Re: [PyMOL] Help: Linux active Stereo on screen seems OK with flickering in pymol window, but glasses dont seem to be shuttering

tion "Screen" >     Identifier     "Screen[1]" >     Device         "Device0" >     Monitor        "Monitor[1]" >     DefaultDepth    24 >     Option         "Stereo" "10" >     SubSection     "Display" >         Viewport    0 0 >         Depth    

Re: [PyMOL] save new coordinate

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

Re: [PyMOL] save new coordinate

strengths and weaknesses of these DLP solutions. > http://www.accelacomm.com/jaw/sfnl/114/51385063/ > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.

Re: [PyMOL] Directional chevrons in mainchain ribbon representation

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 > -- Jason Vertrees, PhD PyMOL Product Manager Schrodi

Re: [PyMOL] Sequence Analysis Methodology

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 -- Jason Vertrees, PhD

Re: [PyMOL] Superimposing 2 or more Selections PyMOL GUI

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

Re: [PyMOL] Superimposing 2 or more Selections PyMOL GUI

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

Re: [PyMOL] Selecting residues for mutagenesis

nfo 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] Render transparent cartoons

e.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 dcd trajectory in Pymol

ense. And common sense. > http://p.sf.net/sfu/splunk-d2d-c2 > ___ > 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.n

Re: [PyMOL] PYMOL MOVIE

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

[PyMOL] Off-topic: Openings at Schrödinger

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 (

Re: [PyMOL] color surface by bfactor discrepancy between range reported on shell and range used

re. Splunk takes this data and makes > sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-d2d-c2 > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.ma

Re: [PyMOL] movie.produce

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] Performance Tip: Texture Fonts

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

Re: [PyMOL] Retention of ANISO Records was How to merge molecules in Pymol?

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

Re: [PyMOL] Retention of ANISO Records was How to merge molecules in Pymol?

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

Re: [PyMOL] How to merge molecules in 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

Re: [PyMOL] How to avoid the message "ObjectMoleculeGuessValences" in pymol1.4.1?

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

Re: [PyMOL] How to avoid the message "ObjectMoleculeGuessValences" in pymol1.4.1?

s compliant with Accessibility Checking. > http://p.sf.net/sfu/ephox-dev2dev > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.ma

Re: [PyMOL] Need help with RMSD ( I am a member of this community now , yayy)

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

Re: [PyMOL] Need help with RMSD ( I am a member of this community now , yayy)

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

Re: [PyMOL] Problems with Pymol 1.4.1 under Ubuntu 11.04

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 &

Re: [PyMOL] problems cloring sticks

. > > Cheers, > ariel > > > On Thu, 2011-06-09 at 10:16 -0500, Jason Vertrees wrote: >> PyMOL to last night's version > > > Centro de Inmu

Re: [PyMOL] Problems with Pymol 1.4.1 under Ubuntu 11.04

and ensure content is compliant with Accessibility Checking. > http://p.sf.net/sfu/ephox-dev2dev > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-a

Re: [PyMOL] problems cloring sticks

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 >> >> >> >> >> >> >>

Re: [PyMOL] Making dashed line transparent

essibility Checking. > http://p.sf.net/sfu/ephox-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

Re: [PyMOL] Problem with distutils build 3951 on Ubuntu Lucid 10.04 : X Error of failed request: BadRequest

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 --

Re: [PyMOL] problems cloring sticks

> http://p.sf.net/sfu/quest-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.source

Re: [PyMOL] problems cloring sticks

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

Re: [PyMOL] problems cloring sticks

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 > -- Ja

Re: [PyMOL] Mutagenesis for DNA

_ > 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.sourc

[PyMOL] JyMOL v1.1 Released

(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

Re: [PyMOL] change angle

ications - including clusters. > http://p.sf.net/sfu/intel-dev2devmay > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.ma

[PyMOL] Schrӧdinger Offers a Second PyMOL Open-Source Fellowship Position

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 (o) +1 (603) 374

Re: [PyMOL] animating 2 sets of pdbs

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

Re: [PyMOL] How to construct a view showing only a single contiguous cavity

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

Re: [PyMOL] mdo command

> ___ > 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@lis

Re: [PyMOL] store/recall stick_transparency in scene?

> 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 > --

Re: [PyMOL] New 16 char length restriction of object names in menu?

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

Re: [PyMOL] New 16 char length restriction of object names in menu?

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

Re: [PyMOL] pymol 1.4.1 (incentive), segfault upon "help->about"

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

Re: [PyMOL] New 16 char length restriction of object names in menu?

_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

Re: [PyMOL] change atom coordiates?

