Dear Thomas,
Thanks for good pointing for the weird problem, which I couldn't notice at all.
> You do compile with -D_FORTIFY_SOURCE=2, could you remove that?
I'm afraid, I know not related PyMOL itself, but I wish to know how to
do that. Searching 'setup.py', 'setup2.py' or some 'Makefile*' with
Dear colleagues,
We would like to announce the availability of mmView - the web-based
application which allows to comfortably explore the structural data of
biomacromolecules stored in the mmCIF (macromolecular Crystallographic
Information File) format. The mmView software system is primarily
inte
That reminds me of:
http://www.proteopedia.org/wiki/index.php/4ins
What is the difference between the two web pages?
Best
Troels
2011/12/6 Daniel Svozil
> Dear colleagues,
>
> We would like to announce the availability of mmView - the web-based
> application which allows to comfortably explo
Hi Troels,
mmView is intended as a web-based viewer (and nothing more) of the
textual mmCIF format, which i used by the PDB database as its archival
format. mmCIF offers, with its flexible syntax, much better solution
for storing biomolecular structures than the PDB format. However,
mmCIF format i
Is there a difference in the sigma values assigned by pymol and coot
I am able to see the density at 8 sigma in coot for the Fo-Fc map but can
go to maximum at 4.5 sigma in pymol after which it disappears
On Mon, Dec 5, 2011 at 11:33 PM, Roger Rowlett wrote:
> I think the isomesh comman
Hi Manas,
have you tried turning the normalize_* setting off?
set normalize_ccp4_maps, off
set normalize_o_maps, off
set normalize_grd_maps, off
http://pymolwiki.org/index.php/Normalize_ccp4_maps
http://pymolwiki.org/index.php/Display_CCP4_Maps#User_Notes
Cheers,
Thomas
On 12/06/2011 03:12
Hi Manas Sule,
this is a bit more complicated:
For PyMOL, you usually calculate an electron density map covering your
molecule. As far as I understand PyMOL, the sigma is taken directly from
your input map.
For Coot, this is completely different. Coot tries to reconstruct from
your input ma
Dear all :)
I want to find Hbonds beetween different helices in the membrane receptor (
H bonds beetween sidechains only)
I know possible way to do it wihin selection if I defined different helixes
but is there any way to find almost all Hbonds between polar sidecains
groups ?
Could I use
find
Hi Andrew,
The main limitation for problems like this is that you need to have
parameters for the ligand. Making sure that you have "good" parameters
is often an expert-level topic, and you're probably best served by the
APBS or PDB2PQR listservs as well as the literature ... but, you can
get a de
Hi Andrew.
I experienced something similar for the autodock_plugin.
http://www.pymolwiki.org/index.php/Autodock_plugin
During my trials, I notified two things for autodock.
It did not like "funny atom names" or "Alternative configuration"
Could this be a case for your protein / ligand?
I don't k
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