was solved after I upgraded my OS. Robin Emig wrote: Does anyone else have the problem where pymol dies, or wont update the display after minimizing on windows? Is there

Re: [PyMOL] pymol dies when minimizing

2010-06-02 Thread Joel Tyndall
Hi, Yeah I have a similar issue and have been meaning to post it. On windows 7 following minimization, the viewer doesn't update when you open it again, no menus either. Using PyMOL 1.2r2 Looking forward to a solution J _ Joel Tyndall, PhD Senior Lecturer in

[PyMOL] convert surface from pymol into a CCP4 map

2010-06-02 Thread Mark A Saper
I have a nice cavity surface that I've made in PyMOL. I'd like to convert it to some type of envelope in CCP4 map format, for input into Coot. I know that surfaces can be saved in .wrl format. I've also tried using Voidoo to prepare a pseudo-map representing the cavity, but it doesn't look

[PyMOL] Fwd: abalone

2010-06-02 Thread mohan raj
hello all: any abalone users -- Forwarded message -- From: mohan raj mohanrajdec2...@gmail.com Date: Wed, Jun 2, 2010 at 11:41 AM Subject: abalone To: PyMOL-users@lists.sourceforge.net hi all: i have came across the sowftware abalone for molecular