ce it when I finish and it's posted.
Cheers,
-- Jason
--
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PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
Enable your software for Intel(R) Act
el(R) vPro (TM) technology - will your software
> be a part of the solution? Download the Intel(R) Manageability Checker
> today! http://p.sf.net/sfu/intel-dev2devmar
> ___
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ne and some other Linux machines
we'll test this on.
At this point it looks like a simple initialization error with GLEW,
but we're still looking into it.
Thanks for bringing this to our attention. I expect this to be
resolved quickly.
Cheers,
-- Jason
--
Jason Vertrees, PhD
(TM) technology - will your software
> be a part of the solution? Download the Intel(R) Manageability Checker
> today! http://p.sf.net/sfu/intel-dev2devmar
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> Info Page: https:
on is 12000+ lines long, so
there's quite a few changes.
Cheers,
-- Jason
--
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PyMOL Product Manager
Schrodinger, LLC
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Create and publish w
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lists/listinfo/pymol-users
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---
; layer4/Cmd.c:8709: error: 'lenA' undeclared (first use in this function)
> layer4/Cmd.c:8718: error: 'lenB' undeclared (first use in this function)
> ...
>
> Possible fix at http://www.python.org/dev/peps/pep-0353/
> Which I added to layer0/os_python.h, patch attache
e settings that control the shader behavior, or do I have to mess
> with the code in data/shaders?
The new basic shaders don't yet support transparencies. They're there
basically to complement the volumes and will be further developed
soon.
Cheers,
-- Jason
--
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__
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>
--
Jason Vertre
nk there are any pdbs yet that contain pi helices (because of the
> loose packing and steric hindrance of the side chains), does anyone know of
> any?
> Thanks
> Adam
> On Apr 6, 2011, at 8:16 AM, Jason Vertrees wrote:
>
> Hi Ramiro,
>
> PyMOL doesn't differentiate helic
found the bug and fixed it. We have
plans to release the updated Incentive PyMOL v1.4.1 in a few weeks'
time, which will have this fix.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vert
nfo Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> 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
--
s with the middle mouse button.
> Finally is it possible to use Pymol from within iPython? For example I
> wanted recently to see the properties of a C object. That would have been
> extremly easy in iPython
>
> import pymol
> cube = pymol.cmd.load("my.cube")
> cube
artphone on the nation's most reliable network.
> And it wants your games.
> http://p.sf.net/sfu/verizon-sfdev
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,
It sounds like your PyMOL is out of date; that command is relatively
new. Which PyMOL version are you using?
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@sc
Hi Kanika,
That version is too old, hence the missing command. It's probably
wise to upgrade.
Cheers,
-- Jason
On Mon, Apr 11, 2011 at 2:50 AM, kanika sharma wrote:
> version 1.1 r1
>
> On Mon, Apr 11, 2011 at 12:04 PM, Jason Vertrees
> wrote:
>>
>> Hi Kanika,
A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
>
> --
n-source branch.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
Xperia(TM) PLAY
It's a major breakthrough. An authentic gaming
sm
help. Please send them directly
to me so we do not clog up the list with debugging messages. We've
tried to debug these drivers for months now. On all machines I've
tried, we cannot ever get them to fail locally, making debugging
extremely challenging.
Cheers,
-- Jason
--
Jason Vert
Hi Christoph,
I just pushed an update that fixes this.
Cheers,
-- Jason
On Mon, Apr 11, 2011 at 4:55 PM, Christoph Gohlke wrote:
>
>
> On 4/11/2011 10:05 AM, Jason Vertrees wrote:
>> Hi Marius,
>>
>>>> Also right clicking on the volume representation raises th
for making and distributing this.
I like the idea of people citing plugins. It could help readers find
the plugin for their own use.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1
e Report - Recovery time is now measured in hours and minutes
> not days. Key insights are discussed in the 2010 Forrester Wave Report as
> part of an in-depth evaluation of disaster recovery service providers.
> Forrester found the best-in-class provider in terms of services and vision.
> Re
update the PyMOLWiki pages with
anything you've learned. I'll try to keep facilitating as time
permits.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodi
s@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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-
mware-sfdev2dev
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ontroller: ATI Technologies Inc NI Whistler [AMD
> Radeon HD 6600M Series]
>
> Debian Squeeze AMD64.
>
>
> Thanks and best regards,
>
> lina
>
> On Sun, Apr 17, 2011 at 10:51 PM, Jason Vertrees
> wrote:
>>
>> Hi Zhao,
>>
>> The ATI drivers are
ore about boosting
> the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev
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OL-users mailing list (PyMOL-users@lists.sourceforge.net)
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>
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Jason V
west initial
> acquisition cost and overall TCO of any competing solution.
> http://p.sf.net/sfu/whatsupgold-sd
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cquisition cost and overall TCO of any competing solution.
> http://p.sf.net/sfu/whatsupgold-sd
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>
f Incentive PyMOL visiting http://pymol.org/dsc.
> I'm coming to this after a very long time so please bear with my
> somewhat ignorant questions.
