ervices without long-term contracts
> Personal 24x7 support from experience hosting pros just a phone call away.
> http://p.sf.net/sfu/theplanet-com
> ___
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> Info Page: h
al 24x7 support from experience hosting pros just a phone call away.
> http://p.sf.net/sfu/theplanet-com
> _______
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> Info Page: https://
ave( "1nmr_partial.pdb", "1nmr.cut", state=0 )
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
SOLARIS 10 is the OS for
tive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
> http://p.sf.net/sfu/solaris-dev2dev
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.m
ows OS, this
> problem doesnt erupt. Can someone help me out, to efficiently use Pymol in
> Linux.
>
> Chandan
Chandan,
I cannot reproduce this bug, but I will keep an eye out for it. Feel
free to send me a PyMOL session of your in which this bug takes place.
Thanks,
-- Jason
--
J
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
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>
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(e
ve control over the FreeMOL
project. When I get back to my office (where the files live) I'll
update FreeMOL.
Thanks,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1
stoph
>
>
> On 2/17/2010 11:35 AM, Jason Vertrees wrote:
>> PyMOLers,
>>
>> * In order to keep all bugs in one place please email your bugs to
>> h...@schrodinger.com instead of using the SourceForge tracker.
>> Schrodinger has a very nice bug tracker that we use
indows and Mac; some issues on Linux
fullscreen
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
Download Intel® Parallel Studio Eval
Try t
x27;s servers only had FTP access, we now have ssh).
Please let me know if anything's missing.
Thanks for being patient,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603
PyMOLers,
As promised:
* FreeMOL is back up.
* CEalign has been built into the PyMOL source code. You can check
out the SourceForge code and test it out.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374
51568949, 0.584285855,\
> -0.417025983, -0.758588016, 0.500633180,\
> 0.0, 0.0, -635.205078125,\
> -42.521865845, 33.457977295, 19.863151550,\
> 530.689270020, 739.720764160, -20.0 )
> mview store
> mview interpolate
> mview reinterpol
> But alignto command is not found ....
>
> I don't know if this is a bug.
> Any help to align all molecules onto the first entry is also appreciated.
>
> Cheers,
> Hugo
> Jason Vertrees wrote:
>> PyMOLers,
>>
>> As promised:
>>
>> *
rs@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
> --
> Joachim
> --
> Download
an change it, but there are some good reasons for leaving it as is.
If there's enough community response, then I'll consider changing it.
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schr
easons for leaving it as is.
>>
>> Can you expand on that?
>>
>> Cheers,
>>
>> Tsjerk
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> Computational Chemist
>> Medicinal Chemist
>> Neuropharmacologist
>>
>
&g
ware tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______
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l Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
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during beta.
> http://p.sf.net/sfu/intel-sw-dev
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sers
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
Download Intel® Paral
applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
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res
fetch 1cll
This offers some more flexibility for the user to choose lines or
other default representation.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
concise than to have everything in a separate setting.
>
> set default,[cartoon, lines, nonbonded, cbaw]
>
> The default value as pymol starts up now would be [lines, nonbonded, cbag].
>
> Just my 2 eurocents...
>
> Cheers,
>
> Tsjerk
>
>
> On Tue, Mar 16, 2010
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
--
Jason Vertrees, PhD
PyMOL Prod
_
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ographica D, co-editor
>
> e-mail: mbfro...@post.tau.ac.il
> Tel: ++972 3640 8723
> Fax: ++972 3640 9407
> Cellular: ++972 547 459 608
>
> On Mar 12, 2010, at 08:16 , Jason Vertrees wrote:
>
>> Harry,
>>
>> Here's how I would do i
nce.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
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>
t the entire object,
so try "br." instead to get just the ligand.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
nux-i686-2.6/contrib/pyopengl/openglutil.o -L/usr/X11R6/lib
>> > -L/usr/lib -lGL -lGLU -lglut -lpython2.6 -o
>> > build/lib.linux-i686-2.6/pymol/opengl/gl/openglutil.so
>> > building 'pymol.opengl.gl.openglutil_num' extension
>> > gcc -pthread -fno-strict-alias
d the problems
set matrix_mode, 2
# move object one
cmd.transform_object("one", mm)
# store its new position which
# PyMOL automaticaly reinterpolates for us
mview store, object=one
mplay
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schroding
beta.
