Hi all,
Yes, it worked for me, the problem is i was using the older version of pymol.
Now the mutagenesis works. Now how to interprete the results of mutation and
what are the different ways to see the effect of mutation in pymol
thanks in avance
regards
sankari
Mike,
The routines that Scott cites were nicely incorporated into
MasterMovie.py by Seth Harris (shar...@msg.ucsf.edu) that is derived
from Kristian Rother's rTools (www.rubor.de) and modified . Email
Seth to see where he hides the program.
Warren ... Glad to hear there is a new command i
What is the recommended approach with apbs for creating a pqr file
from a pdb which has SEP residues? Under gromacs I have been able to
do MD on this peptide by using the user donated ffG43a1p force field which
supports phosphoserine residues. Unfortunately none of the force fields
available a
Richard,
Actually I don't have a copy of Delphi available (hence the use
of APBS). I did notice that I see more positive surface area on a
molecule with a -13 net charge when the run is done with pdie of 2.0
compared to 20.0 even in the presence of 0.150 mM NaCl ions. I also
noticed an oddity
Hi Jack,
> In all of the examples distributed with APBS, the pdie (solute dielectric)
The pdie must be the protein dielectric constant though the comment for
pdie in the pymol generated .in-file reads "# Solute dielectric" ...
that is probably a mistake. The APBS-plugin says Protein Dielectric.
T
Mike,
This may be the first public mention I've made of this, but recent betas
include an experimental "mview" command than can be used to perform the same
kind of interpolation as the scene transitions. Here is an example script:
load $TUT/1hpv.pdb
as ribbon
show sticks, organic
util.cbc elem c
Hi Mike,
I use a nifty little script from Laurence Pearl/ Lieven Buts called
camera_view_travel, which creates smooth transitions between multiple
views of your molecule. I then call their script from my movie script.
Here is my movie.pml
and below that is camera_view_travel.py
I hope thi
I have stumbled across the parameter causing the difference.
In all of the examples distributed with APBS, the pdie (solute dielectric)
value is set to 2.0 whereas ABPS-tools.py defaults this to 20.0. I find
that if I use 2.0 instead of 20.0 for pdie, the resulting electrostatic
potential map i
Hi Jianhai,
load yourmap.xplor
isomesh map1, yourmap, 1.5, LIGAND, carve=1.6
color green, map1
show mesh, map1
The carve command allows you to selectively show density around
whatever selection you want.
I hope this gives you some ideas. You can also type "help isomesh" in
the GUI to get a b
Has anyone noticed major differences between the results obtained in
GRASP when using the method...
1) Read| PDB file
2) Read|Radius Charge File(+Assign)
Input AMBER.crg
3) Build|Molecular Surface|All atoms
4) Calculate|New Potentail Map
5) Calculate|Pot. via Map at Surfaces/Atoms|All atoms
Hello again pymolers
I have a question about the view matrices. Basically I would like to go from
one view to another view gradually in a movie.
Is there a way to calculate from the view matrices, how much I need to rotate
around x,y, and Z and move in x, y and z?
I'm sure it can be done, but h
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