[PyMOL] Error: unknown type
Hello List, Any ideas on why this script keeps failing in the newer PyMOL builds... http://pymolwiki.org/index.php/Zero_residues I keep getting the error message: Error: unknown type: '1hpv' where 1hpv is an actual pdb file/object I am running pymol 1.2b5 rev. 3706 (compiled from svn) on Ubuntu 8.10 Anyone else face a similar issue, or is it just me Thanks! --Shiven -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Color By RMSD -- New Script
Hello List, A new PyMol script for coloring two objects by mutual RMS Deviation is now available on the PyMol wiki: http://pymolwiki.org/index.php/ColorByRMSD Hope some of you will find it useful... Many thanks to Jason Vertrees for help with turning the initial proof-of-principle into useful code!! Best, Shiven Shivender Shandilya, Graduate Student, Schiffer Lab, Dept. of Biochemistry Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01604. -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge ___ 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] figure of buried surface area
Hi Jiamu, Have you looked at VASCo : http://genome.tugraz.at/VASCo/ I have found it to be very useful and very capable. Contact interfaces, electrostatics (with Delphi) and many other features are available. And best of all, it works extremely well with PyMOL. Do read the manual carefully and you should be able to get very high quality surface images with a little tweaking. Best, Shiven On Sat, Aug 8, 2009 at 11:09 PM, Jiamu Dujiam...@gmail.com wrote: Dear Pymol BBSers, I want to generate a figure to show the overlap of two binding epitopes. Both two proteins A and B can interact with protein C, while their binding epitopes on C are overlapped. So I want to generate a figrue as this: the surface of protein C is colored as white, the buried surface area of A on C is colored as red, the buried surface area of B on C is colored as yellow, and the overlapped region is colored as orange. I tried several time, all the figures are not so beautiful. Is there anyone who can perform this well? Thanks and best wishes. -- Jiamu Du, Ph.D. State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 320 Yue-Yang Road Shanghai 200031 P. R. China Tel: +86-21-5492-1117 E-mail: jiam...@gmail.com -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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 -- ~^v^~ the cgull ... -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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] disjoint surfaces
Raluca, Something that helps is: tabbing into edit mode, selecting all vertices (ctrl-a) and removing doubles (Mesh Vertices Remove Doubles). Turning on smooth display also helps. What exactly are you having problems with? In what way are things disjointed ? Best, Shiven On Mon, Dec 21, 2009 at 6:51 AM, Raluca Mihaela ANDREI r.and...@sns.it wrote: Hi, I imported into Blender (a 3D modelling and animation software) a surface created in PyMOL and I realized that there are some disjoint surfaces inside. Is it possible to remove these surfaces in PyMOL? Thank you, Raluca -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-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 -- ~^v^~ the cgull ... -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-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
Re: [PyMOL] disjoint surfaces
Hi Raluca, So I am guessing this something like the surface being in fragments, with small vertices floating within the larger object? Unfortunately there is no easy way to do this from within PyMOL, unless you can separate out the residues/atoms that are contributing the disjointed meshes into new objects and then turn them off before export. Right now the best thing I can think of going into edit mode in Blender and deleting those vertices by hand. :-( Best, Shiven On Mon, Dec 21, 2009 at 12:11 PM, Raluca Mihaela ANDREI r.and...@sns.it wrote: Thank you Shiven, I know how to remove the double vertices in Blender but I would like to remove them directly from PyMOL. By disjoint meshes I mean non-connected meshes, inside my mesh I have some smaller meshes that are non connected to the big mesh. I would like to know how to remove these meshes before saving. Thank you, Raluca On Mon, 21 Dec 2009 11:24:11 -0500 Shiven Shandilya shiven.shandi...