Happy to help.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vert
ey wrote:
> Dear Pymolers,
>
> I would like to be able to write a script with the a command that is
> available in actions (preset, pretty).
>
> How to do that?
>
> Maia
>
--
Jason Vertrees, PhD
PyMOL Product Manag
n SVN,
corresponds to commit 3947, and a corresponding tar file has been
uploaded.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
---
rt
in the Linux VM. (But, Parallels doesn't yet support OpenGL in Ubuntu
11.04 with Unity, it's planned for their next update.) Both Parallels
and VMWare offer OpenGL for Windows.
Good luck,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@sc
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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(e) jason.vertr...@schrodinger.com
(o) +1 (6
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>
--
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S
.net/sfu/intel-dev2devmay
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ction before
fetching. I've seen this cause problems some time.
Just by chance, do you have fetch_host or fetch_path set to something
non-standard (maybe in your .pymolrc)?
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger
This setting
has nothing to do with saving data.
I don't believe PyMOL is currently capable of saving these fields to file.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@sc
pymol-users
> 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
--
Achie
to help Windows* and Linux* C/C++ and Fortran
> developers boost performance applications - including clusters.
> http://p.sf.net/sfu/intel-dev2devmay
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> Info Page: https:
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PyMOL Product Manager
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--
What Every C/C++ and Fort
Hi Thomas,
Thanks for submitting the bug. I've modified and applied the patch
and pushed the code.
It's fixed.
Cheers,
-- Jason
On Wed, May 18, 2011 at 11:43 AM, Thomas Holder
wrote:
> On 05/18/2011 05:01 PM, Jason Vertrees wrote:
>>
>> This is a bug. Please file
; http://p.sf.net/sfu/intel-dev2devmay
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state 2
set state, 2
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
What Every C/C++ and Fortran developer Should Know!
Read
_counter_mode, 0". Alternatively, you could
just increase the internal_gui_width--eg
set internal_gui_width, 300
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
rsion number, please use
"get_version" in the meantime.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
What Ever
then save your session.
I'll look into fixing this ASAP.
Cheers,
-- Jason
On Thu, May 19, 2011 at 11:33 AM, Jason Vertrees
wrote:
> Hi Carsten,
>
>> Has the length of the object name entry in the right hand menu been
>> restricted to 16 characters in v1.4.x? Prior to 1.4.x
DUS]
wrote:
> Hi Jason,
>
> thanks for the follow-up. Let us know when the issue is fixed.
>
> Cheers,
>
> Carsten
>
>> -----Original Message-
>> From: Jason Vertrees [mailto:jason.vertr...@schrodinger.com]
>> Sent: Thursday, May 19, 2011 12:11 PM
> 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
>
--
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boratory of Computational Biology NIH/NHLBI
> 5635 Fishers Lane, Room T909, MSC 9314
> Rockville, MD 20852 (UPS/FedEx/Reality)
> Bethesda MD 20892-9314 (USPS)
>
> --
> What Every C/C++ and Fortran developer Should Know!
> Read this
ame 10, object one
transitions from state 1 to state 100 over 100 frames. Likewise,
object 2 transitions from state 100 down to state 1 over 100 frames.
See also,
* -- http://www.pymolwiki.org/index.php/MovieSchool
Hope this helps.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Pro
ng of applying, you might want to
start planning a project that will benefit PyMOL and the open-source
project in general.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
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ications - including clusters.
> http://p.sf.net/sfu/intel-dev2devmay
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.ma
(even inside the browser!)
* -- over a dozen new functions
* -- improved documentation and demos
* -- updated third party components
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374
_
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sfdev2dev
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>
--
Ja
r you, too.
>
> Regards,
> Andreas
>
>
> Am 05.06.2011, 08:29 Uhr, schrieb Ariel Talavera :
>
>> Hi Jason,
>>
>> After some struggle, I finally compiled the last open source version,
>> Pymol 1.4.1. Unfortunately, the same problem persist. I still not abl
> http://p.sf.net/sfu/quest-sfdev2dev
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of failed request: 169 ()
> Serial number of failed request: 46
> Current serial number in output stream: 46
This sounds like a driver problem. Can you run the 'glxgears'
program? Does it give the same error? Do you have the latest driver
installed?
Cheers,
-- Jason
--
essibility Checking.
> http://p.sf.net/sfu/ephox-dev2dev
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9:58 Uhr, schrieb Gianluigi Caltabiano
> :
>
>> With Ubuntu 10.04 LTS - Lucid Lynx and Pymol 1.4.1 it seems to solve the
>> problem.
>>
>> thanks,
>>
>> Gianluigi
>>
>>
>>
>>
>>
>>
>>
and ensure content is compliant with Accessibility Checking.
> http://p.sf.net/sfu/ephox-dev2dev
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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.
>
> Cheers,
> ariel
>
>
> On Thu, 2011-06-09 at 10:16 -0500, Jason Vertrees wrote:
>> PyMOL to last night's version
>
>
> Centro de Inmu
ave any other ideas?