> http://p.sf.net/sfu/intel-sw-dev
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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lications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
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-dev
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>
--
Jason Vertree
proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Pa
See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archi
bon
(*) assumes you want to ignore atoms not in other objects
(*) no cutoffs
(*) the original selection is in neither of the two new selections
etc...
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@s
//lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
--
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--
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sers
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
--
Jason Vertrees, PhD
PyMOL Product Manager
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(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
Download Intel
at about a forecast of when an official implementation of
> such thing in pymol framework?
>
> Best,
> Quyen
>
> On Fri, Apr 2, 2010 at 4:08 PM, Jason Vertrees
> wrote:
>>
>> Quyen,
>>
>> No, not yet. It's something I very excited to get don
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PyMO
ourceforge.net)
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> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed
heers,
>
> Lucas
>
>
> - Mensagem original
> De: Jason Vertrees
> Para: Lucas Santos
> Cc: pymol-users@lists.sourceforge.net
> Enviadas: Sexta-feira, 9 de Abril de 2010 11:45:23
> Assunto: Re: [PyMOL] Pymol 64-bits MacOSX
>
> Lucas,
>
> Try reduci
ormance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-
>
> Thank you very much - it worked perfectly! I did not realize it is possible
> to apply that for individual objects.
>
> Vitaly
>
>
> - Original Message -
> From: Jason Vertrees
> Date: Tuesday, April 13, 2010 1:58 pm
> Subject: Re: [PyMOL] Label size in
tudio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
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gt; http://p.sf.net/sfu/intel-sw-dev
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y them is around 200kd) and a short stretch of DNA (40bp).
> Furthermore, I just don't want to ray only the cartoon, but the the cartoon
> together with the surface - pymol rays perfectly the cartoon but when I add
> the surface it becomes memory-demanding.
>
>
> Thank you
://pymolwiki.org/index.php/ManualSymExp.
I am working on a fix.
Last, PyMOLers wrote three other cool scripts and deposited them on
the wiki this week--check those out, too.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374
d only generate the first biomolecule I think. Try 2x1g
> (has 2 biomolecules in asymetric unit).
>
> Cheers,
> Thomas
>
> On Thu, 2010-04-15 at 23:39 -0400, Jason Vertrees wrote:
>> PyMOLers,
>>
>> A bug was brought to my attention to day in the symmetry expansi
o get correct result:
>
> fetch 2bop
> sym = cmd.get_symmetry('2bop')
> sym[-1] = 'R 3 2 :R'
> cmd.set_symmetry('2bop', *sym)
> symexp mates, 2bop, 2bop, 6.0
>
> Cheers,
> Thomas
>
> Jason Vertrees wrote, On 04/16/10 05:39:
>>
>
is, is it possible to store the quality settings in a
> Pymol scene?
>
> Thank you.
>
> Vitaly
>
> - Original Message -
> From: Jason Vertrees
> Date: Tuesday, April 13, 2010 4:47 pm
> Subject: Re: [PyMOL] Label size in different scenes
> To: Vitaly Vos
was
> added to the same phosphate.
>
> Any help is much appreciated,
>
> Alaena
>
> --
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives:
I guess I need to dig in the mailing list archive to find a bit more
> information on the usage of "mdo", since at this time I am rather confused
> at the proper application of "mview" and "mdo" for the scene transitions
> (aka movies).
>
> Vitaly
>
>
; Renuka.
>
>
>
> --
>
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Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
--
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PyMOL Product Manager
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(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
__
and object independently of other objects.
Good luck,
-- Jason
>
> Maia
>
> Jason Vertrees wrote:
>>
>> PyMOLers,
>>
>> Due to the popularity of using PyMOL as a portal to other programs and
>> integrating programs with PyMOL, we are developin
am wondering if I have the same version of pymol.