@gmail.com wrote: Raluca, Something that helps is: tabbing into edit mode, selecting all vertices (ctrl-a) and removing doubles (Mesh Vertices Remove Doubles). Turning on smooth display also helps. What exactly are you having problems with? In what way are things disjointed ? Best, Shiven On Mon, Dec 21, 2009 at 6:51 AM, Raluca Mihaela ANDREI r.and...@sns.it wrote: Hi, I imported into Blender (a 3D modelling and animation software) a surface created in PyMOL and I realized that there are some disjoint surfaces inside. Is it possible to remove these surfaces in PyMOL? Thank you, Raluca -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-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 -- ~^v^~ the cgull ... -- ~^v^~ the cgull ... -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-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
[PyMOL] PyMOL Blender
Hello List, An initial attempt at a PyMOL + Blender tutorial is now on the pymolwiki: http://pymolwiki.org/index.php/Blender Hope some of you will find it useful. Fellow Blenderheads, crits are welcome. Also, please help improve/add to the tutorial. Best, Shiven Shivender Shandilya, Graduate Student, Schiffer Lab, Dept. of Biochemistry Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01604. -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-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
Re: [PyMOL] PyMOL-users Digest, Vol 45, Issue 10
Hello Sing,
Perhaps going over the basic tutorial will help make things clear:
http://wwwuser.gwdg.de/~dseelig/plugin_tutorial.html
Best,
Shiven
On Fri, Feb 19, 2010 at 1:13 PM, Kin Sing Stephen Lee
s...@chemistry.msu.edu wrote:
Dear all,
Sorry I fixed the prepare_ligand4.py problem. However, when I try to
do the autodock in the plugin, the plugin cannot recognize the
receptor so there is no choice available in the receptor in the
docking page. If I click autogrid or autodock, the program shows no
response. Is there any setting I could check and fix it?
Thank you very much
Sing
On Feb 19, 2010, at 9:33 AM, pymol-users-requ...@lists.sourceforge.net
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Today's Topics:
1. Re: coordinate systems of pymol and povray (Tsjerk Wassenaar)
2. FreeMOL (Jason Vertrees)
3. Re: PyMOL-users Digest, Vol 45, Issue 9 (Kin Sing Stephen Lee)
4. Save movie not working (Kent Rossman)
--
Message: 1
Date: Thu, 18 Feb 2010 21:42:39 +0100
From: Tsjerk Wassenaar tsje...@gmail.com
Subject: Re: [PyMOL] coordinate systems of pymol and povray
To: gabriela.schlau-co...@alumni.brown.edu, pymol-users
pymol-users@lists.sourceforge.net
Message-ID:
8ff898151002181242o50721274q14324f2a14209...@mail.gmail.com
Content-Type: text/plain; charset=iso-8859-1
Hi Gabriela,
If you only want to get the molecule back in view and rotate/translate
it to your liking, you can use commands like:
#declare Protein = union { #include protein.inc }
#declare Center = (min_extent(Protein)+max_extent(Protein))/2;
object { Protein translate -Center }
If you want to preserve the view you had in Pymol, you'll need
something more. For this purpose I wrote a set of POV-Ray macros,
which are attached. For this to work, you have to save the view from
get_view(). If you used the (better ;)) second version of make_pov
from the wiki, the view is already saved in the pov-ray file. Place
the macro file somewhere where POV-Ray can find it, and uncomment the
section in the .pov file starting with Uncomment the following
lines :) Now, if you want to add objects to your scene that you have
defined based on the coordinates in the pdb file, you can use
something like:
// This draws a sphere of radius 1 at the origin of your .pdb
coordinate system
sphere { 0, 1 SET_PYMOL_VIEW( PYMOL_VIEW )) }
For more extensive information, read the first section of the file. If
things are still unclear, feel free to contact me. And if you find
that you've managed to do really cool stuff with it, please let me
know :)
Hope it helps,
Tsjerk
On Wed, Feb 17, 2010 at 5:07 PM, Gabriela Schlau-Cohen
gsad...@hotmail.com wrote:
Hi all,
I am trying to load a pymol graphic into povray and then add on
geometric
objects.? I exported and loaded the molecular model from pymol
successfully
using the make_pov.py script from the wiki. ?I can then copy and
paste that
file into povray to generate the molecules through povray. ?Then,
when I
save the object in pymol to get the molecular coordinates, the
coordinates
are in a different system.
