From crenshaw at endlessalgae.org Fri Jan 2 03:45:40 2009 From: crenshaw at endlessalgae.org (Breann Crenshaw) Date: 2 Jan 2009 06:45:40 -0500 Subject: [Chimera-users] Motivational Posters, Demotivators Message-ID: Rofl Motivational Posters http://www.roflposters.com From mpancera at mail.nih.gov Mon Jan 5 11:13:59 2009 From: mpancera at mail.nih.gov (Pancera, Marie (NIH/VRC) [E]) Date: Mon, 5 Jan 2009 14:13:59 -0500 Subject: [Chimera-users] Question regarding saving PDB in Chimera Message-ID: <2F7FB66E9CAC6C46AF2A2C412D50DEB707880E11@NIHCESMLBX4.nih.gov> Hello, I am using Chimera to fit coordinates into EM density. However I have problems when I save with Chimera as the coordinates that I am saving are not the one I see on the screen. Here is what I do: File Save PDB chose the folder A file name A file type The model that I want to save, i.e the one I see on the screen And then I have to select save relative to model, otherwise I am saving the original molecule, the problem is that I am not sure relative to which model I have to save it. IS there an easier way to just save what I can see on the screen? Thanks, Marie -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Mon Jan 5 14:21:12 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 05 Jan 2009 14:21:12 -0800 Subject: [Chimera-users] Question regarding saving PDB in Chimera In-Reply-To: <2F7FB66E9CAC6C46AF2A2C412D50DEB707880E11@NIHCESMLBX4.nih.gov> References: <2F7FB66E9CAC6C46AF2A2C412D50DEB707880E11@NIHCESMLBX4.nih.gov> Message-ID: <496287D8.8030104@cgl.ucsf.edu> Hi Marie, To save your Chimera session including the fit position use File / Save Session As.... Later you can open that session in Chimera to get back to where you were. To save an image use File / Save Image.... But if you want to save the fit coordinates so they can be used in other software then you should use File / Save PDB... and save relative to the EM map you fit into. Tom Pancera, Marie (NIH/VRC) [E] wrote: > Hello, > > > > I am using Chimera to fit coordinates into EM density. > > However I have problems when I save with Chimera as the coordinates that > I am saving are not the one I see on the screen. > > > > Here is what I do: > > File > > Save PDB > > chose the folder > > A file name > > A file type > > The model that I want to save, i.e the one I see on the screen > > And then I have to select save relative to model, otherwise I am saving > the original molecule, the problem is that I am not sure relative to > which model I have to save it. > > IS there an easier way to just save what I can see on the screen? > > Thanks, > > Marie > > > ------------------------------------------------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From meng at cgl.ucsf.edu Mon Jan 5 14:28:59 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 5 Jan 2009 14:28:59 -0800 Subject: [Chimera-users] Question regarding saving PDB in Chimera In-Reply-To: <2F7FB66E9CAC6C46AF2A2C412D50DEB707880E11@NIHCESMLBX4.nih.gov> References: <2F7FB66E9CAC6C46AF2A2C412D50DEB707880E11@NIHCESMLBX4.nih.gov> Message-ID: Hi Marie, If you just want the transformed coordinates (as shown on the screen), don't check any options. That is, don't use "save relative to" some model. However, that only saves the atomic structure and not the map, so if you had rotated the entire view you would lose their relationship and the fitting. I believe you want to save the atomic model relative to the density map model. To save the original coordinates of a model, you would "save relative to" itself, for example, save model #0 relative to model #0. Normally that would be done if you did something like rotated a bond or added hydrogens but otherwise wanted the same coordinates as input. Another use is if you superimposed or docked #0 and #1 and wanted to save their relative orientations. In that case you could either save #1 relative to #0 (so that the saved #1 would work with the original file for #0) or vice versa, assuming both are atomic structures. In your case, with a density map and an atomic structure, you can only save the atomic structure as PDB, of course. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jan 5, 2009, at 11:13 AM, Pancera, Marie (NIH/VRC) [E] wrote: > Hello, > > I am using Chimera to fit coordinates into EM density. > > However I have problems when I save with Chimera as the coordinates > that I am saving are not the one I see on the screen. > > Here is what I do: > > File > > Save PDB > > chose the folder > > A file name > > A file type > > The model that I want to save, i.e the one I see on the screen > > And then I have to select save relative to model, otherwise I am > saving the original molecule, the problem is that I am not sure > relative to which model I have to save it. > > IS there an easier way to just save what I can see on the screen? > > Thanks, > > Marie From meng at cgl.ucsf.edu Mon Jan 5 17:28:31 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 5 Jan 2009 17:28:31 -0800 Subject: [Chimera-users] delphi In-Reply-To: References: Message-ID: <7974A921-C744-43C0-ADBC-7ADBB96F6908@cgl.ucsf.edu> Hi Darren and others, I forgot to mention a recent development that might interest you: We recently added a Coulombic Surface Coloring tool (under Tools... Surface/Binding Analysis, not yet documented). This is for people who want to color by electrostatic potential but can't or prefer not to run any of the continuum electrostatics programs (DelPhi, APBS, UHBD) - it associates the atoms with partial charges from AMBER, calculates a Coulombic potential, and allows you to color the molecular surface by those values. The Coulombic potential is cruder than what you get from Poisson-Boltzmann calculations, but our comparisons on a handful of structures showed the same qualitative results (bluest and reddest patches generally in the same places). This is only available in the daily builds, not the recent production release. Users should also be aware it is still being improved upon and various behaviors may change. Best, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Dec 30, 2008, at 4:55 PM, Elaine Meng wrote: > Hi Darren, > Unfortunately it is an unsolved problem getting a pre-made delphi > executable for Mac OSX that gives results that can be shown in > Chimera. Just to clarify for everybody, DelPhi is a program freely > provided by another group, but without official support. > > I went through several weeks of trying to get an older executable from > the Honig site to work, installing various files myself just as you > have. Here is the chimera-users message where I describe running up > against this wall: > 001113.html >> > > I reported these problems to the Honig group, and some months later > (July 2008) they updated their Mac OSX Intel executable so it does not > require these additional libraries. Maybe you downloaded an > executable before that time or have a PPC Mac rather than Intel. > Honig group DelPhi download page: > Software:DelPhi_System_Requirements >> > > However, although the Intel executable runs nicely and can be > controlled by DelPhiController, something about the map format changed > and Chimera cannot read the result. We were unable to get information > from the Honig lab on how the format changed, or even reverse-engineer > the changes given our example maps. There is nothing else we can do - > it is a limitation recorded in our database as problem report #6228. > > Possible solutions are to use DelPhi on a different type of computer, > use one of the other Poisson-Boltzmann programs that produces files > that Chimera understands (Grasp, APBS, UHBD): > filetypes.html#esp >> > > Actually in May 2008 I found one web server that will calculate an > electrostatic potential map and let you download it (so results can be > viewed in Chimera). There are some complications with using it, but > perhaps that's still easier than the alternatives. Here is what I > wrote in May - haven't tried it since then: > ------------ > webPIPSA web server for Protein Interaction Property Similarity > Analysis > http://pipsa.eml.org > focused on performing a calculation on multiple proteins and comparing > them (won't let you proceed until you specify at least two), choice of > using UHBD or APBS > input: upload PDB files or specify PDB IDs, email address for getting > results > output: dendrogram and heat map comparing the results for the multiple > proteins, optional download of zip file with intermediate results > (includes map files and corresponding PDBs) > - my first attempt with two structures and align "none" and use UHBD > failed...I guess you are only supposed to use "none" if the proteins > are already superimposed, which they weren't because I didn't care > about the comparison > - second attempt with align option "sup2pdbs" and use UHBD was > successful. In Chimera, should probably only view the maps along with > the corresponding PDBs from the intermediate results since they may > have been transformed (in the superposition step) > ----------- > > Good luck, > Elaine > ----- > Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu > UCSF Computer Graphics Lab and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > > > > On Dec 30, 2008, at 12:41 PM, Darren Thompson wrote: > >> I installed the ibm compiler libraries on Mac OSX tiger, but delphi >> still does not see them >> >> Applications System Folder mach.sym >> Applications (Mac OS 9) TheVolumeSettingsFolder mach_kernel >> Desktop (Mac OS 9) Trash opt >> Desktop DB Users private >> Desktop DF Volumes sbin >> Desktop Folder automount sw >> Developer bin tmp >> Documents cores usr >> Library dev var >> Network etc >> System mach >> >> the opt folder (ibm) is there. >> >> I did a symbolic link to the Mac OSX executable in the /usr/local/ >> release1.1/exe directory to /usr/bin/delphi, downloaded the example >> files from delphi's website, >> [psb-232-45:release1.1/examples/example_1] darren% delphi param_1 >> dyld: Library not loaded: /opt/ibmcmp/lib/libxlf90.dylib >> Referenced from: /usr/bin/delphi >> Reason: image not found >> Trace/BPT trap >> >> when I try directly >> [psb-232-45:local/release1.1/exe] darren% ./delphiMacOSX >> dyld: Library not loaded: /opt/ibmcmp/lib/libxlf90.dylib >> Referenced from: /usr/local/release1.1/exe/./delphiMacOSX >> Reason: image not found >> Trace/BPT trap >> >> Does it matter that it's looking for /libxlf90.dylib and I have / >> libxlf90.A.dylib? >> >> Have some xmas charity >> Help a newb >> >> Darren Thompson >> Graduate Student >> UCSC >> 1156 High St. >> Santa Cruz, CA 95064 >> 831-459-3390 voice >> 831-459-2395 fax >> http://people.ucsc.edu/~ministry > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From lionel.nauton at univ-bpclermont.fr Tue Jan 6 00:00:06 2009 From: lionel.nauton at univ-bpclermont.fr (Lionel Nauton) Date: Tue, 06 Jan 2009 09:00:06 +0100 Subject: [Chimera-users] problem with new release Message-ID: <49630F86.20805@univ-bpclermont.fr> hi all, I don't know if everyone else have this problem, but i 'm not able to use the last release of chimera (chimera-1.3.2577-linux.exe ) installation script works well, but when I try to start the program, i have a black screen , and my session shutdown and restart, it seems that chimera fall down my Xorg. I'm working on PC linux ( X86_64), but i used the 32 bits version of chimera, ( test with X86_64 version give the same result), my pc linux work with fedora 10 , i have no problem with chimera-1.3.2540-linux.exe thanks per advance for your answer ================================================= NAUTON Lionel Ing?nieur d'?tudes. Laboratoire de Synth?se Et Etude de Syst?mes ? Int?r?t Biologique UMR6504 : universit? Blaise Pascal ? CNRS 24, avenue des Landais ? Campus des C?zeaux 63177 AUBIERE Cedex France Tel : 04 73 40 55 06 m?l : lionel.nauton at univ-bpclermont.fr site web : http://seesib.univ-bpclermont.fr/site_web/pageaccueil.htm ================================================= From mpancera at mail.nih.gov Tue Jan 6 06:29:28 2009 From: mpancera at mail.nih.gov (Pancera, Marie (NIH/VRC) [E]) Date: Tue, 6 Jan 2009 09:29:28 -0500 Subject: [Chimera-users] Question regarding saving PDB in Chimera In-Reply-To: Message-ID: <2F7FB66E9CAC6C46AF2A2C412D50DEB707880E19@NIHCESMLBX4.nih.gov> Thanks, it definitively helps. Finally I was able to save relative to the map and that was fine. Marie -----Original Message----- From: Elaine Meng [mailto:meng at cgl.ucsf.edu] Sent: Monday, January 05, 2009 5:29 PM To: Pancera, Marie (NIH/VRC) [E] Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] Question regarding saving PDB in Chimera Hi Marie, If you just want the transformed coordinates (as shown on the screen), don't check any options. That is, don't use "save relative to" some model. However, that only saves the atomic structure and not the map, so if you had rotated the entire view you would lose their relationship and the fitting. I believe you want to save the atomic model relative to the density map model. To save the original coordinates of a model, you would "save relative to" itself, for example, save model #0 relative to model #0. Normally that would be done if you did something like rotated a bond or added hydrogens but otherwise wanted the same coordinates as input. Another use is if you superimposed or docked #0 and #1 and wanted to save their relative orientations. In that case you could either save #1 relative to #0 (so that the saved #1 would work with the original file for #0) or vice versa, assuming both are atomic structures. In your case, with a density map and an atomic structure, you can only save the atomic structure as PDB, of course. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jan 5, 2009, at 11:13 AM, Pancera, Marie (NIH/VRC) [E] wrote: > Hello, > > I am using Chimera to fit coordinates into EM density. > > However I have problems when I save with Chimera as the coordinates > that I am saving are not the one I see on the screen. > > Here is what I do: > > File > > Save PDB > > chose the folder > > A file name > > A file type > > The model that I want to save, i.e the one I see on the screen > > And then I have to select save relative to model, otherwise I am > saving the original molecule, the problem is that I am not sure > relative to which model I have to save it. > > IS there an easier way to just save what I can see on the screen? > > Thanks, > > Marie From gregc at cgl.ucsf.edu Tue Jan 6 14:55:51 2009 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Tue, 6 Jan 2009 14:55:51 -0800 (PST) Subject: [Chimera-users] problem with new release In-Reply-To: <49630F86.20805@univ-bpclermont.fr> References: <49630F86.20805@univ-bpclermont.fr> Message-ID: Please file a bug report using the working chimera so I can learn more about your system (in particular what graphics setup you have). Then I will try to load fedora 10 on a similar system to see if I can reproduce the bug. There is also a chance that the bug is fixed in the daily builds, but this bug sounds new to me. Greg Couch UCSF Computer Graphics Lab On Tue, 6 Jan 2009, Lionel Nauton wrote: > hi all, > > I don't know if everyone else have this problem, but i 'm not able to > use the last release of chimera (chimera-1.3.2577-linux.exe > ) > installation script works well, but when I try to start the program, i > have a black screen , and my session shutdown and restart, > it seems that chimera fall down my Xorg. > I'm working on PC linux ( X86_64), but i used the 32 bits version of > chimera, ( test with X86_64 version give the same result), > my pc linux work with fedora 10 , i have no problem with > chimera-1.3.2540-linux.exe > > thanks per advance for your answer > > ================================================= > > > NAUTON Lionel > > Ing?nieur d'?tudes. > > Laboratoire de Synth?se Et Etude de Syst?mes ? Int?r?t Biologique > > UMR6504 : universit? Blaise Pascal ? CNRS > > 24, avenue des Landais ? Campus des C?zeaux > > 63177 AUBIERE Cedex > > France > > Tel : 04 73 40 55 06 > > m?l : lionel.nauton at univ-bpclermont.fr > > > site web : http://seesib.univ-bpclermont.fr/site_web/pageaccueil.htm > > > > ================================================= > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > From bruno.villoutreix at gmail.com Tue Jan 6 14:35:28 2009 From: bruno.villoutreix at gmail.com (Bruno Villoutreix) Date: Tue, 6 Jan 2009 23:35:28 +0100 Subject: [Chimera-users] question about measuring volume via command line and the nogui option Message-ID: <72e02c860901061435g64b29895u5627ed3cf13148e8@mail.gmail.com> Dear Chimera Users i am new to chimera, is it possible using something like: chimera --nogui open myfile.mol2 and then i would like to measure the area and volume...but i am not sure which command to use. I can get the surface with this command but to get the volume, i have to use the graphic interface, i do not see either the name of the command in the command history list... thanks if you can give me some advices Bruno -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Wed Jan 7 18:32:34 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Wed, 07 Jan 2009 18:32:34 -0800 Subject: [Chimera-users] question about measuring volume via command line and the nogui option In-Reply-To: <72e02c860901061435g64b29895u5627ed3cf13148e8@mail.gmail.com> References: <72e02c860901061435g64b29895u5627ed3cf13148e8@mail.gmail.com> Message-ID: <496565C2.103@cgl.ucsf.edu> Hi Bruno, There is no Chimera command to report volume enclosed in a surface, so I've added one. Example chimera --nogui --nostatus > open 1a0m > surf #0 ... > measure volume #0 MSMS main surface of 1a0m: volume = 3212.8 > measure area #0 MSMS main surface of 1a0m: area = 1887.7 It will be in tonight's Chimera daily builds if they succeed. Note the use of --nostatus on the Chimera command-line to suppress the extra messages. Many Chimera functions are only available in Python scripts and we recommend using Python if you run into cases where Chimera commands are lacking. Tom Bruno Villoutreix wrote: > Dear Chimera Users > i am new to chimera, is it possible using something like: > chimera --nogui > open myfile.mol2 > > and then i would like to measure the area and volume...but i am not > sure which command to use. I can get the surface with this command > but to get the volume, i have to use the graphic interface, i do not > see either the name of the command in the command history list... > > thanks if you can give me some advices > Bruno > ------------------------------------------------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > From jrumbley at d.umn.edu Tue Jan 6 13:11:41 2009 From: jrumbley at d.umn.edu (Jon Rumbley) Date: Tue, 6 Jan 2009 15:11:41 -0600 Subject: [Chimera-users] Changes after 1.3 Message-ID: <412312E5307A4360BA0456EFBC28C899@RumbleyLaptop> I noticed you were going to remove the DelPhi interface after Chimera ver 1.3. I have used this interface to generate electrostatic surfaces in Chimera for both teaching and research, will there be something replacing it? Thank you, Jon Rumbley Dr. Jon N. Rumbley Assistant Professor Dept. of Chemistry and Biochemistry/ Dept. of Pharmaceutical Sciences University of Minnesota-Duluth 253C SSB 1035 Kirby Dr. Duluth, MN 55812 Phone: 218-726-7423 email: jrumbley at d.umn.edu From meng at cgl.ucsf.edu Thu Jan 8 09:21:45 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 8 Jan 2009 09:21:45 -0800 Subject: [Chimera-users] Changes after 1.3 In-Reply-To: <412312E5307A4360BA0456EFBC28C899@RumbleyLaptop> References: <412312E5307A4360BA0456EFBC28C899@RumbleyLaptop> Message-ID: <553E3F11-775F-4D25-9A55-F13DD8E086D7@cgl.ucsf.edu> Dear Dr. Rumbley, We were waiting on feedback before