[PyMOL] Piecewise rotations while viewing in surface

Hi All, This isn't really a problem per se, I'm just wondering. Is there any way to more efficiently code the rotation protocol when the items being viewed are in surface view? Maybe my computer isn't fast/strong enough or something, but it seems whenever I try tweaking the position of one subunit

[PyMOL] Renumber Script problem

Hi All, I've been having a bit of trouble recently with the renumber script. I have a pdb file that I'm trying to renumber, but unlike the other times I've used it, it is renumbering incorrectly. The numbers are usually spaced out 5 residues apart, but I have one number right near the beginning th

Re: [PyMOL] Shrinking the sidebar

Sorry, I forgot the [PyMOL] subject header. On Mon, Dec 10, 2012 at 3:02 PM, Alex Truong wrote: > Hi All, > > I was just wondering if it was possible to shrink the sidebar width so I > have more viewing space? I regularly work with multiple windows open, > usually splitscreen (v

[PyMOL] Shrinking the sidebar

Hi All, I was just wondering if it was possible to shrink the sidebar width so I have more viewing space? I regularly work with multiple windows open, usually splitscreen (vertically split). Since I do most of my work on a laptop with a 14-inch screen, that doesn't afford me much space to investig

[PyMOL] Fuse gaps

these gaps are...unacceptable. Does anyone know the reason for them, and how to fix them? Additionally, the residue order in the sequence view is scrambled. They are attached in the correct order, but the middle subunit is displayed first, then the N-terminus, then the C-terminus. Thanks, Alex T

[PyMOL] Rotation of entire helix

Hi All, So I have a structure that's fully modeled, but I have one alpha helix that is turned in a non-optimal way. Is there anyway to "rotate" the entire helix along its barrel while keeping everything else fixed? The objective is to turn it such that a critical side chain that was facing inward

[PyMOL] How to rotate entire section of structure relative to rest

Hi All, I'm relatively new to this software, and even though I've been using it for a few months, I haven't really had to use some of the more advanced options yet. This would be my first foray into actual manipulation. That being said, I'm trying to figure out how to move a small section at the

[PyMOL] Forcing alpha-helices

Hi All, I'm trying to manually model a linker region using computational information (such as which residues are predicted to be in helical form, etc.). I have the sequence in PyMOL as an unmodeled linear chain (or whatever the program chose to do with bond angles when I manually generated the seq

[PyMOL] Unable to open pse files (Win7)

Hi All, I was recently fiddling around with some other Python-executable stuff like SCons and Rosetta, but somewhere down the line, my PyMol installation seemed to have corrupted itself. I was originally using the 64-bit version (with 64-bit Python 2.7.2), but stuff like SCons needed 32-bit, and a

[PyMOL] [PyMol] Fuse command issues

Hi All, I am trying to append four residues (MQFF) to the N-terminus (G) of a protein fragment, and whenever I generate the 4-residue peptide and fuse the appropriate atoms together, it always reads MQFGF instead of MQFFG, like the fragment has somehow invaded the N-terminus instead of latching to