Can someone tell me how to get the molecular coordinates and a
povray file
in the same coordinate system?
Thanks,
Gabriela
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Computational Chemist
Medicinal Chemist
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Message: 2
Date: Thu, 18 Feb 2010 16:36:40 -0500
From: Jason Vertrees jason.vertr...@schrodinger.com
Subject: [PyMOL] FreeMOL
To:
Re: [PyMOL] Pymol and APBS
Hi Jon, Perhaps you could look at VASCo http://genome.tugraz.at/VASCo/ I have found it to work extremely well on Windows and Linux platforms. You not only get electrostatics but also hydrophobic surface coloring, and all without the APBS and Python hassles and headaches. Sorry to be knocking down APBS+PyMOL integration like this, but IMHO VASCo does a stellar job as far as integrating outside programs with PyMOL goes. Good luck! Best, Shiven On Thu, Apr 15, 2010 at 12:01 AM, J. Fleming moloch...@gmail.com wrote: Hi all, I've been trying to get APBS Tools and/or APBSTools2 running for a few weeks now on multiple linux systems (RedHat and Fedora). I've Installed MALOC and APBS Tools. I can start up Pymol through Phenix, load a .pqr generated from a PDB2PQR server, start APBS Tools, set the grid, but when I click on Run APBS I get: ObjectMapLoadDXFile-Error: Unable to open file! If I use the pymol generated PQR option with my .pqr even though it is a PDB2PQR server generated file APBS runs and states X atoms did not have properties assigned and to either remove or fix the atoms. How can I fix them? The problem residues are just regular amino acids; no split confrimations etc. I've also tried editing out the PDBs chain name before converting to the PDB to PQR but that didn't work. Another things I've tried is using APBSTools 2 but it errors as soon as I click set grid with: Error: 2 ... Attribute Error: elec_radius. I really need to get this to work but I have no clue what to try next. Thanks in advance for any thoughts. -Jon -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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 -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ 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 and APBS
Dear Michael, First, let me thank you for your time and effort in providing the community with your contributions. I do sincerely appreciate your hard work and your willingness to share it with us all. Without the contributions of users such as yourself, PyMOL's stature and utility would be far less than what it is now. I have used the APBS plugin in the past, successfully and without problems. And yes, it has been helpful in solving the problem(s) at hand. As for the knocking down, it was more of a comparison with VASCo than a direct criticism of your work. I am no expert at programming PyMOL/python plugins but I have used quite a few over the years. All I speak is from my own user experience when I say that some plugins work better than others. VASCo, in my experience, happens to belong to the better category. Now why the better plugins work the way do may depend on many factors but some that I feel important are listed below (nothing specifically for/against the APBS plugin). I only speculate when I write the following, but in hopes that it may be considered constructive feedback: (1). Whenever possible, farm out the heavy lifting to external executables (apbs, python scripts, black magic shamans etc.)... (2). Clearly ask for all the defaults a user must specify at first run (executable location, temporary directory, other knick-knacks your plugin requires) Do not allow execution to begin unless you are reasonably sure you have everything needed to properly finish the job. (3). And, for heaven's sake, save those user-specified defaults for the rest of posterity in a location (pymolrc, yourpluginrc) that your plugin can always find... never, ever make a user specify such mundane things over and over again... nothing kills the user experience quicker than that. (4). Overwrite result files only if you have to... create a new directory for every new run (and clearly display