[PyMOL] cylinder fuzzy color when ray traced
Hi All, I am trying to highlight a specific residue (black color) in a helix (orange color) displayed in cylinder mode. When I perform ray tracing, the black region becomes a fuzzy gradient on the ends. Is there a ray tracing setting to make a crisp, sharp transition from orange to black to orange? I’ve attached an image example, hopefully it comes through. Thanks, Doug -- 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] Ca sphere size from b-factor value
Hi Jason, Thanks -- is there any way to add some limits to the scaling, say to alter the vdw radius from a value of 1 to 5 based on a b-factor range of values? Doug On Jul 31, 2012, at 4:44 PM, Jason Vertrees wrote: Hi Douglas, You can do something as simple as this: # fetch a protein fetch 1ejg, async=0 # show as spheres as spheres, n. CA # set the vdw radii = some factor of the b-factor alter n. CA, vdw=b/5 rebuild Cheers, -- Jason On Tue, Jul 31, 2012 at 3:36 PM, Douglas Kojetin douglas.koje...@gmail.com wrote: Hi All, I would like to set the sphere size for each Ca atom proportional to the b-factor value (the larger the b-factor the larger the sphere size) and also color the sphere based on the b-factor value. Is there an easy way to adjust the sphere size according to b-factor value? Thanks, Doug -- 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- 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
[PyMOL] Ca sphere size from b-factor value
Hi All, I would like to set the sphere size for each Ca atom proportional to the b-factor value (the larger the b-factor the larger the sphere size) and also color the sphere based on the b-factor value. Is there an easy way to adjust the sphere size according to b-factor value? Thanks, Doug -- 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
[PyMOL] c-alpha only model show cartoon
Hi All, ( I am unable to search the PyMOL mailing list archives for this question, per this message: http://sourceforge.net/mailarchive/forum.php?thread_name=200807281639.m6SGcvAe006759%40apollo.hosting4less.comforum_name=pymol-users ) How can a cartoon cylinder diagram be displayed for a c-alpha only model? show cartoon and set cartoon_cylindrical_helices, 1 only seems to show a smooth backbone trace. Thanks, Doug
[PyMOL] distorted electrostatic surface color with PyMOL/APBS
Hi All, I am having some problems with surface display of the output from the APBS plugin distributed with PyMOL (version 1.1r0) using the color by potential on sol. acc. surf. option. Steps to reproduce the problem: 1. Load in a structure. 2. Perform the APBS calculation (execute Set grid and Run APBS functions/buttons). 3. Show the electrostatics on the molecular surface under the Visualization tab. I used the following options Low = -5 High = 5 solvent accessible surface = selected color by potential on sol. acc. surf. = selected The initial surface displayed looks OK, and there are no problems if I rotate the molecule using the mouse. However, if I attempt to rotate the molecule using a command such as rotate y, 180,, the surface coloring is distorted. If I execute rotate y, 180 again, then rotate by hand, the distortion on the problematic surface-side disappears. However, if I execute rotate y, 180 once, or some iteration != 360, then rotate the molecule using the mouse, the color distortion is present and will not disappear with subsequent rotate commands. Thanks in advance for help, Doug
Re: [PyMOL] putty/sausage NMR figure
Many thanks for the suggestion. I worked something up using CNS/ python scripts -- but if anyone comes up with an all PyMOL alternative, please share with the list! Doug On Jul 20, 2005, at 1:18 PM, Cartailler, Jean-Philippe wrote: One way to do this would be to calculate RMSD between your models (using whatever package) and replace the B-factor column with those values (make sure you respect the PDB format (B-factors are in columns 61 - 66, with first column as 1 - see http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_62.html for details), load that into pymol, and voila. If the effect isn't enough, you could always multiply your RMS values by some value (eg. 10). Good luck! JP Cartailler -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Douglas Kojetin Sent: Tuesday, July 19, 2005 3:48 PM To: pymol Subject: [PyMOL] putty/sausage NMR figure Hello All- From what I've read, the 'cartoon putty' command uses the PDB B- factor value to determine the appearance of the sausage diagram. How can I use the 'cartoon putty' command with NMR structures in a way that represents the structure ensemble, similar to that as the MOLMOL sausage diagram? Thanks, Doug --- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_id=7477alloc_id=16492op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_idt77alloc_id492op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] putty/sausage NMR figure
