It took a while for me to figure out a means of doing what
I needed to do with a protein molecule in pymol (mutate
certain residues to cysteine and then create crosslinks
between them). One thing that seems to be missing, and
it caused me no end of problems until I worked out a
different method was that there is no button option/key
option for pk2. I see a pk1 for RMB (depending on which
configuration for keys/mouse you go with) but no pk2 yet
some commands seem to suggest using a pk1 and pk2.
Another issue that I came across was once I did manage
to create a disulfide between two cysteines, I could see
an option in the "SHOW" menu for showing disulfides but
there is not a corresponding entry in "HID" to hide
disulfides. Perhaps for every entry in SHOW there could
be the corresponding entry in HIDE?
It would also be very helpful to be able to select bonds
in addition to the current atoms, residues, etc. I had
many instances where I would like to simply eliminate a
disulfide bond I created, or change the properties of the
bond (line width, color) but could find no way to do this
without changing the display nature of the actual
residues involved. This sort of selection would make
eliminating disulfides very easy as well - just pick it and
"hide" it or delete it.
There appears to be no setting in the full settings list
for changing the line width of the projected molecule (I
am using ribbons). I can find a line width setting but
when I set it, it only changed the line width for sidechain
residues, NOT the backbone trace. In this case I am
displaying a ribbon diagram of the protein with only a few
cysteine side residues displayed, plus their crosslinks. If
I alter the line_width setting, the only lines changed are
the sidechain and crosslink line widths, NOT the ribbon
width. Perhaps a separate setting for that could be
added?
Finally, labeling is a problem. I have read many
messages on mailing lists that suggests that the preferred
method for labeling is to do it with Photoshop or similar
third party app. A problem as Photoshop is a
bitmap-based editor (vector is preferable), as is GIMP.
What I needed to do was simply create a single label for
each mutated cysteine residue in the protein with a
corresponding line pointing to it. The image is
stereoscopic so it would be nice to have the labels also
be stereoscopic (molmol and a few other apps do this but
are not so good with editing the sequence/mutating the
sequence as I need to do - pymol wins this hands-down
thus far). Every attempt I made at labeling within pymol
ended up with every atom of the residue labeled. Just
one label per residue was desired. Could this capability
be added/improved?