the location)... Remember, (storage) space is cheap and (a user's) time is expensive, respect that. (5). If possible, give the users a clear indication of the status of the back-end job doing the heavy lifting... (6). Once you are done running the back-end job(s), prompt the user immediately and (if agreed) automatically load the results. (7). If your back-end job fails, parse the error in your plugin and inform the user where in the entire process the error occurred, why it may have occurred and what the user should do to prevent this error from occurring again. If it is an error your plugin does not understand let the user know, clearly and loudly. If an error log file, hopefully text, was written, specify its location (full path) in your error prompts. Prefrably, display that error file in the system %editor% so that the user does not have to go hunting for it. ...and I'll leave it at that... ;-) I welcome your feedback and views of other community members on this. Thank you! With best regards, Shiven P.S. Apologies again if my criticism hit a personal note. Like everyone else writing to the list and answering questions, my aim was to help a fellow user get that job done. --- On Thu, Apr 15, 2010 at 12:00 PM, Michael Lerner mgler...@gmail.com wrote: On Thu, Apr 15, 2010 at 10:30 AM, Shiven Shandilya shiven.shandi...@gmail.com wrote: Sorry to be knocking down APBS+PyMOL integration like this, but IMHO VASCo does a stellar job as far as integrating outside programs with PyMOL goes. I initially wrote the PyMOL/APBS plugin for my own use and I now maintain/develop it as a community resource in my limited free time. Despite this, several hundred users (at least) have found it quite helpful in their research, and I've included many newer features based on their feedback. The plugin is certainly not perfect, and I don't mind people knocking it down, but I appreciate it when that knocking down comes with constructive feedback. Additionally, unlike VASCo, the PyMOL/APBS/PDB2PQR toolchain is provided as completely free and open source suite of programs. For many reasons, I believe that free and open source software is vital to to good science. I would strongly urge users to consider such issues before settling on a suite of software products, especially when you're already working with programs like PyMOL and APBS. Cheers, -Michael Good luck! Best, Shiven On Thu, Apr 15, 2010 at 12:01 AM, J. Fleming moloch...@gmail.com wrote: Hi all, I've been trying to get APBS Tools and/or APBSTools2 running for a few weeks now on multiple linux systems (RedHat and Fedora). I've Installed MALOC and APBS Tools. I can start up Pymol through Phenix, load a .pqr generated from a PDB2PQR server, start APBS Tools, set the grid, but when I click on Run APBS I get: ObjectMapLoadDXFile-Error: Unable to open file! If I use the pymol generated PQR option with my .pqr even though it is a PDB2PQR server generated file APBS runs and states X atoms did not have properties
Re: [PyMOL] for evaluation only
hi victor, if you are on windows and need the latest pymol version, please take a look at christoph's pymol builds (thanks christoph!): http://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol best, shiven On Thu, Apr 29, 2010 at 6:32 PM, Nathaniel Echols nathaniel.ech...@gmail.com wrote: On Thu, Apr 29, 2010 at 3:03 PM, victor kenyon vicken...@gmail.comwrote: i am an academic using pymol and the new build places a for evaluation only graphic on top of the rendered structure. not very helpful for presentations, publications and the like. how do i circumvent this without using chimera to generate my images for pubs. Use the open-source version, I would be very surprised if that overlays anything. Or download one of the builds of version 0.99, which is missing some nifty features but still more than adequate for publication graphics as long as you don't need to show anisotropic Bs. http://www.pymol.org/rel/099/ -- ___ 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 -- ___ 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 MacPros and PyMOL - Radeon only?