Hello All- From what I've read, the 'cartoon putty' command uses the PDB B- factor value to determine the appearance of the sausage diagram. How can I use the 'cartoon putty' command with NMR structures in a way that represents the structure ensemble, similar to that as the MOLMOL sausage diagram? Thanks, Doug
Re: [PyMOL] OSX: fink image libs, pymol and the command line
Hi Warren- Thanks for the reply. Fink adds /sw/lib to the beginning of the DYLD_LIBRARY_PATH. Adding the following to the beginning of the shell script fixed the problem: DYLD_LIBRARY_PATH=/usr/local/lib Thanks, Doug On Jun 10, 2005, at 2:11 PM, Warren DeLano wrote: Doug, I can't be sure, but this looks like a problem with MacOS X binding PyMOL to the wrong shared object, quite possibly due to some change in the resolution order...your analysis is on track. To fix this, try to figure out what entry in PATH, LD_LIBRARY_PATH, (or whatever mechanism MacOS uses for shared object resolution) is causing the problem. You may then be able to simply change the order of the entries in order to get things to work correctly. Alternatively, you could reset the environment variable within your macpymol shell script... Cheers, Warren -Original Message- Hi All- I've been using a shell script called 'macpymol' to start PyMOL from the command line under OS X (pre-Tiger): #!/bin/sh /Applications/PyMOLX11Hybrid.app/Contents/MacOS/PyMOL $* usage: macpymol file.pdb I noticed if I use Fink to install an application under OS X (Tiger) that requires image libraries to be complied and installed (e.g. /sw/ lib/libJPEG.dylib), PyMOL fails to start using the above command and gives the following error output (from the terminal): File /Applications/PyMOLX11Hybrid.app/pymol/modules/pymol/ __init__.py, line 90, in ? import pymol File /Applications/PyMOLX11Hybrid.app/pymol/modules/pymol/ __init__.py, line 306, in ? import _cmd ImportError: Failure linking new module: /Applications/ PyMOLX11Hybrid.app/pymol/modules/pymol/_cmd.so: Symbol not found: __cg_jpeg_resync_to_restart Referenced from: /System/Library/Frameworks/ ApplicationServices.framework/Versions/A/Frameworks/ ImageIO.framework/ Versions/A/ImageIO Expected in: /sw/lib/libJPEG.dylib If I uninstall all Fink installed image libraries (jpeg, png, etc.), PyMOL starts w/ no problems. If I click directly on the PyMOLX11Hybrid.app icon, PyMOL starts w/ no problems. Any idea of how to resolve this so that I can start PyMOL from the command line? I think it could have something to do with Fink's /sw/ bin/init.csh adding some /sw info near the beginning of my $PATH. Many thanks, Doug
[PyMOL] OSX: fink image libs, pymol and the command line
Hi All- I've been using a shell script called 'macpymol' to start PyMOL from the command line under OS X (pre-Tiger): #!/bin/sh /Applications/PyMOLX11Hybrid.app/Contents/MacOS/PyMOL $* usage: macpymol file.pdb I noticed if I use Fink to install an application under OS X (Tiger) that requires image libraries to be complied and installed (e.g. /sw/ lib/libJPEG.dylib), PyMOL fails to start using the above command and gives the following error output (from the terminal): File /Applications/PyMOLX11Hybrid.app/pymol/modules/pymol/ __init__.py, line 90, in ? import pymol File /Applications/PyMOLX11Hybrid.app/pymol/modules/pymol/ __init__.py, line 306, in ? import _cmd ImportError: Failure linking new module: /Applications/ PyMOLX11Hybrid.app/pymol/modules/pymol/_cmd.so: Symbol not found: __cg_jpeg_resync_to_restart Referenced from: /System/Library/Frameworks/ ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/ Versions/A/ImageIO Expected in: /sw/lib/libJPEG.dylib If I uninstall all Fink installed image libraries (jpeg, png, etc.), PyMOL starts w/ no problems. If I click directly on the PyMOLX11Hybrid.app icon, PyMOL starts w/ no problems. Any idea of how to resolve this so that I can start PyMOL from the command line? I think it could have something to do with Fink's /sw/ bin/init.csh adding some /sw info near the beginning of my $PATH. Many thanks, Doug
[PyMOL] atom selection: wildcard
Hi All- Is it possible to select all oxygen atoms (backbone sidechain) with a command similar to the following: select oxy, name o* I cannot seem to get any variation of that to work without specifying all atoms (e.g. o+oe1+oe2) Thanks, Doug
Re: [PyMOL] Getting Closer to Wiki Time!
Another potentially useful category: Plugin/Modules -- ex. Michael George Lerner's APBS plugin -- other existing and future plugins This would make it easy for others to contribute tips/explanations/experiences/etc. to these extremely useful add-ons. On Feb 15, 2005, at 1:11 PM, Warren DeLano wrote: PyMOL Users, Jason Vertrees (UTMB) has volunteered to lead the creation of a PyMOL Wiki, and has found a suitable location for hosting. We now need your input on how the Wiki should be organized. Please summarize your ideas to the mailing list in the next 24-48 hours so that Jason has your input as he lays down an initial framework for content on the Wiki. ... Please revise, extend, and embellish.
