ing I am missing in the number format? When I check
coordinates via the cmd.iterate_state, I can see that most of them are
numbers with around 15 to 16 significative figures... where the pdb file has
only three figures!! Is there something that is added by the iterate_state
command, and might this coul
Sorry for my first post, I just relaized it was kind of hard to read
with all the funny tags I am reposting for clarity!!!
I am trying to run a script to translate all pdb structures so that an
atom of the protein gets the coordinate (0,0,0)
I have written a small script for that:
for i
an make every atom move by saying:
cmd.alter_state("1", "my_structure", "x, y, z = x + 1, y + 1, z + 1")
So, the "x,y,z=x-a,y-b,z-c" would probably work, too. I hadn't
realised that variables in the current scope were accessible from the
alter_state
ilto:pymol-users-boun...@lists.sourceforge.net] De la part de
lie...@ultr.vub.ac.be
Envoyé : mardi 19 juin 2007 16:41
À : pymol-users@lists.sourceforge.net
Objet : Re: [PyMOL] TR : alter_state for y coordinates?
On Tuesday 19 June 2007 16:24, Gilles Truan wrote:
> cmd.alter_state ("1",(
I have noticed a strange behaviour of the APBS module. I used it a lot
recently and it works perfectly for 95% of the structures I analyzed. I
usually fetch the pdb code, then remove waters, heteroatoms and so on. I
also noticed that in some cases, when the b factor is quite big (over
100) APBS
e workaround is to make sure no B-factors exceed
100.
alter all, b=min(b,99.9)
should about do it.
Cheers,
Warren
-Original Message-
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Gilles
Truan
Sent: Wednesday, Septe
must eventually sort this out, because it causes continued grief
for our users in common.
For now, however, the workaround is to make sure no B-factors
exceed 100.
alter all, b=min(b,99.9)
should about do it.
Cheers,
Warren
-Original Message-
From: pymol-users-boun...@lists.source
RH2, 2V8B, 2VB1, 2Z6W, 3AL1,
3B3R, 3C78, 3CNJ, 3D1P, 8A3H
Cheers!
-Tom
-Original Message-----
From: Gilles Truan [mailto:gilles.tr...@cgm.cnrs-gif.fr]
Sent: Mon 9/22/2008 6:14 AM
To: Nathan Baker
Cc: David Gohara; apbs-us...@lists.sourceforge.net list;
pymol-users@lists.sourceforge.net
Subj
assigned charges with pymo, I can still
generated the pqr file, the apbs ini file and calculate the potential
with apbs and read it with pymol
Gilles
Gilles Truan a écrit :
Dear all,
Sorry for the late answer but I finally managed to find what the error
is...
First thing, I work on a
Hi all,
I just upgraded to the pymol 1.2b2. The install works perfectly etc.
I have a strange phenomenon though, all the colors in the menu on the
right side of the graphics windows have disappeared as well as the
colors in the sequence panel.
Any hint what it might be?
I have not change my con
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