[PyMOL] extra bonds
Hi, In my trajectory movie, there are some minor distortions of some of the residues, but the sticks presentation in pymol seems fine. However, after I loaded the trajectory pdb file use discrete=1, extra bonds would be shown in sticks in those slightly distorted residues. Is there is way to avoid those extra bonds? Thanks a lot. --Jianghai -- Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET Get 100% visibility into your production application - at no cost. Code-level diagnostics for performance bottlenecks with <2% overhead Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap1 ___ 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] SS in a trajectory
Hi, I have a trajectory file, in which two short helices would merge into one long helix. However, when I play the trajectory in Pymol as cartoon, the long helix would still be shown as two helices with a loop in between. Is there a way to force Pymol to show a long helix for a specific range of frames in a trajectory? Thanks a lot. --Jianghai -- Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, & servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ 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] Quicktime movie saving
Hi, In MacPymol, I can save a movie as a quicktime movie by "File->Save Movie As->Quicktime…". What is the equivalent command for this function? Thanks. --Jianghai -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis & visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter___ 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] movie for morphing
Hi, I have a pdb containing the morphing. I can play the movie with the loaded pdb file. Now I want to start the movie with rocking the first state for a few seconds and end the movie with rocking the last state for a few seconds. How do I do that? Can I rock or nutate a state in the middle for a few seconds as well? Thanks. --Jianghai -- Minimize network downtime and maximize team effectiveness. Reduce network management and security costs.Learn how to hire the most talented Cisco Certified professionals. Visit the Employer Resources Portal http://www.cisco.com/web/learning/employer_resources/index.html ___ 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] movie for morphing
Hi, I have a pdb containing the morphing. I can play the movie with the loaded pdb file. Now I want to start the movie with rocking the first state for a few seconds and end the movie with rocking the last state for a few seconds. How do I do that? Can I rock a state in the middle for a few seconds as well? Thanks. --Jianghai -- Minimize network downtime and maximize team effectiveness. Reduce network management and security costs.Learn how to hire the most talented Cisco Certified professionals. Visit the Employer Resources Portal http://www.cisco.com/web/learning/employer_resources/index.html ___ 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] refinement in morph
Hi, If I turn on the refinement option in morph, the non-covalently bonded atoms like metals and waters are moving around a lot. However, if I turn off the refinement, there are some distortions in my protein. Is there a way to make the non-covalently bonded atoms just move along the transition path? Thanks. --Jianghai -- Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the endpoint security space. For insight on selecting the right partner to tackle endpoint security challenges, access the full report. http://p.sf.net/sfu/symantec-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] eMovie question
Simon, Thanks for the suggestion. That is exactly my workaround. But I found out that I don't have to render the first 70 frames. I used "mpng xxx, 70, 300" and it worked fine. So this should save some rendering time. -- Jianghai On May 10, 2009, at 7:59 AM, Simon Kolstoe wrote: > Hi Jianghai, > > I've had a similar problem. I think it is to do with a mismatch > between the mpng command and moving the movie to the next frame. It > looks to me as if the mpng command saves what's in the pymol viewer > regardless of whether the next frame has actually played. The main > solution I've found is to use a computer with more RAM as this seems > to minimise the problem. The alternative is to put a pause