Hi Martin,
you may also consider these scripts from PyMOLWiki that generate the
biological assembly from the asymmetric unit.
http://pymolwiki.org/index.php/BiologicalUnit/Quat
or
http://pymolwiki.org/index.php/BiologicalUnit
Cheers,
Thomas
Martin Hediger wrote, On 05/03/11 22:00:
> Dear al
Hi,
This is a specific question about how to compile Pymol for Mac with xtc support.
The regular Pymol version that is compiled with "port" does not
include support for xtc files (and thus can't play movies).
However, the best thing about Pymol are its movie-making tools.
How do you compile Pymo
Hi Martin,
You can download the biological assembly directly from the pdb website. Under
download files (RHS) usually the last entry is Biological Assembly. Once
downloaded you can unzip it and change the file suffix back to pdb e.g.
1AVD.pdb1 ==> 1AVD_1.pdb
Hope this helps
Joel
___
Hi Martin,
Do you mean something like this? If so, use the "type=" parameter with fetch.
# grab the biological unit; this PDB1 is in
# 2 states, so split them with multiplex
fetch 1avd, type=pdb1, multiplex=1, async=0
# color the chains
util.color_chains()
# show as cartoon
as cartoon
Chee
http://www.rcsb.org/pdb/files/1avd.pdb1
The key is adding 1 to the suffix. Sometimes there is more than one biological
unit, in which case, there is a pdb2, pdb3, etc.
-David
On May 3, 2011, at 4:00 PM, Martin Hediger wrote:
> Dear all
> I would like to ask how it is possible to download the
Dear all
I would like to ask how it is possible to download the coordinate file
for the biological assembly of a protein structure from the PDB.
Naturally, this is not a question directly related to PyMOL, but I
thought I'll be reaching at least a couple of
Biochemists/Chrystallographers who kno