Re: [PyMOL] Getting Closer to Wiki Time!
While we're throwing out all these ideas and possibilities: Is it ... possible? ... relatively painless? ... difficult? ... to use BioPython modules in PyMOL scripts? Doug
Re: [PyMOL] effect of number of pixels on ray image quality
Building on the two previous posts, is it necessary to use 'viewport' before executing 'ray'? this: ray 2000, 2000 instead of: viewport 700, 700 ray 2000, 2000 Thanks, Doug On Jan 20, 2005, at 10:11 AM, Ezequiel H Panepucci wrote: - so you should execute the command: viewport 700, 700 - and then fine tune your figure and then run the ray command: ray 2000, 2000
Re: [PyMOL] selection help + align question
Thanks for that one; it works as advertised. Another question: if I have 10 different structures read into PyMOL, what is the best (most accurate) method for aligning the structures as an ensemble? Currently, I'm aligning all to the first structure read in (i.e. 21, 31, etc.) using a for loop and the 'align' command. Since the structures have different sequences, I cannot use 'intra_fit', etc., is that right? Are there any other commands or methods of aligning that might be easy to script? Thanks, Doug On Jan 20, 2005, at 2:12 PM, Warren DeLano wrote: Doug, Setwise logical ANDs and ORs are tricky at first. In this case, you want to create a new set that contains atoms in a1 *or* a2. There aren't any atoms that are in both a1 and a2 which is why you're ending up with an empty object. create one, a1 or a2 -Original Message- I'm having some problems with selection syntax w/ multiple objects. I've loaded four different PDB files (in sequence structure): load 1.pdb, a1 load 2.pdb, a2 load 3.pdb, b1 load 4.pdb, b2 I wanted to create two new selections: one = a1 a2 two = b1 b2 I've tried many different combinations of PyMOL selection syntax, but I cannot get the objects to add to the same selection (using 'create' or 'select'): create one, a1 + a2 create one, a1 and a2 create one, object a1 + object a2 create one, a* From what I've read in the manual, I think these commands are not working because they actually work to select atoms that are the same between a1 a2. The manual says it 'selects atoms included in both s1 and s2'. Any clues or hints? Thanks, Doug
Re: [PyMOL] Need Feedback Testing: 0.98 beta 17
Is it possible to make this an option by means of a switch? i.e. set mouse_toggle=0 (or 1) Or manually configure each click-and-release? I see how it could be useful, however I often double click the left mouse button randomly when ... thinking ... and in this beta release I accidentally invoke selection toggle (multiple times). On the flip side, this might be good way for me to pick random atoms. Thanks, Doug On Nov 19, 2004, at 12:53 PM, Warren DeLano wrote: - If you left-click-and-release, you get selection toggle behavior. - If you middle-click-and-release you get centering behavior. - If you right-click-and-release you get a context-sensitive pop-up menu. Also, if you right click on an active selection, the pop-up menu is now selection-oriented menu rather than being the standard atom-click menu. Is this better? Let me know...I very much think so.
Re: [PyMOL] Coloring gradient
Will this work for what you want to do? spectrum palette=green_yellow Dear All, I'm trying to color a protein cartoon structure from N- to C-terminal with a green to yellow gradient. Had a browse around and couldn't quite find the correct command. Any pointers are welcomed. Peter
[PyMOL] transparent background
Hi All- Is it possible to create an image in PyMOL with a transparent background (without having to feed it through a second program, such as the ImageMagick suite)? rant: MS PowerPoint has the ability to make images transparent, however Apple's Keynote does not -- a missing feature that's likely to make me switch back from switching (presentation software; I'm not giving up OS X). Thanks, Doug
Re: [PyMOL] transparent background
Works perfectly. Many thanks. If anyone has any strong arguments for Apple's Keynote over MS's Powerpoint, I'd be interested in hearing them (off list or on). Thanks again, Doug On Aug 12, 2004, at 12:11 PM, Cartailler, Jean-Philippe wrote: Set the ray_opaque_background to off The PNG file format supports transparency. Render your scene with the above, open up in an image editor and you should have a transparent background. JP Is it possible to create an image in PyMOL with a transparent background (without having to feed it through a second program, such as the ImageMagick suite)? rant: MS PowerPoint has the ability to make images transparent, however Apple's Keynote does not -- a missing feature that's likely to make me switch back from switching (presentation software; I'm not giving up OS X). Thanks, Doug
[PyMOL] selection of residues with negative numbers