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

Re: [PyMOL] movie: interpolate between different states

; http://p.sf.net/sfu/intel-dev2devmay > ___ > 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.sourcefo

Re: [PyMOL] nucleic acid (one or two letter) residue names

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

Re: [PyMOL] change transparency for only a selection

s > 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 -- What Every C/C++ and Fort

Re: [PyMOL] nucleic acid (one or two letter) residue names

to help Windows* and Linux* C/C++ and Fortran > developers boost performance applications - including clusters. > http://p.sf.net/sfu/intel-dev2devmay > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https:

Re: [PyMOL] set pdb_reformat_names_mode

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 -- Achie

Re: [PyMOL] Set pdb_echo_tags, HEADER

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

Re: [PyMOL] Error in Fetch command

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

Re: [PyMOL] installation from cvs fails

.net/sfu/intel-dev2devmay > ___ > 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/py

Re: [PyMOL] Pymol 1.4.1 does not load PDBs from command line anymore

> 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 S

Re: [PyMOL] Downloading the biological assembly from the PDB

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 > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (6

Re: [PyMOL] Virtual machines and graphics cards

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

[PyMOL] PyMOL v1.4.1 Released

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 ---

Re: [PyMOL] How to script preset actions

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

Re: [PyMOL] Difference between open source and licensed versions?

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

Re: [PyMOL] hardware for quad-buffered stereo

cquisition cost and overall TCO of any competing solution. > http://p.sf.net/sfu/whatsupgold-sd > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >

Re: [PyMOL] Editing map visualisation

___ > 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.sourcefor

Re: [PyMOL] Hiding individual dash/distance objects within a merged-dash object

west initial > acquisition cost and overall TCO of any competing solution. > http://p.sf.net/sfu/whatsupgold-sd > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-a

Re: [PyMOL] PDB: How to extract

OL-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 V

Re: [PyMOL] Visualizing protein-ligand complexes of metalloproteins

L-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...@schro

Re: [PyMOL] suface display protein-protein interactions...residues getting bleached.

ore about boosting > the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http

Re: [PyMOL] pymol

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

Re: [PyMOL] Problems with set solvent_radius

mware-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

Re: [PyMOL] pymol

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

[PyMOL] Volumes video

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

Re: [PyMOL] EDS maps switched upon fetch?

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

Re: [PyMOL] How to color in a different way different helix types?

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

Re: [PyMOL] global illumination, volume representation and ipython

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

Re: [PyMOL] segmentation fault pymol 1.4 rev 3938

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

Re: [PyMOL] global illumination, volume representation and ipython

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

Re: [PyMOL] segmentation fault pymol 1.4 rev 3938

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 > > --

Re: [PyMOL] center of mass

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,

Re: [PyMOL] center of mass

, 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

Re: [PyMOL] Convert pml script to Pymol Python script

artphone on the nation's most reliable network. > And it wants your games. > http://p.sf.net/sfu/verizon-sfdev > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.ma

Re: [PyMOL] global illumination, volume representation and ipython

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

Re: [PyMOL] distances between rotated molecules

nfo 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 1.4 OpenGL issue with openSuSE 11.3 / 11.4

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

Re: [PyMOL] How to color in a different way different helix types?

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

Re: [PyMOL] How to color in a different way different helix types?

__ > 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 Vertre

Re: [PyMOL] funny transparent stick rendering when use_shaders = 1

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 -- Jason Vertrees,

Re: [PyMOL] PyMOL Project Updates & Open Source PyMOL v1.4b1

; 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

Re: [PyMOL] PyMOL Project Updates & Open Source PyMOL v1.4b1

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] Ligand surface

t; ___ > 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.

[PyMOL] PyMOL Project Updates & Open Source PyMOL v1.4b1

on is 12000+ lines long, so there's quite a few changes. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Create and publish w

Re: [PyMOL] Newline character in labels

(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 > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https:

Re: [PyMOL] Pymol 1.4 OpenGL issue with openSuSE 11.3 / 11.4

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

Re: [PyMOL] MacPyMOL 1.4 on OS X 10.5.8 load command error

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 > ___ > PyMOL-users mailing list (P

Re: [PyMOL] How to get pymol 1.4

ce it when I finish and it's posted. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Enable your software for Intel(R) Act

Re: [PyMOL] Pymol no longer fetches from pdb

Great, thanks, David. Just ensuring the problems been isolated. Cheers, -- Jason On Tue, Mar 22, 2011 at 9:53 AM, David Hall wrote: > Resolves fine for me. > > -David > > On Mar 22, 2011, at 12:30 PM, Jason Vertrees > wrote: > >> Hi Roger, >> >>

Re: [PyMOL] Pymol no longer fetches from pdb

anyone else having this error or just Roger? Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Enable your software for Intel(R)

Re: [PyMOL] Pymol no longer fetches from pdb

able to download. PyMOL v1.3 will most likely not work, because the PDB changed their PDB paths last year. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ---

[PyMOL] PyMOL at West Coast Meetings

heers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Enable your software for Intel(R) Active Management Technology to meet the gr

Re: [PyMOL] Ubuntu 10.04 and pymol 1.4

pymol > 1.3.1 in the same VM (other than the missing binary graphics driver). This was due to a mistake I made before posting the release builds. It's now fixed and the downloads are updated. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.ver

Re: [PyMOL] Pymol 1.4 OpenGL issue with Ubuntu 9.04

it's broken? The software renderer you're using is on the openGL 1.5 standard--which is quite old and possibly buggy. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1

[PyMOL] Incentive PyMOL v1.4 Released

g them to the open-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)

Re: [PyMOL] get all user defined selections?

ame # end block python end 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 g

Re: [PyMOL] ray_trace_mode, 1 - white outline

.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.v

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