From: ccp4...@hotmail.com
To: pymol-users@lists.sourceforge.net
Date: Fri, 8 Nov 2013 19:53:50 -0600
Subject: [PyMOL] alignment of metal coordination
Hi,
Is it possible to align two structure based on metal coordination or
metal-coordinating
I have a similar requirement, taking density and potential dstriutbutions from
jdftx which are written as plain binarry doubles. I use a script and
some code to create an xplor file which seems to work but I have
to adjust the position and scale to let it
overlay the ion positions that I read
From: blaine-moo...@ouhsc.edu
To: tlin...@gmail.com
Date: Wed, 13 Mar 2013 04:45:59 -0500
CC: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] PyMOL to 3D PDF
PyMOL will also save surfaces in addition to cartoons to vwrl and idtf.
Any
Mike Marchywka
marchy...@hotmail.commailto:marchy...@hotmail.com
From: blaine-moo...@ouhsc.edumailto:blaine-moo...@ouhsc.edu
To: tlin...@gmail.commailto:tlin...@gmail.com
Date: Wed, 13 Mar 2013 04:45:59 -0500
CC:
pymol-users
Where do you get the x_shift and y_shift values? I ended up writing a program to
take bond lengths and directions relative to select coord systems to generate
periodic or
almost periodic things. Right now polyenes but extensible. Is there some
program that
does this easily? This allows me to
: Re: [PyMOL] Building of the Carbon lattice
Hi Mike,
I simply measured x_shift and y_shift from a cyclohexane fragment. Use
the graphical Builder or the fragment command to load stuff from the
fragment library.
PyMOL fragment cyclohexane
Cheers,
Thomas
Mike Marchywka wrote, On 01/04/13 15
format which is not yet supported by PyMOL, the
easiest solution is to convert it to some already supported format on
the fly and feed that to PyMOL, if possible.
Cheers,
Thomas
Mike Marchywka wrote, On 01/02/13 17:01:
I'm trying to load a self-generated xplor file and pymol keeps
,
own_the_options=optimized out) at main.c:1955
#41 was_main () at main.c:2006
#42 0x75853dd4 in CmdRunPyMOL (self=0x76177df0,
args=optimized out) at Cmd.c:4771
#43 0x004b66b9 in PyEval_EvalFrameEx ()
note new address
Mike Marchywka 2295 Collinworth Drive Marietta GA
What does Chimera do? I finally wrote my own c++ tool that let's a TcL script
specify a molecule's layout in terms of relevance like bond length and angle.
I decided it was worth the effort since I didn't want to look around much for
existing
stuff and would eventually add my own stuff for
I don't want to hijack the thread but I was curious if you can point to few
pymol
features for generating and rotating molecules and how they would play with
other tools. For example, if I just go download pdb files or take output from
DFT,
it may be easier to do analysis with certain
From: jason.vertr...@schrodinger.com
Date: Mon, 26 Nov 2012 10:37:52 -0600
Subject: Re: was: [PyMOL] Mobile PyMOL Problem and Solution/ Now: pdb or
related libraries
To: marchy...@hotmail.com
CC: pymol-users@lists.sourceforge.net
Hi Mike,
I
From: jason.vertr...@schrodinger.com
Date: Tue, 27 Nov 2012 12:37:41 -0600
Subject: Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or
related libraries
To: marchy...@hotmail.com
CC: pymol-users@lists.sourceforge.net
Mike,
pymol have
for an API to get molecule structures from various locations or do you just
have an
interface for pdb.org? Besides deciding on what to eat today, I was curious if
pymol has more generalized means of finding structure files.
Thanks.
note new address
Mike Marchywka 2295 Collinworth Drive
=5280443disopt=3DSaveSDF,
format=sdf
Also, Mobile PyMOL (for the iPad) has it's own server capabilities,
including support for PubChem, PDB, Dropbox, etc.
Cheers,
Thomas
Mike Marchywka wrote, On 11/25/12 17:26:
I was trying to figure out what to eat today so naturally I started looking
for PDB
.
Cheers,
Thomas
Mike Marchywka wrote, On 11/25/12 17:26:
I was trying to figure out what to eat today so naturally I started
looking for PDB libraries
with food components. I was looking for garlic related chemicals when I
came across this,
http://molecules.gnu-darwin.org
From: jason.vertr...@schrodinger.com
Date: Fri, 2 Nov 2012 18:57:38 -0500
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Mobile PyMOL Problem and Solution
Greetings,
On Oct 28th, the folks at the PDB made some changes to their PDB Web
Date: Tue, 9 Oct 2012 03:07:08 +0200
From: ivan...@gmail.com
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Stucked...
Dear PyMol users,
I'm facing very unusual runtime problem. After successful compiling of
PyMol 1.5.0.1 on
on this behaviour LOL).
Cheers,
-- Jason
On Thu, Oct 4, 2012 at 9:18 PM, Mike Marchywka marchy...@hotmail.com
wrote:
CC: pymol-users@lists.sourceforge.net
From: li...@cowsandmilk.net
Subject: Re: [PyMOL] I just built pymol
was missing -lGLEW.
In any case it looks like I am all set but I thought the download would come
closer to working right
away.
And the xyz files I wanted to display do appear to come up just great.
So do I need a license for the open source version?
Thanks.
note new address
Mike Marchywka 2295
-lglut -ldl -O2
-Wl,-soname -Wl,libpymol.so.0 -o .libs/libpymol.so.0.0.0
marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$
-David
On Oct 4, 2012, at 9:22 PM, Mike Marchywka marchy...@hotmail.com wrote:
fwiw, I never figured out why the out-of-the-box build hung using
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