Re: [PyMOL] Updates

)! Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology / University of Groningen The Netherlands -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr

Re: [PyMOL] Citing PyMOL

) 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 Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [PyMOL] Rendering issues

/pymol-users 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 -- Sell apps

Re: [PyMOL] how to understand the symmetry operators coding?

/RIM-dev2dev ___ 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

Re: [PyMOL] educational build?

-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 Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [PyMOL] Writing Hbond list

-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 -- Sell apps to millions through the Intel(R) Atom(Tm

Re: [PyMOL] about script

___ 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 Product Manager Schrodinger

[PyMOL] AxPyMOL and the new AxPyMOL Reader

computer. If you are a current AxPyMOL subscriber, you do not need AxPyMOL Reader, as the full version of AxPyMOL includes Reader capabilities. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [PyMOL] how to call the align command without opening Pymol GUI window

) 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 Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [PyMOL] Mutagenesis How many rotamers per amino acid

. Then to extract a sequence, I tend to go for a construction like: sequence = [ aa321[i.resn] for i in cmd.get_model(selection + and n. ca).atom ] Cheers, Tsjerk On Mon, Sep 13, 2010 at 12:30 AM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Martin, iterate first my_res

[PyMOL] Cool New Script -- Angle Between Helices

for many. The PyMOLWik page is http://www.pymolwiki.org/index.php/AngleBetweenHelices. Great job, Thomas. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [PyMOL] Set cartoon_transparency bug?

/lists/listinfo/pymol-users 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

Re: [PyMOL] Setting outline thickness during ray tracing

-users 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 -- Start

Re: [PyMOL] Running pymol without display

@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Start uncovering the many advantages of virtual appliances and start using

Re: [PyMOL] Mutagenesis How many rotamers per amino acid

. Thanks a lot. I am wondering, are there any scripts/ plugins for PyMOL out there that facilitate the generation of a large amount of rotamers for different mutants? I might take the effort and start building this into a plugin. Martin Am 16.09.10 19:51, schrieb Jason Vertrees: Hi

Re: [PyMOL] Mutagenesis How many rotamers per amino acid

wizard be used for this? Thanks a lot for any suggestions. Martin Am 19.09.10 19:00, schrieb Jason Vertrees: Martin, I am wondering, are there any scripts/ plugins for PyMOL out there that facilitate the generation of a large amount of rotamers for different mutants? I might take

Re: [PyMOL] zoom w/o ray-trace

/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Start uncovering the many advantages of virtual appliances

Re: [PyMOL] Deleting and Loading multiple SDF files

@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 Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [PyMOL] zoom w/o ray-trace

-sfdev2dev ___ 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 Product

Re: [PyMOL] Fwd: emovie scripting

/listinfo/pymol-users 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 -- Start

Re: [PyMOL] Access viewport size

-- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Start uncovering the many advantages of virtual appliances and start using them to simplify

Re: [PyMOL] How to measure the angle between two aromatic rings?

/lists/listinfo/pymol-users 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

Re: [PyMOL] New MacPros and PyMOL - Radeon only?

version for a while, but the Tcl/Tk toolkit was not ready. I think it's still in alpha/beta. 64-bit MacPyMOL will be released when we're sure that works. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [PyMOL] Outline in Ray trace mode 1

://lists.sourceforge.net/lists/listinfo/pymol-users 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

Re: [PyMOL] pymol dies when switching edit/view modes

/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Beautiful is writing same markup. Internet Explorer 9

Re: [PyMOL] [PYMOL] error with pair fitting

-users 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 -- Beautiful

Re: [PyMOL] [PYMOL] error with pair fitting

___ 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 Product Manager Schrodinger, LLC (e

Re: [PyMOL] Delete states function?

-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 Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [PyMOL] object matrix not updated with pair_fit

@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Beautiful is writing same markup. Internet Explorer 9 supports standards

Re: [PyMOL] Delete states function?

@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 Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [PyMOL] h_add - proton nomenclature

@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 Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [PyMOL] How do I use the 'alter' command on a single chain?

@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5

Re: [PyMOL] OpenDX files from opendx.org

___ 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 Product Manager Schrodinger, LLC (e) jason.vertr

Re: [PyMOL] OpenDX files from opendx.org

___ 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 Product

Re: [PyMOL] Displaying PDB files that were determined via fiber diffraction

://p.sf.net/sfu/adobe-dev2dev ___ 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] Fwd: What is the difference between Atom ID and Index

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 Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603

Re: [PyMOL] maximum sphere-quality ?

