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Re: [PyMOL] PyMOL-users Digest, Vol 69, Issue 12
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From: Troels E. L. <tl...@gm...> - 2012-02-15 12:27:47
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If you need publication citation, I would go for the Cealign ww.pymolwiki.org/index.php/Cealign There is references you can read and understand. :-) See a list of alignment methods and tools http://www.pymolwiki.org/index.php/Align#SEE_ALSO Best T Troels Emtekær Linnet Lyongade 24. 4.mf, 2300 København S Mobil: +45 60210234 2012/2/15 Bachar Cheaib <che...@gm...> > Dear All, > > I am a Pymol's user > > I would like to know how could I find the algorithm publication of three > functions for superimposition of multi-structures? > > 1- fit > 2- align > 3- super > > I would thanks in advance for your reply > > Sincerely > > > > BaCh > > On Wed, Feb 15, 2012 at 11:31 AM, < > pym...@li...> wrote: > >> Send PyMOL-users mailing list submissions to >> pym...@li... >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://lists.sourceforge.net/lists/listinfo/pymol-users >> or, via email, send a message with subject or body 'help' to >> pym...@li... >> >> You can reach the person managing the list at >> pym...@li... >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of PyMOL-users digest..." >> >> >> Today's Topics: >> >> 1. Re: Open Source PyMOL v1.5.0.1 (David Hall) >> 2. Re: solid objects (Jason Vertrees) >> 3. compiling Open Source PyMOL v1.5.0.1 (Thomas Stout) >> 4. 1.5 version runs slow with "large" objects (Vitali Stanevich) >> 5. Re: Open Source PyMOL v1.5.0.1 (?????? ??????) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Tue, 14 Feb 2012 12:03:33 -0500 >> From: David Hall <li...@co...> >> Subject: Re: [PyMOL] Open Source PyMOL v1.5.0.1 >> To: Jason Vertrees <jas...@sc...> >> Cc: pym...@li... >> Message-ID: >> < >> CAP...@ma...> >> Content-Type: text/plain; charset=ISO-8859-1 >> >> On Mon, Feb 13, 2012 at 2:27 PM, Jason Vertrees >> <jas...@sc...> wrote: >> > Greetings, >> > >> > It is my pleasure to announce the release of open source PyMOL >> > v1.5.0.1. The source code has been committed to the open-source >> > repository. It is revision 3976. An svn tag and downloadable bz2 >> > source file were also created. All of this is accessible form the >> > PyMOL project page on SourceForge >> > (http://sourceforge.net/projects/pymol/). >> >> For those of you on openSUSE, I've updated the pymol packages in the >> openSUSE Build Service to this release. You can test this new version >> by visiting >> http://software.opensuse.org/download.html?project=devel:languages:python&package=pymol >> and choosing the appropriate openSUSE release and architecture. >> >> -David >> >> >> >> ------------------------------ >> >> Message: 2 >> Date: Tue, 14 Feb 2012 12:40:02 -0500 >> From: Jason Vertrees <jas...@sc...> >> Subject: Re: [PyMOL] solid objects >> To: Daniel Larsson <la...@xr...> >> Cc: pym...@li... >> Message-ID: >> < >> CAA...@ma...> >> Content-Type: text/plain; charset=ISO-8859-1 >> >> Daniel, >> >> Filling clipped spheres is not yet available. We'll look at adding it. >> >> Cheers, >> >> -- Jason >> >> On Tue, Feb 14, 2012 at 12:00 PM, Daniel Larsson <la...@xr...> >> wrote: >> > Thanks for the quick reply. >> > >> > A closely related issue is that clipped spheres are rendered very >> strangely. It seems they only consists of a half-sphere and if the clipping >> plane intersects the sphere in the front-most half, then you can see >> straight through it. >> > >> > Daniel >> > >> > >> > On Feb 14, 2012, at 17:50 , Jason Vertrees wrote: >> > >> >> Daniel, >> >> >> >> # reset the setting >> >> >> >> set ray_interior_color, default >> >> >> >> # set the setting for each object >> >> >> >> set ray_interior_color, marine, protA >> >> >> >> set ray_interior_color, magenta, protB >> >> >> >> >> >> PyMOL does not support this via the 'draw' command (unless you set >> >> draw_mode, 3, but that's just ray tracing). Please file an RFE and >> >> we'll look into it. >> >> >> >> Cheers, >> >> >> >> -- Jason >> >> >> >> On Tue, Feb 14, 2012 at 11:17 AM, Daniel Larsson < >> la...@xr...