[PyMOL] low res surfaces, CRYST headers, rotamers

[Seth H. <sh...@ms...>]

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