[PyMOL] moving objects
Hi Pymol Users, I have 2 objects (objects 1 and 2) and I would like to re-orient object 1 so that the distance from either end of object 1 becomes the same to object 2 (see image). Is there a way to achieve this in PyMol? I have tried using the mouse in edit mode and I have tried using the rotate/translate commands. Neither method can move object 1 without altering the position of the lower end of object 1. Regards, Marcelo -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y___ 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] (no subject)
Hi Leila, No problem, here is the content of the site. If you need the reference manager files (BibTex or EndNote files), I am happy to email them to you as well. Cheers, Marcelo Citation Format Please cite PyMOL, AxPyMOL and JyMOL as shown below. Be sure to edit the version number in accordance with your usage. If you use BibTex or EndNote, download the handy citation files below. PyMOL The PyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC. JyMOL The JyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC. AxPyMOL The AxPyMOL Molecular Graphics Plugin for PowerPoint, Version 1.7.4 Schrödinger, LLC. BibTex Files PyMOL BibTex Entries [.bib] http://pymol.org/sites/default/files/pymol.bib For help with BibTex see: http://en.wikipedia.org/wiki/BibTeX http://en.wikipedia.org/wiki/BibTeX http://www.bibtex.org/Using/ http://www.bibtex.org/Using/ EndNote Files PyMOL EndNote Entries [.xml] http://pymol.org/sites/default/files/pymol_0.xml (right-click and save this file to your computer; most browsers dont' render XML nicely) On Apr 19, 2015, at 12:08 AM, leila karami karami.lei...@gmail.com wrote: Dear Marcelo Thanks for your quick answer. Unfortunately, I can't open the link (https://www.pymol.org/citing https://www.pymol.org/citing) you suggested me. Thanks in advance. -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF___ 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 -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF___ 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] (no subject)
Hi Leila, Take a look at the link below: https://www.pymol.org/citing https://www.pymol.org/citing Cheers, Marcelo On Apr 18, 2015, at 11:55 PM, leila karami karami.lei...@gmail.com wrote: Dear all How to cite pymol in my paper? Thanks. -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF___ 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 -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF___ 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] creating a virus capsid using supercell.py
Hi Ezra, Capsid was a typo, I ment to say the matrix of the virus. The pdb1 file is a trimer of the protein. I now how the trimeric form of the protein interacts to form the matrix and was hoping that a script could help me build the complete matrix sphere. Marcelo On Apr 17, 2015, at 4:53 AM, Ezra Peisach ezra.peisach+py...@rcsb.org wrote: The full biological unit should be available in biological assembly file. Have you tried using the fetch command? i.e.: fetch 1avd, type=pdb1 set all_states, on The first retrieves BA #1, the all_states shows the models. If there is something wrong with the assembly file - then by all means contact the PDB... Ezra On Fri, Apr 17, 2015 at 1:34 AM, Marcelo Marcet mmar...@nait.ca mailto:mmar...@nait.ca wrote: Hi Everyone, I have been trying to build a virus capsid using pymol. The biological unit for the complete structure is not available. :( My first attempt at getting this done was by using the “rotate” and “translate” commands. Unfortunately, these commands can only move objects either relative to the main axes or the viewer’s position (not relative to existing objects), thus I had to calculate the rotation angles and translation angle/distances for every single object (not practical). I have been advised to try the ‘supercell.py’ script. Is supercell the right tool for the job? Any advice would be much appreciated. Marcelo -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net mailto:PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF___ 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] creating a virus capsid using supercell.py
Hi Everyone, I have been trying to build a virus capsid using pymol. The biological unit for the complete structure is not available. :( My first attempt at getting this done was by using the “rotate” and “translate” commands. Unfortunately, these commands can only move objects either relative to the main axes or the viewer’s position (not relative to existing objects), thus I had to calculate the rotation angles and translation angle/distances for every single object (not practical). I have been advised to try the ‘supercell.py’ script. Is supercell the right tool for the job? Any advice would be much appreciated. Marcelo -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF ___ 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] making liposomes
Hi Everyone, Does anyone know of a way to generate/make liposome structures that can then be viewed in PyMol? Thanks, Marcelo -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=164703151iu=/4140/ostg.clktrk ___ 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] implementing focal_blur in movies
Dear PyMol community, I would like to create a movie with two objects where neither the camera nor the objects move. Instead, I would like to focus on the object closest to me while blurring out the background object and gradually bring the background into focus and blurring the closer object. Other than saving one frame at a time and compiling the movie later, could a script be the solution here? Your help is most appreciated! Regards, Marcelo PyMol ver. 1.7.2.1 (Incentive) Mac OS 10.9.5 -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311iu=/4140/ostg.clktrk ___ 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 3D movies
Hi Christian,
Thanks so much for your email. I am looking forward to testing your approach
and scripts soon. Again, thanks for the detailed explanations and the scripts.
