From meng at cgl.ucsf.edu Mon Mar 3 09:26:53 2008 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 3 Mar 2008 09:26:53 -0800 Subject: [Chimera-users] longer bonds in image In-Reply-To: <91F147390CA53D44BFADECB36C489D13026A85@n1ex> References: <91F147390CA53D44BFADECB36C489D13026A83@n1ex> <91F147390CA53D44BFADECB36C489D13026A85@n1ex> Message-ID: <0C8F6056-605E-43E6-9FE5-3D6BBD253B6E@cgl.ucsf.edu> Hi Bala, This is an expected behavior of Chimera: the ribbon is a smoothed path that does not go exactly through the atom positions. When ribbon is shown, the default is to simply draw the longer or shorter bonds where the ribbon is farther from or closer to the displayed atoms (ribose/base or amino acid side chain) than are the backbone atoms that the ribbon represents. However, there are ways to change the behavior: (A) use the command "ribbackbone" to allow display of both backbone atoms and ribbon. This will not make any bonds look longer or shorter, but it is usually ugly because the ribbon is not in the same place as the backbone atoms. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribbackbone.html (B) with Ribbon Style Editor, "Residue Class" section, you can set which atoms control the ribbon path and which are hidden automatically (by default, without using "ribbackbone") when ribbon is shown: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ ribbonstyle.html 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 P.S. you can send attachments such as images to chimera-users, but the message will not appear until the moderator has a chance to approve it... just be patient and it will be sent! On Mar 2, 2008, at 9:00 PM, bala wrote: > -----Original Message----- > From: bala > Sent: Fri 2/29/2008 12:13 PM > To: chimera-users at cgl.ucsf.edu > Subject: longer bonds in image > > Hi all, > > Thank you for the suggestions for my previous query. > > When the ribbons are displayed for the backbone of a RNA molecule. > Some of the bonds look longer than usual. Herewith i have attached > the image of a RNA molecule in which residues colored in cyan have > some bonds longer in appearance. Kindly help me to get this of this. > > Thanks, > Bala -------------- next part -------------- A non-text attachment was scrubbed... Name: query.jpg Type: image/jpeg Size: 177540 bytes Desc: not available URL: -------------- next part -------------- From triffo at rice.edu Mon Mar 3 09:59:27 2008 From: triffo at rice.edu (William Jeffrey Triffo) Date: Mon, 03 Mar 2008 09:59:27 -0800 Subject: [Chimera-users] saving positions Message-ID: <47CC3C7F.80402@rice.edu> hello, if I have used 'savepos' to save several orientations in a chimera session, is there a way to list these positions if I have forgotten what I named some of them? thanks, -Jeff From meng at cgl.ucsf.edu Mon Mar 3 10:04:18 2008 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 3 Mar 2008 10:04:18 -0800 Subject: [Chimera-users] saving positions In-Reply-To: <47CC3C7F.80402@rice.edu> References: <47CC3C7F.80402@rice.edu> Message-ID: Hi Jeff, The command "savepos list" should show the list in the status line and Reply Log: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/savepos.html You can call up this man page from inside Chimera with the command "help savepos" (in general "help command" will show the man page for "command"). Best, 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 Mar 3, 2008, at 9:59 AM, William Jeffrey Triffo wrote: > hello, > if I have used 'savepos' to save several orientations in a chimera > session, is there a way to list these positions if I have forgotten > what > I named some of them? > thanks, > -Jeff From pett at cgl.ucsf.edu Mon Mar 3 11:54:49 2008 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 3 Mar 2008 11:54:49 -0800 Subject: [Chimera-users] Step through trajectory from command line? In-Reply-To: <1204309130.47c84c8aec55a@webmail.nd.edu> References: <1204309130.47c84c8aec55a@webmail.nd.edu> Message-ID: <8A96E46F-A904-42E3-8AF0-2BE5AA6C47DA@cgl.ucsf.edu> Hi Kristina, There is no command for advancing trajectory frames. Perhaps you can detail the scenario that you need this for and why the per-frame scripting of the MD Movie tool doesn't cover your needs. Are you trying to completely automate the production of a movie from a trajectory or some such? Even if there were a command to advance the trajectory, how would you know when to stop? There are no "flow control" statements (if statements/for loops/functions) in the Chimera command language. I think you will have to use Python scripting for completely automating trajectory-related scripting. I can provide assistance there. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Feb 29, 2008, at 10:18 AM, Kristina Furse wrote: > Hi- > > Can you advance a trajectory by one frame from the command line, or > do you have > to use the controls in the MD Movie panel? > > Thanks, > Kristina > > -- > Kristina Furse > Postdoctoral Research Associate > 262 Stepan Chemistry Hall > Notre Dame, IN 46556 > (574)631-3904 > > > > _______________________________________________ > 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 Klaas.Decanniere at pandora.be Mon Mar 3 12:10:53 2008 From: Klaas.Decanniere at pandora.be (Klaas Decanniere) Date: Mon, 03 Mar 2008 21:10:53 +0100 Subject: [Chimera-users] scens/movies rendered with povray Message-ID: <47CC5B4D.6000708@pandora.be> Hello, The option to make movies using povray works nice and easy, so I want to push the boundaries a bit :-) - the standard texture included in the .pov files has a very simple finish - is there an easy way to include a spiced-up version? - when not using a "wait" command, several movements (roll, move, scale) are combined. When using the wait command, movements become separated with a small "hesitation" before the second movement starts. Is there a way to minimize this hesitation? Thanks, Klaas P.S.: if you know why powerpoint would play a movie fine 3 or 4 times in a row and then fail after that (nothing else changes, except maybe time), please let me know. From pett at cgl.ucsf.edu Mon Mar 3 14:22:42 2008 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 3 Mar 2008 14:22:42 -0800 Subject: [Chimera-users] scens/movies rendered with povray In-Reply-To: <47CC5B4D.6000708@pandora.be> References: <47CC5B4D.6000708@pandora.be> Message-ID: On Mar 3, 2008, at 12:10 PM, Klaas Decanniere wrote: > - when not using a "wait" command, several movements (roll, move, > scale) > are combined. When using the wait command, movements become separated > with a small "hesitation" before the second movement starts. Is > there a > way to minimize this hesitation? I don't know about your other questions but I have some info on this one. Until recently, Chimera was putting an implicit "wait 1" after every line of a script, including comment lines, blank lines, and lines that already end in an explicit "wait" of some sort. Now it does not wait after those three types of lines. Depending on the structure of your script, this behavior may have been causing the "hesitation" you describe. If you get a daily build (www.cgl.ucsf.edu/chimera and follow the "Daily Builds" link) this behavior is fixed there. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From gregc at cgl.ucsf.edu Mon Mar 3 16:07:38 2008 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Mon, 3 Mar 2008 16:07:38 -0800 (PST) Subject: [Chimera-users] scens/movies rendered with povray In-Reply-To: <47CC5B4D.6000708@pandora.be> References: <47CC5B4D.6000708@pandora.be> Message-ID: On Mon, 3 Mar 2008, Klaas Decanniere wrote: > Hello, > > The option to make movies using povray works nice and easy, so I want to > push the boundaries a bit :-) > > - the standard texture included in the .pov files has a very simple > finish - is there an easy way to include a spiced-up version? > - when not using a "wait" command, several movements (roll, move, scale) > are combined. When using the wait command, movements become separated > with a small "hesitation" before the second movement starts. Is there a > way to minimize this hesitation? > > Thanks, > > Klaas > > P.S.: if you know why powerpoint would play a movie fine 3 or 4 times in > a row and then fail after that (nothing else changes, except maybe > time), please let me know. Hello, We don't have a simple way to change the POV-ray finish. What you could do today, is to use chimera's x3dsave command to export your scene as a X3D file, next run CHIMERA/bin/x3d2pov to convert it to a .pov file, and then edit the result. If the editting is done by a program, you could invoke it and x3d2pov with chimera's system command, so all of the commands could be in a command script. FYI, I will be deprecating the x3dsave command with a more general export command that will let you export directly to .pov before for the next production release. As for PowerPoint, we have a list of troubleshooting web links in the Chimera documentation on "Making Movies". If you have already done what they recommend and it didn't help, we like to know. Greg Couch UCSF Computer Graphics Lab From meng at cgl.ucsf.edu Mon Mar 3 16:16:57 2008 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 3 Mar 2008 16:16:57 -0800 Subject: [Chimera-users] scens/movies rendered with povray In-Reply-To: References: <47CC5B4D.6000708@pandora.be> Message-ID: Hi Klaas, Here is the Chimera documentation page Greg mentioned: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html Near the bottom are links to two pages at Microsoft about movie/ PowerPoint issues. However, I just looked at these pages and don't see anything relating to a movie that first plays fine and then won't play, assuming you haven't changed your system in the meanwhile. They seem to relate to cases where the movie has never played correctly. I'm curious: if you exit from PowerPoint and then reopen the presentation, then will the movie play, or does it stop working "forever"? Best, 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 Mar 