RE: [PyMOL] low res surfaces, CRYST headers, rotamers

[Thomas S. <ts...@ex...>]

Since we do this all the time, I can answer #3!

From our local user's tip-sheet:

"
Tip #2 - To make lower-res "BLOB" figures:

pymol> set surface_quality,1
pymol> set solvent_radius,4.0, object
pymol> alter object, vdw=3Dvdw+1.0
pymol> rebuild
pymol> show surface


*Note: you may need to adjust these values (the solvent radius and the =
amount you add to the VdW radii) to get something that does not have =
gaps or drop-outs in the surface.  I'd suggest starting with just the =
"solvent_radius" command first (also try values as low as 3), and then =
move to adding in the vdw alteration if necessary.
"

Don't forget to use your object name of interest in place of the word =
"object" above!
-Tom


-----Original Message-----
From: pym...@li...
[ mailto:pym...@li...]On Behalf Of Seth =
Harris
Sent: Tuesday, December 21, 2004 2:15 PM
To: pym...@li...
Subject: [PyMOL] low res surfaces, CRYST headers, rotamers


Hi PyMOLarians (sorry, I've been reading Bush quotes and
his tragic knack for inventive names for nationalities..)

Hope it's not terrible form to bundle questions:

Is there a way to have PyMOL save header information?  It
would help, for instance, if the CRYST card were preserved
after editing a pdb, building new residues, etc.

In terms of building, can someone remind me how to change
rotamers on side chains?  I think I've seen you doing
this, Warren, and also remember your warning that the
rotamer libraries were not yet mature, accurate, or
complete, but I'd still like to try it even as an
exploratory measure.

Finally, a request/wish list thing for me would be the
ability to make lower resolution molecular surfaces.  I've
seen neat images usually based on EM maps, but recently
realized that some people were making them from atomic PDB
files.  They're very smoothed out blobs that serve well
for  schematic style representations that still directly
relate to the structure (as opposed to hand-drawn blobs or
plain ovoids).  Also good for generating images of larger
multimers like virus particles, etc I understand since
these low res surfaces, being more featureless (less
featuremore?), are computationally simpler to manipulate,
yeah?  I think the Chimera program does this with some
multiscale model module, but I haven't used that package.
 They also look great rendered with transparency.

Just thought I'd ask since I've seen several times before
the happy surprise of Warren's replies that he has already
included such features or they are imminently to be
released.  I have briefly tried some work arounds by
making maps or masks at low resolution and then smoothing
them in Gerard Kleywegt's MAMA, but they seem to always
have a stepped-edge pixelated look as opposed to the
desired liquid smoothness.  And I don't think this was
just a map grid fineness/coarseness issue, but if anyone
has suggestions on this...?

Thanks,
Seth


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