actually deleting anything on this list, so it is good you said something! I would also encourage anybody else who relies on any of those features to let us know. The idea is to remove features that are less useful so that Chimera doesn't just get bigger and bigger, making it harder to access the features that are the most useful. We haven't made a final decision yet, but perhaps considering your input, DelPhiController will be retained. There is not anything to directly replace it, that is, no graphical interface for running finite-difference Poisson-Boltzmann (FDPB) calculations with DelPhi or any other FDPB program. In the version 1.4 builds, we just added a tool to color surfaces by Coulombic electrostatic potential calculated within Chimera, which could partly compensate for a lack of FDPB calculations, but that is a more approximate approach. Thanks for the information, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jan 6, 2009, at 1:11 PM, Jon Rumbley wrote: > I noticed you were going to remove the DelPhi interface after > Chimera ver > 1.3. I have used this interface to generate electrostatic surfaces in > Chimera for both teaching and research, will there be something > replacing > it? > > Thank you, > Jon Rumbley > > > Dr. Jon N. Rumbley > Assistant Professor > Dept. of Chemistry and Biochemistry/ > Dept. of Pharmaceutical Sciences > University of Minnesota-Duluth > 253C SSB > 1035 Kirby Dr. > Duluth, MN 55812 > > Phone: 218-726-7423 > email: jrumbley at d.umn.edu From kay_jay at earthlink.net Thu Jan 8 10:59:46 2009 From: kay_jay at earthlink.net (Kenward Vaughan) Date: Thu, 08 Jan 2009 10:59:46 -0800 Subject: [Chimera-users] Changes after 1.3 In-Reply-To: <553E3F11-775F-4D25-9A55-F13DD8E086D7@cgl.ucsf.edu> References: <412312E5307A4360BA0456EFBC28C899@RumbleyLaptop> <553E3F11-775F-4D25-9A55-F13DD8E086D7@cgl.ucsf.edu> Message-ID: <1231441186.11550.8.camel@hpotter.vaughan.home> On Thu, 2009-01-08 at 09:21 -0800, Elaine Meng wrote: > Dear Dr. Rumbley, > We were waiting on feedback before actually deleting anything on this > list, > > > > so it is good you said something! I would also encourage anybody else > who relies on any of those features to let us know. The idea is to > remove features that are less useful so that Chimera doesn't just get > bigger and bigger, making it harder to access the features that are > the most useful. > I definitely use the Delphi controller, so it would be a loss for me as well. :-( As I am not a theoretician deeply imbedded within the field, nor well trained in all the intricacies of each of the apps. I use, having such an interface is a tremendous boon for me. I'd guess that us "merely mortal" teachers teaching themselves this stuff always welcome such things (though I don't know how many of us are out here... ???) My $0.02 ;-) Cheers, Kenward > We haven't made a final decision yet, but perhaps considering your > input, DelPhiController will be retained. There is not anything to > directly replace it, that is, no graphical interface for running > finite-difference Poisson-Boltzmann (FDPB) calculations with DelPhi or > any other FDPB program. In the version 1.4 builds, we just added a > tool to color surfaces by Coulombic electrostatic potential calculated > within Chimera, which could partly compensate for a lack of FDPB > calculations, but that is a more approximate approach. > > > > Thanks for the information, > Elaine > ----- > Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > > > > On Jan 6, 2009, at 1:11 PM, Jon Rumbley wrote: > > > I noticed you were going to remove the DelPhi interface after > > Chimera ver > > 1.3. I have used this interface to generate electrostatic surfaces in > > Chimera for both teaching and research, will there be something > > replacing > > it? > > > > Thank you, > > Jon Rumbley > > > > > > Dr. Jon N. Rumbley > > Assistant Professor > > Dept. of Chemistry and Biochemistry/ > > Dept. of Pharmaceutical Sciences > > University of Minnesota-Duluth > > 253C SSB > > 1035 Kirby Dr. > > Duluth, MN 55812 > > > > Phone: 218-726-7423 > > email: jrumbley at d.umn.edu > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users -- The church says the earth is flat, but I know that it is round, for I have seen the shadow on the moon, and I have more faith in a shadow than in the church. --Ferdinand Magellan From meng at cgl.ucsf.edu Thu Jan 8 11:35:55 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 8 Jan 2009 11:35:55 -0800 Subject: [Chimera-users] delphi Message-ID: <23CA79E3-7158-4009-BA09-E90423A556D1@cgl.ucsf.edu> Hi everybody, I'm happy to report that Chimera (version 1.4 builds Jan 8, 2009 and later) can now read electrostatic potential maps from the Intel Mac version of DelPhi provided by the Honig lab as of mid-2008: The problem was that part of the potential file was written in double precision. Their group may be updating that executable so that it does not write double precision, but either way, the newer builds of Chimera will be able to read the maps. This does not solve the problem Darren was having, I assume using a PPC Mac rather than an Intel Mac. The PPC Mac version of DelPhi from the Honig lab still requires certain library files that I don't think are freely available. The Honig web site (URL above) does mention this issue. Best, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Dec 30, 2008, at 4:55 PM, Elaine Meng wrote: > Hi Darren, > Unfortunately it is an unsolved problem getting a pre-made delphi > executable for Mac OSX that gives results that can be shown in > Chimera. Just to clarify for everybody, DelPhi is a program freely > provided by another group, but without official support. > > I went through several weeks of trying to get an older executable from > the Honig site to work, installing various files myself just as you > have. Here is the chimera-users message where I describe running up > against this wall: > 001113.html >> > > I reported these problems to the Honig group, and some months later > (July 2008) they updated their Mac OSX Intel executable so it does not > require these additional libraries. Maybe you downloaded an > executable before that time or have a PPC Mac rather than Intel. > Honig group DelPhi download page: > Software:DelPhi_System_Requirements >> > > However, although the Intel executable runs nicely and can be > controlled by DelPhiController, something about the map format changed > and Chimera cannot read the result. We were unable to get information > from the Honig lab on how the format changed, or even reverse-engineer > the changes given our example maps. There is nothing else we can do - > it is a limitation recorded in our database as problem report #6228. From hsosa at aecom.yu.edu Sun Jan 11 05:53:37 2009 From: hsosa at aecom.yu.edu (hsosa at aecom.yu.edu) Date: Sun, 11 Jan 2009 08:53:37 -0500 Subject: [Chimera-users] Higher order Message-ID: <4969F9E1.60007@aecom.yu.edu> Hi, Is it possible to use the tools in: Higher Order Structures > Multiscale Models to generate full atomic models (with atoms and all the display capabilities of chimera) from the symmetry entries in the PDB file (SMTRY entries) ? So far I been able to produce only a rough surface representation of the symmetry related molecules. Thanks Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa at aecom.yu.edu ----------------------------------- From meng at cgl.ucsf.edu Sun Jan 11 08:58:31 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sun, 11 Jan 2009 08:58:31 -0800 Subject: [Chimera-users] Higher order In-Reply-To: <4969F9E1.60007@aecom.yu.edu> References: <4969F9E1.60007@aecom.yu.edu> Message-ID: <75B28320-EE6A-402F-AFC1-ECEE07F56C43@cgl.ucsf.edu> Hi Hernando, The low-res surfaces are for efficiency, but you can force loading all of the atomic coordinates as follows: After you make the Multiscale Model, in that dialog select "All" chains and then change the "Style" to anything other than "Surface" to force Chimera to load the atomic coordinates. This was described with a few more details in previous posts: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jan 11, 2009, at 5:53 AM, hsosa at aecom.yu.edu wrote: > Hi, > Is it possible to use the tools in: Higher Order Structures > > Multiscale Models to generate full atomic models (with atoms and all > the display capabilities of chimera) from the symmetry entries in the > PDB file (SMTRY entries) ? > > So far I been able to produce only a rough surface representation of > the symmetry related molecules. > Thanks > Hernando > From hsosa at aecom.yu.edu Sun Jan 11 11:05:06 2009 From: hsosa at aecom.yu.edu (hsosa at aecom.yu.edu) Date: Sun, 11 Jan 2009 14:05:06 -0500 Subject: [Chimera-users] Higher Order Message-ID: <496A42E2.5030908@aecom.yu.edu> I have another related question: If I were to deposit a PDB coordinates file of a helical structure, what would be the best place to put helical symmetry information (the file includes the full coordinates for only one asymmetric unit) so that chimera can generate a model with more than one asymmetric unit ?. The idea being to be able to see the contacts between asymmetric units and the symmetry of the complex. Should I use the the SMTRY, or the MTRIX entries ?. Does it make any difference in chimera ?. Thanks Hernando . -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa at aecom.yu.edu ----------------------------------- From goddard at cgl.ucsf.edu Sun Jan 11 16:26:09 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Sun, 11 Jan 2009 16:26:09 -0800 Subject: [Chimera-users] Higher Order In-Reply-To: <496A42E2.5030908@aecom.yu.edu> References: <496A42E2.5030908@aecom.yu.edu> Message-ID: <496A8E21.5020308@cgl.ucsf.edu> Hi Hernando, The SMTRY and MTRIX records in PDB files are only used to describe crystal packing. SMTRY describes only crystallographic symmetries. MTRIX describes only symmetries within the crystallographic asymmetric unit when the deposited coordinates do not contain the full crystal asymmetric unit (typically used for virus capsids). Other cases, e.g. all electron microscopy structures use REMARK 350 biological unit BIOMT matrices. See PDB 2tmv for an example of REMARK 350 for a helical structure. Tom hsosa at aecom.yu.edu wrote: > I have another related question: If I were to deposit a PDB > coordinates file of a helical structure, what would be the best place > to put helical symmetry information (the file includes the full > coordinates for only one asymmetric unit) so that chimera can generate a > model with more than one asymmetric unit ?. The idea being to be able > to see the contacts between asymmetric units and the symmetry of the > complex. Should I use the the SMTRY, or the MTRIX entries ?. Does > it make any difference in chimera ?. > > Thanks > > Hernando > . > > From papai at igbmc.fr Thu Jan 8 23:52:47 2009 From: papai at igbmc.fr (Gabor Papai) Date: Fri, 09 Jan 2009 08:52:47 +0100 Subject: [Chimera-users] Changes after 1.3 In-Reply-To: <553E3F11-775F-4D25-9A55-F13DD8E086D7@cgl.ucsf.edu> References: <412312E5307A4360BA0456EFBC28C899@RumbleyLaptop> <553E3F11-775F-4D25-9A55-F13DD8E086D7@cgl.ucsf.edu> Message-ID: <4967024F.70503@igbmc.fr> Hi, I wonder if you discontinue keyboard shortcuts, the features - like "erase outside" - will be discontinued also? I use some of these features. An other question: is it possible to cut out a subregion from a density map in old style, I mean to set the position, size and resolution of the cube, which defines the new volume? Gabor -- Gabor Papai IGBMC Department of Structural Biology and Genomics 1, rue Laurent Fries, BP 10142 67404 Illkirch, France phone +33-3-88655748 Fax +33-3-88653201 E-mail: papai at igbmc.u-strasbg.fr From goddard at cgl.ucsf.edu Mon Jan 12 09:48:24 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 12 Jan 2009 09:48:24 -0800 Subject: [Chimera-users] Changes after 1.3 In-Reply-To: <4967024F.70503@igbmc.fr> References: <412312E5307A4360BA0456EFBC28C899@RumbleyLaptop> <553E3F11-775F-4D25-9A55-F13DD8E086D7@cgl.ucsf.edu> <4967024F.70503@igbmc.fr> Message-ID: <496B8268.9030006@cgl.ucsf.edu> Hi Gabor, If we eliminated keyboard shortcuts there would be new commands or buttons that do the things that only shortcuts can currently do. But I more and more think we need to keep the shortcuts because I frequently give demonstrations and use them very heavily. It doesn't seem right to give demonstrations using shortcuts that are not available to users. You can still extract a subregion of a volume by outlining it with a box using the volume dialog subregion panel, or by using the "vop" command resample option. The subregion panel has improved in Chimera 1.3 and 1.4 so it allows rotating the subregion box to an arbitrary orientation. Tom Gabor Papai wrote: > Hi, > > I wonder if you discontinue keyboard shortcuts, the features - like > "erase outside" - will be discontinued also? I use some of these features. > An other question: is it possible to cut out a subregion from a density > map in old style, I mean to set the position, size and resolution of the > cube, which defines the new volume? > > Gabor > From adolphsdchiu at ufl.edu Mon Jan 12 11:54:40 2009 From: adolphsdchiu at ufl.edu (CHIU,YEUNG) Date: Mon, 12 Jan 2009 14:54:40 -0500 (EST) Subject: [Chimera-users] "Extra" hydrogens in Dockprep and addH steps Message-ID: <1783795324.303081231790080717.JavaMail.osg@osgjas03.cns.ufl.edu> Dear colleagues and friends, I notice that during "Tools -> Dockprep" and "Tools -> addH" steps Chimera sometimes will automatically add hydrogens to the positions considered necessary by the program itself. However, these positions do not always really have these hydrogens imposed on them. One situation is when I added hydrogen to the molecule containing nitrogen with lone-pair electrons, Chimera added hydrogen to the position of this lone-pair. One other situation is in the disulfide bond. It seems that Chimera can not recognize the disulfide bond, so hydrogen is added to each of the thiol group, which is obviously inappropriate. I'm wondering what causes these situations and how users can prevent them happening. Any help is appreciated. If you coincidently encountered with similar situation, I'm glad to hear your story as well~ Happy new year and best wishes to your research! Sincerely yours CHIU,YEUNG From meng at cgl.ucsf.edu Mon Jan 12 13:05:33 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 12 Jan 2009 13:05:33 -0800 Subject: [Chimera-users] "Extra" hydrogens in Dockprep and addH steps In-Reply-To: <1783795324.303081231790080717.JavaMail.osg@osgjas03.cns.ufl.edu> References: <1783795324.303081231790080717.JavaMail.osg@osgjas03.cns.ufl.edu> Message-ID: Dear Yeung, Chimera automatically identifies atom types using the input coordinates and bonding pattern. In the case of the disulfide, the input structure is lacking the S-S bond. You can either edit the input file (CONECT section) or just add the bond in Chimera before adding hydrogens. You can add a bond by selecting the two atoms (Ctrl-click, Shift-Ctrl-click) and then using the command "bond sel" or the Build Structure tool (under Tools.. Structure Editing. See the Add/Delete Bonds section of Build Structure). Sometimes input bond lengths and angles are not very accurate, so that the types are harder to figure out, and some may be identified incorrectly. The number and location of hydrogens added to an atom depend on that atom's type. Here are the explanations of the Chimera atom types: As mentioned on the Dock Prep page, the protonation states of any ambiguous groups and of those with possibly perturbed pKa values (for example, in active sites or coordinating metal ions) should be checked manually and corrected as needed. If the result is just an extra hydrogen, you could simply select it with Ctrl-click and delete it (Actions... Atoms/Bonds... delete). If it is missing hydrogens or wrong geometries (e.g. planar when you were expecting tetrahedral) then the fix is to delete any wrong-geometry hydrogens, change the atom types as needed (described below), and then add hydrogens again. Charge assignment should be repeated after any manual correction of protonation states. If you want to see what the atom types are: Actions... Label... IDATM type To change atom type, you can use the Build Structure tool, Modify Atom tab, or the command "setattr" -- for example, the following command would change the type of the currently selected atom(s) to N2: setattr a idatmType N2 sel I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jan 12, 2009, at 11:54 AM, CHIU,YEUNG wrote: > Dear colleagues and friends, > > I notice that during "Tools -> Dockprep" and "Tools -> addH" steps > Chimera sometimes will automatically add hydrogens to the > positions considered necessary by the program itself. However, > these positions do not always really have these hydrogens imposed > on them. > > One situation is when I added hydrogen to the molecule containing > nitrogen with lone-pair electrons, Chimera added hydrogen to the > position of this lone-pair. > > One other situation is in the disulfide bond. It seems that > Chimera can not recognize the disulfide bond, so hydrogen is added > to each of the thiol group, which is obviously inappropriate. > > I'm wondering what causes these situations and how users can > prevent them happening. Any help is appreciated. If you > coincidently encountered with similar situation, I'm glad to hear > your story as well~ > > Happy new year and best wishes to your research! > > Sincerely yours > CHIU,YEUNG > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From pett at wooster.edu Mon Jan 12 13:07:08 2009 From: pett at wooster.edu (Virginia Pett) Date: Mon, 12 Jan 2009 16:07:08 -0500 Subject: [Chimera-users] Generating symmetry-related molecule Message-ID: <27C6437B-750C-475D-9150-FCBEE05381AE@wooster.edu> I am trying to display PDB file 2O1I, which is a DNA structure. I would like to generate the biological macromolecule with 2 strands of DNA, but I'm having a hard time figuring out how to do this. The PDB file has BIOMT records in it and I thought I could use the sym command to generate the other strand of DNA. What do I use for the refmol? Is there a tutorial on this topic? Virginia _______________________________ Virginia B. Pett Professor of Chemistry The College of Wooster 943 College Mall Wooster, OH 44691-2363 voice: 330-263-2114 fax: 330-263-2386 From meng at cgl.ucsf.edu Mon Jan 12 13:14:30 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 12 Jan 2009 13:14:30 -0800 Subject: [Chimera-users] Generating symmetry-related molecule In-Reply-To: <27C6437B-750C-475D-9150-FCBEE05381AE@wooster.edu> References: <27C6437B-750C-475D-9150-FCBEE05381AE@wooster.edu> Message-ID: <9DD9F397-5733-41EE-A955-7E23EA015F9B@cgl.ucsf.edu> Hi Virginia, To generate BIOMT-described copies, you would just use the same model as the molecule model and the reference model. For example: open 2o1i sym 0 0 This is mentioned on the "sym" man page, but perhaps it is insufficiently prominent: "A secondary use of sym is to generate BIOMT-described copies of a molecule model, where that model is specified as both molmodel and refmodel." Best, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jan 12, 2009, at 1:07 PM, Virginia Pett wrote: > I am trying to display PDB file 2O1I, which is a DNA structure. I > would like to generate the biological macromolecule with 2 strands of > DNA, but I'm having a hard time figuring out how to do this. The PDB > file has BIOMT records in it and I thought I could use the sym command > to generate the other strand of DNA. What do I use for the refmol? > Is there a tutorial on this topic? > Virginia > _______________________________ > Virginia B. Pett > Professor of Chemistry > The College of Wooster > 943 College Mall > Wooster, OH 44691-2363 > voice: 330-263-2114 > fax: 330-263-2386 > From dchen at caltech.edu Mon Jan 12 13:32:26 2009 From: dchen at caltech.edu (David Chenoweth) Date: Mon, 12 Jan 2009 13:32:26 -0800 Subject: [Chimera-users] precise overlay of ligands Message-ID: Dear Chimera team, Hi! I have two ligands in two different PDB files which have a very similar core structure. I have constructed a framework of dummy atoms based on the centroids of several aromatic rings to use as a positioning system for the two ligands. I have three points/dummy atoms for each ligand in space in their respective pdb files and I would like to overlay or map the three points of one onto the three points of the other so I can make measurements in chimera. Is there a simple way to open the two pdb files, select the three points that belong to each ligand and overlay them (maybe even minimize the rms deviation between them with some kind of fit to the plane defined by the three points). I can do this by hand and get them close but not exact. I would also like to be able to calculate the rms deviation between similar atoms in the core structure if possible. Thanks in advance, Dave Chenoweth ********************************************** David M. Chenoweth California Institute of Technology Division of Chemistry and Chemical Engineering Mail Code: 164-30 1200 California Boulevard, 91125 Pasadena California, USA Phone: 626-395-6074 Email: dchen at caltech.edu ********************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Jan 12 13:33:18 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 12 Jan 2009 13:33:18 -0800 Subject: [Chimera-users] precise overlay of ligands In-Reply-To: References: Message-ID: Hi Dave, With the "match" command you can specify the exact atoms to fit, and the resulting RMSD will be reported in the Reply Log. The main thing to be careful about is specifying the atoms in the proper order. One way is by name, another is to pick them in order from the graphics window (Shift-Ctrl-click). Specifics on how to use the "match" command: More general information on various matching methods: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jan 12, 2009, at 1:32 PM, David Chenoweth wrote: > Dear Chimera team, > > Hi! I have two ligands in two different PDB files which have a very > similar core structure. I have constructed a framework of dummy > atoms based on the centroids of several aromatic rings to use as a > positioning system for the two ligands. I have three points/dummy > atoms for each ligand in space in their respective pdb files and I > would like to overlay or map the three points of one onto the three > points of the other so I can make measurements in chimera. Is there > a simple way to open the two pdb files, select the three points that > belong to each ligand and overlay them (maybe even minimize the rms > deviation between them with some kind of fit to the plane defined by > the three points). I can do this by hand and get them close but not > exact. I would also like to be able to calculate the rms deviation > between similar atoms in the core structure if possible. > > Thanks in advance, > Dave Chenoweth From meng at cgl.ucsf.edu Mon Jan 12 13:56:24 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 12 Jan 2009 13:56:24 -0800 Subject: [Chimera-users] Generating symmetry-related molecule In-Reply-To: <95A7D5C9-9F2D-4FCC-A468-8F35218FE743@wooster.edu> References: <27C6437B-750C-475D-9150-FCBEE05381AE@wooster.edu> <9DD9F397-5733-41EE-A955-7E23EA015F9B@cgl.ucsf.edu> <95A7D5C9-9F2D-4FCC-A468-8F35218FE743@wooster.edu> Message-ID: Hi Virginia, I definitely tried it myself before sending the message, but in a much newer version (daily build Jan 9, 2009!). However, I just now tried it in both 1.2540 and the most recent production release 1.3 (Dec 2008), and in both of those versions the command works either with or without the pound signs (#). The error message sounds like you have additional models besides the DNA structure with model number 0. If so, I think the command would work if you close those, use sym, and then reopen or regenerate them as possible. You may want to update to a newer version to get other new features, but my experiments suggest it will not affect this particular problem. Best, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jan 12, 2009, at 1:41 PM, Virginia Pett wrote: > Elaine, > Thanks for the fast reply! > > I had tried what you suggested. > sym #0 #0 > and just now I tried > sym 0 0 > and generated error message: > Multiple models with id: 0 > > I am using Chimera ver 1.2540 and perhaps the problem is that I need > to update the software? > > Virginia From meng at cgl.ucsf.edu Mon Jan 12 18:35:22 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 12 Jan 2009 18:35:22 -0800 Subject: [Chimera-users] precise overlay of ligands In-Reply-To: References: Message-ID: <116672FE-DE64-44FC-9877-FDAB15FFFF08@cgl.ucsf.edu> Hi Dave, Me again - I forgot to mention that there is also a command to measure RMSD between sets of atoms without fitting them (it just uses their current positions): You could fit on the three pairs of atoms using the "match" command, then use this "rmsd" command to measure RMSD between other sets of atoms without changing the fit. I wasn't sure from your mail whether that was something you wanted to do. Best, Elaine On Jan 12, 2009, at 1:33 PM, Elaine Meng wrote: > Hi Dave, > With the "match" command you can specify the exact atoms to fit, and > the resulting RMSD will be reported in the Reply Log. The main thing > to be careful about is specifying the atoms in the proper order. One > way is by name, another is to pick them in order from the graphics > window (Shift-Ctrl-click). > > Specifics on how to use the "match" command: > > > More general information on various matching methods: > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > > > On Jan 12, 2009, at 1:32 PM, David Chenoweth wrote: > >> Dear Chimera team, >> >> Hi! I have two ligands in two different PDB files which have a very >> similar core structure. I have constructed a framework of dummy >> atoms based on the centroids of several aromatic rings to use as a >> positioning system for the two ligands. I have three points/dummy >> atoms for each ligand in space in their respective pdb files and I >> would like to overlay or map the three points of one onto the three >> points of the other so I can make measurements in chimera. Is there >> a simple way to open the two pdb files, select the three points that >> belong to each ligand and overlay them (maybe even minimize the rms >> deviation between them with some kind of fit to the plane defined by >> the three points). I can do this by hand and get them close but not >> exact. I would also like to be able to calculate the rms deviation >> between similar atoms in the core structure if possible. >> >> Thanks in advance, >> Dave Chenoweth From hsosa at aecom.yu.edu Mon Jan 12 19:39:08 2009 From: hsosa at aecom.yu.edu (hsosa at aecom.yu.edu) Date: Mon, 12 Jan 2009 22:39:08 -0500 Subject: [Chimera-users] Higher order Message-ID: <496C0CDC.3020403@aecom.yu.edu> Is it possible to assign colors by chain to the surfaces created my the multiscale models tool ? Thanks Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa at aecom.yu.edu ----------------------------------- From goddard at cgl.ucsf.edu Tue Jan 13 08:44:28 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Tue, 13 Jan 2009 08:44:28 -0800 Subject: [Chimera-users] Higher order In-Reply-To: <496C0CDC.3020403@aecom.yu.edu> References: <496C0CDC.3020403@aecom.yu.edu> Message-ID: <496CC4EC.8070604@cgl.ucsf.edu> Hi Hernando, Multiscale models assigns colors by chain by default. All copies of chain B will initially get the same color. All copies of chain C get another color. If you wish to change those colors, select a chain surface, click the select Copies button, then use the Color button or the Actions / Color menu (in Chimera 1.3 or newer). Maybe the case you are thinking of is where chains B and C are really copies of the same protein with different conformations. If you select the surface for chain B you can then select all chains which have identical amino acid sequences with shortcut xc, then color those. Now if you have several chains that are the same protein but have different sequences (maybe some residues not observed in some of the copies) then they are not identical. Then you'd just have to hand-select one copy of each chains known to be the same, press the Copies button and color. This is the situation with rice dwarf virus 1uf2. Might be nice to have the ability to extend selection to all chains that have the same chain name (given in PDB file though not currently used in Chimera). Tom hsosa at aecom.yu.edu wrote: > Is it possible to assign colors by chain to the surfaces created my the > multiscale models tool ? > > Thanks > > Hernando > > From bala.biophysics at gmail.com Tue Jan 13 09:57:18 2009 From: bala.biophysics at gmail.com (Bala subramanian) Date: Tue, 13 Jan 2009 18:57:18 +0100 Subject: [Chimera-users] chimera on fedora10 Message-ID: <288df32a0901130957w56c493dej61e22a1536f1ab43@mail.gmail.com> Hello, I installed chimera on fedor10. The installation was done but when I try to open, it gives me the following error. How should i resolve the problem python2.5: can't open file '/usr/local/share/checkOpenGL.py': [Errno 2] No such file or directory Thanks, Bala -------------- next part -------------- An HTML attachment was scrubbed... URL: From dchen at caltech.edu Tue Jan 13 11:31:03 2009 From: dchen at caltech.edu (David Chenoweth) Date: Tue, 13 Jan 2009 11:31:03 -0800 Subject: [Chimera-users] precise overlay of ligands In-Reply-To: <116672FE-DE64-44FC-9877-FDAB15FFFF08@cgl.ucsf.edu> References: <116672FE-DE64-44FC-9877-FDAB15FFFF08@cgl.ucsf.edu> Message-ID: Hi Elaine, Thanks so much for all the advice. I'm still having trouble getting the match/alignment command to work and I'm not quite sure what I'm doing wrong but I think it's in my pdb format. I have attached two files with four atoms in each that I would like to overlay and get the rms deviation for. Maybe you could look at the files and let me know where my formatting mistake is. The files are attached and the coordinates are listed below. They both open in Chimera and work fine but I think maybe the problem lies in chain id #'s or something. Thanks again for your help, Dave 1st pdb file: 2to1_coordinates_test.pdb HETATM 114 B2 CE2 22 8.649 -5.055 13.615 1.00 1.00 B HETATM 115 B3 CE2 22 10.976 -7.450 8.675 1.00 1.00 B HETATM 117 S1 CE3 22 8.845 -8.275 11.641 1.00 1.00 S HETATM 118 S2 CE3 22 10.227 -5.377 10.923 1.00 1.00 S END 2nd pdb file: Cycle_coordinates_test.pdb HETATM 96 B2 CE2 Z 1 -3.480 14.686 -11.018 1.00 1.00 B HETATM 97 B3 CE2 Z 1 -5.877 19.992 -9.560 1.00 1.00 B HETATM 99 S1 CE3 G 1 -6.701 16.412 -10.234 1.00 1.00 S HETATM 107 S9 CE3 G 1 -3.731 17.766 -10.322 1.00 1.00 S END On Jan 12, 2009, at 6:35 PM, Elaine Meng wrote: > Hi Dave, > Me again - I forgot to mention that there is also a command to > measure RMSD between sets of atoms without fitting them (it just > uses their current positions): > > > > You could fit on the three pairs of atoms using the "match" command, > then use this "rmsd" command to measure RMSD between other sets of > atoms without changing the fit. I wasn't sure from your mail whether > that was something you wanted to do. > Best, > Elaine > > On Jan 12, 2009, at 1:33 PM, Elaine Meng wrote: > >> Hi Dave, >> With the "match" command you can specify the exact atoms to fit, and >> the resulting RMSD will be reported in the Reply Log. The main thing >> to be careful about is specifying the atoms in the proper order. One >> way is by name, another is to pick them in order from the graphics >> window (Shift-Ctrl-click). >> >> Specifics on how to use the "match" command: >> >> >> More general information on various matching methods: >> >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> http://www.cgl.ucsf.edu/home/meng/index.html >> >> >> On Jan 12, 2009, at 1:32 PM, David Chenoweth wrote: >> >>> Dear Chimera team, >>> >>> Hi! I have two ligands in two different PDB files which have a very >>> similar core structure. I have constructed a framework of dummy >>> atoms based on the centroids of several aromatic rings to use as a >>> positioning system for the two ligands. I have three points/dummy >>> atoms for each ligand in space in their respective pdb files and I >>> would like to overlay or map the three points of one onto the three >>> points of the other so I can make measurements in chimera. Is there >>> a simple way to open the two pdb files, select the three points that >>> belong to each ligand and overlay them (maybe even minimize the rms >>> deviation between them with some kind of fit to the plane defined by >>> the three points). I can do this by hand and get them close but not >>> exact. I would also like to be able to calculate the rms deviation >>> between similar atoms in the core structure if possible. >>> >>> Thanks in advance, >>> Dave Chenoweth > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 2to1_coordinates_test.pdb Type: application/octet-stream Size: 320 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Cycle_coordinates_test.pdb Type: application/octet-stream Size: 320 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Jan 13 11:38:30 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 13 Jan 2009 11:38:30 -0800 Subject: [Chimera-users] precise overlay of ligands In-Reply-To: References: <116672FE-DE64-44FC-9877-FDAB15FFFF08@cgl.ucsf.edu> Message-ID: <99FEBB20-2B6C-445E-AB01-1F923736E428@cgl.ucsf.edu> Hi Dave, If I open the file 2to1... as model 0 and Cycle... as model 1, then the command in Chimera to fit the 4 pairs of atoms and get the RMSD is: match #0 at b2@b3 at s1@s2 #1 at b2@b3 at s1@s9 or vice versa. The above will move #0 and keep #1 fixed. The RMSD is 0.035 angstroms. If you are using a relatively recent daily build, the following command gives exactly the same result: match #0 at b2,b3,s1,s2 #1 at b2,b3,s1,s9 I was assuming you wanted the atoms to pair in the same order as they are listed in the files. If you wanted to pair the atoms differently, change the order of their names. I'm not sure what you were doing, so I don't know what was causing the problem. Best, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jan 13, 2009, at 11:31 AM, David Chenoweth wrote: > Hi Elaine, > > Thanks so much for all the advice. I'm still having trouble getting > the match/alignment command to work and I'm not quite sure what I'm > doing wrong but I think it's in my pdb format. I have attached two > files with four atoms in each that I would like to overlay and get > the rms deviation for. Maybe you could look at the files and let me > know where my formatting mistake is. The files are attached and the > coordinates are listed below. They both open in Chimera and work > fine but I think maybe the problem lies in chain id #'s or something. > > Thanks again for your help, > Dave > > > 1st pdb file: 2to1_coordinates_test.pdb > > HETATM 114 B2 CE2 22 8.649 -5.055 13.615 1.00 > 1.00 B > HETATM 115 B3 CE2 22 10.976 -7.450 8.675 1.00 > 1.00 B > HETATM 117 S1 CE3 22 8.845 -8.275 11.641 1.00 > 1.00 S > HETATM 118 S2 CE3 22 10.227 -5.377 10.923 1.00 > 1.00 S > END > > > 2nd pdb file: Cycle_coordinates_test.pdb > > HETATM 96 B2 CE2 Z 1 -3.480 14.686 -11.018 1.00 > 1.00 B > HETATM 97 B3 CE2 Z 1 -5.877 19.992 -9.560 1.00 > 1.00 B > HETATM 99 S1 CE3 G 1 -6.701 16.412 -10.234 1.00 > 1.00 S > HETATM 107 S9 CE3 G 1 -3.731 17.766 -10.322 1.00 > 1.00 S > END From hsosa at aecom.yu.edu Tue Jan 13 12:04:04 2009 From: hsosa at aecom.yu.edu (hsosa at aecom.yu.edu) Date: Tue, 13 Jan 2009 15:04:04 -0500 Subject: [Chimera-users] Higher order In-Reply-To: <496CC4EC.8070604@cgl.ucsf.edu> References: <496C0CDC.3020403@aecom.yu.edu> <496CC4EC.8070604@cgl.ucsf.edu> Message-ID: <496CF3B4.3060204@aecom.yu.edu> Thanks Tom, Now I can change the colors on each chain. Another issue is that after displaying the surfaces of a big complex (33 copies as BIOMT entries) chimera seems to freeze for very long periods of time. It may be related to not having enough computer power (Dual Xeon 1.4 GHz,, 1GB RAM, Windows XP, Graphics ATI Radeon 9550, Chimera 1.3) ?. Hernando Tom Goddard wrote: > Hi Hernando, > > Multiscale models assigns colors by chain by default. All copies of > chain B will initially get the same color. All copies of chain C get > another color. If you wish to change those colors, select a chain > surface, click the select Copies button, then use the Color button or > the Actions / Color menu (in Chimera 1.3 or newer). > > Maybe the case you are thinking of is where chains B and C are really > copies of the same protein with different conformations. If you > select the surface for chain B you can then select all chains which > have identical amino acid sequences with shortcut xc, then color > those. Now if you have several chains that are the same protein but > have different sequences (maybe some residues not observed in some of > the copies) then they are not identical. Then you'd just have to > hand-select one copy of each chains known to be the same, press the > Copies button and color. This is the situation with rice dwarf virus > 1uf2. Might be nice to have the ability to extend selection to all > chains that have the same chain name (given in PDB file though not > currently used in Chimera). > > Tom > > > hsosa at aecom.yu.edu wrote: >> Is it possible to assign colors by chain to the surfaces created my >> the multiscale models tool ? >> >> Thanks >> >> Hernando >> >> > > -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa at aecom.yu.edu ----------------------------------- From goddard at cgl.ucsf.edu Tue Jan 13 12:18:15 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Tue, 13 Jan 2009 12:18:15 -0800 Subject: [Chimera-users] Higher order In-Reply-To: <496CF3B4.3060204@aecom.yu.edu> References: <496C0CDC.3020403@aecom.yu.edu> <496CC4EC.8070604@cgl.ucsf.edu> <496CF3B4.3060204@aecom.yu.edu> Message-ID: <496CF707.7080103@cgl.ucsf.edu> Hi Hernando, If you make multiscale surfaces totaling millions of triangles it can take a while to create the surfaces and it can be slow rotating them. To see how many triangles you've got press the select "All" button on the multiscale dialog and then use Actions / Inspect, set the Inspect menu to Surface (probably already set that way) and the last line says "triangles 522960" when I try with the biological unit of 1uf2 and default surface resolution 8 Angstroms. That rotates fast but took several seconds to create the surfaces on my Mac laptop. If you get into millions of triangles it can be quite slow. To speed it up you can set the resolution to a larger value in the multiscale dialog, select all chains and press Resurface. Or set the resolution value larger before you make the model in the first place. With resolution 15 Angstroms I get 121000 triangles for 1uf2. Tom hsosa at aecom.yu.edu wrote: > Thanks Tom, Now I can change the colors on each chain. > Another issue is that after displaying the surfaces of a big complex (33 > copies as BIOMT entries) chimera seems to freeze for very long periods > of time. It may be related to not having enough computer power (Dual > Xeon 1.4 GHz,, 1GB RAM, Windows XP, Graphics ATI Radeon 9550, Chimera > 1.3) ?. > > Hernando > > Tom Goddard wrote: > >> Hi Hernando, >> >> Multiscale models assigns colors by chain by default. All