> wrote: >> >>> Hi, >> >>> >> >>> Is there a way to render truncated/clipped objects as "dense". I.e. a >> "lid" on clipped objects, such as surfaces or spheres. >> >>> >> >>> Want I want is something similar to the "A sliced image" example in >> the wiki gallery (http://www.pymolwiki.org/index.php/Gallery), but with >> that technique I can only pick one color for all molecules. I would like to >> set "ray_interior_color" different for different molecules or objects. >> Basically, I want the color to be the same on the inside as on the outside. >> It would be great if it would work with the "draw" command as well. >> >>> >> >>> Is it possible with version 1.5? Or is there a chances of having this >> implemented anytime soon? >> >>> >> >>> Daniel >> >>> >> >>> >> >>> >> ------------------------------------------------------------------------------ >> >>> Keep Your Developer Skills Current with LearnDevNow! >> >>> The most comprehensive online learning library for Microsoft >> developers >> >>> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, >> MVC3, >> >>> Metro Style Apps, more. Free future releases when you subscribe now! >> >>> http://p.sf.net/sfu/learndevnow-d2d >> >>> _______________________________________________ >> >>> PyMOL-users mailing list (PyM...@li...) >> >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> >>> Archives: >> http://www.mail-archive.com/pym...@li... >> >> >> >> >> >> >> >> -- >> >> Jason Vertrees, PhD >> >> PyMOL Product Manager >> >> Schr?dinger, LLC >> >> >> >> (e) Jas...@sc... >> >> (o) +1 (603) 374-7120 >> > >> >> >> >> -- >> Jason Vertrees, PhD >> PyMOL Product Manager >> Schr?dinger, LLC >> >> (e) Jas...@sc... >> (o) +1 (603) 374-7120 >> >> >> >> ------------------------------ >> >> Message: 3 >> Date: Tue, 14 Feb 2012 09:32:54 -0800 >> From: "Thomas Stout" <ts...@ex...> >> Subject: [PyMOL] compiling Open Source PyMOL v1.5.0.1 >> To: <pym...@li...> >> Message-ID: >> <C5F...@EX...> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Hi All - >> >> I am trying to compile the open-source code for PyMOL for the first time >> (on CentOS) and running into all sorts of issues. Is there a listing >> somewhere of all the dependencies (and their versions) that I could use as >> a guide to get everything I need all at once, rather than continuing to fix >> compile failures one-at-a-time (which is confusing and frustrating) >> >> Conversely, is there a distro that more-or-less "just works"? I can >> create a virtual machine in which I compile, but I'm only allowed to have >> RHEL or CentOS on my physical machine... >> >> Thanks! >> -Tom >> >> >> >> ________________________________ >> >> From: Jason Vertrees [mailto:jas...@sc...] >> Sent: Mon 2/13/2012 11:27 AM >> To: pym...@li... >> Subject: [PyMOL] Open Source PyMOL v1.5.0.1 >> >> >> >> Greetings, >> >> It is my pleasure to announce the release of open source PyMOL >> v1.5.0.1. The source code has been committed to the open-source >> repository. It is revision 3976. An svn tag and downloadable bz2 >> source file were also created. All of this is accessible form the >> PyMOL project page on SourceForge >> (http://sourceforge.net/projects/pymol/). >> >> Before upgrading PyMOL -- please -- upgrade your video drivers! NVidia >> and AMD/ATI cards are known to work well. But, Intel Mobile and other >> low-end cards might have issues with the new rendering. The majority >> of rendering anomalies are fixed by simply upgrading your video >> drivers. >> >> You should be able to pull and build just like normal. You will need >> Python 2.7. >> >> Some simple testing on my Linux machine shows the following >> improvements in real-time rendering performance for a large protein >> (58,000 atom Gro-EL, PDB 1AON) with the new open-source PyMOL code: >> >> Lines: >> 240% increase (81 FPS to 270 FPS) >> Spheres: >> 864% increase (28 FPS to 270 FPS) >> Sticks: >> 2100% increase (8 FPS to 180 FPS) >> Cartoon: >> 3757% increase (27 to 270 FPS) >> Surface: >> 2600% increase (10 to 270 FPS) >> Mesh: >> 33% (180 FPS to 270 FPS) >> >> Your numbers will be different. This Linux machine has a powerful card >> used for development >> ( >> http://www.amd.com/us/products/workstation/graphics/ati-firepro-3d/v8800/Pages/v8800.aspx >> ). >> It was generously donated by AMD. If you use an AMD/ATI card and PyMOL >> works for you it's because AMD/ATI helped out. You may want to thank >> them. What I've seen is that the more powerful your card the greater >> the _difference_ in speed. That is, low-end cards should see >> improvements in the range of tens to hundreds of percent while more >> powerful cards should register improvements like mine, in the >> thousands of percent for some representations. >> >> To quickly test performance of the new code on your machine just load >> a large structure (eg. 1AON; 3R8O and 3R8T) and quickly >> rotate/translate it. To see the refresh rate, type "set >> show_frame_rate". The refresh rate shows up in the lower right hand >> corner. Compare the frame rate, smoothness, and rendering quality when >> the setting "use_shaders" is turned off and when it's turned on. >> Compare different representations, each time turning on and off the >> "use_shaders" setting. >> >> You can quickly update old PyMOL session files to the new rendering by >> clicking, Settings > Rendering > Modernize after loading the old >> session file. PyMOL will flip all the right settings to update >> rendering. If the new code doesn't render properly, you can revert to >> the old style rendering by typing: >> >> set use_shaders, 0 >> >> set sphere_mode, 0 >> >> >> Please let us know how it goes. >> >> Cheers, >> >> -- Jason, Blaine & the PyMOL Team >> >> -- >> Jason Vertrees, PhD >> PyMOL Product Manager >> Schr?dinger, LLC >> >> (e) Jas...