>
> Thanks,
> Bernhard
>
> -----Original Message-
> From: Jason Vertrees
> To: Bernhard Lechtenberg
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] Problems with Pymol 1.4.1 under Ubuntu 11.04
> Date: Thu, 9 Jun 2011 11:24:27 -0400
&
thout any changes to the structures)
If you want PyMOL to do the calculation, but leave the structures
untouched use "cmd.rms" instead of "cmd.fit". They both have a
similar syntax.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) j
ould use
> to get rmsd between these PDBS
> both my pdbs are of the same protein
Please read the help I suggested earlier. If you type "help fit" you
will see that there are lots of alignment and fitting commands in
PyMOL, including: align, super, pair_fit, rms, rms_cur, intra_fit
s compliant with Accessibility Checking.
> http://p.sf.net/sfu/ephox-dev2dev
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de with the command: svn co
> https://pymol.svn.sourceforge.net/svnroot/pymol pymol
> (2) go to pymol/trunk/pymol, and see the ChangeLog: 2011-06-16 Jason
> Vertrees
>
> * suppress guess valences warning message to Blather
> (3) In pymol/trunk/pymol:
> python setup.py install --prefi
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not carry them over into the combined file,
> neither are CRYST/SCALE records retained. Any flags I need to set?
>
> Cheers,
>
> Carsten
>
>> -Original Message-
>> From: Jason Vertrees [mailto:jason.vertr...@schrodinger.com]
>> Sent: Thur
quest? I know Pymol is more
> a 'consumer' and not a 'producer' but in certain instances
> this would be a nice feature to have.
>
> Cheers,
>
> Carsten
>
>> -Original Message-
>> From: Jason Vertrees [mailto:jason.vertr...@schrod
plex scene _without_ texture_fonts set, gives me about 30
FPS. After typing,
set texture_fonts, 1
my frame rate jumps to 60 FPS.
Hope this helps.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603
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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PyMOL Product Manager
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(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
-
re. Splunk takes this data and makes
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2d-c2
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l Methods)
* Senior Software Developer (Scientific Libraries)
* Senior Database Developer
If you're interested, please consider applying! If you know someone
who might be, please pass along the info.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(
y, Imperial College London
>> http://www.msf.bio.ic.ac.uk
>
>
> --
> All of the data generated in your IT infrastructure is seriously valuable.
> Why? It contains a definitive record of appli
ense. And common sense.
> http://p.sf.net/sfu/splunk-d2d-c2
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e.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
--
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PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
---
nfo Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
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(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
---
color-code my selections, and visualize them
> simultaneously on the structure to see if there is any overlap?
The most flexible way to do this is as Tsjerk suggested: changing the
colors, or representations of your selections.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger
h show residue 227 being right before residue 266.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
AppSumo Presents a FREE Vide
pendent of one another, whereas in fact it is likely
> that functional residues form in clusters? Is there any statistical
> methodology that would be appropriate and take this into account?
> Again, sorry for the slightly off-topic question and many thanks.
> Spyros
--
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ist (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
>
--
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PyMOL Product Manager
Schrodi
strengths and weaknesses of these DLP solutions.
> http://www.accelacomm.com/jaw/sfnl/114/51385063/
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Hi Lina,
Use the command line:
save newPDB.pdb, rotatedObject
Cheers,
-- Jason
On Tue, Jul 19, 2011 at 11:13 AM, lina wrote:
> On Tue, Jul 19, 2011 at 10:29 PM, Jason Vertrees
> wrote:
>> Hi Lina,
>>
>>> I don't know how to save a NEW.pdb which based on th
tion "Screen"
> Identifier "Screen[1]"
> Device "Device0"
> Monitor "Monitor[1]"
> DefaultDepth 24
> Option "Stereo" "10"
> SubSection "Display"
> Viewport 0 0
> Depth
cartoons at 23 Hz
on the left screen and 12 Hz on the right (but only when display_lists
are turned on). If you find a combination that gets you a significant
boost in rendering speeds, feel free to share.
Hope this helps.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schroding
nt of the user.
> 3. It is possible that the newer driver could be less stable. The customer
> can try an older driver, but it must be 260.19.36 or newer.
Hope this helps.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schro
of these DLP solutions.
> http://www.accelacomm.com/jaw/sfnl/114/51385063/
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Greetings,
Just a quick note to let you know that the latest versions of MacPyMOL
(1.4.x+) should work without issue on Mac OS X 10.7 (Lion). I did some
quick testing and everything worked well. If you update and find any
problems with PyMOL, please let me know.
Cheers,
-- Jason
--
Jason
elevant piece of output of my glxinfo command on
> linux :
> OpenGL vendor string: Tungsten Graphics, Inc
> OpenGL renderer string: Mesa DRI Mobile Intel® GM45 Express Chipset GEM
> 20100330 DEVELOPMENT x86/MMX/SSE2
> OpenGL version string: 2.1 Mesa 7.9-devel
After seeing this,
mailing list (PyMOL-users@lists.sourceforge.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
(
r the new fellowship.
Fellows are listed on our website (http://pymol.org/fellowship).
Cheers,
Jason & the PyMOL Team at Schrödinger
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603)
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--
Jason Vertrees, PhD
PyMOL Product Manager
Schro
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