copies of >> chain B will initially get the same color. All copies of chain C get >> another color. If you wish to change those colors, select a chain >> surface, click the select Copies button, then use the Color button or >> the Actions / Color menu (in Chimera 1.3 or newer). >> >> Maybe the case you are thinking of is where chains B and C are really >> copies of the same protein with different conformations. If you >> select the surface for chain B you can then select all chains which >> have identical amino acid sequences with shortcut xc, then color >> those. Now if you have several chains that are the same protein but >> have different sequences (maybe some residues not observed in some of >> the copies) then they are not identical. Then you'd just have to >> hand-select one copy of each chains known to be the same, press the >> Copies button and color. This is the situation with rice dwarf virus >> 1uf2. Might be nice to have the ability to extend selection to all >> chains that have the same chain name (given in PDB file though not >> currently used in Chimera). >> >> Tom >> >> >> hsosa at aecom.yu.edu wrote: >> >>> Is it possible to assign colors by chain to the surfaces created my >>> the multiscale models tool ? >>> >>> Thanks >>> >>> Hernando >>> >>> >>> >> > > From dchen at caltech.edu Tue Jan 13 13:36:11 2009 From: dchen at caltech.edu (David Chenoweth) Date: Tue, 13 Jan 2009 13:36:11 -0800 Subject: [Chimera-users] Coloring bonds/sticks independent of the atom color Message-ID: Dear Chimera team, Is it possible to color bonds / sticks independent of the atoms so that I could have colored balls corresponding to atom types but have all the sticks connecting the balls/atoms to be a different color or colors. Thanks again, Dave From meng at cgl.ucsf.edu Tue Jan 13 13:45:53 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 13 Jan 2009 13:45:53 -0800 Subject: [Chimera-users] Coloring bonds/sticks independent of the atom color In-Reply-To: References: Message-ID: Hi Dave, Yes, see command "bondcolor": Best, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jan 13, 2009, at 1:36 PM, David Chenoweth wrote: > Dear Chimera team, > > Is it possible to color bonds / sticks independent of the atoms so > that I could have colored balls corresponding to atom types but have > all the sticks connecting the balls/atoms to be a different color or > colors. > > Thanks again, > Dave From rabyrd at ncifcrf.gov Tue Jan 13 20:17:59 2009 From: rabyrd at ncifcrf.gov (R. Andrew Byrd) Date: Tue, 13 Jan 2009 23:17:59 -0500 Subject: [Chimera-users] Saving a Morph movie Message-ID: <1231906679.496d677784acb@webmail.ncifcrf.gov> Greetings, I have been trying to use the Morph tool in the production release from summer 2008. The tool works very well and allows playing the trajectory in the graphics window. However, when I try to save the file as a movie, it consistently crashes. I am running Win XP SP3, on a Dell M1330 laptop. It has also crashed on a Dell desktop running XP SP3. Are there special tricks to saving the movie for use in a Powerpoint presentation? Thanks for any help/suggestions! Andy ------------------------------------------------- From pett at cgl.ucsf.edu Wed Jan 14 11:35:28 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 14 Jan 2009 11:35:28 -0800 Subject: [Chimera-users] Saving a Morph movie In-Reply-To: <1231906679.496d677784acb@webmail.ncifcrf.gov> References: <1231906679.496d677784acb@webmail.ncifcrf.gov> Message-ID: <81775F71-4438-4B68-BE29-D2BE024E1FC8@cgl.ucsf.edu> On Jan 13, 2009, at 8:17 PM, R. Andrew Byrd wrote: > Greetings, > I have been trying to use the Morph tool in the production release > from summer > 2008. The tool works very well and allows playing the trajectory in > the > graphics window. However, when I try to save the file as a movie, it > consistently crashes. I am running Win XP SP3, on a Dell M1330 > laptop. It has > also crashed on a Dell desktop running XP SP3. Hi Andy, I guess I have a few questions. When you "save the file as a movie", are you using File->Record Movie... from the movie-playing interface, or the Movie Recorder tool (in Utilities)? Probably the former (which is what you should use) but I just want to make sure. And when "it crashes" is Chimera completely quitting or are you getting an error dialog? If the latter, you should use the "Report Bug" button in the error dialog to report the bug since that will give us additional info about your system and what Chimera was doing when it crashed. If Chimera is completely crashing, you should probably first upgrade to the 1.3 release, which has some fixes specifically for lower-end Windows graphics cards. If that release still crashes, use the Help- >Report a Bug... menu item to make a bug report, which will include details about your system as above. I can then give you a few things to try and we can try to replicate your error here in our lab. > Are there special tricks to saving the movie for use in a Powerpoint > presentation? There are. See: Making Movies --Eric -------------- next part -------------- An HTML attachment was scrubbed... URL: From rabyrd at ncifcrf.gov Wed Jan 14 11:44:18 2009 From: rabyrd at ncifcrf.gov (R. Andrew Byrd) Date: Wed, 14 Jan 2009 14:44:18 -0500 Subject: [Chimera-users] Saving a Morph movie In-Reply-To: <81775F71-4438-4B68-BE29-D2BE024E1FC8@cgl.ucsf.edu> References: <1231906679.496d677784acb@webmail.ncifcrf.gov> <81775F71-4438-4B68-BE29-D2BE024E1FC8@cgl.ucsf.edu> Message-ID: <1231962258.496e409215220@webmail.ncifcrf.gov> Thanks Eric, I had already tried the download of the latest production release...and this fixed the problem. For others...I was using the File>Record Movie. It yielded an Error dialog. It seems that things are fixed in the latest version, and it worked well. As for Powerpoint...I have used the help docs and used movies often prior to this. I was only wondering if there was something special about the MORPH Movie creation...seems the answer is no in the latest release. Andy Quoting Eric Pettersen : > On Jan 13, 2009, at 8:17 PM, R. Andrew Byrd wrote: > > > Greetings, > > I have been trying to use the Morph tool in the production release > > from summer > > 2008. The tool works very well and allows playing the trajectory in > > the > > graphics window. However, when I try to save the file as a movie, it > > consistently crashes. I am running Win XP SP3, on a Dell M1330 > > laptop. It has > > also crashed on a Dell desktop running XP SP3. > > Hi Andy, > I guess I have a few questions. When you "save the file as a movie", > are you using File->Record Movie... from the movie-playing interface, > or the Movie Recorder tool (in Utilities)? Probably the former (which > is what you should use) but I just want to make sure. And when "it > crashes" is Chimera completely quitting or are you getting an error > dialog? If the latter, you should use the "Report Bug" button in the > error dialog to report the bug since that will give us additional info > about your system and what Chimera was doing when it crashed. > If Chimera is completely crashing, you should probably first upgrade > to the 1.3 release, which has some fixes specifically for lower-end > Windows graphics cards. If that release still crashes, use the Help- > >Report a Bug... menu item to make a bug report, which will include > details about your system as above. I can then give you a few things > to try and we can try to replicate your error here in our lab. > > > Are there special tricks to saving the movie for use in a Powerpoint > > presentation? > > There are. See: Making Movies > > --Eric ------------------------------------------------- From pett at cgl.ucsf.edu Wed Jan 14 12:04:37 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 14 Jan 2009 12:04:37 -0800 Subject: [Chimera-users] Saving a Morph movie In-Reply-To: <1231962258.496e409215220@webmail.ncifcrf.gov> References: <1231906679.496d677784acb@webmail.ncifcrf.gov> <81775F71-4438-4B68-BE29-D2BE024E1FC8@cgl.ucsf.edu> <1231962258.496e409215220@webmail.ncifcrf.gov> Message-ID: On Jan 14, 2009, at 11:44 AM, R. Andrew Byrd wrote: > Thanks Eric, > > I had already tried the download of the latest production > release...and this > fixed the problem. Great! > For others...I was using the File>Record Movie. It yielded an Error > dialog. > It seems that things are fixed in the latest version, and it worked > well. > > As for Powerpoint...I have used the help docs and used movies often > prior to > this. I was only wondering if there was something special about the > MORPH Movie > creation...seems the answer is no in the latest release. Right, all the Chimera movie-saving mechanisms use the same underlying code base so they all produce the same results -- and all have the same strengths and weaknesses. --Eric From gregc at cgl.ucsf.edu Wed Jan 14 12:19:00 2009 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Wed, 14 Jan 2009 12:19:00 -0800 (PST) Subject: [Chimera-users] chimera on fedora10 In-Reply-To: <288df32a0901130957w56c493dej61e22a1536f1ab43@mail.gmail.com> References: <288df32a0901130957w56c493dej61e22a1536f1ab43@mail.gmail.com> Message-ID: On Tue, 13 Jan 2009, Bala subramanian wrote: > Hello, > > I installed chimera on fedor10. The installation was done but when I try to > open, it gives me the following error. How should i resolve the problem > > python2.5: can't open file '/usr/local/share/checkOpenGL.py': [Errno 2] No > such file or directory > > Thanks, > Bala Do you have the CHIMERA environment set? If so, it must be set to the top of the chimera installation, i.e., the directory you gave when you installed chimera. If not, we'll need to dig deeper into how you installed and are invoking chimera (but no other explanation seems possible). Type "env CHIMERA" to see the current value. And "unset CHIMERA" to clear it in bash/sh or "unsetenv CHIMERA" in csh/tcsh. It is best left unset. And for Linux users, I'd like to recommend that you not put the chimera/bin directory on your path, but instead put a symbolic link to the chimera executable in one of the directories on your PATH. For example, if chimera is installed in /opt/chimera and ~/bin is on your path, then ln -s /opt/chimera/bin/chimera ~/bin You could also place a symbolic link on your Desktop, so you can double-click on it to start chimera up: ln -s /opt/chimera/bin/chimera ~/Desktop Good luck and please let me know if I figured out your bug or not, Greg Couch UCSF Computer Graphics Lab From emailanindito at yahoo.co.in Wed Jan 14 12:45:29 2009 From: emailanindito at yahoo.co.in (Anindito Sen) Date: Thu, 15 Jan 2009 02:15:29 +0530 (IST) Subject: [Chimera-users] Docking crystal structure in density map Message-ID: <127924.18684.qm@web8507.mail.in.yahoo.com> Dear All I have docked the crystal structure of a protein monomer manually in the density map ( of a filament) and with some movements done with a long alpha helix(part of the crystal structure) to make a decent fit. However when I generated multiple copies of the docked structure- regions where manual adjustments on the alpha helix were made- came out like thin wires instead of being a ribbon. Thanks Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908 -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Jan 14 13:21:45 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 14 Jan 2009 13:21:45 -0800 Subject: [Chimera-users] Docking crystal structure in density map In-Reply-To: <127924.18684.qm@web8507.mail.in.yahoo.com> References: <127924.18684.qm@web8507.mail.in.yahoo.com> Message-ID: <8E8D16C3-0F56-479A-9FF8-D38955CCE3B8@cgl.ucsf.edu> Hi Andy, Probably the adjustments to the coordinates caused them not be recognized as "helix" - however, you can force them to be labeled as helix as follows: - select all the residues you want to be labeled as "helix" (there are many different ways, and it depends on the details of your situation which is easiest... if your copies all have the same residue numbering, you could do something like use the command "select : 43-57.a,103-119.b" which would select residues 43-57 in chain A and 103-119 in chain B in all models... but there are many other possible routes) - open the Selection Inspector (by clicking the greenish button on the bottom right corner of the Chimera window or choosing menu item Actions... Inspect) -- in that dialog, Inspect "Residue" and change "in helix" to "true" I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jan 14, 2009, at 12:45 PM, Anindito Sen wrote: > Dear All > I have docked the crystal structure of a protein monomer manually in > the density map ( of a filament) and with some movements done with a > long alpha helix(part of the crystal structure) to make a decent > fit. However when I generated multiple copies of the docked > structure- regions where manual adjustments on the alpha helix were > made- came out like thin wires instead of being a ribbon. > Thanks > Andy From goddard at cgl.ucsf.edu Wed Jan 14 16:44:27 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Wed, 14 Jan 2009 16:44:27 -0800 Subject: [Chimera-users] Rotating about an axis In-Reply-To: References: Message-ID: <496E86EB.30604@cgl.ucsf.edu> Hi Kevin, The command "turn x 23" will rotate active models about the screen x axis by 23 degrees. The command "turn 1,1,0 180 center 0,2.5,2.5 coord #1 models #1" rotates just model #1 by 180 degrees about axis 1,1,0 defined in the local coordinates of model #1 about center point 0,2.5,2.5 also in model #1 local coordinates. The fancier forms of the turn command are only in Chimera 1.4 daily builds. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html You align multiple structures by aligning them all to one reference structure. You can align specific residues with the "match" command: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html Do do a sequence based structure alignment look at the MatchMaker tool or command: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html Best to send questions to chimera-users at cgl.ucsf.edu. Tom Kevin Koehntop wrote: > Hi Tom, > > In Chimera, how do you rotate a structure along an axis by X degrees? > How is the specific axis selected? Finally, is it possible to align > multiple structures (e.g. their tops, bottoms, centers, etc.)? Thank you > > Kevin From meng at cgl.ucsf.edu Thu Jan 15 10:12:41 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 15 Jan 2009 10:12:41 -0800 Subject: [Chimera-users] Protskin In-Reply-To: References: Message-ID: <1170EFC9-0DAE-4619-9F22-A7AEEC85FEF3@cgl.ucsf.edu> On Jan 15, 2009, at 7:07 AM, Patton, John (NIH/NIAID) wrote: > > Hi Elaine, > Do you have any information concerning using Protskin in conjunction > with > Chimera? The only information I have come across applies to PyMol. > Thanks, > John Hi John, I haven't tried Protskin, but my understanding is that its purpose is to map conservation in a multiple sequence alignment to protein display. (Protskin page: ) Chimera itself can (A) read your multiple sequence alignment (many formats, just use File... Open) (B) calculate any of several measures of conservation (entropy, variability, etc.) - in the sequence window menu, choose Preferences... Analysis, set "Conservation style" to "AL2CO" to access further options for calculating conservation, which is shown as a histogram above the alignment (C) show them on your structure(s) with any color mapping you desire, or with "worm" thickness - any open structure(s) will associate automatically with sequence(s) in the alignment - in the sequence window menu, choose Structure... Render by Conservation, change attribute to "mavConservation" and show with color or worms Example image, 1bzm colored by conservation in PFAM Carb_anhydrase seed alignment: This tutorial includes coloring by conservation: Back to ProtSkin: ----------------- It sounds like ProtSkin emits some file listing the residues and associated values. Certainly you could reformat that into a Chimera "define attribute" file, read it in, and then show the values as in (C) above. Since Chimera already performs the preceding steps quite well and with many powerful options, there hasn't been much impetus to hooking it up to ProtSkin. However, I don't see any barrier other than your needing to convert the output file into the simple "define attribute" format described here: Getting a sequence alignment: ----------------------------- Perhaps you didn't already have a sequence alignment, and find ProtSkin to be helpful in generating one. There are many alternative approaches. For example, the ConSurf server does a great job of automatically generating an alignment of a diverse set of sequences related to your single uploaded structure. (ConSurf server: ) There are more ideas in this page I wrote on "sources of sequence alignments" for use in Chimera: I would be happy provide more detailed help on using Chimera to color by conservation as it applies to your system of interest, i.e. feel free to write back. Best, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html From matthewd at bcm.edu Sun Jan 18 19:56:42 2009 From: matthewd at bcm.edu (Matthew Dougherty) Date: Sun, 18 Jan 2009 21:56:42 -0600 Subject: [Chimera-users] command files Message-ID: <83827820-FE20-4963-A7CF-13A86694BE99@bcm.edu> I have a command file that has a number of reset commands. I would like to 1) interrupt a command file during execution, aborting all further commands, stopping the graphics configuration at the abort (e.g. threshold values, active models, etc) 2) be able to place a hold in a command file, say after the a reset command, and be able to continue the command processing after pressing a key on the keyboard. Does this capability exist? thanks, Matt From hsosa at aecom.yu.edu Mon Jan 19 12:45:22 2009 From: hsosa at aecom.yu.edu (hsosa at aecom.yu.edu) Date: Mon, 19 Jan 2009 15:45:22 -0500 Subject: [Chimera-users] Matchmaker Message-ID: <4974E662.2070108@aecom.yu.edu> Is it possible to retrieve the transformation matrix (or angle of rotation and translation) that the Matchmaker tool used to align two atomic models ?. I know that you can get this information when fitting an atomic model into a density map using the tool Fit in Map and then pressing the Results button. Is there anything similar for the MatchMaker tool ?. Thanks Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa at aecom.yu.edu ----------------------------------- From goddard at cgl.ucsf.edu Tue Jan 20 10:25:30 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Tue, 20 Jan 2009 10:25:30 -0800 Subject: [Chimera-users] Matchmaker In-Reply-To: <4974E662.2070108@aecom.yu.edu> References: <4974E662.2070108@aecom.yu.edu> Message-ID: <4976171A.6040705@cgl.ucsf.edu> Hi Hernando, Just a week ago I added a Chimera command that will do this: measure rotation #0 #1 reports in the reply log the same info about the orientation of model #0 relative to model #1 that the Fit Map tool does. You can abbreviate the command "me rot #0 #1". It also displays the rotation axis and that can't currently be turned off. This command is so new it has not yet been documented. You'll need a current daily build to use it. Tom hsosa at aecom.yu.edu wrote: > Is it possible to retrieve the transformation matrix (or angle of > rotation and translation) that the Matchmaker tool used to align two > atomic models ?. > > I know that you can get this information when fitting an atomic model > into a density map using the tool Fit in Map and then pressing the > Results button. Is there anything similar for the MatchMaker tool ?. > > Thanks > > Hernando > > > From martin.kampmann at mail.rockefeller.edu Tue Jan 20 12:09:04 2009 From: martin.kampmann at mail.rockefeller.edu (Martin Kampmann) Date: Tue, 20 Jan 2009 15:09:04 -0500 Subject: [Chimera-users] Coulombic Surface Coloring Message-ID: <0E3FF679-A9D0-4C35-8731-FC7FFDDA0772@rockefeller.edu> Hello, I saw on the Chimera online manual that there is a Coulombic Surface Coloring function, which displays an approximate electrostatic potential without having to calculate a file with delphi etc. This sounds great and I would love to use the function. However, in the Tools > Surface/Binding Analysis menu, I don't find it. Is it something to be implemented in future versions of Chimera? Or is there a way of using it in the current release (I have version 1.3 build 2577 from December 9) Thanks a lot! Martin From chiendarret at gmail.com Tue Jan 20 14:18:01 2009 From: chiendarret at gmail.com (Francesco Pietra) Date: Tue, 20 Jan 2009 23:18:01 +0100 Subject: [Chimera-users] marginal issues on installation (linux) Message-ID: hi: replaced hd, installed chimera-1.3.2577-linux.exe on debian i386 lenny ok, though i have to give the full path /usr/local/chimera/bin/./chimera to launch chimera. notice that the directory /chimera is chown to me as user. with previous versions and debian i386 etch (last installation daily built 17 Sept 2008), execution of chimera from anywhere was provided on installation. never mind, are there available env variables for the executable? thanks francesco pietra From gregc at cgl.ucsf.edu Tue Jan 20 14:31:32 2009 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Tue, 20 Jan 2009 14:31:32 -0800 (PST) Subject: [Chimera-users] marginal issues on installation (linux) In-Reply-To: References: Message-ID: On Tue, 20 Jan 2009, Francesco Pietra wrote: > hi: > replaced hd, installed chimera-1.3.2577-linux.exe on debian i386 lenny > > ok, though i have to give the full path > > /usr/local/chimera/bin/./chimera > > to launch chimera. notice that the directory /chimera is chown to me > as user. with previous versions and debian i386 etch (last > installation daily built 17 Sept 2008), execution of chimera from > anywhere was provided on installation. never mind, are there available > env variables for the executable? > > thanks > francesco pietra So what's going wrong exactly? You only have to give the full path if the chimera executable is not on your shell's path nor do you have a symbolic link to it (e.g., ln -s /usr/local/chimera/bin/chimera ~/bin/chimera and ~/bin is on your shell's path). The chimera installation does not make that symbolic link. The only enviroment variable you might want to use with chimera is the CHIMERA_PATH enviroment variable. It replaces PYTHON_PATH for chimera's python, so it can be different from the PYTHON_PATH your system python uses. Greg Couch UCSF Computer Graphics Lab From chiendarret at gmail.com Tue Jan 20 14:37:08 2009 From: chiendarret at gmail.com (Francesco Pietra) Date: Tue, 20 Jan 2009 23:37:08 +0100 Subject: [Chimera-users] Fwd: marginal issues on installation (linux) In-Reply-To: References: Message-ID: Sorry. please disregard this mail. I did some mistake. actually, setting the PATH is enough francesco ---------- Forwarded message ---------- From: Francesco Pietra Date: Tue, Jan 20, 2009 at 11:18 PM Subject: marginal issues on installation (linux) To: chimera hi: replaced hd, installed chimera-1.3.2577-linux.exe on debian i386 lenny ok, though i have to give the full path /usr/local/chimera/bin/./chimera to launch chimera. notice that the directory /chimera is chown to me as user. with previous versions and debian i386 etch (last installation daily built 17 Sept 2008), execution of chimera from anywhere was provided on installation. never mind, are there available env variables for the executable? thanks francesco pietra From meng at cgl.ucsf.edu Tue Jan 20 15:00:49 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 20 Jan 2009 15:00:49 -0800 Subject: [Chimera-users] Coulombic Surface Coloring In-Reply-To: <0E3FF679-A9D0-4C35-8731-FC7FFDDA0772@rockefeller.edu> References: <0E3FF679-A9D0-4C35-8731-FC7FFDDA0772@rockefeller.edu> Message-ID: <8F51C3EF-E9F9-4DBE-9D62-EED062541BDC@cgl.ucsf.edu> Hi Martin, You must be looking at the "development" documentation online. The Coulombic Surface Coloring tool was added after release 1.3, so to use it you would want to get a Chimera daily build (just give that a different name or put it in a different place if you want to also keep 1.3 around). Daily build download: Here is the list of what's new since the production release: Best, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jan 20, 2009, at 12:09 PM, Martin Kampmann wrote: > Hello, > > I saw on the Chimera online manual that there is a Coulombic Surface > Coloring function, which displays an approximate electrostatic > potential without having to calculate a file with delphi etc. > > This sounds great and I would love to use the function. > > However, in the Tools > Surface/Binding Analysis menu, I don't find > it. > > Is it something to be implemented in future versions of Chimera? > Or is there a way of using it in the current release (I have version > 1.3 build 2577 from December 9) > > Thanks a lot! > Martin From pett at cgl.ucsf.edu Tue Jan 20 15:46:35 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 20 Jan 2009 15:46:35 -0800 Subject: [Chimera-users] command files In-Reply-To: <83827820-FE20-4963-A7CF-13A86694BE99@bcm.edu> References: <83827820-FE20-4963-A7CF-13A86694BE99@bcm.edu> Message-ID: On Jan 18, 2009, at 7:56 PM, Matthew Dougherty wrote: > I have a command file that has a number of reset commands. > > I would like to > 1) interrupt a command file during execution, aborting all further > commands, stopping the graphics configuration at the abort (e.g. > threshold values, active models, etc) > 2) be able to place a hold in a command file, say after the a reset > command, and be able to continue the command processing after pressing > a key on the keyboard. > > Does this capability exist? We don't have #1, though it used to exist in Midas by pressing the Escape key during script execution. I will open a feature request in our Trac database to get this capability back. It will probably take a couple of months for me to get to it. You'll get automated mail from Trac when the implementation happens. I went ahead and implemented #2 since I thought it would be trivial. It turned out to be a little less trivial than I had thought, but not too bad. It will be available as the "pause" command starting with tonight's daily builds. I don't know what your need for these commands are precisely, but you should be aware that the Demo capability of Chimera offers #2 already, though maybe creating a demo is a little more elaborate than what you want. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From n.a.ranson at leeds.ac.uk Wed Jan 21 07:48:08 2009 From: n.a.ranson at leeds.ac.uk (Neil Ranson) Date: Wed, 21 Jan 2009 15:48:08 +0000 Subject: [Chimera-users] transparency change for a whole model Message-ID: Dear All, I am revisiting a movie I made in chimera some time ago with a painfully long script. In this script, I used a command syntax like this: transition transparency #0 0 0.1 1 copy file 'filename' To change the global transparency of model #0 (with lots of different elements all coloured and represented differently) This command seems to have disappeared. Is there an equivalent way now? The only way I can find is to use transparency in the colordef command, but that will be extremely cumbersome. What is the preferred way to fade a model in and out now? Thanks in advance, Neil Ranson Neil Ranson PhD Level 2 Biochemistry Tutor University Research Fellow Astbury Centre for Structural Molecular Biology IMCB University of Leeds, Leeds, LS2 9JT, UK. EM Image Processing Suite - Miall 6.02 Tel: 44 (0) 113 343 7065 email: n.a.ranson at leeds.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Wed Jan 21 09:18:49 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Wed, 21 Jan 2009 09:18:49 -0800 Subject: [Chimera-users] transparency change for a whole model In-Reply-To: References: Message-ID: <497758F9.1020005@cgl.ucsf.edu> Hi Neil, The "transition" command comes from a Chimera plug-in (not distributed by default). The plug-in is on the "Experimental Features" web page and is called "Animation Commands". Unfortunately we do not have any built-in capability to do color fades. Tom Neil Ranson wrote: > Dear All, > I am revisiting a movie I made in chimera some time ago with a > painfully long script. > In this script, I used a command syntax like this: > > transition transparency #0 0 0.1 1 > copy file 'filename' > > To change the global transparency of model #0 (with lots of different > elements all coloured and represented differently) > This command seems to have disappeared. Is there an equivalent way > now? The only way I can find is to use transparency in the colordef > command, but that will be extremely cumbersome. What is the preferred > way to fade a model in and out now? > > Thanks in advance, > Neil Ranson > > Neil Ranson PhD > Level 2 Biochemistry Tutor > University Research Fellow > Astbury Centre for Structural Molecular Biology > IMCB > University of Leeds, Leeds, LS2 9JT, UK. > > EM Image Processing Suite - Miall 6.02 > Tel: 44 (0) 113 343 7065 > email: n.a.ranson at leeds.ac.uk > > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > From hsosa at aecom.yu.edu Wed Jan 21 10:02:30 2009 From: hsosa at aecom.yu.edu (hsosa at aecom.yu.edu) Date: Wed, 21 Jan 2009 13:02:30 -0500 Subject: [Chimera-users] Higher Order In-Reply-To: <496CF707.7080103@cgl.ucsf.edu> References: <496C0CDC.3020403@aecom.yu.edu> <496CC4EC.8070604@cgl.ucsf.edu> <496CF3B4.3060204@aecom.yu.edu> <496CF707.7080103@cgl.ucsf.edu> Message-ID: <49776336.4090704@aecom.yu.edu> Dear Tom , Elaine David Thanks a lot for the help. As suggested we placed helical symmetry information in the BIOMT entries of the PDB file (3EDL). A representation of the molecule made with chimera using the Higher Order Structures tool and PovRay is attached. As mentioned making these type of figures in my computer was relatively slow. What would be the best graphic card choice to accelerate the display and manipulation of surfaces ? (I need to replace the graphic card anyway). A graphic card with the biggest amount of graphics memory ?. From your benchmark scores it seems that memory is not the most important parameter, right ?. Would the Quadro FX 1700 be the best choice to display many surfaces ?. Thanks again Hernando Tom Goddard wrote: > Hi Hernando, > > If you make multiscale surfaces totaling millions of triangles it can > take a while to create the surfaces and it can be slow rotating them. > To see how many triangles you've got press the select "All" button on > the multiscale dialog and then use Actions / Inspect, set the Inspect > menu to Surface (probably already set that way) and the last line says > "triangles 522960" when I try with the biological unit of 1uf2 and > default surface resolution 8 Angstroms. That rotates fast but took > several seconds to create the surfaces on my Mac laptop. If you get > into millions of triangles it can be quite slow. To speed it up you > can set the resolution to a larger value in the multiscale dialog, > select all chains and press Resurface. Or set the resolution value > larger before you make the model in the first place. With resolution > 15 Angstroms I get 121000 triangles for 1uf2. > > Tom > > > hsosa at aecom.yu.edu wrote: >> Thanks Tom, Now I can change the colors on each chain. >> Another issue is that after displaying the surfaces of a big complex >> (33 copies as BIOMT entries) chimera seems to freeze for very long >> periods of time. It may be related to not having enough computer >> power (Dual Xeon 1.4 GHz,, 1GB RAM, Windows XP, Graphics ATI Radeon >> 9550, Chimera 1.3) ?. >> >> Hernando >> >> Tom Goddard wrote: >> >>> Hi Hernando, >>> >>> Multiscale models assigns colors by chain by default. All copies >>> of chain B will initially get the same color. All copies of chain C >>> get another color. If you wish to change those colors, select a >>> chain surface, click the select Copies button, then use the Color >>> button or the Actions / Color menu (in Chimera 1.3 or newer). >>> >>> Maybe the case you are thinking of is where chains B and C are >>> really copies of the same protein with different conformations. If >>> you select the surface for chain B you can then select all chains >>> which have identical amino acid sequences with shortcut xc, then >>> color those. Now if you have several chains that are the same >>> protein but have different sequences (maybe some residues not >>> observed in some of the copies) then they are not identical. Then >>> you'd just have to hand-select one copy of each chains known to be >>> the same, press the Copies button and color. This is the situation >>> with rice dwarf virus 1uf2. Might be nice to have the ability to >>> extend selection to all chains that have the same chain name (given >>> in PDB file though not currently used in Chimera). >>> >>> Tom >>> >>> >>> hsosa at aecom.yu.edu wrote: >>> >>>> Is it possible to assign colors by chain to the surfaces created >>>> my the multiscale models tool ? >>>> >>>> Thanks >>>> >>>> Hernando >>>> >>>> >>> >> >> > > -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa at aecom.yu.edu ----------------------------------- -------------- next part -------------- A non-text attachment was scrubbed... Name: ring_povray3.jpg Type: image/jpeg Size: 149265 bytes Desc: not available URL: From goddard at cgl.ucsf.edu Wed Jan 21 11:30:43 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Wed, 21 Jan 2009 11:30:43 -0800 Subject: [Chimera-users] Higher Order In-Reply-To: <49776336.4090704@aecom.yu.edu> References: <496C0CDC.3020403@aecom.yu.edu> <496CC4EC.8070604@cgl.ucsf.edu> <496CF3B4.3060204@aecom.yu.edu> <496CF707.7080103@cgl.ucsf.edu> <49776336.4090704@aecom.yu.edu> Message-ID: <497777E3.7000306@cgl.ucsf.edu> Hi Hernando, From your image it looks like your surface has a lot of detail -- a lot of triangles. A fast graphics card will allow you to rotate it more smoothly. It won't speed up calculating the surface the first time you show it. The Chimera graphics benchmark page is the best info I have about cards: http://www.cgl.ucsf.edu/chimera/benchmarks.html The top two cards in the table differ by a factor of 3 in price but by just a tiny amount in surface rendering speed. So it depends how much money you want to spend. The top half of the table are all pretty fast. And many standard cards like Geforce 8800 GTX are not even listed. A second probably more important consideration is how buggy is the graphics driver for the card. Our information on this is incomplete and out of date. Here's that info: http://www.cgl.ucsf.edu/chimera/graphics/graphicsbugs.html#cards Tom hsosa at aecom.yu.edu wrote: > Dear Tom , Elaine David > > Thanks a lot for the help. As suggested we placed helical symmetry > information in the BIOMT entries of the PDB file (3EDL). A > representation of the molecule made with chimera using the Higher > Order Structures tool and PovRay is attached. > As mentioned making these type of figures in my computer was > relatively slow. What would be the best graphic card choice to > accelerate the display and manipulation of surfaces ? (I need to > replace the graphic card anyway). A graphic card with the biggest > amount of graphics memory ?. From your benchmark scores it seems > that memory is not the most important parameter, right ?. Would the > Quadro FX 1700 be the best choice to display many surfaces ?. > > > Thanks again > > Hernando > > Tom Goddard wrote: >> Hi Hernando, >> >> If you make multiscale surfaces totaling millions of triangles it >> can take a while to create the surfaces and it can be slow rotating >> them. To see how many triangles you've got press the select "All" >> button on the multiscale dialog and then use Actions / Inspect, set >> the Inspect menu to Surface (probably already set that way) and the >> last line says "triangles 522960" when I try with the biological unit >> of 1uf2 and default surface resolution 8 Angstroms. That rotates >> fast but took several seconds to create the surfaces on my Mac >> laptop. If you get into millions of triangles it can be quite slow. >> To speed it up you can set the resolution to a larger value in the >> multiscale dialog, select all chains and press Resurface. Or set the >> resolution value larger before you make the model in the first >> place. With resolution 15 Angstroms I get 121000 triangles for 1uf2. >> >> Tom >> >> >> hsosa at aecom.yu.edu wrote: >>> Thanks Tom, Now I can change the colors on each chain. >>> Another issue is that after displaying the surfaces of a big complex >>> (33 copies as BIOMT entries) chimera seems to freeze for very long >>> periods of time. It may be related to not having enough computer >>> power (Dual Xeon 1.4 GHz,, 1GB RAM, Windows XP, Graphics ATI >>> Radeon 9550, Chimera 1.3) ?. >>> >>> Hernando >>> >>> Tom Goddard wrote: >>> >>>> Hi Hernando, >>>> >>>> Multiscale models assigns colors by chain by default. All copies >>>> of chain B will initially get the same color. All copies of chain >>>> C get another color. If you wish to change those colors, select a >>>> chain surface, click the select Copies button, then use the Color >>>> button or the Actions / Color menu (in Chimera 1.3 or newer). >>>> >>>> Maybe the case you are thinking of is where chains B and C are >>>> really copies of the same protein with different conformations. If >>>> you select the surface for chain B you can then select all chains >>>> which have identical amino acid sequences with shortcut xc, then >>>> color those. Now if you have several chains that are the same >>>> protein but have different sequences (maybe some residues not >>>> observed in some of the copies) then they are not identical. Then >>>> you'd just have to hand-select one copy of each chains known to be >>>> the same, press the Copies button and color. This is the situation >>>> with rice dwarf virus 1uf2. Might be nice to have the ability to >>>> extend selection to all chains that have the same chain name (given >>>> in PDB file though not currently used in Chimera). >>>> >>>> Tom >>>> >>>> >>>> hsosa at aecom.yu.edu wrote: >>>> >>>>> Is it possible to assign colors by chain to the surfaces created >>>>> my the multiscale models tool ? >>>>> >>>>> Thanks >>>>> >>>>> Hernando >>>>> >>>>> >>>> >>> >>> >> >> > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > From matthewd at bcm.edu Wed Jan 21 17:05:33 2009 From: matthewd at bcm.edu (Matthew Dougherty) Date: Wed, 21 Jan 2009 19:05:33 -0600 Subject: [Chimera-users] suggested feature/model panel Message-ID: <5AD417B4-0A63-46DB-9627-11BF3F1344F6@bcm.edu> 1) ability to create folders in the model panel so models can be grouped 2) ability to have a model in multiple folders 3) ability to show/hide in a folder by a a single checkbox 4) ability to name the folder From emailanindito at yahoo.co.in Wed Jan 21 20:53:13 2009 From: emailanindito at yahoo.co.in (Anindito Sen) Date: Thu, 22 Jan 2009 10:23:13 +0530 (IST) Subject: [Chimera-users] Chimera on Ubuntu mounted on MAC using VMware Fusion Message-ID: <170804.63209.qm@web8508.mail.in.yahoo.com> Dear All This may be a bit unusual problem- I am using Chimera (from Daily build) on Ubuntu mounted on my MAC using VMware Fusion (reason- some software packages that run only on LINUX and not on a MAC). The problem is - when I try to get the color panel by clicking on the color tab on the volume viewer- it does not appear. I am not sure if any of you have encountered such