at the > beginning of the move before getting into the animation. In your > case I would put a 70 frame pause at the beginning of the movie and > then edit it out at a later date. > > Simon > > > On 10 May 2009, at 02:01, Jianghai Zhu wrote: > >> Thanks for the suggestion. I have brought the movie back to frame 1 >> before I save the movie or images. So I still have no fix for this >> yet. >> >> -- Jianghai >> >> >> >> >> >> >> On May 9, 2009, at 8:13 PM, Carlos Huerta wrote: >> >>> Jianghai, >>> >>> I hope I am not over-simplifying your problem, as I had a similar >>> situation as you in saving the sequential images. If you play a >>> movie you made in PyMol using eMovie, it is best to go back to your >>> first Scene by clicking on your Scene button before saving the >>> images. Also, you can use the rewind button on the PyMol tool bar >>> menu. Hope this solves your problem. >>> >>> Sincerely, >>> >>> Carlos >>> >>> >>>>>> Jianghai Zhu 05/08/09 10:51 PM >>> >>> Hi all, >>> >>> I am trying to make a simple movie using eMovie. I rotate the >>> molecule >>> 360 degrees and then move to another region. The movie is fine >>> when I >>> play it in pymol. However, when I tried to save the movie as >>> sequential images or as a movie, the movie won't play until 70ish >>> frames and it won't finish the 360 degree rotation but just move to >>> the other region. So my first 70 or so images are just repeating >>> frame 1. Has anybody know a fix for this? Thanks. >>> >>> -- Jianghai >>> >>> >>> >>> >>> >>> >>> >>> -- >>> 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 >>> >>> >>> -- >>> 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 >>> >> >> >> -- >> 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 > -- 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
Re: [PyMOL] eMovie question
Thanks for the suggestion. I have brought the movie back to frame 1 before I save the movie or images. So I still have no fix for this yet. -- Jianghai On May 9, 2009, at 8:13 PM, Carlos Huerta wrote: > Jianghai, > > I hope I am not over-simplifying your problem, as I had a similar > situation as you in saving the sequential images. If you play a > movie you made in PyMol using eMovie, it is best to go back to your > first Scene by clicking on your Scene button before saving the > images. Also, you can use the rewind button on the PyMol tool bar > menu. Hope this solves your problem. > > Sincerely, > > Carlos > > >>>> Jianghai Zhu 05/08/09 10:51 PM >>> > Hi all, > > I am trying to make a simple movie using eMovie. I rotate the molecule > 360 degrees and then move to another region. The movie is fine when I > play it in pymol. However, when I tried to save the movie as > sequential images or as a movie, the movie won't play until 70ish > frames and it won't finish the 360 degree rotation but just move to > the other region. So my first 70 or so images are just repeating > frame 1. Has anybody know a fix for this? Thanks. > > -- Jianghai > > > > > > > > -- > 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 > > > -- > 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 > -- 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] eMovie question
Hi all, I am trying to make a simple movie using eMovie. I rotate the molecule 360 degrees and then move to another region. The movie is fine when I play it in pymol. However, when I tried to save the movie as sequential images or as a movie, the movie won't play until 70ish frames and it won't finish the 360 degree rotation but just move to the other region. So my first 70 or so images are just repeating frame 1. Has anybody know a fix for this? Thanks. -- Jianghai -- 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] question about SUPER
Hi, I am using SUPER to superimpose different structures in PyMOL. And I noticed that when I try to superimpose a lot of different structures onto one reference structure, the number of aligned atoms is getting smaller and smaller as I keep using SUPER command. And eventually structures cannot be aligned anymore even though the first few structures are aligned quite well. So is this a bug? Jianghai Jianghai Zhu, PhD Immune Disease Institute Dept. of Pathology Harvard Medical School 200 Longwood Ave. Boston, MA 02115 Tel: 617-278-3211 Fax: 617-278-3232
