Thank you very much to both of you for your help.
Have a good day.
Fred
> Matt,
>
> There isn't an escape sequence, but PyMOL will automatically disable the
> asterisk as a wildcard for atom names if any PDB file loaded contains an
> asterisk in that field.
>
> To manually choose another wildcard
Dear Warren,
this little thread points nicely to the major problem that I have quite
often with PyMol: it is a really powerful program, but the documentation
is somewhere scattered between various incomplete sources (manual,
reference list, wiki, bulletin board, user home pages, ...). This mak
http://www.ebi.ac.uk/~gareth/pymol/images/walls.png
how to draw this walls.png ?
On Mon, 3 Apr 2006 pymol-users-requ...@lists.sourceforge.net wrote:
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Dear all.
I need to select surface atoms. Friend of mine recommended me this way:
For solvent accessible surface one can try Molmol:
Load your molecule, say " SelectAtom '' " in command line, say "CalcSurface"
- select the solvent radius (1.4A for water by default), put "by atom" radio
button on
Dear Warren,
I would second Dirk's statement below. The manuals on web are a
couple of years out of date now, and while the wiki and bulletin
board are very useful sources of information, I too would prefer to
have good up to date documentation, rather than more and more
improvements with poo
Dear Warren,
I could not agree more with Mark and Dirk. I recently received my "PyMOL
Subscription Renewal" email from DeLano Scientific, and I must admit I
will not renew my subscription, and for only one reason; the
documentation is not up-to-date! Especially since (according to the
Manual
> this little thread points nicely to the major problem that I have
> quite often with PyMol: it is a really powerful program, but the
> documentation is somewhere scattered between various incomplete
> sources (manual, reference list, wiki, bulletin board, user home
> pages, ...). This makes it ve
PyMOL Users,
I concur with both of the statements below -- lack of good documentation and
training materials has become much more limiting of PyMOL's utility than lack
of functionality.
Furthermore, as illustrated by Stéphane's post, if DeLano Scientific LLC is to
continue to thrive as a busin
Just to pipe up for the other side, while I would by no means defend the
lack of documentation as a good thing, given limited resources I actually
prefer new features at the expense of documentation. I realize there is a
large range of computer expertise in the pymol user community, and obviously
t
Hi folks,
what I did for now is that I selected a subset of residues that sit
around a cavity. Then I showed the surface of the original protein
inside the selection to get only the inside surface of the cavity. Now
it looks sort of like a hose with inside and outside just as I wanted.
Now I'd
Paul,
I'm actually quite interested in an answer to this question as well.
An example of what I have been able to do is this:
http://kinemage.biochem.duke.edu/~immormino/neca_new.png
I like using this type of rendering to look at a protein cavity from
inside the protein. For me it has been hel
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