problem. Thanks Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908 -------------- next part -------------- An HTML attachment was scrubbed... URL: From skmolugu at miners.utep.edu Thu Jan 22 12:17:29 2009 From: skmolugu at miners.utep.edu (skmolugu at miners.utep.edu) Date: Thu, 22 Jan 2009 13:17:29 -0700 Subject: [Chimera-users] Movie Recording Message-ID: Hi, I am having problems with movie recording. I saved the movie as .avi file and when I upload the movie in to a windows power point slide, it crashes or shows a dark cube. Can you please suggest me a possible solution for this.. Thank you very much for your time. Regards, Sudheer. -------------- next part -------------- An HTML attachment was scrubbed... URL: From sdecarlo at ccny.cuny.edu Thu Jan 22 12:52:11 2009 From: sdecarlo at ccny.cuny.edu (Sacha De Carlo) Date: Thu, 22 Jan 2009 15:52:11 -0500 (EST) Subject: [Chimera-users] Movie Recording Message-ID: <20090122155211.BSD54774@pelican.admin.ccny.cuny.edu> Hi, it sounds lime you're having problems with Windows & Powerpoint, not Chimera... can you play the movie correctly with media player or VLC? Do you have all the video codecs installed correctly? Did you check the Chimera temp directory to see whether the frames have been created? hope this helps. Sacha ------------------------------------------ Sacha De Carlo, Asst. Professor Marshak Building Room 1335 The City College of NY (212) 650-6070 E-mail: sdecarlo at ccny.cuny.edu http://www.planetesacha.com/Work.htm ------------------------------------------ From meng at cgl.ucsf.edu Thu Jan 22 13:19:04 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 22 Jan 2009 13:19:04 -0800 Subject: [Chimera-users] Movie Recording In-Reply-To: References: Message-ID: <42839426-C74E-478F-B292-55553B961342@cgl.ucsf.edu> Hi Sudheer, I agree with Sacha... just wanted to add there are some suggestions and links on troubleshooting this kind of problem at: Best, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jan 22, 2009, at 12:17 PM, wrote: > Hi, > > I am having problems with movie recording. I saved the movie as .avi > file and when I upload the movie in to a windows power point slide, > it crashes or shows a dark cube. Can you please suggest me a > possible solution for this.. > > Thank you very much for your time. > > Regards, > Sudheer. From pett at cgl.ucsf.edu Thu Jan 22 15:15:08 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 22 Jan 2009 15:15:08 -0800 Subject: [Chimera-users] suggested feature/model panel In-Reply-To: <5AD417B4-0A63-46DB-9627-11BF3F1344F6@bcm.edu> References: <5AD417B4-0A63-46DB-9627-11BF3F1344F6@bcm.edu> Message-ID: <61DB644E-9AD3-4B96-B862-C79A8D04C971@cgl.ucsf.edu> On Jan 21, 2009, at 5:05 PM, Matthew Dougherty wrote: > 1) ability to create folders in the model panel so models can be > grouped > 2) ability to have a model in multiple folders > 3) ability to show/hide in a folder by a a single checkbox > 4) ability to name the folder These are good suggestions, and we have discussed adding some kind of grouping mechanism in Chimera given that there are a lot of situations where you want to treat a set of models as a single entity (e.g. multiple structures fit into a EM map). I think #2 and #3 are in conflict though. Really, I don't think you want #2 -- it's too confusing. Say a model is in two groups: you close one group -- what happens? You hide one group -- what happens? You deactivate one group and move the other -- what happens? Perhaps if you elaborated on the motivation for putting a model in multiple groups then some other alternative could be devised that provides what you need. I'll open a change-request in our Trac database for "grouping mechanism" and include the above. I don't really want to promise a timeline, but the issue is a concern of ours. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthewd at bcm.tmc.edu Thu Jan 22 16:05:26 2009 From: matthewd at bcm.tmc.edu (Dougherty, Matthew T.) Date: Thu, 22 Jan 2009 18:05:26 -0600 Subject: [Chimera-users] suggested feature/model panel References: <5AD417B4-0A63-46DB-9627-11BF3F1344F6@bcm.edu> <61DB644E-9AD3-4B96-B862-C79A8D04C971@cgl.ucsf.edu> Message-ID: Hi Eric, You are correct about #2 & #3, there would be an ambiguity in the design & coding. what I would propose: If a folder shuts off (hide), all multiple instantiations would be turned off. If a folder turns on (show), it only turns the model on in that folder. If a protein were in to two folders, it would require a third checkbox option of mixed, along with show & hide states. definitely needs more analysis. Initially I would prefer #2 over #3 as for the motivation: each folder would represent a scenario, easy switching between scenes, improved convenience in working with dozens or hundreds of models. > 1) ability to create folders in the model panel so models can be grouped > 2) ability to have a model in multiple folders > 3) ability to show/hide in a folder by a a single checkbox > 4) ability to name the folder I think #2 and #3 are in conflict though. Really, I don't think you want #2 -- it's too confusing. Say a model is in two groups: you close one group -- what happens? You hide one group -- what happens? You deactivate one group and move the other -- what happens? Perhaps if you elaborated on the motivation for putting a model in multiple groups then some other alternative could be devised that provides what you need. -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Fri Jan 23 10:05:41 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Fri, 23 Jan 2009 10:05:41 -0800 Subject: [Chimera-users] Chimera on Ubuntu mounted on MAC using VMware Fusion In-Reply-To: <170804.63209.qm@web8508.mail.in.yahoo.com> References: <170804.63209.qm@web8508.mail.in.yahoo.com> Message-ID: <497A06F5.5020705@cgl.ucsf.edu> Hi Andy, Sounds like a windowing system problem, not a Chimera problem. If you show the Surface Color dialog (Tools / Volume / Surface Color) and click on one of its color buttons, does the color dialog appear? Tom Anindito Sen wrote: > Dear All > > This may be a bit unusual problem- I am using Chimera (from Daily > build) on Ubuntu mounted on my MAC using VMware Fusion (reason- some > software packages that run only on LINUX and not on a MAC). The > problem is - when I try to get the color panel by clicking on the > color tab on the volume viewer- it does not appear. I am not sure if > any of you have encountered such problem. > > Thanks > Andy > > > Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and > Molecular Genetics University of Virginia Box 800733 Charlottesville, > VA 22908 > > > ------------------------------------------------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > From emailanindito at yahoo.co.in Fri Jan 23 23:15:02 2009 From: emailanindito at yahoo.co.in (Anindito Sen) Date: Sat, 24 Jan 2009 12:45:02 +0530 (IST) Subject: [Chimera-users] Chimera on Ubuntu mounted on MAC using VMware Fusion Message-ID: <184678.44534.qm@web8508.mail.in.yahoo.com> Hi Tom You are correct! The color dialog does appear as you mentioned! In addition -? While using Chimera-? the display window keeps flickering when I move the density map/pdb files. What can be a possible remedy to solve the problem? Thanks Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908 --- On Fri, 23/1/09, Tom Goddard wrote: From: Tom Goddard Subject: Re: [Chimera-users] Chimera on Ubuntu mounted on MAC using VMware Fusion To: emailanindito at yahoo.co.in Cc: chimera-users at cgl.ucsf.edu Date: Friday, 23 January, 2009, 11:35 PM Hi Andy, Sounds like a windowing system problem, not a Chimera problem. If you show the Surface Color dialog (Tools / Volume / Surface Color) and click on one of its color buttons, does the color dialog appear? Tom Anindito Sen wrote: > Dear All > > This may be a bit unusual problem- I am using Chimera (from Daily build) on Ubuntu mounted on my MAC using VMware Fusion (reason- some software packages that run only on LINUX and not on a MAC). The problem is - when I try to get the color panel by clicking on the color tab on the volume viewer- it does not appear. I am not sure if any of you have encountered such problem. > > Thanks > Andy > > > Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908 > > > ------------------------------------------------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthewd at bcm.edu Sat Jan 24 19:49:43 2009 From: matthewd at bcm.edu (Matthew Dougherty) Date: Sat, 24 Jan 2009 21:49:43 -0600 Subject: [Chimera-users] suggested feature/model panel In-Reply-To: <61DB644E-9AD3-4B96-B862-C79A8D04C971@cgl.ucsf.edu> References: <5AD417B4-0A63-46DB-9627-11BF3F1344F6@bcm.edu> <61DB644E-9AD3-4B96-B862-C79A8D04C971@cgl.ucsf.edu> Message-ID: another suggestion would be to put open and export buttons on the model panel. Makes it easier than going up to menu pull down. From bala.biophysics at gmail.com Mon Jan 26 03:20:57 2009 From: bala.biophysics at gmail.com (Bala subramanian) Date: Mon, 26 Jan 2009 12:20:57 +0100 Subject: [Chimera-users] need a script Message-ID: <288df32a0901260320h6291214dqb974185ec8d62f0e@mail.gmail.com> Dear Chimerians, Kindly help me If anybody has a script to do the following. Given two pdb files, the script should calculate the vector distance between the atoms, say CA atoms and draw an arrow representing the magnitude and direction of the vector. Do i need to add some plugin to draw arrows through atoms in Chimera. Thanks in advance, Bala -------------- next part -------------- An HTML attachment was scrubbed... URL: From hjunlee at gmail.com Mon Jan 26 03:40:10 2009 From: hjunlee at gmail.com (Hyung Jun Lee) Date: Mon, 26 Jan 2009 20:40:10 +0900 Subject: [Chimera-users] How to display automatically the atoms in Gaussian cube file format Message-ID: <69ca71c20901260340k7d189df1u7c298efd77e2a0db@mail.gmail.com> Gaussian cube file formats include the information about each atom's positions as well as the volumetric data. But, Chimera only displays the volumetric data when importing the cube file format. I want to know how to display automatically the atoms whose positions is included in the cube file, together with the volumetric data. -------------- next part -------------- An HTML attachment was scrubbed... URL: From papai at igbmc.fr Mon Jan 26 04:43:00 2009 From: papai at igbmc.fr (Gabor Papai) Date: Mon, 26 Jan 2009 13:43:00 +0100 Subject: [Chimera-users] marker coordinates Message-ID: <497DAFD4.4040700@igbmc.fr> Hi, I would like to do the following: I placed markers on density spots. I want to get their coordinates and excise a box around the marked density and save it as a separate file. For this I would like to know how I can retrieve the coordinates of a marker set and possibly how to position exactly a box around a marker to set a subregion (and of course how to set the dimensions of that box). This second feature existed before, but disappeared in the latest releases with the subregion selection tool in the Volume Viewer. Thanks in advance, Gabor -- Gabor Papai IGBMC Department of Structural Biology and Genomics 1, rue Laurent Fries, BP 10142 67404 Illkirch, France phone +33-3-88655748 Fax +33-3-88653201 E-mail: papai at igbmc.u-strasbg.fr From meng at cgl.ucsf.edu Mon Jan 26 09:48:22 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 26 Jan 2009 09:48:22 -0800 Subject: [Chimera-users] need a script In-Reply-To: <288df32a0901260320h6291214dqb974185ec8d62f0e@mail.gmail.com> References: <288df32a0901260320h6291214dqb974185ec8d62f0e@mail.gmail.com> Message-ID: Hi Bala, The "distance" command measures distances and (by default) shows dashed lines and the distance values in the main window. The distance at the time of command execution is also reported in the Reply Log. Example: dist #0:35 at ca #1:35 at ca You can control the appearance of those distance monitors, for example to hide the distance values: setattr p label " " To show arrows, however, the only way I know aside from python coding is to create a BILD format file describing the arrows and read it in. The format is pretty simple. For example, reading in a file arrow.bild containing this line: .arrow 17.675 49.049 21.434 16.956 48.582 17.728 makes an arrow between the two sets of xyz coordinates. You can also control its thickness, color, etc. and make other shapes, and of course put many of them in one file. See the BILD description: Best, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jan 26, 2009, at 3:20 AM, Bala subramanian wrote: > Dear Chimerians, > > Kindly help me If anybody has a script to do the following. > Given two pdb files, the script should calculate the vector distance > between the atoms, say CA atoms and draw an arrow representing the > magnitude and direction of the vector. Do i need to add some plugin > to draw arrows through atoms in Chimera. > > Thanks in advance, > Bala From meng at cgl.ucsf.edu Mon Jan 26 09:58:01 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 26 Jan 2009 09:58:01 -0800 Subject: [Chimera-users] marker coordinates In-Reply-To: <497DAFD4.4040700@igbmc.fr> References: <497DAFD4.4040700@igbmc.fr> Message-ID: <3315FDAF-65A0-47A4-9ACE-B54A681F8F44@cgl.ucsf.edu> Hi Gabor, I am pretty sure the capabilities are still there, but maybe the dialog has been rearranged - In the Volume Viewer dialog, choose Features... Atom box - is that what you had in mind? Another possibility is to use Features... Zone to get everything within some distance of your markers (not necessarily a rectangular box): For both of those, you would first need to select all the markers of interest. To get the (untransformed) coordinates of the markers, you could save them to a file from the Volume Tracer tool, or select them and use the command: getcrd sel which sends the coordinates to the Reply Log (under Favorites). Best, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jan 26, 2009, at 4:43 AM, Gabor Papai wrote: > Hi, > > I would like to do the following: I placed markers on density spots. I > want to get their coordinates and excise a box around the marked > density > and save it as a separate file. For this I would like to know how I > can > retrieve the coordinates of a marker set and possibly how to position > exactly a box around a marker to set a subregion (and of course how > to > set the dimensions of that box). This second feature existed before, > but > disappeared in the latest releases with the subregion selection tool > in > the Volume Viewer. > Thanks in advance, > Gabor From cardoneg at mail.nih.gov Mon Jan 26 11:38:39 2009 From: cardoneg at mail.nih.gov (Giovanni Cardone) Date: Mon, 26 Jan 2009 14:38:39 -0500 Subject: [Chimera-users] marker coordinates In-Reply-To: <497DAFD4.4040700@igbmc.fr> References: <497DAFD4.4040700@igbmc.fr> Message-ID: <9CDFA2E2-D369-4689-945D-A5C2DA8A66E6@mail.nih.gov> Hi Gabor, here attached is a python script that I adapted from a pug-in that I am writing. You need to adjust the box size to your needs, then you can save it as a file and open it in Chimera. The script extracts subregions from the active volume, around only the selected markers. The subregions are visualized as separate maps, but they are not saved to file (can anyone contribute with that?). Since it uses a function (region_matrix) that has been recently modified, I can only guarantee that it works with the latest nightly builds (however, in the script there is a commented line that should work with version 1.2552). I hope it helps, Giovanni # ----------------------------------------------------------------------------- # Script to extract subregions around selected markers from the active volume # from chimera import selection from VolumeData import Array_Grid_Data from VolumeViewer import volume_from_grid_data, active_volume # box size around markers (pixels) boxSize = 10 region = active_volume() data = region.data for i,atom in enumerate(selection.currentAtoms()): coord = atom.coord() # calculate limits and extract subregions ijkcoord = map(lambda a: int(round(a)), data.xyz_to_ijk(coord)) ijk_size = [boxSize]*len(ijkcoord) ijk_min = map(lambda a,b: max(0,a-b/2), ijkcoord, ijk_size) ijk_size = map(lambda a,b,c,d: min(a-1,b+c/2)-d, data.size, ijkcoord, ijk_size, ijk_min) ijk_max = map(lambda a,b: a+b-1, ijk_min, ijk_size) new_origin = data.ijk_to_xyz(ijk_min) step = (1,1,1) r = (ijk_min, ijk_max, step) mtx = region.region_matrix(r) # version 1.2552 # mtx = region.region_matrix(origin = ijk_min, size = ijk_size, subsampling = (1,1,1), step = (1,1,1), read_matrix = True) # show selection name = region.name + (' (subregion %d) '%(i+1)) gg = Array_Grid_Data(mtx, new_origin, data.step, data.cell_angles, data.rotation, name = name) gv = volume_from_grid_data(gg, show_data = False) gv.copy_settings_from(region, copy_region = False) gv.show() On Jan 26, 2009, at 7:43 AM, Gabor Papai wrote: > Hi, > > I would like to do the following: I placed markers on density spots. I > want to get their coordinates and excise a box around the marked > density > and save it as a separate file. For this I would like to know how I > can > retrieve the coordinates of a marker set and possibly how to position > exactly a box around a marker to set a subregion (and of course how > to > set the dimensions of that box). This second feature existed before, > but > disappeared in the latest releases with the subregion selection tool > in > the Volume Viewer. > Thanks in advance, > Gabor > > -- > Gabor Papai > IGBMC > Department of Structural Biology and Genomics > 1, rue Laurent Fries, BP 10142 > 67404 Illkirch, France > phone +33-3-88655748 > Fax +33-3-88653201 > E-mail: papai at igbmc.u-strasbg.fr > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From pett at cgl.ucsf.edu Mon Jan 26 11:40:34 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 26 Jan 2009 11:40:34 -0800 Subject: [Chimera-users] suggested feature/model panel In-Reply-To: References: <5AD417B4-0A63-46DB-9627-11BF3F1344F6@bcm.edu> <61DB644E-9AD3-4B96-B862-C79A8D04C971@cgl.ucsf.edu> Message-ID: <70FABF75-E563-4502-B797-30AB51E0B83C@cgl.ucsf.edu> On Jan 24, 2009, at 7:49 PM, Matthew Dougherty wrote: > another suggestion would be to put open and export buttons on the > model panel. > Makes it easier than going up to menu pull down. I'm hesitant to add buttons to the model panel since the button list is already kind of long, particularly for functions that aren't all that hard to access. As a power user, you might want to consider using keyboard shortcuts, as documented here: Chimera Keyboard Shortcuts (Accelerators) In particular, 'op' will bring up the open-file dialog, and 'ov' the open-volume dialog. There are shortcuts for opening the last file you opened, the second-to-last, the last two, etc. which is convenient for quickly opening the same file(s) you were working on in a previous session when you start a new session. Also, 'xs' will export a scene. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Mon Jan 26 11:46:58 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 26 Jan 2009 11:46:58 -0800 Subject: [Chimera-users] Chimera on Ubuntu mounted on MAC using VMware Fusion In-Reply-To: <184678.44534.qm@web8508.mail.in.yahoo.com> References: <184678.44534.qm@web8508.mail.in.yahoo.com> Message-ID: <497E1332.8030803@cgl.ucsf.edu> Hi Andy, Your flickering display again sounds like a problem with your virtual linux machine, specifically its graphics driver, not a problem that can be solved within Chimera. I wonder if your color dialog not appearing is because it is hidden behind another dialog. When you press the color button Chimera asks to raise the color dialog so it is visible, but I saw last week a linux system where that did not happen. That would be a problem with the window manager or perhaps the Tk window toolkit. It correctly raises the color dialog on the Mac Aqua version of Chimera. Tom Anindito Sen wrote: > Hi Tom > > You are correct! The color dialog does appear as you mentioned! In > addition - While using Chimera- the display window keeps flickering > when I move the density map/pdb files. > > What can be a possible remedy to solve the problem? > > Thanks > Andy > > Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and > Molecular Genetics University of Virginia Box 800733 Charlottesville, VA > 22908 > > > --- On *Fri, 23/1/09, Tom Goddard //* wrote: > > From: Tom Goddard > Subject: Re: [Chimera-users] Chimera on Ubuntu mounted on MAC using > VMware Fusion > To: emailanindito at yahoo.co.in > Cc: chimera-users at cgl.ucsf.edu > Date: Friday, 23 January, 2009, 11:35 PM > > Hi Andy, > > Sounds like a windowing system problem, not a Chimera problem. If you show > the Surface Color dialog (Tools / Volume / Surface Color) and click on one of > its color buttons, does the color dialog appear? > > Tom > > > Anindito Sen wrote: > > Dear All > > > > This may be a bit unusual problem- I am using > > Chimera (from Daily build) > on Ubuntu mounted on my MAC using VMware Fusion (reason- some software packages > that run only on LINUX and not on a MAC). The problem is - when I try to get the > color panel by clicking on the color tab on the volume viewer- it does not > appear. I am not sure if any of you have encountered such problem. > > > > Thanks > > Andy > > > > > > Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and > Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908 > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users at cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > From goddard at cgl.ucsf.edu Mon Jan 26 14:21:35 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 26 Jan 2009 14:21:35 -0800 Subject: [Chimera-users] Mac 64-bit Chimera version In-Reply-To: References: <200805141716.m4EHGwJW1886560@guanine.cgl.ucsf.edu> <482C67D7.20207@cgl.ucsf.edu> Message-ID: <497E376F.8000906@cgl.ucsf.edu> Hi Denis, Conrad Huang in our lab tried building a 64-bit Mac Chimera several months ago. Many of the third-party packages we rely on failed to compile. We decided to pursue this only after Mac OS 10.6 is released. I believe the rationale of that was that Mac OS 10.5 is the oldest Mac OS that supports 64-bit graphical apps. We still support Mac OS 10.4 and our current automated build system targets 10.4. When 10.6 comes out we may target our builds to 10.5. Currently we only provide 64-bit Chimera on Linux. Tom Denis Chr?tien wrote: > Dear Thomas, > > We were discussing some time ago about a 64 bit Mac version of Chimera. > Did you progress in this project ? (I'm still very limited for > visualization of large volumes with my mac, although its not a hardware > problem : 16 Gb Ram installed). > > Best regards, > > Denis > > Le 15 mai 08 ? 18:41, Thomas Goddard a ?crit : > >> Hi Denis, >> >> The Chimera error you reported means there was insufficient memory to >> compute the Fourier transform you wanted. I see from the report that >> your Mac has 18 Gbytes (wow). But our Mac Chimera version is a 32-bit >> program so its memory address space is only 4 Gbytes. In that 4 >> Gbytes has to fit not only data, but all shared libraries, program >> stack and (I think) operating system code. So really you might have >> just 3 Gbytes to work with. Also my Fourier transform code does a >> full complex value FT where it could do a real value FT taking half >> the memory. And the Python library that actually does the FT can only >> use double precision, so 16 bytes per complex value. More memory is >> used when Chimera takes just the magnitude of the FT coefficients. In >> short it is using 20 bytes per grid point. So a 512^3 FT will use 2.5 >> Gb, about the maximum that will fit in the 32-bit address space >> (assuming it isn't already fragmented by other data/libraries since >> you need a 2.5 Gb free block). >> >> We plan on fixing this. We plan on distributing a 64-bit Mac >> Chimera, and have tried compiling it. But some of the ~30 third-party >> libraries Chimera depends on did not compile. So we still need to >> work on that -- maybe within 3 months. Also I plan on making the FT >> code not such a hog, do a real FT and investigate 32-bit float FT >> values for a factor of 4 memory savings. For now your only option >> would be to use one of our 64-bit Chimera versions on Linux or Tru64 >> operating systems. >> >> Tom > > ___________________________ > Universit? de Rennes 1 > UMR 6026, ?quipe TIPs > Campus de Beaulieu, B?t. 13 > 35042 Rennes Cedex > France > > Tel. +33 (0)2 23 23 67 64 > http://www.umr6026.univ-rennes1.fr/ > ___________________________ > From goddard at cgl.ucsf.edu Mon Jan 26 14:30:05 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 26 Jan 2009 14:30:05 -0800 Subject: [Chimera-users] How to display automatically the atoms in Gaussian cube file format In-Reply-To: <69ca71c20901260340k7d189df1u7c298efd77e2a0db@mail.gmail.com> References: <69ca71c20901260340k7d189df1u7c298efd77e2a0db@mail.gmail.com> Message-ID: <497E396D.2040107@cgl.ucsf.edu> Hi Hyung, The Chimera Gaussian cube file reader ignores the atoms specified in the file and just displays the volume data. I'll add to our requested features list an entry to also display the atoms. There are hundreds of new features requested and I do not know when this one might get done. Eric Pettersen says that if you have a Gaussian checkpoint file with the same atoms you can open that and it will display the atoms. Tom Hyung Jun Lee wrote: > Gaussian cube file formats include the information about each atom's > positions as well as the volumetric data. But, Chimera only displays the > volumetric data when importing the cube file format. > > I want to know how to display automatically the atoms whose positions is > included in the cube file, together with the volumetric data. > > > ------------------------------------------------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From pett at cgl.ucsf.edu Mon Jan 26 14:33:35 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 26 Jan 2009 14:33:35 -0800 Subject: [Chimera-users] How to display automatically the atoms in Gaussian cube file format In-Reply-To: <497E396D.2040107@cgl.ucsf.edu> References: <69ca71c20901260340k7d189df1u7c298efd77e2a0db@mail.gmail.com> <497E396D.2040107@cgl.ucsf.edu> Message-ID: On Jan 26, 2009, at 2:30 PM, Thomas Goddard wrote: > Eric Pettersen says that if you have a Gaussian checkpoint file with > the > same atoms you can open that and it will display the atoms. Mmmm, Gaussian formatted checkpoint file, that is. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Mon Jan 26 14:38:27 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 26 Jan 2009 14:38:27 -0800 Subject: [Chimera-users] marker coordinates In-Reply-To: <497DAFD4.4040700@igbmc.fr> References: <497DAFD4.4040700@igbmc.fr> Message-ID: <497E3B63.6070900@cgl.ucsf.edu> Hi Gabor, Not sure what you are talking about in the subregion selection panel that has disappeared. Sounds like what you want is the "atom box" panel as Elaine mentioned. Once you use Atom Box, then use volume dialog File / Save Map As.... If you are refering to the subregion panel Resample button. That is now down by the "Crop" button if you have the "Rotate selection box" checkbutton enabled. Tom Gabor Papai wrote: > Hi, > > I would like to do the following: I placed markers on density spots. I > want to get their coordinates and excise a box around the marked density > and save it as a separate file. For this I would like to know how I can > retrieve the coordinates of a marker set and possibly how to position > exactly a box around a marker to set a subregion (and of course how to > set the dimensions of that box). This second feature existed before, but > disappeared in the latest releases with the subregion selection tool in > the Volume Viewer. > Thanks in advance, > Gabor > From meng at cgl.ucsf.edu Mon Jan 26 15:25:58 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 26 Jan 2009 15:25:58 -0800 Subject: [Chimera-users] suggested feature/model panel In-Reply-To: <70FABF75-E563-4502-B797-30AB51E0B83C@cgl.ucsf.edu> References: <5AD417B4-0A63-46DB-9627-11BF3F1344F6@bcm.edu> <61DB644E-9AD3-4B96-B862-C79A8D04C971@cgl.ucsf.edu> <70FABF75-E563-4502-B797-30AB51E0B83C@cgl.ucsf.edu> Message-ID: <83BBB2A9-AF1D-4C0A-A3A1-5678440369D3@cgl.ucsf.edu> Hi Matt, If you prefer commands to shortcuts, simply entering "open" without arguments will bring up a file browser. There is also an "export" command, and if you omit the output filename argument, it will bring up the file browser for specifying output name and location. Neither of these is an operation on specific models ("export" gets the whole scene). Best, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jan 26, 2009, at 11:40 AM, Eric Pettersen wrote: > On Jan 24, 2009, at 7:49 PM, Matthew Dougherty wrote: > >> another suggestion would be to put open and export buttons on the >> model panel. >> Makes it easier than going up to menu pull down. > > I'm hesitant to add buttons to the model panel since the button list > is already kind of long, particularly for functions that aren't all > that hard to access. As a power user, you might want to consider > using keyboard shortcuts, as documented here: > > Chimera Keyboard Shortcuts (Accelerators) > > In particular, 'op' will bring up the open-file dialog, and 'ov' the > open-volume dialog. There are shortcuts for opening the last file > you opened, the second-to-last, the last two, etc. which is > convenient for quickly opening the same file(s) you were working on > in a previous session when you start a new session. Also, 'xs' will > export a scene. > > --Eric > From goddard at cgl.ucsf.edu Mon Jan 26 16:13:52 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 26 Jan 2009 16:13:52 -0800 Subject: [Chimera-users] marker coordinates In-Reply-To: <9CDFA2E2-D369-4689-945D-A5C2DA8A66E6@mail.nih.gov> References: <497DAFD4.4040700@igbmc.fr> <9CDFA2E2-D369-4689-945D-A5C2DA8A66E6@mail.nih.gov> Message-ID: <497E51C0.90108@cgl.ucsf.edu> Hi Giovanni, The call to save your individual maps would be like gv.write_file('/tmp/volume%d.mrc' % (i+1), format = 'mrc') Allowed formats are mrc, dsn6 (O brix format), cmap (Chimera map format uses HDF5), or netcdf (Chimera only). Tom Giovanni Cardone wrote: > Hi Gabor, > > here attached is a python script that I adapted from a pug-in that I > am writing. > You need to adjust the box size to your needs, then you can save it as > a file and open it in Chimera. > The script extracts subregions from the active volume, around only the > selected markers. > The subregions are visualized as separate maps, but they are not saved > to file (can anyone contribute with that?). > Since it uses a function (region_matrix) that has been recently > modified, I can only guarantee that it works with the latest nightly > builds (however, in the script there is a commented line that should > work with version 1.2552). > > I hope it helps, > Giovanni > > > > > # > ----------------------------------------------------------------------------- > # Script to extract subregions around selected markers from the active > volume > # > from chimera import selection > from VolumeData import Array_Grid_Data > from VolumeViewer import volume_from_grid_data, active_volume > > # box size around markers (pixels) > boxSize = 10 > > region = active_volume() > data = region.data > > for i,atom in enumerate(selection.currentAtoms()): > coord = atom.coord() > # calculate limits and extract subregions > ijkcoord = map(lambda a: int(round(a)), data.xyz_to_ijk(coord)) > ijk_size = [boxSize]*len(ijkcoord) > ijk_min = map(lambda a,b: max(0,a-b/2), ijkcoord, ijk_size) > ijk_size = map(lambda a,b,c,d: min(a-1,b+c/2)-d, data.size, > ijkcoord, ijk_size, ijk_min) > ijk_max = map(lambda a,b: a+b-1, ijk_min, ijk_size) > new_origin = data.ijk_to_xyz(ijk_min) > > step = (1,1,1) > r = (ijk_min, ijk_max, step) > mtx = region.region_matrix(r) > # version 1.2552 > # mtx = region.region_matrix(origin = ijk_min, size = ijk_size, > subsampling = (1,1,1), step = (1,1,1), read_matrix = True) > > # show selection > name = region.name + (' (subregion %d) '%(i+1)) > gg = Array_Grid_Data(mtx, new_origin, data.step, data.cell_angles, > data.rotation, name = name) > > gv = volume_from_grid_data(gg, show_data = False) > gv.copy_settings_from(region, copy_region = False) > gv.show() > > > > On Jan 26, 2009, at 7:43 AM, Gabor Papai wrote: > >> Hi, >> >> I would like to do the following: I placed markers on density spots. I >> want to get their coordinates and excise a box around the marked >> density >> and save it as a separate file. For this I would like to know how I >> can >> retrieve the coordinates of a marker set and possibly how to position >> exactly a box around a marker to set a subregion (and of course how >> to >> set the dimensions of that box). This second feature existed before, >> but >> disappeared in the latest releases with the subregion selection tool >> in >> the Volume Viewer. >> Thanks in advance, >> Gabor >> >> -- >> Gabor Papai >> IGBMC >> Department of Structural Biology and Genomics >> 1, rue Laurent Fries, BP 10142 >> 67404 Illkirch, France >> phone +33-3-88655748 >> Fax +33-3-88653201 >> E-mail: papai at igbmc.u-strasbg.fr >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From vamsee at chemistry.montana.edu Mon Jan 26 16:23:35 2009 From: vamsee at chemistry.montana.edu (vamsee) Date: Mon, 26 Jan 2009 17:23:35 -0700 Subject: [Chimera-users] Volume information Message-ID: Hello All, I am working on a virus and I am trying to figure out its volume. I would want to find out the volume of the nucleic acid and the water inside the virus capsid. That way, if I am thinking right, that should give me the total internal volume of the virus. This volume would be a constant even with the movement of water in and out. Is it possible to use chimera to calculate any of such data, with no prior information about how the nucleic acid is packed inside? Thanks in advance, Vamsee Graduate Student Dept of Chemistry and Biochemistry Montana State University Bozeman, MT - 59715 -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Mon Jan 26 16:37:16 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 26 Jan 2009 16:37:16 -0800 Subject: [Chimera-users] Volume information In-Reply-To: References: Message-ID: <497E573C.7070904@cgl.ucsf.edu> Hi Vamsee, Chimera can report the volume enclosed in any surface using menu entry Tools / Volume Data / Measure Volume and Area The hard part is getting a surface for your situation. I don't know how you plan on defining the part that is just nucleic acid and water. For icosahedral viruses you could fit an icosahedral/spherical inside the density map creating it with the Icosahedron Surface dialog (Tools / Higher-Order Structure) and moving it to the right place using the Model Panel "active" buttons. http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#icosfit http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#measurevolume Tom vamsee wrote: > Hello All, > > > I am working on a virus and I am trying to figure out its volume. > I would want to find out the volume of the nucleic acid and the water > inside the virus capsid. That way, if I am thinking right, that should > give me the total internal volume of the virus. This volume would be a > constant even with the movement of water in and out. Is it possible to > use chimera to calculate any of such data, with no prior information > about how the nucleic acid is packed inside? > > > Thanks in advance, > > Vamsee > Graduate Student > Dept of Chemistry and Biochemistry > Montana State University > Bozeman, MT - 59715 > > > ------------------------------------------------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From papai at igbmc.fr Tue Jan 27 00:19:09 2009 From: papai at igbmc.fr (Gabor Papai) Date: Tue, 27 Jan 2009 09:19:09 +0100 Subject: [Chimera-users] marker coordinates In-Reply-To: <497E3B63.6070900@cgl.ucsf.edu> References: <497DAFD4.4040700@igbmc.fr> <497E3B63.6070900@cgl.ucsf.edu> Message-ID: <497EC37D.6020809@igbmc.fr> Hi Tom, I was talking about this: "Resample map commands newmap 100 100 100 2.4 2.4 2.4 -120 -120 -120 This command creates a new map containing zero values of size 100^3 grid points with grid plane spacing equal to 2.4 and origin (i.e. physical xyz position of grid value at index 0,0,0) equal to (-120,-120,-120). An outline box is shown for the new map." Here I could create a new map at a specified position with specified size but the Atom Box feature will be fine and the "getcrd sel" command also. Thank you, Elaine and Giovanni! At last, a feature request: it would be convenient if I could open IMAGIC files directly in Chimera. Bye, Gabor -- Gabor Papai IGBMC Department of Structural Biology and Genomics 1, rue Laurent Fries, BP 10142 67404 Illkirch, France phone +33-3-88655748 Fax +33-3-88653201 E-mail: papai at igbmc.u-strasbg.fr From ayassin at wadsworth.org Mon Jan 26 08:06:49 2009 From: ayassin at wadsworth.org (ayassin at wadsworth.org) Date: Mon, 26 Jan 2009 11:06:49 -0500 (EST) Subject: [Chimera-users] 3D on Chimera. Message-ID: <58233.199.184.30.59.1232986009.squirrel@info.wadsworth.org> Hello, I am trying to use Chimera to model pdb files into EM maps. When I select the red cyan stereo, the EM map is stereo but the pdb structure is not. -Is there anyway to display pdb in stereo in Chimera, how? -Is there another program that would allow me to do the same thing: fit pdb in EM density map-in stereo(other than "O")? -When I use Chimera on windows VISTA the side view panel does not appear and a message about graphic card appear, anyway to solve this? Thank you all very much. Aymen Yassin. Postdoc Research Affiliate Wadsworth Center, Albany,NY. IMPORTANT NOTICE: This e-mail and any attachments may contain confidential or sensitive information which is, or may be, legally privileged or otherwise protected by law from further disclosure. It is intended only for the addressee. If you received this in error or from someone who was not authorized to send it to you, please do not distribute, copy or use it or any attachments. Please notify the sender immediately by reply e-mail and delete this from your system. Thank you for your cooperation. From giulia at strubi.ox.ac.uk Mon Jan 26 11:10:35 2009 From: giulia at strubi.ox.ac.uk (Giulia Zanetti) Date: Mon, 26 Jan 2009 19:10:35 +0000 (GMT) Subject: [Chimera-users] color zone on command line Message-ID: <20090126191035.DCD94450@mail.strubi.ox.ac.uk> Hi all, I would like to make a movie in which areas of my map are coloured while the surface is rotating. Any idea how to use color zone from the command line? thanks Giulia From goddard at cgl.ucsf.edu Tue Jan 27 09:08:27 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Tue, 27 Jan 2009 09:08:27 -0800 Subject: [Chimera-users] marker coordinates In-Reply-To: <497EC37D.6020809@igbmc.fr> References: <497DAFD4.4040700@igbmc.fr> <497E3B63.6070900@cgl.ucsf.edu> <497EC37D.6020809@igbmc.fr> Message-ID: <497F3F8B.4080000@cgl.ucsf.edu> Hi Gabor, The "newmap" command is part of a plug-in "Resample map commands" still available on the following web page. http://www.cgl.ucsf.edu/chimera/experimental/experimental.html It has never been included in the Chimera distributions. In cases where the new map is part of an existing map the volume dialog subregion panel can be used. Also the "vop #0 resample onGrid #1" command can resample one map on the grid of another map. If there are