[PyMOL] color key using ConSurf
Hi all, I am using ConSurf server to calculate the consurf scores and trying to generate pictures in Pymol. I followed their instructions and everything worked fine. I just have one question. Does anyone know how to generate the color key in Pymol? The color key image on the website doesn't match the color in pymol. Is there a way to generate a color panel like the color panel we use in electrostatic surface picture? Thanks. Jianghai
Re: [PyMOL] backbone in cartoon
I will make the last question more general. How do I make cartoon go through a specific backbone atom in pymol? Thanks. Jianghai +++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++
Re: [PyMOL] backbone in cartoon
Another question. After I show C=O as stick, how do I make the cartoon go through the carbonyl carbon? "Side chain helper" can only make sure the cartoon go through the Ca atoms. Thanks. Jianghai +++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++ On Sep 30, 2007, at 4:08 AM, Tsjerk Wassenaar wrote: Hi Jianghai, How can I show the carbonyl oxygen as a stick? show sticks, (n. c,o) What is the best way to show the backbone nitrogen? show sticks, (n. n,h) Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623
Re: [PyMOL] backbone in cartoon
Hi Tsjerk, Thanks. This works. The sticks didn't show up when I selected oxygen and nitrogen alone. But after I select c+o and n+h, sticks worked very well. Jianghai +++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++ On Sep 30, 2007, at 4:08 AM, Tsjerk Wassenaar wrote: Hi Jianghai, How can I show the carbonyl oxygen as a stick? show sticks, (n. c,o) What is the best way to show the backbone nitrogen? show sticks, (n. n,h) Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623
[PyMOL] backbone in cartoon
Hi all, I would like to draw some H-bonds between the ligand and the backbone nitrogen and carbonyl oxygen. The protein is shown in cartoon and the ligand and other side chains are shown in stick. "Side chain helper" is on. How can I show the carbonyl oxygen as a stick? What is the best way to show the backbone nitrogen? Thanks. Jianghai +++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++
Re: [PyMOL] ray_trace_mode
Yes, this strategy works very well. Thanks. Jianghai +++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++ On Jun 16, 2007, at 6:42 PM, DeLano Scientific wrote: Jianghai, The ray_trace_mode tracing mechanism operates at a per-pixel level. Thus, to get a small image with a nice outline, you simply render a large image and then shrink it down. Cheers, Warren From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users- boun...@lists.sourceforge.net] On Behalf Of Jianghai Zhu Sent: Saturday, June 16, 2007 3:36 PM To: pymol-users Subject: [PyMOL] ray_trace_mode Hi all, The black outline made by "set ray_trace_mode, 1 (or 2, 3)" is very nice if the picture is a zoom in view. However, when I look at a whole structure, a big one, the black outline is way too thick and the loops just turn into some thick black lines. Is there a way to adjust the thickness of the black outline in the ray-traced image? Thanks. Jianghai +++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++
[PyMOL] ray_trace_mode
Hi all, The black outline made by "set ray_trace_mode, 1 (or 2, 3)" is very nice if the picture is a zoom in view. However, when I look at a whole structure, a big one, the black outline is way too thick and the loops just turn into some thick black lines. Is there a way to adjust the thickness of the black outline in the ray-traced image? Thanks. Jianghai +++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++
[PyMOL] hydrogen bonds displaying
Hi all, How can I display hydrogen bonds of one protein in pymol just like the "Roving Detail" in Demonstration? Thanks. Jianghai +++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++
Re: [PyMOL] Mac Flicker Issue Workaround
