Is there a similar command to force PyMOL to use only CONECT lines in
the pdb file instead of generating connectivity by distance?
Eric
Warren DeLano wrote:
A quick fix is to use the "retain_order" setting.
set retain_order
which will force PyMOL to honor the order of ATOMs in the PDB file o
Marcus,
Here is one way (courtesy Kyle Lassila):
Check out VOIDOO:
http://xray.bmc.uu.se/usf/voidoo.html
Then:
Use VOIDOO to make a map of the cavity. That gives a
map in one of the electron density formats, .ezd. Then use MAPMAN (also
found as Uppsala Software Factory) to
convert to
Check out Robert Cambell's scripts
data2bfactor.py
color_b.py
at http://adelie.biochem.queensu.ca/%7Erlc/work/pymol/
Eric
Eva Vanamee wrote:
Hi,
How can I color residues by a certain property?
Let's say I have a list of property (e.g. mutation frequency from 0-1)
for each amino acid residue
Anyone who works with nucleic acids will certainly prefer the current
situation. From the PDB format guidelines:
* The asterisk (*) is used in place of the prime character (')
for naming atoms of the sugar group. The prime was avoided historically
because of non-uniformity of its external repr
with those sidechains with
multiple conformations. Anyone else have this problem? Is there a
quick fix?
Pymol 0.93 on Fedora Core 1.
Thanks.
Eric Zollars
All-
I have been attempting to add atoms to proteins that are missing
electron density, mostly surface positions. In most cases I have been
able to just add an atom or two (Build->Fragment->group); sometimes
adding a whole rotamer is required. I have been unable to add a planar
guanidino
