[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] 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

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] 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] select single state with the mouse?

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Re: [PyMOL] label_size in pymol 1.3 on Mac

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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] 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

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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] 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] 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] 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

[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] 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

Re: [PyMOL] maximum sphere-quality ?

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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] 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] OpenDX files from opendx.org

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Re: [PyMOL] OpenDX files from opendx.org

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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] 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] 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] [PYMOL] error with pair fitting

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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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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

[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] about script

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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] 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] 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] Updates

where we all present from. I'll announce this when it's ready. Cheers, -- Jason On Thu, Aug 19, 2010 at 3:30 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Greetings, I'd like to pass on a few notes to let you know some of what's going on in the world of PyMOL. First, the PyMOL

Re: [PyMOL] Updates

/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] 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] Newbie question : what command to use for changing color of inside of helix

-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 -- This SF.net email

Re: [PyMOL] Fetch Command

On Thu, Aug 5, 2010 at 5:47 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Greetings, Fetch has been fixed and the code checked into SVN with some other changes.  I'm calling this v1.3r1 because 'fetch' is so integral to PyMOL. For Incentive PyMOL subscribers, the new v1.3r1

Re: [PyMOL] Fetch Command

, -- Jason On Wed, Aug 4, 2010 at 12:33 AM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Daphna, The PDB servers underwent some reorganization and moved the files on us!  I will post a fix for this by tomorrow night. Thanks! -- Jason On Sun, Aug 1, 2010 at 3:44 AM, Daphna Meroz

Re: [PyMOL] obtaining of protein-dna complex by pymol

/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 -- The Palm

Re: [PyMOL] Select a residue within a state

/ ___ 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

Re: [PyMOL] draw vector

-com-first ___ 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] get coordinates

: 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] loading plugins from user home directories

-- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone

Re: [PyMOL] print out distance

/sfu/sprint-com-first ___ 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

Re: [PyMOL] PyMOL Help

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 (o) +1

Re: [PyMOL] Question on how to identify residue number on protein surface

) 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 does PyMol add hydrogen atoms?

-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 -- This SF.net email is sponsored by Sprint What will you do

Re: [PyMOL] How does PyMol add hydrogen atoms?

, and then h_adding them back. Remove/add them a few times to the lone carbon to see the effect of the randomized placement.) Cheers, -- Jason On Thu, Jul 1, 2010 at 10:40 AM, Jason Vertrees jason.vertr...@schrodinger.com wrote: João, Thanks for being patient on this.  I just moved to a big

Re: [PyMOL] DSS

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 (o) +1 (603

Re: [PyMOL] Question about ray

___ 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] Segmentation fault r3910 on linux with Python 2.5/2.6 and tcl/tk 8.5.5 and 8.6b1.

-- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE

Re: [PyMOL] Alignments in Pymol

/thinkgeek-promo ___ 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] Possible bug in set cartoon_cylindrical_helices

of ubuntu builds were compiled by me , but everything is working just fine , other than this property setting as far as I know. Are your or anyone else seeing this  on their machine. Thanks Hari On Thu, Jun 17, 2010 at 7:04 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi

Re: [PyMOL] Possible bug in set cartoon_cylindrical_helices

/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 minimizing

-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 -- ThinkGeek

[PyMOL] PyMOL v1.3

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, moving forward. Cheers, -- Jason -- Jason Vertrees, PhD

Re: [PyMOL] help with moving objects separately

@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] label bond type and molecule name

/phachem/lemcke/mitarbeiter.html -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad

Re: [PyMOL] pymol dies when minimizing

://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 minimizing

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 and PyMOL are you using? Cheers, -- Jason On Wed, Jun 2, 2010 at 10:52 AM

Re: [PyMOL] Problem with coloring of sticks

will either find a machine or go buy an ATI card for my Linux box and let you know the results. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120

Re: [PyMOL] Problem with coloring of sticks

, -- Jason On Fri, May 28, 2010 at 11:37 AM, Jason Vertrees jason.vertr...@schrodinger.com 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's how

Re: [PyMOL] PyMOL Print Limitation

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] Problem with display on Intel graphics card

://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] some help

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 -- Jason Vertrees, PhD PyMOL

Re: [PyMOL] Mutagenesis tool failing on rotameric amino acids

@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] dihedral

-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] Moveable Camera

) 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 draw the line in images

-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] segmentation fault in 1.2r3pre 64-bit on linux

-- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- ___ PyMOL-users mailing list (PyMOL-users

Re: [PyMOL] taking snapshots from a 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

Re: [PyMOL] label

-- ___ 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

Re: [PyMOL] Add a small molecule to a protein

(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] How to get the coordinates of the center of a group of atoms?

@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] Fit command for 24 vs 18 amino acids

) 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] Load without bonding

@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- ___ PyMOL-users mailing list (PyMOL-users

Re: [PyMOL] Label size in different scenes

scene? Thank you. Vitaly - Original Message - From: Jason Vertrees jason.vertr...@schrodinger.com Date: Tuesday, April 13, 2010 4:47 pm Subject: Re: [PyMOL] Label size in different scenes To: Vitaly Vostrikov vvos...@uark.edu Cc: pymol-users@lists.sourceforge.net Vitaly, Great

Re: [PyMOL] attaching phosphate

-- ___ 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

Re: [PyMOL] Label size in different scenes

. 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 - Original Message - From: Jason Vertrees

Re: [PyMOL] Symmetry Expansion

= 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: PyMOLers, A bug was brought to my attention to day in the symmetry expansion command (try it on 2bop).  If you have issues

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