Best regards,
Marcelo
On Aug 25, 2014, at 6:02 PM, Christian Becke christian.be...@fu-berlin.de
wrote:
Hi,
Am 25.08.2014 21:44, schrieb Marcelo Marcet:
Thank you for taking the time to reply to this question and for
offering your help. I am also interested in quad-buffered stereo play
back.
Sorry, maybe I wasn't clear in my first mail: I don't have experience
with quad-buffered stereo playback. All I have done is preparing 3D
stereo movie files using PyMOL and ffmpeg[1] which I can play on a 3D TV
(using a side-by-side stereo movie file and polarization glasses) or on a
regular beamer (anaglyph red/cyan movie with red/cyan glasses).
I expect that one could play these (or similarly prepared) movie files with a
movie player that makes use of OpenGL quad-buffered 3D capabilities of a
graphics card - but I never tried this myself.
AFAIU, there is no such thing as a quad-buffered movie file - it's just the
movie player that plays back a 3D stereo movie file using OpenGL
quad-buffered stereo on hardware that supports it. A player that might work
is bino[2], but, as I said, I never got around to try it out.
Would you be able to provide us with a bit more methodology information?
It sounds like you have a script that helps you save the side-by-side
images and later you use a software called ffmpeg to render the movie.
Is this correct?
Yes, this is correct. Here is how I did it:
1) Prepare a movie in PyMOL
2) run the attached python script (run /path/to/mpng_3d.sh). This will add
a new command to pymol: mpng_3d
It works similar to the mpng command, but saves 2 images for each movie
frame, one for the left and one for the right eye. If ray traced frames are
desired, do set ray_trace_frames, 1. You can also play around with the
stereo_angle setting (e.g. set stereo_angle, 3). This defines the
difference in viewing angle of the images for the left and right eye.
The mpng_3d command takes the following options:
mpng_3d prefix, width, height, [start=1], [end=-1]
render stereoscopic frames sized width x height pixels.
Files will be named prefix_%04d.png.
Render frames start to end (default: all frames)
Example: mpng_3d my_movie, 1920, 1080 will write png files called
my_movie_0001.png, my_movie_0002.png, ...
If ray_trace_frames is set (recommended), the images will be ray traced and
have a size of 1920x1080 pixels (i.e. full HD).
3) Use ffmpeg to encode a movie from the individual frames saved with mpng_3d:
For h.264 encoding:
ffmpeg -i my_movie_%04d.png \
-an \
-r 30 -aspect 1.78 -pix_fmt yuv420p \
-c:v libx264 -tune animation \
-vf stereo3d=al:sbsl \
-profile:v baseline -level 3.0 -refs 4 -qmin 4 \
my_movie.mp4
For WMV encoding:
ffmpeg -i my_movie_%04d.png \
-an \
-r 30 -aspect ${aspect} \
-vf stereo3d=al:sbsl \
-q:v 2 -c:v msmpeg4v3 \
my_movie.wmv
These are the commands I used on linux. Similar ffmpeg commands should also
work on Windows or OS X. Video quality and file size were reasonable with the
above settings, and the files played all right on almost all video players I
tested (the wmv files work with all versions of PowerPoint I tested, the
h.264 movies do not work with WinXP).
If you change the size of the images, also change the -aspect parameter in
the ffmpeg commands accordingly (for 1920x1080 pixel images:
aspect=1920/1080=1.78).
The above commands produce side-by-side stereo movies, i.e. the images for
the left and right eye are shown next to each other in each frame
of the movie. Check the ffmpeg docs[3] for other output options.
For some movie players (e.g. the one on my LG 3D TV) it might be necessary to
scale the pymol-rendered frames to half-width before encoding them to a
side-by-side stereo movie with ffmpeg. This can be done e.g. with the
convert command from the imagmagick[4] suite.
I hope this helps!