The new beta works fine on my new Powerbook now. No flickering anymore. Thanks. On Nov 5, 2005, at 11:33 PM, Warren DeLano wrote: Hmm... Working now. -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com -Original Message- From: Jianghai Zhu [mailto:z...@purdue.edu] Sent: Saturday, November 05, 2005 7:49 PM To: Warren DeLano Subject: Re: [PyMOL] Mac Flicker Issue Workaround I have problem to uncompress the data. Anybody has the same problem? On Nov 5, 2005, at 10:32 PM, Warren DeLano wrote: Mac users: We lucked out and obtained a little help from an off-duty Apple engineer today who figured out how to work around the issue in 10.4.3. It was one of these combined bugs -- we weren't doing things sensibly in PyMOL, and the ATI driver wasn't quite complying with normal OpenGL behavior with respect to screen updates. They changes seem to have done the trick, so I have posted an updated MacPyMOL build at: http://delsci.com/beta Please let me know if this does NOT solve the issue on your machine. Also, since I had to change the lighting and draw-buffer code, please let me know right away if anything strange or new surfaces. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com --- SF.Net email is sponsored by: Tame your development challenges with Apache's Geronimo App Server. Download it for free - -and be entered to win a 42" plasma tv or your very own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --- SF.Net email is sponsored by: Tame your development challenges with Apache's Geronimo App Server. Download it for free - -and be entered to win a 42" plasma tv or your very own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] question on cctbx and pymol
Hi, I could not get cctbx work under either MacPymol or PymolX11Hybrid in Mac OS X. Anywhere I can find some instructions to get cctbx work in OS X? Thanks. Jianghai On Aug 23, 2005, at 1:18 PM, Sabuj Pattanayek wrote: Hi, This worked. Thanks, ..Sabuj Robert Campbell wrote: prefixing a directory path. If you were like me and had: /usr/bin/python $PYMOL_PATH/modules/launch_pymol.py $* in your pymol.com file, then it would not run that cctbx_build/bin/python script. So you need to either change the above line to: python $PYMOL_PATH/modules/launch_pymol.py $*
[PyMOL] background color
Hi, all, I am trying to change the color of the background in pymol. I know I can change the background color from menu to white, black, light grey and grey. But I want some other color. set bg_rgb, [51,153,153] or set_color newcolor=[51,153,153] bg_color newcolor but none of them worked. The background just turned to white. What did I do wrong? Thanks. Jianghai
[PyMOL] transparency surface
Hi, all, I have several objects using surface presentation. Is there a way to make the surface of one object to be transparent and the the surfaces of other objects still solid? Thanks. Jianghai
[PyMOL] perspective rendering
Hi, all, I am trying to render my picture in a perspective view in pymol 0.98. Is there a way to make the perspective effect more dramatic than the default way? I mean to make the far end smaller and the close end bigger. Thanks. Jianghai
[PyMOL] density around ligand
Hi, all, Is there a way in Pymol to draw electron density only around my ligand? Thanks. Jianghai
[PyMOL] question about "side chain helper"
Hi, all I am trying to make a picture in pymol. I have my protein in cartoon presentation and some residues in stick presentation. When I turn on "side chain helper", it works beautifully except that my glycines disappeared. Is there any way to get the glycines back? Thanks. Jianghai
[PyMOL] a minor bug in MacPymol 0.98 beta 27
Hi, I found out that once in a while macpymol lost memories of previous commands. so the "up" key could not bring the previous commands back in the external window. I don't know if this only happened to me. It could be a minor bug. Jianghai
Re: [PyMOL] macpymol beta bug
Thanks. The new beta is very good. Especially like the side_chain_helper. Now I just wonder how I can get APBS plugin work under MacPymol. Jianghai == Jianghai Zhu Molecular Biology & Biochemistry Purdue University == On Dec 4, 2004, at 12:55 PM, Warren DeLano wrote: Hmm... The problems are fixed in MacPyMOL beta24 (http://delsci.com/macbeta). Also note that there is a new setting "cartoon_side_chain_helper" that greatly simplifies figure preparation when you mix cartoons and side chains. It takes care of making sure the cartoon goes through the CA position, and it automatically hides main chain atoms when the cartoon representation is visible for a residue. You can activate it under the Display/Cartoon menu, or with "set cartoon_side_chain_helper" Cheers, Warren