interesting cases where newmap is needed please explain them to me. Reading IMAGIC maps is item #100 on the feature request list. http://www.cgl.ucsf.edu/chimera/plans.html I'm not sure when it will be implemented, there are at least a dozen higher priority requests. Tom Gabor Papai wrote: > Hi Tom, > > I was talking about this: > > "Resample map commands > > newmap 100 100 100 2.4 2.4 2.4 -120 -120 -120 > This command creates a new map containing zero values of size 100^3 > grid points with grid plane spacing equal to 2.4 and origin (i.e. > physical xyz position of grid value at index 0,0,0) equal to > (-120,-120,-120). An outline box is shown for the new map." > > Here I could create a new map at a specified position with specified > size but the Atom Box feature will be fine and the "getcrd sel" > command also. Thank you, Elaine and Giovanni! > > At last, a feature request: it would be convenient if I could open > IMAGIC files directly in Chimera. > > Bye, > > Gabor > From goddard at cgl.ucsf.edu Tue Jan 27 10:16:07 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Tue, 27 Jan 2009 10:16:07 -0800 Subject: [Chimera-users] 3D on Chimera. In-Reply-To: <58233.199.184.30.59.1232986009.squirrel@info.wadsworth.org> References: <58233.199.184.30.59.1232986009.squirrel@info.wadsworth.org> Message-ID: <497F4F67.4070400@cgl.ucsf.edu> Hi Aymen, In my tests the red-cyan stereo works fine on PDB models and maps. Perhaps you are using a color near red or cyan for the PDB model. That will make it work exceedingly poorly. In general, the red-cyan stereo only works well for monochrome (gray) images. I guess the Windows Vista message about the Side View not working means your graphics driver or graphics card is not capable of making that second 3-d graphics window. That almost never happens. Perhaps you can install a graphics driver that will make it work. Greg Couch in our lab knows more about this and can advise you. Tom ayassin at wadsworth.org wrote: > Hello, > > I am trying to use Chimera to model pdb files into EM maps. When I select > the red cyan stereo, the EM map is stereo but the pdb structure is not. > > -Is there anyway to display pdb in stereo in Chimera, how? > -Is there another program that would allow me to do the same thing: fit > pdb in EM density map-in stereo(other than "O")? > -When I use Chimera on windows VISTA the side view panel does not appear > and a message about graphic card appear, anyway to solve this? > > Thank you all very much. > > Aymen Yassin. > Postdoc Research Affiliate > Wadsworth Center, Albany,NY. > > > > > > > > IMPORTANT NOTICE: This e-mail and any attachments may contain > confidential or sensitive information which is, or may be, legally > privileged or otherwise protected by law from further disclosure. It > is intended only for the addressee. If you received this in error or > from someone who was not authorized to send it to you, please do not > distribute, copy or use it or any attachments. Please notify the > sender immediately by reply e-mail and delete this from your > system. Thank you for your cooperation. > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > From gregc at cgl.ucsf.edu Tue Jan 27 10:28:09 2009 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Tue, 27 Jan 2009 10:28:09 -0800 (PST) Subject: [Chimera-users] 3D on Chimera. In-Reply-To: <497F4F67.4070400@cgl.ucsf.edu> References: <58233.199.184.30.59.1232986009.squirrel@info.wadsworth.org> <497F4F67.4070400@cgl.ucsf.edu> Message-ID: The message about your graphics card also mentions that you might be able to fix the problem by updating your graphics driver. If you have with Intel graphics, you should get a newer driver directly from Intel at . If you tell me more about your computer (run the dxdiag program, save all information, and email me the result), I could be more specific. Greg Couch UCSF Computer Graphics Lab On Tue, 27 Jan 2009, Tom Goddard wrote: > Hi Aymen, > > In my tests the red-cyan stereo works fine on PDB models and maps. > Perhaps you are using a color near red or cyan for the PDB model. That > will make it work exceedingly poorly. In general, the red-cyan stereo > only works well for monochrome (gray) images. > > I guess the Windows Vista message about the Side View not working > means your graphics driver or graphics card is not capable of making > that second 3-d graphics window. That almost never happens. Perhaps > you can install a graphics driver that will make it work. Greg Couch in > our lab knows more about this and can advise you. > > Tom > > > ayassin at wadsworth.org wrote: >> Hello, >> >> I am trying to use Chimera to model pdb files into EM maps. When I select >> the red cyan stereo, the EM map is stereo but the pdb structure is not. >> >> -Is there anyway to display pdb in stereo in Chimera, how? >> -Is there another program that would allow me to do the same thing: fit >> pdb in EM density map-in stereo(other than "O")? >> -When I use Chimera on windows VISTA the side view panel does not appear >> and a message about graphic card appear, anyway to solve this? >> >> Thank you all very much. >> >> Aymen Yassin. >> Postdoc Research Affiliate >> Wadsworth Center, Albany,NY. >> >> >> >> >> >> >> >> IMPORTANT NOTICE: This e-mail and any attachments may contain >> confidential or sensitive information which is, or may be, legally >> privileged or otherwise protected by law from further disclosure. It >> is intended only for the addressee. If you received this in error or >> from someone who was not authorized to send it to you, please do not >> distribute, copy or use it or any attachments. Please notify the >> sender immediately by reply e-mail and delete this from your >> system. Thank you for your cooperation. >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > From goddard at cgl.ucsf.edu Tue Jan 27 10:30:46 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Tue, 27 Jan 2009 10:30:46 -0800 Subject: [Chimera-users] color zone on command line In-Reply-To: <20090126191035.DCD94450@mail.strubi.ox.ac.uk> References: <20090126191035.DCD94450@mail.strubi.ox.ac.uk> Message-ID: <497F52D6.6060601@cgl.ucsf.edu> Hi Giulia, Unfortunately there is no command equivalent of the color zone dialog. The color zone operation can be invoked by opening a file containing Python code as shown below. One of the main limitations of using Chimera to make animations is that there are no command equivalents for many dialog actions. Another approach is to use the Movie Recorder dialog (Tools / Utilities menu) and stop recording, then use the dialog to add some color, continue recording, then stop and adjust again with the dialog. Tedious but maybe simplest. Tom # # Color zone the first surface using the selected atoms and radius set below. # from chimera import selection as s, openModels as om from _surface import SurfaceModel radius = 5 surface = om.list(modelTypes = [SurfaceModel])[0] xform_to_surface = surface.openState.xform.inverse() atoms = s.currentAtoms() bonds = s.currentBonds() import ColorZone as cz points, colors = cz.points_and_colors(atoms, bonds, xform_to_surface) cz.color_zone(surface, points, colors, radius, auto_update = True) Giulia Zanetti wrote: > Hi all, I would like to make a movie in which areas of my map are coloured while the surface is rotating. > > Any idea how to use color zone from the command line? > > thanks > > Giulia > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > From YHWANG1 at PARTNERS.ORG Tue Jan 27 09:50:48 2009 From: YHWANG1 at PARTNERS.ORG (Hwang, Youngha,Ph.D.) Date: Tue, 27 Jan 2009 12:50:48 -0500 Subject: [Chimera-users] fit in map output : coordinate representation of axis, axis point Message-ID: <52368789F9A31D43B7D335E33F45868201B1FE93@PHSXMB24.partners.org> Hi, could anyone explain to me what axis points mean in chimera? What unit is used for them? Is it related to the volume dimension? Is the rotation matrix based on Euler-angle representation? Thanks, Youngha. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. From goddard at cgl.ucsf.edu Tue Jan 27 15:27:25 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Tue, 27 Jan 2009 15:27:25 -0800 Subject: [Chimera-users] fit in map output : coordinate representation of axis, axis point In-Reply-To: <52368789F9A31D43B7D335E33F45868201B1FE93@PHSXMB24.partners.org> References: <52368789F9A31D43B7D335E33F45868201B1FE93@PHSXMB24.partners.org> Message-ID: <497F985D.7090304@cgl.ucsf.edu> Hi Youngha, Here's the description of the Fit in Map output from the Chimera manual, displayed in a web browser by pressing the Help button on the Fit in Map dialog. "Transformation matrices. The transformation matrix of the fit model relative to the reference map is reported in the Reply Log. The first three columns of the matrix describe a rotation and the fourth describes a translation (performed after the rotation). The transformation is also described as an axis of rotation (a unit vector), point on the axis, degrees of rotation, and shift parallel to the axis." If you have specified the map voxel size in Angstroms in the Coordinates panel of volume dialog then those are the units of the translation and shift. If you are fitting map #1 into map #0 then all positioning parameters are relative to the coordinate frame of map #0. The first 3 columns of the 3 by 4 transformation matrix are a rotation matrix, the last column is a translation vector (rotation applied first then translation). The axis, axis point, rotation angle, and shift are just another way of expressing the same transformation. Euler angles are not provided. Tom Example output fitting groel to rotated copy of itself: Fit map groel.mrc in map groel.mrc using 1254 points correlation = 0.7305, overlap = 1.131e+04 steps = 40, shift = 0.0106, angle = 2.64 degrees Position of groel.mrc (#1) relative to groel.mrc (#0) coordinates: Matrix rotation and translation 0.62732525 -0.77875617 -0.00136447 1.34502847 0.77875534 0.62732665 -0.00117890 -0.47283012 0.00177404 -0.00032304 0.99999837 -0.00375893 Axis 0.00054950 -0.00201508 0.99999782 Axis point 1.16654379 1.16890014 0.00000000 Rotation angle (degrees) 51.14694922 Shift along axis -0.00206703 Tom Hwang, Youngha,Ph.D. wrote: > Hi, could anyone explain to me what axis points mean in chimera? What unit is > used for them? Is it related to the volume dimension? Is the rotation matrix > based on Euler-angle representation? > > Thanks, Youngha. > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > From kparra at mail.usf.edu Wed Jan 28 07:22:27 2009 From: kparra at mail.usf.edu (Katherine Parra) Date: Wed, 28 Jan 2009 10:22:27 -0500 Subject: [Chimera-users] error message Message-ID: <44c5ac740901280722o23e17484v8423765ec8299c07@mail.gmail.com> Hello! I'm trying to get the hydrogen bonds between some selected residues during a trajectory, using per frame commands from tools. But when I get the possible hydrogen bonds formed between the selected residues I also get the following error message in the Reply Log: *Skipping possible acceptor with bad geometry: #0:2108 at O Wrong number of grandchild atoms for phi/psi acceptor #0:2108 at O *What could be happening? Thank you in advance. KP -------------- next part -------------- An HTML attachment was scrubbed... URL: From giulia at strubi.ox.ac.uk Wed Jan 28 03:08:01 2009 From: giulia at strubi.ox.ac.uk (Giulia Zanetti) Date: Wed, 28 Jan 2009 11:08:01 +0000 (GMT) Subject: [Chimera-users] color zone on command line In-Reply-To: <497F52D6.6060601@cgl.ucsf.edu> References: <20090126191035.DCD94450@mail.strubi.ox.ac.uk> <497F52D6.6060601@cgl.ucsf.edu> Message-ID: <20090128110801.DCE04493@mail.strubi.ox.ac.uk> Hi Tom, thanks for your suggestion. I have managed a reproducible movie with color zone in the following way: upload map and pdb start rolling start ColorZone (at least this you can do from the command line) wait n record movie wait n color whatever pdb part wait n color another pdbpart ecc in this way, i get the color zone window opened up before the movie starts and i just keep pressing color so that colors on the map will appear quite immediately after the command "color part of the pdb" has been executed, while the map is rolling. I needed to show the map getting colored in a movie, and the pdb getting colored in the same way in another movie, the 2 movies to be shown together in a slide. This method worked. Giulia ---- Original message ---- >Date: Tue, 27 Jan 2009 10:30:46 -0800 >From: Tom Goddard >Subject: Re: [Chimera-users] color zone on command line >To: Giulia Zanetti >Cc: chimera-users at cgl.ucsf.edu > >Hi Giulia, > > Unfortunately there is no command equivalent of the color zone >dialog. The color zone operation can be invoked by opening a file >containing Python code as shown below. One of the main limitations of >using Chimera to make animations is that there are no command >equivalents for many dialog actions. Another approach is to use the >Movie Recorder dialog (Tools / Utilities menu) and stop recording, then >use the dialog to add some color, continue recording, then stop and >adjust again with the dialog. Tedious but maybe simplest. > > Tom > ># ># Color zone the first surface using the selected atoms and radius set >below. ># >from chimera import selection as s, openModels as om >from _surface import SurfaceModel >radius = 5 >surface = om.list(modelTypes = [SurfaceModel])[0] >xform_to_surface = surface.openState.xform.inverse() >atoms = s.currentAtoms() >bonds = s.currentBonds() >import ColorZone as cz >points, colors = cz.points_and_colors(atoms, bonds, xform_to_surface) >cz.color_zone(surface, points, colors, radius, auto_update = True) > > > >Giulia Zanetti wrote: >> Hi all, I would like to make a movie in which areas of my map are coloured while the surface is rotating. >> >> Any idea how to use color zone from the command line? >> >> thanks >> >> Giulia >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> From pett at cgl.ucsf.edu Wed Jan 28 11:24:22 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 28 Jan 2009 11:24:22 -0800 Subject: [Chimera-users] error message In-Reply-To: <44c5ac740901280722o23e17484v8423765ec8299c07@mail.gmail.com> References: <44c5ac740901280722o23e17484v8423765ec8299c07@mail.gmail.com> Message-ID: <61402E5E-7B6E-41F1-9644-DA3F68C44C52@cgl.ucsf.edu> On Jan 28, 2009, at 7:22 AM, Katherine Parra wrote: > Hello! > I'm trying to get the hydrogen bonds between some selected residues > during a trajectory, using per frame commands from tools. But when I > get the possible hydrogen bonds formed between the selected residues > I also get the following error message in the Reply Log: > Skipping possible acceptor with bad geometry: #0:2108 at O > Wrong number of grandchild atoms for phi/psi acceptor #0:2108 at O > What could be happening? Hi Katherine, A more verbose version of the error message might be: atom #0:2108 at O has been classified as a phi/psi acceptor as per Mills et al (full cite in FindHBond docs) but the number of atoms bonded to #0:2108 at O's neighbor atoms ("grandchild atoms") is in conflict with that classification. The most likely cause is that #0:2108 at O's bonds are wrong or that its neighbor atoms' bonds are wrong. There is also some chance that Chimera has computed the wrong atom type for #0:2108 at O or its neighbors. If you were working with a single structure instead of a trajectory then it might also be possible that :2108 is a standard residue with missing atoms (Chimera assigns standard residue atom types using templates instead of computing them) but trajectories typically don't have missing atoms. To investigate, you should have a look at #0:2108 at O's atom type and it and its neighbor's bonds. To see the atom type open the command lines (Favorites->Command Line) and type "sel #0:2108 at o" and then use Actions->Label->IDTAM type. To see what the atom type means, look at this table: Atom Types in Chimera . If the atom type seems wrong, you can change it using the "setattr" command (e.g. to change it to O3, type: "setattr a idatmType O3 #0:2108 at o"). If the atom type seems okay, look at the bonds and particularly the neighbor's bonds. If there are extra or missing bonds you can fix that using the bond/~bond command (type "help bond" in the command line for info). You could send me the trajectory to look at if you feel think the problem is wrong atom typing or Chimera getting the bonding information wrong, and I would try to fix it. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From duncant at upstate.edu Fri Jan 30 14:49:28 2009 From: duncant at upstate.edu (Tom Duncan) Date: Fri, 30 Jan 2009 17:49:28 -0500 Subject: [Chimera-users] Calc buried surface area between 2 chains Message-ID: I saw an earlier post (Dec. 29, 2008; Digest vol. 68, issue 28) in which Elaine Meng described a procedure for calculating surface area for selected atoms. I did this for atoms on chain A that were selected as contacting atoms on neighboring chain B, but the sum(atom.areaSES) probably includes area buried within the chain A, not just between the 2 chains. I tried checking this by calculating the sum(atom.areaSES) for chain A (all atoms in A) in the whole model, then again for a model from which chain B was deleted before calculating the surface. However, the results indicated a larger areaSES for chain A in the absence of chain B! There were some errors reported in calculating the surfaces; perhaps this contributed. Is there a better way to calculate the buried surface on 1 chain due to contacts with a 2nd chain? Thanks, Tom Duncan From meng at cgl.ucsf.edu Fri Jan 30 15:15:40 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 30 Jan 2009 15:15:40 -0800 Subject: [Chimera-users] Calc buried surface area between 2 chains In-Reply-To: References: Message-ID: Hi Tom, Happily there is a command to do it, but first I'll explain your current results: Even though you are summing over a certain set of atoms, the surface does not necessarily enclose that set. If you have a single surface enclosing both A and B, any sums will not include the part buried between A and B. Thus it makes complete sense that the surface area of A alone, with surface enclosing A only, is larger than the surface area of A in the AB combined surface, because B buries part of A. You could tell Chimera to make separate surfaces for A and B and sum the areas in those. However, if it is really the buried surface area you care about, use the new "measure buriedarea" command -- it calculates the combined and individual surfaces (without creating displays) and takes the difference. More details on this command and how to use it: To use "measure" you need a recent daily build (it isn't in the Dec 2008 production release). Best, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jan 30, 2009, at 2:49 PM, Tom Duncan wrote: > I saw an earlier post (Dec. 29, 2008; Digest vol. 68, issue 28) in > which Elaine Meng described a procedure for calculating surface area > for selected atoms. I did this for atoms on chain A that were selected > as contacting atoms on neighboring chain B, but the sum(atom.areaSES) > probably includes area buried within the chain A, not just between the > 2 chains. > I tried checking this by calculating the sum(atom.areaSES) for chain A > (all atoms in A) in the whole model, then again for a model from which > chain B was deleted before calculating the surface. However, the > results indicated a larger areaSES for chain A in the absence of chain > B! > There were some errors reported in calculating the surfaces; perhaps > this contributed. > > Is there a better way to calculate the buried surface on 1 chain due > to contacts with a 2nd chain? > > Thanks, > Tom Duncan >