@sc... >> (o) +1 (603) 374-7120 >> >> >> ------------------------------------------------------------------------------ >> Try before you buy = See our experts in action! >> The most comprehensive online learning library for Microsoft developers >> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, >> Metro Style Apps, more. Free future releases when you subscribe now! >> http://p.sf.net/sfu/learndevnow-dev2 >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> >> >> >> This email (including any attachments) may contain material >> that is confidential and privileged and is for the sole use of >> the intended recipient. Any review, reliance or distribution by >> others or forwarding without express permission is strictly >> prohibited. If you are not the intended recipient, please >> contact the sender and delete all copies. >> Exelixis, Inc. reserves the right, to the extent and under >> circumstances permitted by applicable law, to retain, monitor >> and intercept e-mail messages to and from its systems. >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> >> ------------------------------ >> >> Message: 4 >> Date: Tue, 14 Feb 2012 16:27:32 -0600 >> From: Vitali Stanevich <sta...@wi...> >> Subject: [PyMOL] 1.5 version runs slow with "large" objects >> To: pym...@li... >> Message-ID: >> < >> CAE...@ma...> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Hi, >> >> I recently installed a new version of licensed pymol 1.5. It works ok with >> small molecules (<25 kDa). But, unfortunately, I found that after I load >> relatively large molecules (>60 kDa) everything really slows down, >> movements become somewhat abrupt and etc. At the same time, I can open >> this >> molecule with coot, generate bunch of symmetry mates, add maps, but >> everything runs really smooth. How can I make pymol run smooth again >> (version 1.2 worked well before)? >> >> Pymol: PyMOL-v1.5.0-Linux-x86_32-TclTk8.5 (I tried 64-bit with the same >> result) >> OS: Ubuntu 10.10 >> Video card: nVidia GeForce 7150M >> CPU: AMD Turion(tm) 64 X2 TL-62 (2100 MHz, 64 bits) >> >> Thanks, >> Vitali >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> >> ------------------------------ >> >> Message: 5 >> Date: Wed, 15 Feb 2012 13:30:30 +0300 >> From: ?????? ?????? <gon...@gm...> >> Subject: Re: [PyMOL] Open Source PyMOL v1.5.0.1 >> To: pym...@li... >> Message-ID: >> < >> CAC...@ma...> >> Content-Type: text/plain; charset=UTF-8 >> >> Hi all! >> I've just installed a new version of PyMol, but when I select a >> repersentation different to the default, it displays a blank screen >> and returns >> >> unsupported IR in fragment shader 13 >> unsupported IR in fragment shader 13 >> unsupported IR in fragment shader 13 >> unsupported IR in fragment shader 13 >> unsupported IR in fragment shader 13 >> >> I run PyMol n Debian Squeeze x64, I have an integrated video >> >> Detected OpenGL version 2.0 or greater. Shaders available. >> Detected GLSL version 1.20. >> OpenGL graphics engine: >> GL_VENDOR: Tungsten Graphics, Inc >> GL_RENDERER: Mesa DRI Intel(R) G41 GEM 20091221 2009Q4 >> GL_VERSION: 2.1 Mesa 7.7.1 >> >> -- >> >> Andrew Gonchar >> >> >> >> ------------------------------ >> >> >> ------------------------------------------------------------------------------ >> Virtualization & Cloud Management Using Capacity Planning >> Cloud computing makes use of virtualization - but cloud computing >> also focuses on allowing computing to be delivered as a service. >> http://www.accelacomm.com/jaw/sfnl/114/51521223/ >> >> ------------------------------ >> >> _______________________________________________ >> PyMOL-users mailing list >> PyM...@li... >> https://lists.sourceforge.net/lists/listinfo/pymol-users >> >> >> End of PyMOL-users Digest, Vol 69, Issue 12 >> ******************************************* >> > > > > ------------------------------------------------------------------------------ > Virtualization & Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |
