[PyMOL] Parallelize mutation script

2012-10-03 Thread Martin Hediger
Dear PyMOL Users I use the following script to prepare small side chain fragment PDB files of mutants in PyMOL: http://pastebin.com/nDTZApHP I use the PyMOL built-in mutagenesis wizard and the sculpting wizard to locally optimize the side chains within the environment of the protein. For large am

Re: [PyMOL] Movie School 4

2012-10-03 Thread Jason Vertrees
Sean, > My mistake, I omitted "set matrix_mode, 1" and realized in Movie School 5 > that not setting this to "1" would cause the object motions to not be > captured. I will add this to the PyMOL-Wiki. That tutorial is mostly correct, but as you've noticed, a bit out of date. Please feel free to

[PyMOL] question about biological units, states, etc.

2012-10-03 Thread Bourgaize David
Hello, all. First let me announce that I am not a PyMOL poweruser, and I have virtually no experience with crystallography and its data files. I have been plugging along using the PyMOLwiki as my knowledge-base for years, but cannot seem to wrap my head around certain issues. For example, 6pfk

Re: [PyMOL] question about biological units, states, etc.

2012-10-03 Thread Pete Meyer
Hi, Look into the "create" command - this should allow you to create a new object from multiple starting objects/selections. Pete Bourgaize David wrote: > Hello, all. > > First let me announce that I am not a PyMOL poweruser, and I have virtually > no experience with crystallography and its d

Re: [PyMOL] question about biological units, states, etc.

2012-10-03 Thread Tsjerk Wassenaar
Hi Dave, You can set the chain identifier for each object alter object, chain="A" And then you can create a new object create alltogether, chain A+B+C+D That object you can then use for fitting. Hope it helps, Tsjerk On Wed, Oct 3, 2012 at 7:22 PM, Bourgaize David wrote: > Hello, all. > >