[PyMOL] Quick PyMOLWiki Update

Greetings PyMOLers, Traffic on the PyMOLWiki continues to grow. It serves far over 100k page views/month. In 2015 we got traffic from almost every country on the planet. Very cool. While operating well, the site, schemas, and plugins were outdated. So, I went through and upgraded everything (and

Re: [PyMOL] PyMOLWiki: Quick Update

like the server's down? > > Any page returns: > > (Can't contact the database server: Can't connect to local MySQL server > through socket '/var/run/mysqld/mysqld.sock' (111) (localhost)) > > Is there a mirror anywhere that can be used? > > Shane Caldwell > McGill Univ

Re: [PyMOL] PyMOLWiki: Quick Update

t; (Can't contact the database server: Can't connect to local MySQL server > through socket '/var/run/mysqld/mysqld.sock' (111) (localhost)) > > Is there a mirror anywhere that can be used? > > Shane Caldwell > McGill University > > On Wed, Sep 9, 2015 at 1:02 AM, Jason Vertr

[PyMOL] PyMOLWiki Update

fixed. Please let me know if you find any other problems.) Please join me in thanking Microlytic http://Melanie Adams-Cioaba m...@microlytic.com for helping serve the PyMOL community. Cheers, -- Jason -- Jason Vertrees, PhD (e) jason.vertr...@gmail.com (o) +1 (603) 374-7120

Re: [PyMOL] PyMOLWiki Update

Hi Suzanne, Everything should look and act exactly like it has in the past, including the address. Cheers, -- Jason -- Jason Vertrees, PhD (e) jason.vertr...@gmail.com (o) +1 (603) 374-7120 On Fri, Jun 20, 2014 at 10:18 AM, Lapolla, Suzanne M (HSC) suzanne-lapo...@ouhsc.edu wrote: Great

[PyMOL] Farewell

ideas and actions have touched the lives of millions, whether they know it or not. He is missed. It's been great fun. I wish you all the best. Cheers, -- Jason -- Jason Vertrees, PhD (e) jason.vertr...@gmail.com (o) +1 (603) 374-7120

Re: [PyMOL] forward and backward keyboard shortcuts

...@pharm.uoa.gr'); teva...@gmail.comjavascript:_e(%7B%7D,'cvml','teva...@gmail.com'); website: thomasevangelidishomepagehttps://sites.google.com/site/thomasevangelidishomepage/ -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr

Re: [PyMOL] RNA stick depiction with filled-out rings

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Re: [PyMOL] arbitrary distance label for atom pair

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[PyMOL] PyMOL on Coursera

would like to learn more about this free online course visit https://www.coursera.org/course/bioinfomethods2. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [PyMOL] List residues functionality ?

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Re: [PyMOL] Write map from list of coordinates.

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Re: [PyMOL] Error while starting Pymol 1.7

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Re: [PyMOL] Font problem

, Justin Lecher j.lec...@fz-juelich.dewrote: On 22/11/13 17:44, Jason Vertrees wrote: Hi Justin, We'll fix that, too. Cheers, -- Jason Hi Jason, did you find time to look into that? Thanks justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural

Re: [PyMOL] PyMOL v1.7 Released

Michael, Nice catch—we'll fix it. Thanks for letting us know. Cheers, -- Jason On Mon, Jan 20, 2014 at 9:11 AM, Michael Banck mba...@gmx.net wrote: Hi, On Tue, Jan 14, 2014 at 05:11:51PM -0600, Jason Vertrees wrote: We are happy to announce the release of PyMOL v1.7.0.0! Congrats

Re: [PyMOL] Pymol, number and label the helices

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Re: [PyMOL] mutagenesis wizard data file loading

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Re: [PyMOL] combining multiple objects into one multistate object

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Re: [PyMOL] combining multiple objects into one multistate object

trying to avoid writing a script, figuring that it should just be an option in 'create'. That is, if the selection old_obj has a wild card, then create new_obj, old_obj*,1,-1 should work. Clearly not; could this be a future feature? Jed On 1/16/2014 10:56 AM, Jason Vertrees wrote: Jed

[PyMOL] PyMOL v1.7 Released

feedback and bug reports. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- CenturyLink Cloud: The Leader in Enterprise

Re: [PyMOL] Pymol and Oculus Rift

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Re: [PyMOL] Selection algebra issue

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Re: [PyMOL] what is an object colored ?

- 287561, FAX: (+44) - 1865 - 287547 On 12 Dec 2012, at 17:24, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Jon, ive been given a pse file.and i am trying to work out what color an object is.. i used the command get cartoon_color, pT_A and got back

Re: [PyMOL] ERROR: CGOOptimizeScreenTexturesAndPolygons() glGenBuffers returns err=1282

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Re: [PyMOL] ERROR: CGOOptimizeScreenTexturesAndPolygons() glGenBuffers returns err=1282

Томашевский croov...@gmail.comwrote: 2013/11/24 Jason Vertrees jason.vertr...@schrodinger.com: Hi, Hi Jason Is there any chance you can send me your input file(s)? Also, please let me know what computer, video card, and architecture (32-bit/64-bit) you're running on. So basically

Re: [PyMOL] Font problem

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Re: [PyMOL] Pymol sas

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Re: [PyMOL] Font problem

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Re: [PyMOL] UCSD pymol workshop

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Re: [PyMOL] How to make outlines to spheres drawn in PyMOL ?

