I'm using MacPymol0.99beta14, and I've just noticed some strange behaviour:
Using the mutagenesis wizard, I've changed the rotameric conformation of
a residue, and I've saved the new molecule. When I open this 'new'
protein, If I edit the chi1 dihedral angle (i.e. the N-CA-CB-SG, in my
case) of that same residue for further editing (either with the command
"edit 285/CB, 285/CA" or control-right clicking on the CA-CB bond), any
change in the value of the angle (either with the command 'torsion', or
control-left clicking and dragging) make the whole protein, not the
sidechain, rotate around the bond. If I swap the order of the atoms
selected in the 'edit' command, the rotation is in the oposite
direction, but it is still the whole protein what rotates.
What's interesting is that this *only* happens with the residue that I
changed through the wizard (the rest behave 'as expected'), and it
happens even after reinitializing or restarting the program. It also
happens if I swap to MacPymol0.98. This seems certainly strange to me...
I thought that maybe the pdb file written by PyMOL after changing the
rotamer was somehow corrupted, but it seems ok.
I'm doing all this conformational editing through scripts which used to
work properly. The only 'different' thing I've made that I can think of
is the mutation of the residue through the wizard. And I can reproduce
this 'bug' changing the conformation of some other residue...
So, has anybody experienced this situation before? Any solution to
restore the 'normal' behaviour of the 'mutated' conformations?
Is it possible that this is a bug?
Xavier Deupi, Ph.D.
Department of Molecular and Cellular Physiology
Beckman Center for Molecular and Genetic Medicine (B161)
279 Campus Drive, Stanford University School of Medicine
Stanford, CA 94305 (USA)
Phone: +1 (650) 725-6497
Fax : +1 (650) 725-8021