Hi All- I cannot make PyMOL make selections of residues with negative (sequence) numbers. Any quick way around this? ex. that works: PyMOLshow sticks, //mod1//10/ ex. that fails: PyMOLshow sticks, //mod1//-4/ Selector-Error: Invalid Range. ( s; mod1 i; :4 )-- I found this post on the mailing list, but no responses were posted: http://sourceforge.net/mailarchive/message.php?msg_id=4223049 Thanks! Doug
Re: [PyMOL] A couple of quick PyMOL + APBS notes
Verified. I downloaded the g77 available from http://hpc.sourceforge.net, copied the files to the respective directories in /usr/local/, and the binary appears to work now (at least no errors when I run it with no input as before). Thanks! Doug On Jul 15, 2004, at 8:02 PM, Jianghai Zhu wrote: 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: --- This SF.Net email is sponsored by BEA Weblogic Workshop FREE Java Enterprise J2EE developer tools! Get your free copy of BEA WebLogic Workshop 8.1 today. http://ads.osdn.com/?ad_id=4721alloc_id=10040op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Powermate dial with Pymol on OS X
A great many thanks for this -- I went out to the local Apple store and purchased a Powermate specifically for this - and it's awesome! Now I just need to work on programming it to interface with NMRView ... Doug On May 6, 2004, at 4:50 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
[PyMOL] pymol locks up - unix pipe
Hi All- I'm using PyMOL through a UNIX pipe within a Tcl/Tk script interface. The script make calls to highlight certain residues, and it also uses the 'dist' command. After the script makes a a few calls (20) to PyMOL, my PyMOL session usually locks up. Anyone know what might be going on? Or what I can do to resolve the issue? Thanks, Doug
Re: [PyMOL] running PyMOL remotely - how to do it without GUI
one other option. if you use ssh (instead of telnet) ... use the '-X' flag and there's no need use the xhost command: ssh -X u...@hostname see 'man ssh' for all options -- your server may need to be setup to use this specific switch. if you are under windows, you can check out 'cygwin' to connect to a remote server too (it provides a nice bash command prompt for windows X). cheers- Doug On Mar 18, 2004, at 12:50 AM, Lihua Wang wrote: If your both your remote and local systems are UNIX/LINUX/IRIX/SUN, you can use the xhost remote_address command before you launch the application. If your local machine is windows based, then you need a 3rd party software, e.g. x-win32 or hummingbird exceed.
[PyMOL] cartoon transparency a possible 'native' bug
[i'm sending again; it seems the pymol sourceforge list was down when i tried to send this] Hi All- In reference to this post: http://sourceforge.net/mailarchive/message.php?msg_id=6977122 When I gave PyMOL this command, I got the following error: Error: unknown setting 'cartoon_transparency'. Is this setting only available on newer versions of PyMOL? If so, anyone working on a *new* Fink version?!? [ edit: just found out this is only available on 0.91 greater on the changes page -- feel free to reply about the Fink version; I believe many are waiting for this to be released! ] I would simply use the native Apple PyMOL released, but a) I prefer the interface of the 'Fink' version, unless there's a way to customize the menu interface and b) often, when I minimize/maximize the PyMOL interface to the Dock a few times, the native PyMOL crashes -- has anyone else experienced this? I have plenty of free and total memory (1.5GB total), so I don't think it's a memory issue. Also, I could not find any reference to 'cartoon_transparency' on the online man pages -- presently, are there updated man pages available (to subscribers only?) that include the new settings/etc.? Many thanks for the help, Doug
[PyMOL] Select Atom Change View
Hi All- Is it possible to do the following through the command line ... -- select an atom (say the CA of residue 25) and bring the view of the molecule within PyMOL so that 25.CA is 'up front' (or closest to the viewer's point of view)? Thanks for the input, Doug
[PyMOL] pymol 0.93, fink source compile issues (os x)
Hi All- It's be over a month since pymol 0.93 has been released ... anyone know when a Fink distribution will be available? Or how to do it manually (using Fink, without the main/online Fink database knowing about it)? I tried compiling the source manually, but I got an error similar to the following error previously reported here: http://sourceforge.net/mailarchive/message.php?msg_id=6454630 Many thanks, Doug
[PyMOL] non-related question related: electrostatics
Hi All- I'll ask my related question first: does anyone know if/when electrostatic calculations might be incorporated into pymol? Or if you can import calcs from another (hopefully free) program? Unrelated question: does anyone know of a secondary structure prediction program that outputs pretty graphics to related 'helix' and 'sheet' structures? similar to how ESPript outputs ... but i do not have an input PDB file (yet) to use that program Thanks, Doug