>
> Could you also give me some explanation what are polymer or organic, byres
> (organic expand 4), and flag fix, not organic
>
>
> Maia
>
>
> Jason Vertrees wrote:
>>
>> Maia,
>>
>>
>>>
>
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s mailing list (PyMOL-users@lists.sourceforge.net)
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>
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Sch
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>
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(e) jason.vertr..
s
>
> Cheers
> Gauri
> --
>
>
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imposition?
> Looking for inputs from community..
> Thanks to all...
>
> Cheers
> Gauri
> --
>
>
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>
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(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
__
n the objects in the script etc.Is there a way to have
> one object with main-chain atoms, and another object-without them.
>
> Maia
>
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schro
l-archive.com/pymol-users@lists.sourceforge.net
>>
>> R. Bryn Fenwick
>> robert.fenw...@irbbarcelona.org
>> Post-doctoral fellow
>> Chemistry and Molecular Pharmacology P
fo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
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-
yMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
--
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t;
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>
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(PyMOL-users@lists.sourceforge.net)
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> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
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(e) jason.vertr...@schrodinger.com
(o
tended only for the use of the individual(s) or
>> > entity named on the e-mail. If the reader of this e-mail is not the
>> > intended
>> > recipient, or the employee or agent responsible for delivering it to the
>> > intended recipient, you are hereby notified that reading it is strictly
>> > prohibited. If you
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>
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>
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Schrodin
y
>
>
>
> --
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>
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> Info Page: https://lists.sourceforge.net/lists/listinfo/py
(e.g. using
> MODELLER).
You can load FASTA files into PyMOL. Good luck understanding the
results though. For example:
# fetch a protein and save its sequence
fetch 1cll, async=0
save 1cll.fasta, 1cll
# delete everything & load the FASTA file
dele *
load 1cll.fasta
Cheers,
-- Jason
--
>
>
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get an
ATI card to more testing.
"""
I cannot be more helpful at this time because my Linux boxes only run
NVidia cards. I will either find a machine or go buy an ATI card for
my Linux box and let you know the results.
Cheers,
,
-- Jason
On Fri, May 28, 2010 at 11:37 AM, Jason Vertrees
wrote:
> Hi Bernhard,
>
> After re-reading Timothy's original email, this very much sounds like
> a driver issue. Timothy reports proper functionality using the same
> laptop, but in Windows. Regardless, here&
-
>
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ther programs stopped
> working etc. Now everything is ok. The pymol version that I have has come
> with ubuntu package, it's Version 1.1r2pre. Works fine.
>
> Maia
>
>
>
> Jason Vertrees wrote:
>>
>> Maia and Robin,
>>
>> What version of Windows an
Institut für Pharmazie
> Bundesstr. 45 | Raum 112 (406)
> D 20146 Hamburg
>
> Tel: +49 (0)40 42838-3626 (-3484)
> mail: krug...@chemie.uni-hamburg.de
> http://www.chemie.uni-hamburg.de/pha/phachem/lemcke/mitarbeiter.html
>
>
--
Jason Vertrees, PhD
PyMOL Product Manager
the
> lucky parental unit. See the prize list and enter to win:
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en a humbling experience to step into the shoes of
my mentor and get a glimpse of what he had been shouldering for the
past decade. He was a genius who worked and gave incessantly. While
it was easier for us when Warren was here, we still need to learn and
move forward.
PyMOL v1.3 is us, movi
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e list and enter to win:
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8 ip 7f00abd88626 sp 7f009444be30
>> error 4 in libX11.so.6.3.0[7f00abd36000+134000]
>>
>> Cheers,
>>
>> Edward
>>
>
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hon version 2.5 and 2.6 , both of
>> them dont do the right thing i.e allow the property to be set only for
>> the object and instead propagate the property to all objects.
>>
>> I must admit that both of ubuntu builds were compiled by me , but
>> everything is working just f
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heers,
-- Jason
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