> 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-coordinatin
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 f
ermarken 9, 1.th<http://1.th>
> 2300 København S
> Mobil: +45 60210234
>
>
> 2013/3/13 Mike Marchywka
> mailto:marchy...@hotmail.com>>
>
>
>
>
> > From: blaine-moo...@ouhsc.edu<mailto:blaine-moo...@
> 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.
> An
users@lists.sourceforge.net
> Subject: 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.
>
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 w
etry information.
>
> If you want to load some 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/
was_main () at main.c:2006
#42 0x75853dd4 in CmdRunPyMOL (self=0x76177df0,
args=) at Cmd.c:4771
#43 0x004b66b9 in PyEval_EvalFrameEx ()
note new address
Mike Marchywka 2295 Collinworth Drive Marietta GA 30062.
formerly 487 Salem Woods Drive Marietta GA 30067 404-788-1
I'm trying to load a self-generated xplor file and pymol keeps segfaulting. I
wanted to debug the
problem but can't get my debug statements to execute. The only thing that greps
for "xplor"
is a few pymol modules and plugin called edmplugin. If I rebuild the plugin and
relink pymol
nothing see
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 ana
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 alignments
> 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,
> 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 Mik
;
> >
> > File type given with "format" argument:
> >
> > PyMOL> load
> > http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=5280443&disopt=3DSaveSDF,
> > format=sdf
> >
> > Also, Mobile PyMOL (for the iPad) has it's own ser
given with "format" argument:
>
> PyMOL> load
> http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=5280443&disopt=3DSaveSDF,
> format=sdf
>
> Also, Mobile PyMOL (for the iPad) has it's own server capabilities,
> including support for PubChem, PDB, Dropbox,
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 C
> 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 PD
> 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 Sl
one was so mangled that
> > it had problems aligning them.
>
> Glad it's working. Fit is a mathematically optimal superposition of
> vector sets. Are your atom pairings correct? If you want to specify
> them manually, check out Wizard > Pair Fitting. If you send me the
>
if files on pdb.org and another
derived from jdftx after 300 position iterations using very
simple C and H models. In any case, I think part of the problem
is just using .53 for atomic/angstrom conversions but it looks like
&
pting to use "fit" on my
2 molecules gave a non-intuitive result I think the one was so mangled that
it had problems aligning them.
>
> I routinely build on Ubuntu without problems. Just make sure the
> python you build with is the same that you run with.
>
> Che
bs/liblayer1.a
layer2/.libs/liblayer2.a layer3/.libs/liblayer3.a layer4/.libs/liblayer4.a
layer5/.libs/liblayer5.a -Wl,--no-whole-archive -L/usr/lib/x86_64-linux-gnu
-lGL -lGLU /usr/lib/x86_64-linux-gnu/libfreetype.so -lz -lpng -lglut -ldl -O2
-Wl,-soname -Wl,libpymol.so.0 -o .libs/libpymol.so.
y the link 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 Marc
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