Dear Jason, I strongly support Adam's suggestion that the PyMOL website and the Wiki display a clear warning to people planning on using PyMOL with ATI/AMD graphics card. I have had numerous issues with ATI graphics cards + PyMOL over the years and nVidia is unquestionably the better choice when it comes to running professional OpenGL intensive software (like PyMOL and Blender) on Linux or Mac OS. Best regards, Shiven On Wed, Sep 29, 2010 at 11:07 AM, H. Adam Steinberg a...@steinbergs.uswrote: Hi All, I bought a new MacPro and now get this message when I open PyMOL: Note: Radeon HD cards tend not to run PyMOL well. Use nVidia or Intel instead, if OpenGL glitches occur. Attempting to compensate for known issues... So the new Macs only come with Radeon video cards... there are no other choices with a Mac. This means the MacPros no are no longer a good platform for running PyMOL? I just tossed $3K down the drain? I tried to render the surface of 3L5Q and PyMOL just crashes (6GB RAM). I tried to render just the top half and it still crashes. What are the OpenGL glitches that occur, are they documented somewhere? What does PyMOL do to compensate? I checked the PyMOL web site and under the supported operating systems and hardware there is no mention of the lack of Radeon support/poor Radeon performance. Maybe that should be added because I wouldn't have bought this new Mac if I would have known this. Is there anything I can do to make this new machine work? I see a 64-bit version is on the horizon, will this address Radeon performance or should I go back to my old MacPro with it's nVidia 7300 video cards? H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/729-5944 -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-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 -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-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
[PyMOL] GLSL Shaders
Hi fellow PyMOLers, Thought some of you may be interested in this: http://pymolwiki.org/index.php/GLSL_Shaders Test, improve, share ... :-) Cheers!! -- Shiven -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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] Real-time black and white view possible?
Hi Martin, I guess you can do this using modified GLSL shaders … Two examples I posted on the PyMOL wiki a while ago: http://www.pymolwiki.org:/index.php/GLSL_Shaders Best, Shiven On Jun 12, 2014, at 5:10 PM, Martin Hediger ma@bluewin.ch wrote: Hi all I wonder if it's possible to have something like ray_trace_mode, 2 (i.e. black and white with outlines) but in the interactive view. Also, is it possible to have part of the structure in color (say some active site amino acids) and the rest in black and white? Thanks for help Martin -- HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions Find What Matters Most in Your Big Data with HPCC Systems Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. Leverages Graph Analysis for Fast Processing Easy Data Exploration http://p.sf.net/sfu/hpccsystems ___ 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 -- HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions Find What Matters Most in Your Big Data with HPCC Systems Open Source. Fast. Scalable. Simple. Ideal for Dirty Data. Leverages Graph Analysis for Fast Processing Easy Data Exploration http://p.sf.net/sfu/hpccsystems___ 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] Cel shading in PyMOL
Hi Jacob, If you have the right mix of display drivers and Pymol version, you can try GLSL shaders. http://www.pymolwiki.org/index.php/GLSL_Shaders Unfortunately, it does not work flawlessly across platforms and I have not invested any more time figuring it out because the shader system in Pymol still appears to be a work-in-progress. Best, Shiven Shivender Shandilya, Senior Post-Doc, Schiffer Lab, Dept. of Biochemistry Molecular Pharmacology, University of Massachusetts Medical School. Worcester, MA 01605. On Jan 13, 2015, at 9:39 AM, Thomas Holder thomas.hol...@schrodinger.com wrote: Hi Jacob Osvaldo, the ray tracer has cel shading as ray trace mode 3. PyMOL set ray_trace_mode, 3 PyMOL ray See also: http://pymolwiki.org/index.php/Ray#Modes Hope that helps. Cheers, Thomas On 13 Jan 2015, at 08:07, Osvaldo Martin aloctavo...@gmail.com wrote: Hi Jacob, What about the Goodsell-like representation from here? Cheers, Osvaldo. On Tue, Jan 13, 2015 at 7:29 AM, Jacob Lewis jl...@uowmail.edu.au wrote: Hi all, Has anyone figured out a good way to do Cel shading in pymol? Or even the sort of variables to play with? Cheers, Jacob -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high performing configs, both with 100TB of bandwidth. Higher redundancy.Lower latency.Increased capacity.Completely compliant. http://p.sf.net/sfu/gigenet ___ 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 -- New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high performing configs, both with 100TB of bandwidth. Higher redundancy.Lower latency.Increased capacity.Completely compliant. http://p.sf.net/sfu/gigenet ___ 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
