I agree that it would nice for PyMOL to handle this automatically, but I
personally think that extra long CA-CB bonds look almost as goofy as
sidechains hanging in space.
As it stands, there are two ways to handle this annoyance manually, assuming
that you're using version 0.95 beta:
1) put the mouse into editing mode and then just
ctrl-shift-left-click-and-drag the CA atoms back onto the sheet.
2) use the command:
flag no_smooth, atom-selection, set
for those sidechains you wish to show. Note that this has the effect of
"unflattening" the sheet for just those residues you wish to show. For
flag no_smooth, resi 12+16+19, set
> Subject: Some Ideas for PyMol
> I would like to emphasize some points that I think are
> missing in PyMol (and I think it's not too difficult to put
> in). When you draw carton sheets with the flat option turned
> on, you can't show any sidechain in there, because it's not
> Why don't you put an option that make the CB-CA bond a little
> bit longer to reach the sheet? (this feature exist in a
> script for MolMol) It will not give away any important
> information, but it will make nicer images.
> Thank you for answering (especially if this is already
> possible, and you have to explain it too me)