Christian
[1] http://ffmpeg.org
[2] http://bino3d.org
[3] http://ffmpeg.org/ffmpeg-filters.html#stereo3d
[4] http://www.imagemagick.org
--
Christian Becke
Freie Universität Berlin
Fachbereich Biologie, Chemie, Pharmazie
Institut für Chemie und Biochemie
AG Strukturbiochemie
Takustr. 6
14195 Berlin
Germany
Phone: +49 (0)30 838-57344
Fax: +49 (0)30 838-56981
E-mail: christian.be...@fu-berlin.de
mpng_3d.py--
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Re: [PyMOL] pymol 3D movies
Hi Christian, Thank you for taking the time to reply to this question and for offering your help. I am also interested in quad-buffered stereo play back. Would you be able to provide us with a bit more methodology information? It sounds like you have a script that helps you save the side-by-side images and later you use a software called ffmpeg to render the movie. Is this correct? Thanks so much, Marcelo On Aug 25, 2014, at 10:38 AM, Christian Becke christian.be...@fu-berlin.demailto:christian.be...@fu-berlin.de wrote: Hi Xevi, I have prepared side-by-side 3D movies that I could play on a 3D TV using pymol and ffmpeg. I ray-traced the movie, one frame for each eye, and used ffmpeg to compile the resulting png files to an h264 movie file. With side-by-side stereo, you of course lose resolution, but ffmpeg can also do alternating-frames stereo with no loss in resolution. If you find a movie player that renders such a movie using your quad-buffer capable hardware, you should be all set. Let me know if you want to try this, I would be happy to share my scripts. Christian Am Montag, den 25.08.2014, 09:35 -0400 schrieb Xavier Fradera: Hi, I am looking into making a quad-buffered stereo 3D movie. Is this possible with mpeg or any other format ? I know I could just play the movie from pymol, but would like to be able to save as mpeg with x-ray traced images for higher quality. Xevi -- Xavier Fradera -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.netmailto: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 -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.netmailto: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 -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Nvision stereo video export
Hi Everyone, If one has a functional Nvidia Nvision 3D setup, can you export a video that retains 3D? How is this done? Thanks in advance! Marcelo -- Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft ___ 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 wrl output
Hi Bob, Before you save your file from pymol try increasing the quality to max, then save as VRML. This increases the number of polygons in the file and after exporting from meshlab the final molecule will look a lot smoother. Cheers, Marcelo On May 2, 2014, at 2:15 PM, Grateful Frog gratefulf...@gmail.com wrote: Hi all, I'm new to this list and to this tool. I have encountered a problem with exporting as wrl in pylolk 1.7 that I compiled on my Ubuntu 12.04 platform. I load a PDB file and it displays fine. I then type the command show surface and this works fine, too. I then save image as VRML 2, and write the file to disk. This file can be visualized fine in MeshLab. However, it cannot be 3D printed at Shapeways. The error message does not say what is wrong. The work-around that I have found is to open the wrl file, generated by Pymol, in Meshlab and re-save another copy as wrl, but generated by Meshlab. This new file can be 3D printed at Shapeways. However, the look of the surface is not as nice when it comes out of Meshlab, as it is in Pymol... Any thoughts would be great! Thanks, Bob -- Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available. Simple to use. Nothing to install. Get started now for free. http://p.sf.net/sfu/SauceLabs___ 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 -- Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available. Simple to use. Nothing to install. Get started now for free. http://p.sf.net/sfu/SauceLabs ___ 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 system ideal hardware
Hi PyMol community, Is there such thing as a site comparing hardware performance for PyMol? What would be the ideal system/OS to run PyMol? Best regards to all, Marcelo -- Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available. Simple to use. Nothing to install. Get started now for free. http://p.sf.net/sfu/SauceLabs ___ 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 1.3 and 1.6 compatability?
Hi Lapolla, Yes, you can keep your pymol v1.3 and v1.6. Just make sure that they have different names. You will also be able to open your old pse files. Cheers, Marcelo On Jan 14, 2014, at 12:18 PM, Lapolla, Suzanne M (HSC) suzanne-lapo...@ouhsc.edu wrote: I would like to upgrade to Pymol 1.6 on my windows 7 64 bit laptop. Right now I have Pymol 1.3 opensource. I have a many session files (.pse) that I have made on PyMol 1.3, and want to make sure that upgrading will not be a problem. Can I uninstall Pymol 1.3, then install Python 2.7 and Pymol 1.6? or can I have pymol 1.3 and 1.6 both on my machine at the same time? Thank you. -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ 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