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Re: [PyMOL] apply spectrum per MODEL in PyMOL script

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Re: [PyMOL] default values in pymol?

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Re: [PyMOL] [WAS: polygonal ring] cyclic peptide

-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 Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr

Re: [PyMOL] [WAS: polygonal ring] cyclic peptide

a ticket be filled ? Jerome On 05/11/13 15:34, Jason Vertrees wrote: Hi Jerome, PyMOL doesn't yet handle cyclic peptides. It's an open case we hope to resolve soon. Cheers, -- Jason On Tue, Nov 5, 2013 at 1:47 AM, Jerome BENOIT g62993...@rezozer.net wrote: Hello Again, let rephrase

Re: [PyMOL] cylindrical helices

-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 Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr

Re: [PyMOL] Is object enabled or disabled?

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Re: [PyMOL] neutral aminoacids

, Osvaldo. On Fri, Oct 11, 2013 at 12:12 AM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Osvaldo, This isn't built in yet. But, if you need to do that, you can edit the Python picked files found here: pymol/data/chempy/fragments Cheers -- Jason On Thu, Oct 10, 2013 at 2

Re: [PyMOL] selection residues with an exact b-factor value

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Re: [PyMOL] neutral aminoacids

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Re: [PyMOL] load surface

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Re: [PyMOL] Background colors in PyMOL 1.6

Uhr Von: Jason Vertrees jason.vertr...@schrodinger.com An: Nils NN n...@gmx.ch Cc: pymol-users@lists.sourceforge.net pymol-users@lists.sourceforge.net Betreff: Re: [PyMOL] Background colors in PyMOL 1.6 Hi Nils, We've updated how PyMOL stores colors in sessions. You can try

Re: [PyMOL] Background colors in PyMOL 1.6

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Re: [PyMOL] C-aplha c-alpha distances

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Re: [PyMOL] Alpha Channels in Pymol Movies

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Re: [PyMOL] Pymol OpenGL ES?

(and likely others now or in the future), pymol would really make it a complete mobile device. --p On 07/17/2013 12:02 PM, Jason Vertrees wrote: Hi Paul, It's been done already. See, PyMOL on the iPad (http://pymol.org/mobile). Cheers, -- Jason On Wed, Jul 17, 2013 at 10:55 AM, Paul

Re: [PyMOL] python module in pymol

/clk?id=48808831iu=/4140/ostg.clktrk ___ 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

Re: [PyMOL] Trouble with mutagenesis script

=0.083 (4 to 4 atoms) Mutagenesis: 12 rotamers loaded. where the RMS will change based on your residues. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [PyMOL] Pymol DLP 3D

. GeForce cards are incapable of presenting windowed OpenGL 3D at 120 Hz. You need a Quadro card. The NVidia 3D Vision ( http://www.nvidia.com/object/3d-vision-main.html) page should have all the info you need. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc

Re: [PyMOL] Anaglyph colours sorted (kind of)

the time–your video card just has to be good enough and you need to be using PyMOL v1.5 or later. Cheers, -- Jason From: Jason Vertrees jason.vertr...@schrodinger.com Date: Wednesday, 26 June 2013 21:53 To: Gary Hunter gary.hun...@um.edu.mt Cc: Thomas Holder thomas.hol...@schrodinger.com

Re: [PyMOL] Anaglyph colours sorted (kind of)

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Re: [PyMOL] PyMOL 1.6 pre-release announcement

Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [PyMOL] PyMOL 1.6 pre-release announcement

to have backward compatibility to PyMOL 1.3 from the open source version 1.6.0.0. Mostly it has to do with CGOs and measurements. Should I just send them to you and/or Thomas? Bob On Thu, Jun 20, 2013 at 7:36 AM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi David, If you save

Re: [PyMOL] Leapmotion ?

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Re: [PyMOL] PyMOL measurements

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Re: [PyMOL] how to get cealign outputs for mulitple structures

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Re: [PyMOL] how to face cartoon

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Re: [PyMOL] trouble with fading for sticks in a movie

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Re: [PyMOL] Problems with H_add when theres alternate conformations present

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Re: [PyMOL] CEalign parameter d0 and d1

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Re: [PyMOL] CGO fixed in space

@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 Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374

Re: [PyMOL] Howto fake mouse events in pymol

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[PyMOL] Invitation to visit at ACS New Orleans

of PyMOL v1.6, PyMOL on the iPad, and even a sneak peek of Leap Motion (https://www.leapmotion.com/) controller integration with PyMOL. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [PyMOL] Invitation to visit at ACS New Orleans

Hi Sabuj, Do you have it working under linux? Yes, I have demonstrated the same functionality on Ubuntu (12.10). Ubuntu is the only Linux distro currently supported by Leap. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr

Re: [PyMOL] How to hide the object control panel

Matthias, As David said, try setting internal_gui to 0. Or, try saving your session as a .psw instead of .pse. Cheers, Jason Sent from my Android. Please excuse the concision and any typos. On Mar 24, 2013 6:55 PM, Matthias Haffke matze_haf...@hotmail.com wrote: Dear all, this might be a

Re: [PyMOL] How to ray trace clipped image without clipping spheres.

