Hi,
Does anybody knows if PyMol is implemented with a cut-off
distance feature, i.e. if I can select some atoms on my
structure and visualize only the portion of the fitted
density map that is located at a defined distance from my
selection?
Thank you
Stefano
Hi,
I've been meaning to update APBS tools so that some of the warnings are
larger and better explained.
WARNING: 53 atoms did not have properties assigned
means that PyMOL couldn't automatically assign properties for 53 atoms in
yoru molecule. This is usually because you have
Nicholas,
For example, each pattern that matches the following is
alanine : a C bonded to CH3, NH2 and COOH.
The algorithm must also deals with peptide bonds and disulfure bonds.
It must also work when the H atoms are not int the xyz file.
You're on the right track. In fact, most
Hi, I am back with a small prob! may be i am missing
something in command line
Q: How to label residue in cartoon selection using
command line.
Sincerely
sn
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Hi,
On Mon, 7 Feb 2005, Sabuj Pattanayek wrote:
Dear Mr. Lerner,
Thanks for letting me know about the PDB2PQR server. I was able to generate a
pqr from the NBCR website that then works with APBS to generate the dx map.
I'm not sure how to get the same electrostatic gradient effect on the
Is there some kind of pymol
startup switch or environment variable to disable loading
into a stereo window?
Use the -M startup option (forces a mono OpenGL graphics context). Is this
documented anywhere? Hmm no.
Say, what do people think about the idea of creating a PyMOL Wiki to hold
show sticks, [selection] around [angstoms]
or more usefully:
show sticks, byres [selection] around [angstoms]
You can load a map in a similiar manner.
This is also in the manual so I would suggest looking there first, it's quicker
than waiting for a list reply.
Cheers,
JTM
We can be sure
only the portion of the fitted density map that is located at a
defined distance from my selection?
This is what the carve option to isosurface and isomesh do:
isomesh mesh-name, map-name, level, selection, carve=distance
load map1.xplor
load ref.pdb
zoom ref and resn LIG, 3
isomesh mesh1,
dude,
what's a WIKI?
Hah! Well, in case you're wondering it has nothing to do with...
this http://www2.gvsu.edu/~oatesr/wookie.jpg
this http://www.geocities.com/Area51/Corridor/8289/wicket.jpg
this http://www.prairielights-croquet.org/wicket.jpg
or this
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