Take a look at this link:
http://www.rubor.de/bioinf/tips_modeling.html#addhbond
It contains two simple examples and one python script.
On 8/23/06, selva raj cryptochrome2...@yahoo.co.in wrote:
Dear Pymol users,
Would anyone tell me how to draw hydrogen bonds between interacting
atoms in
Dear Selvaraj,
You will find useful resources about hydrogen bonding with PyMOL on:
http://www.rubor.de/bioinf/tips_modeling.html#addhbond
Regards,
Jerome Pansanel
Le mercredi 23 août 2006 22:48, selva raj a écrit :
Dear Pymol users,
Would anyone tell me how to draw hydrogen bonds
Hi
I need help. Can some one tell me a way to find out whether 2 molecules are
connected by covalent linkage or not. Say for example in pdb files we have
ligand and protein molecules and I wish to know a way to find out if the
ligand is connected to the protein via a covalent bond or not, The
Hi Mahesh,
There is no way to see whether two atoms are connected. Pymol guesses
the connectivity based on the distances between the particles. But to
be certain whether atoms are bonded, you have to look in the PDB file,
which should mention covalent attachment of a ligand. At the end of
the
You can also check if there is connecting electron density, see for example
the electron density server at http://eds.bmc.uu.se/eds/ . This of course
only works if the authors have deposited the experimental data.
I hope this helps.
Best regards,
Anne
-Original Message-
From:
I'm trying to create a smooth surface representation of a set of 6.5A
diameter spheres read in as CA atoms. Is there a way to override
PyMol's assignment of atomic radii? Also, if I were using a
conventional molecular surface algorithm I would turn up the probe
radius so that the surface
HI all,
This is a follow on from the e-mail below. Frequently I'm also getting this
error when pymol crashes:
*** glibc detected *** /home/fauxn/software/pymol/pymol.exe: double free or
corruption (!prev): 0x0aaef170 ***
=== Backtrace: =
/lib/libc.so.6[0xc69d88]