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Re: [PyMOL] pymol install

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Re: [PyMOL] [PyMol] How to visualize surface within a given radius

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Re: [PyMOL] Lighting script request

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Re: [PyMOL] Zoom + Fading simultaneously in movie

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Re: [PyMOL] Managing Viewport Location

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Re: [PyMOL] cross hair for non-bonded atoms

Hi Pascal, hide nonbonded Cheers, Jason Sent from my Android. Please excuse the concision and any typos. On Jan 30, 2013 1:10 PM, Pascal Auffinger p.auffin...@ibmc-cnrs.unistra.fr wrote: Hi, Just wondering how to remove the cross hair that is shown for each non-bonded atom (for example

Re: [PyMOL] Hight-quality visualisation

. For other neat rendering tricks, please see the PyMOLWiki's Gallery ( http://www.pymolwiki.org/index.php/Gallery). Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [PyMOL] Active stereo on an iMac?

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Re: [PyMOL] Piecewise rotations while viewing in surface

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Re: [PyMOL] names of the residues

-d2d ___ 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 Director

Re: [PyMOL] new line in label

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Re: [PyMOL] Write vector graphics of session

On Tue, Jan 15, 2013 at 6:32 AM, Martin Hediger ma@bluewin.ch wrote: I'm no expert but I guess my favorite would be EPS. Converting to PDF, if required, is easy on the Mac. Best regards Martin On 14.01.13 23:53, Jason Vertrees wrote: Martin, That would be a nice feature. Which format

Re: [PyMOL] Write vector graphics of session

@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 Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374

Re: [PyMOL] stick/ribbon rendering not working

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Re: [PyMOL] unittest for get_coordinate function

files to ensure they're properly formatted before use. If you're lucky, your format will come with a nicely defined BNF grammar. Good luck. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374

Re: [PyMOL] Atom renaming within selection

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Re: [PyMOL] Memory not released after load and delete of structure

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Re: [PyMOL] Memory not released after load and delete of structure

? (Any chance we can see the script or a stub of it?) Cheers, -- Jason On Fri, Dec 21, 2012 at 3:17 AM, Martin Hediger ma@bluewin.ch wrote: Hi Jason, I'm using PyMOL 1.3. Best regards Martin On 20.12.12 15:53, Jason Vertrees wrote: Hi Martin, Which version of PyMOL are you using

Re: [PyMOL] wierd bug in Ubuntu 12.10

___ 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 Director of Core Modeling Product Management

Re: [PyMOL] what is an object colored ?

, but it's not very straightforward: s = cmd.get_session() print cmd.get_color_tuple(s[names][1][5][0][2]) To make sure you have right object ensure that, s[names][1][5][0][1] equals your object name. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger

Re: [PyMOL] make bond between two atoms

pseudoatoms. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LogMeIn Rescue: Anywhere, Anytime Remote

Re: [PyMOL] Help with alignments

-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 Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1

Re: [PyMOL] Rendering memory errors

the images are nice. If you have Intel-based hardware you might try the following settings upon startup: set use_shaders, 0 set sphere_mode, 0 and then try your rendering plugin. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr

[PyMOL] Project Upgrades

be patient. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LogMeIn Rescue: Anywhere, Anytime Remote support

Re: [PyMOL] setting the cutoff radius that determines when atoms are bonded

Terrell ryeterr...@ryeterrell.net wrote: Hi Jason, Thanks for the tip. I still couldn't get it to work. I'll google around some more, but here's the file. Thanks for any help. Cheers, Rye On Mon, Dec 3, 2012 at 4:34 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Rye, How

Re: [PyMOL] setting the cutoff radius that determines when atoms are bonded

-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LogMeIn Rescue: Anywhere

Re: [PyMOL] iPad pymol questions

-- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Keep yourself connected to Go Parallel: INSIGHTS What's next for parallel hardware

Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries

). Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Monitor your physical, virtual and cloud

Re: [PyMOL] ribbon trace, visualizing polymers (resent)

___ 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 Director of Core Modeling Product Management Schrödinger, Inc

Re: [PyMOL] ribbon trace, visualizing polymers (resent)

___ 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 Director of Core Modeling Product Management Schrödinger, Inc. (e

Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries

this out. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LogMeIn Central: Instant, anywhere, Remote PC

Re: [PyMOL] Pymol in command mode - no output

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 Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr

Re: [PyMOL] cgo object tutorials

the demonstrate their usage. In addition, is the pymol volume visualize (http://pymol.org/volume) available for educational use ? Volume visualization is available in the Incentive version and open-source builds, but not the free Educational version. Cheers, -- Jason -- Jason Vertrees, PhD

Re: [PyMOL] (no subject)

___ 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 Director of Core Modeling

Re: [PyMOL] sphere_scale

/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

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