[PyMOL] macpymol beta bug
Hi, all, I am using the MacPymol 0.98beta23. I found in the menu "Setting --> Cartoon" or "Setting --> Transparency" or "Setting --> Rendering" all the submenus are grey and I can't select them. What command should I use to do, for example, "use most memory in rendering"? Jianghai == Jianghai Zhu Molecular Biology & Biochemistry Purdue University ==
Re: [PyMOL] pymol and Desktop Manager on OS X
No. The game mode doesn't even allow me to switch virtual desktop anymore. Jianghai On Oct 26, 2004, at 12:53 PM, Charles Moad wrote: Have you tried "pymol -G" for game mode? On Tue, 2004-10-26 at 00:33, Jianghai Zhu wrote: Hi, all, Anybody has any experiences of using full-screen pymol and desktop manager at the same time on OS X? When I am running desktop manager and put pymol into full screen mode, I found every virtual desktop is full-screen pymol. I like to use this to switch back and forth between my pymol and powerpoint. It is great for real-time pymol demonstration during a powerpoint speech. But I just can't put pymol into full screen mode. If I am playing a movie by full screen, desktop manager can handle it with no problem. Anybody has any idea? Thanks. Jianghai --- This SF.net email is sponsored by: IT Product Guide on ITManagersJournal Use IT products in your business? Tell us what you think of them. Give us Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more http://productguide.itmanagersjournal.com/guidepromo.tmpl ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --- This SF.Net email is sponsored by: Sybase ASE Linux Express Edition - download now for FREE LinuxWorld Reader's Choice Award Winner for best database on Linux. http://ads.osdn.com/?ad_id=5588&alloc_id=12065&op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] pymol and Desktop Manager on OS X
Hi, all, Anybody has any experiences of using full-screen pymol and desktop manager at the same time on OS X? When I am running desktop manager and put pymol into full screen mode, I found every virtual desktop is full-screen pymol. I like to use this to switch back and forth between my pymol and powerpoint. It is great for real-time pymol demonstration during a powerpoint speech. But I just can't put pymol into full screen mode. If I am playing a movie by full screen, desktop manager can handle it with no problem. Anybody has any idea? Thanks. Jianghai
[PyMOL] unit cell
Hi, folks, In pymol, how do you draw a unit cell? The cell constants are in the pdb file and the manual says pymol can display unit cell. I just could not figure out how to do it. Thanks. Jianghai == Jianghai Zhu Molecular Biology & Biochemistry Purdue University ==
Re: [PyMOL] Re: PyMOL-APBS os x
I still can't compile it with scott's method. Do you mind share your binary with us? Jianghai == Jianghai Zhu Molecular Biology & Biochemistry Purdue University == On Jul 15, 2004, at 7:47 PM, William Scott wrote: The best way to overcome this is to compile it, so that you don't have to depend on someone's dynamic library. Fink doesn't build the g77 dynamic library, which allows you to avoid this problem. If you use g77 3.4.1 (which is what is currently in fink) with gcc 3.3 you will have some linking errors. I could not get the LDFLAG to let me do this (i.e., I coudn't figure out how to do this the "right way"), so I instead did the following: 1. start up zsh (to make use of its recursive globbing capability) 2. configure 3. perl -pi -e 's|\-L/usr/local/|\-lcc_dynamic \-L/usr/local/|g' **/Makefile make; make install
Re: [PyMOL] A couple of quick PyMOL + APBS notes
The reason it doesn't work is because, I think, APBS was not compiled by the fink g77. More likely it was compiled by a g77 from http://hpc.sourceforge.net/ or other similar places. So you need to install that version of g77 to get APBS running on you mac. If anybody can compiled APBS using fink g77, that will be great. Jianghai == Jianghai Zhu Molecular Biology & Biochemistry Purdue University == On Jul 15, 2004, at 6:52 PM, Douglas Kojetin wrote: (this might be better suited on an APBS list, but i figured i'd give it a shot here) I downloaded the Mac APBS binary, but I'm seeing this error when trying to run it: % ./apbs-0.3.1-g4 dyld: ./apbs-0.3.1-g4 can't open library: /usr/local/lib/libg2c.0.dylib (No such file or directory, errno = 2) Trace/BPT trap Anyone else see this or know how to overcome it? Thanks, Doug On Jul 15, 2004, at 7:33 PM, Michael George Lerner wrote:
Re: [PyMOL] Powermate dial with Pymol on OS X
This works, but it could ruin my sessions which are very important for us. Warren, is it possible to add the support of powermate into PyMol or MacPyMol? Since it works perfectly with O, I think it could be a very helpful control tool for PyMol too. == Jianghai Zhu Molecular Biology & Biochemistry Purdue University == On May 6, 2004, at 3:50 PM, William Scott wrote: Thanks, Ezequiel! That is exactly what I needed. I guess I need to RTFM some more... So for anyone else who might be interested, here is how to get the Powermate dial to play nice with Pymol (I did this on OS X but I assume it would be very similar on Windows). http://chemistry.ucsc.edu/~wgscott/xtal/powermate_pymol_osx.html Bill On May 6, 2004, at 6:06 AM, Panepucci, Ezequiel wrote: Bill, Use the command set_key from PyMOL (API only) one of the examples on 'help set_key' is precicelly what you want. Cheers, Zac --- This SF.Net email is sponsored by Sleepycat Software Learn developer strategies Cisco, Motorola, Ericsson & Lucent use to deliver higher performing products faster, at low TCO. http://www.sleepycat.com/telcomwpreg.php?From=osdnemail3 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] color choices
Hi, all, When I use color command, how many choices do I have for colors? Can I use direct rgb value? Thanks. Jianghai -- Jianghai Zhu Biochemistry & Molecular Biology Purdue University Tel: (765)494-9247
Re: [PyMOL] protein surface
Hi, kaushik, Thanks for the response. Those metheds sound good first, but when I think about it, they are not real accessible surfaces because these surfaces still show those small reentrant shapes between two consecutive atoms. Is there anyway to get around this? Or can I read any surface file ouput by other programs in pymol? Thanks Jianghai On Tuesday 25 February 2003 09:56 am, Kaushik Raha wrote: > Hi Jianghai, > > Some of these questions have been answered by Warren: > > PyMOL doesn't show the solvent accessible surface, rather it > shows the solvent/protein contact surface. The solvent > accessible surface area is usually defined as the surface > traced out by the center of a water sphere, having a radius > of about 1.4 angstroms, rolled over the protein atoms. The > contact surface is the surface traced out by the vdw surfaces > of the water atoms when in contact with the protein. > > PyMOL can only show solvent accessible surfaces using the dot > or sphere representations: > > for dots: > > show dots > set dot_mode,1 > set dot_density,3 > > for spheres: > > alter all,vdw=vdw+1.4 > show spheres > > - Kaushik. -- === Jianghai Zhu Biochemistry & Molecular Biology Purdue University Tel: 765-4949249 (O) 765-466 (H) ===
[PyMOL] protein surface
Hi, When I used "show surface, protein", what kind of surface did I generate? Molecualr surface, accessible surface (what is the probe radius?)? How can I define the type of surface I want and the probe radius? Besides generating the surface by itself, could pymol read other surface files? like msms format, grasp format, etc. Thanks. Jianghai -- === Jianghai Zhu Biochemistry & Molecular Biology Purdue University Tel: 765-4949249 (O) 765-466 (H) ===
[PyMOL] CA only pdb file
Hi, all, I have a pdb file only contains CA atoms. When I try to show cartoon about this protein, nothing happened. I found I can only show nb_sphere on the screen, is there a way to show cartoon based on those CA only pdb files? The secondary structures have been already defined in the pdb header. Thanks. Jianghai -- === Jianghai Zhu Biochemistry & Molecular Biology Purdue University Tel: 765-4949249 (O) 765-466 (H) ===
[PyMOL] how to use util.rainbow?
Hi, all, I was trying to use a command to do rainbow coloring. After I entered util.rainbow, pymol(0.86) hung up there. I could not find any document or help on how to use util.rainbow. Could someone give me some suggestions? Thanks. Jianghai -- === Jianghai Zhu Biochemistry & Molecular Biology Purdue University Tel: 765-4949249 (O) 765-466 (H) ===