___ 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 Product Manager Schrodinger, LLC (e) jason.vertr

Re: [PyMOL] Electron density map

Quoting Jason Vertrees jason.vertr...@schrodinger.com: Hi Saif, Can you please show us the commands you used in PyMOL to load the data and generate the map?  (Also, can you send me a copy of the map and structure?)  Has anyone else seen this problem? I've looked over a few CCP4 maps in PyMOL

[PyMOL] Poll: openGL versions

PyMOLers, Work on bringing PyMOL's code up to a newer openGL standard has begun. This will bring us access to new openGL features. We're taking a poll of which openGL version your systems support. To cast your vote please visit: http://pymol.org/poll Cheers, -- Jason -- Jason Vertrees, PhD

Re: [PyMOL] pymol

(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 Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374

Re: [PyMOL] small molecule geometry gets whacked in creating multi-state object. rebuild?

information. In Seth's case, it looks like that difference was confusing PyMOL. Cheers, -- Jason On Wed, Nov 10, 2010 at 8:55 AM, Robert Campbell robert.campb...@queensu.ca wrote: Hi Seth, On Tue, 09 Nov 2010 22:54:59 -0500 Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Seth, I

Re: [PyMOL] small molecule geometry gets whacked in creating multi-state object

, 2010 at 5:37 AM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Seth, I don't understand your question.  I think you're looking for the copy or extract command (http://www.pymolwiki.org/index.php/Extract).  If not, please try rewording the question. Cheers, -- Jason On Fri, Nov 12

Re: [PyMOL] Selecting subsequence in PyMol

the 'ps.' (peptide sequence) modifier: select targetSeq, ps. GKTQKV Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [PyMOL] Selecting subsequence in PyMol

. Cheers, -- Jason On Fri, Dec 10, 2010 at 1:48 AM, Keitaro Yamashita yamash...@castor.sci.hokudai.ac.jp wrote: It's very useful. How about RNA/DNA sequence? Thanks in advance, Keitaro 2010/12/10 Jason Vertrees jason.vertr...@schrodinger.com: Hi Julio, I'm using PyMOL 1.3 and I would

Re: [PyMOL] Disappearing right-hand control panel

-- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Oracle to DB2 Conversion Guide: Learn learn about native support for PL/SQL, new data types, scalar

Re: [PyMOL] Dont resequence atoms when saving

for your answers. Martin On 09.11.10 13:26, Jason Vertrees wrote: Hi Martin, set retain_order set pdb_retain_ids Cheers, -- Jason On Tue, Nov 9, 2010 at 4:30 AM, Martin Hedigerma@bluewin.ch  wrote: Dear all It occured to me that PyMOL is resequencing a structure when saving

Re: [PyMOL] label_size in pymol 1.3 on Mac

@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect

Re: [PyMOL] select single state with the mouse?

___ 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 Product

Re: [PyMOL] use PyMOL code in outer tkinter application

-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 PyMOL Product

Re: [PyMOL] Segmentation fault rendering CGO object with all_states one

://p.sf.net/sfu/oracle-sfdevnl ___ 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] Segmentation fault rendering CGO object with all_states one

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 -- Learn how Oracle Real

Re: [PyMOL] Force of pure white background when ray tracing with fog

-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 Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

[PyMOL] New Scripts on the PyMOLWiki

-- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Learn how Oracle Real Application Clusters (RAC) One Node allows customers to consolidate database

Re: [PyMOL] Model pdb section support

@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 Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [PyMOL] Pymol and Powerpiont and MiMac

___ 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 Product Manager Schrodinger, LLC (e) jason.vertr

Re: [PyMOL] Fwd: all_states failure with 500 or more models

with 500 or more models To: Jason Vertrees jason.vertr...@schrodinger.com Hi Jason, Another glitch with all_states it seems. When loading a pdb with 500 frames or more, the OpenGL window starts displaying weird behaviour. It doesn't properly respond to changes in the representation

Re: [PyMOL] Malformed Selection Error when Measuring Dihedral Angle with Measurement Wizard

://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 -- Protect Your Site and Customers from Malware

Re: [PyMOL] Wiki down?

://lists.sourceforge.net/lists/listinfo/pymol-users 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

Re: [PyMOL] can't save pdb from within pymol

___ 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 Product Manager Schrodinger

Re: [PyMOL] Independent Zooming in Grid Mode

/arcsight-sfd2d ___ 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

Re: [PyMOL] can't save pdb from within pymol

:59 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi David, Can you please send me the PSE?  If not, do you have multiple states? Are you using the save command or the GUI? Cheers, -- Jason On Thu, Jan 27, 2011 at 1:50 PM, David A.  Horita dhor...@wfubmc.edu wrote: Hi, I've

Re: [PyMOL] dialogs in pyMOL

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 Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374

[PyMOL] Spam

, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class

Re: [PyMOL] Visualizing two surfaces using APB2tools2.1

on the PyMOLWiki. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD

Re: [PyMOL] Please assess the Pymol interface

-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 Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [PyMOL] Quick Updates

the representation. We'd have to consider how best to utilize it from within PyMOL. Thanks for the great work developing PyMOL further. I'm glad it's appreciated. Even though working on PyMOL can be challenging, it is great fun. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager

Re: [PyMOL] Plugin Tutorial

places its plugins in modules/pmg_tk/startup/. Since PyMOL does not read the script but once, upon initialization, any changes you make will be recognized simply by restarting PyMOL, but you don't need to reinstall. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC

Re: [PyMOL] how to color surface based on electrostatic potential

@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE

Re: [PyMOL] pymol movie scripting for beginners questions

://p.sf.net/sfu/intel-dev2devfeb ___ 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] Smoothing camera movements

-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 Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com

Re: [PyMOL] insertion code

-dev2devfeb ___ 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

Re: [PyMOL] insertion code

PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Interesting question.  PyMOL's wildcards can help here: select allButInsertionsA, not (i. *A) This will look for all residue NUMBERS that end in A and select everything but that. Thanks, that definitely helps a lot.  I just realized

Re: [PyMOL] alter atom coordinates

://lists.sourceforge.net/lists/listinfo/pymol-users 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

Re: [PyMOL] sphere labeling in pymol

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 Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603

Re: [PyMOL] Getting object names

/lists/listinfo/pymol-users 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

Re: [PyMOL] using pymol from python script

://lists.sourceforge.net/lists/listinfo/pymol-users 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

Re: [PyMOL] using pymol from python script

Hi John, I'm running version Version 1.2r2. This is probably why. I don't recall the exact version in which this became doable, but it's now available in the latest version. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com

Re: [PyMOL] visualizing objects via python script

-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 Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [PyMOL] Color scale changed in APBS?

@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Index, Search Analyze Logs and other IT data in Real-Time with Splunk Collect, index

Re: [PyMOL] select clipped atoms

) 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 Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [PyMOL] Saving the Connolly surface of a PDB

/listinfo/pymol-users 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

Re: [PyMOL] labeling by a pseudoatom

mcache 50, as spheres, het mcache 50, show surface, poly within 10 or org ... store scenes, plan movie, etc. ... mCacheApply 50 I made something similar for making movie fades, just cache the string an apply it when necessary. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager

Re: [PyMOL] Selecting ASP and GLU

___ 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 Product Manager Schrodinger, LLC (e) jason.vertr

Re: [PyMOL] Rendering Large Scene Crashes Pymol

-ray, but pymol still crashed.  What are my options for rendering out my scene, if any? Thank you. Last, are you using 32-bit PyMOL or 64-bit PyMOL? I know your OS is 64-bit, but what about the PyMOL binary? Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e

Re: [PyMOL] How to color aligned structures by equivalent SSE?

indicators select none That's cool enough to be it's own script. I'll add that to the PyMOLWiki if I find the time. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [PyMOL] select clipped atoms

: Jason Vertrees wrote: Having said this, you can however, can get the clipping information from P... Hi Jason, thank you again for the hint. First I looked if I can select atoms according to their coordinates, or store new coordinates after a rotation / shift. But implicitly you already

Re: [PyMOL] Different color on each side of strand

://lists.sourceforge.net/lists/listinfo/pymol-users 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

Re: [PyMOL] CGO objects don't disappear when they should...

an object only for a given state/frame? Should I delete the object at the next state/frame? What would be the command to delete a cgo object? Should I store what load_cgo() returns and issue a delete over that object? Thanks! On Mon, Mar 7, 2011 at 9:03 PM, Jason Vertrees jason.vertr

Re: [PyMOL] Question about the .obj file saved by Pymol

://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 -- What You Don't Know About Data Connectivity CAN

Re: [PyMOL] CGO objects don't disappear when they should...

? I hope the example code will help out. Thanks a lot! Nicolas On Mon, Mar 7, 2011 at 10:17 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Nicolas, It sounds like you have the all_states option set.  So, to only have one object state shown at a time, try unset

[PyMOL] MTZ Files

reader on various MTZ files new and old. If you have an MTZ file you'd like to share for testing, please email it directly to me (jason.vertr...@schrodinger.com) and I'll be sure we run it through our tests. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e

Re: [PyMOL] MTZ Files

file that is generated by CNS 1.3 and contains map coefficients/phases. The code also supports CIF and CNS files, but those won't be fully functional until a later update release. I'm very looking forward to PyMOL v1.4 release, Awesome--so am I! Cheers, -- Jason -- Jason Vertrees, PhD PyMOL

Re: [PyMOL] PyMOL breaks printing \b

) for this? Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Colocation vs. Managed Hosting A question and answer guide to determining

Re: [PyMOL] plugin dependencies

___ 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 Product Manager Schrodinger, LLC (e

Re: [PyMOL] protein interaction surface

. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Colocation vs. Managed Hosting A question and answer guide to determining

Re: [PyMOL] Problem reading multiframe pdb file for animation

-sfd2d ___ 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 Product

Re: [PyMOL] Problem reading multiframe pdb file for animation

. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Colocation vs. Managed Hosting A question and answer guide to determining the best

Re: [PyMOL] 3D Projector successful cases

Hi David, Thank you very much. Have you tried to use it with a Mac ? We have not tried it with a Mac. The only stereo I can currently get on the Mac is Zalman. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603

Re: [PyMOL] ray_trace_mode, 1 - white outline

: https://lists.sourceforge.net/lists/listinfo/pymol-users 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

[PyMOL] Incentive PyMOL v1.4 Released

-source project. I will send an update soon when the volume visualization is in the open-source code. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

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