3, 2008, at 4:07 PM, Greg Couch wrote: >> >> P.S.: if you know why powerpoint would play a movie fine 3 or 4 >> times in >> a row and then fail after that (nothing else changes, except maybe >> time), please let me know. > > Hello, > > We don't have a simple way to change the POV-ray finish. What you > could > do today, is to use chimera's x3dsave command to export your scene > as a > X3D file, next run CHIMERA/bin/x3d2pov to convert it to a .pov > file, and > then edit the result. If the editting is done by a program, you could > invoke it and x3d2pov with chimera's system command, so all of the > commands could be in a command script. FYI, I will be deprecating the > x3dsave command with a more general export command that will let you > export directly to .pov before for the next production release. > > As for PowerPoint, we have a list of troubleshooting web links in the > Chimera documentation on "Making Movies". If you have already done > what > they recommend and it didn't help, we like to know. > > Greg Couch > UCSF Computer Graphics Lab From goddard at cgl.ucsf.edu Tue Mar 4 09:55:38 2008 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Tue, 04 Mar 2008 09:55:38 -0800 Subject: [Chimera-users] Graphics cards for Mac Message-ID: <47CD8D1A.8070502@cgl.ucsf.edu> Here's a comparison of Chimera graphics benchmarks for the current standard PowerMac graphics versus the top-of-the-line graphics: Radeon HD 2600 - no additional cost Quadro FX 5600 - $2850 additional cost Surfaces and meshes: 1.8x faster Volume solid style: size 443**3 vs 325**3. Quadro system was limited 32-bit main memory address space. Molecule: Neglible difference for 34000 atom model in wire, stick, ball and stick, ribbon, sphere styles. The Quadro card has 1.5 Gbytes of memory and will probably have significantly higher performance on solid style volume rendering if the Chimera volume display code is optimized. Probably adding more main memory will not help because the limitation is the 32-bit address space (a limit of Mac OS graphical applications). The Quadro card did not correctly display volume data in solid style with 3d textures (solid rendering 2d texture option turned off) -- displayed a chessboard pattern. Did not test 3d textures on Radeon card. Tom From gregc at cgl.ucsf.edu Tue Mar 4 10:48:26 2008 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Tue, 4 Mar 2008 10:48:26 -0800 (PST) Subject: [Chimera-users] Graphics cards for Mac In-Reply-To: <47CD8D1A.8070502@cgl.ucsf.edu> References: <47CD8D1A.8070502@cgl.ucsf.edu> Message-ID: Another take home message is that if you want chimera to run faster drawing molecules, get a faster CPU. This is true for all platforms chimera runs on (Mac OS X, Windows, Linux, ...). For example, both the Quadro system and the HD 2600 systems mentioned had 2.8 Ghz CPU's and Apple sells 3.0 and 3.2 Ghz systems for $800 and $1600 additional cost respectively. I would expect the improvement to be roughly linear with the CPU speed change, so +7% and +14%. But we'll have to wait for someone to do the benchmarks to be sure. Being CPU limited is not a feature, but to fix it will take a rewrite of the chimera internals and we're still evaluating how best to do it. Greg Couch UCSF Computer Graphics Lab On Tue, 4 Mar 2008, Tom Goddard wrote: > Here's a comparison of Chimera graphics benchmarks for the current > standard PowerMac graphics versus the top-of-the-line graphics: > > Radeon HD 2600 - no additional cost > Quadro FX 5600 - $2850 additional cost > > Surfaces and meshes: 1.8x faster > > Volume solid style: size 443**3 vs 325**3. Quadro system was limited > 32-bit main memory address space. > > Molecule: Neglible difference for 34000 atom model in wire, stick, ball > and stick, ribbon, sphere styles. > > The Quadro card has 1.5 Gbytes of memory and will probably have > significantly higher performance on solid style volume rendering if the > Chimera volume display code is optimized. Probably adding more main > memory will not help because the limitation is the 32-bit address space > (a limit of Mac OS graphical applications). > > The Quadro card did not correctly display volume data in solid style > with 3d textures (solid rendering 2d texture option turned off) -- > displayed a chessboard pattern. Did not test 3d textures on Radeon card. > > Tom From speir at scripps.edu Tue Mar 4 12:47:54 2008 From: speir at scripps.edu (Jeff Speir) Date: Tue, 4 Mar 2008 12:47:54 -0800 Subject: [Chimera-users] Graphics cards for Mac In-Reply-To: References: <47CD8D1A.8070502@cgl.ucsf.edu> Message-ID: <6F6AF348-3C75-428B-8FD1-33028D9C882E@scripps.edu> Thanks for the valuable info Tom, Greg. Apple advertised 10.5 Leopard as a 64-bit OS top to bottom. Is this not true for the graphics? Can any of the graphics programs running in Leopard access 64-bit memory space? Thanks, Jeff On Mar 4, 2008, at 10:48 AM, Greg Couch wrote: > Another take home message is that if you want chimera to run faster > drawing molecules, get a faster CPU. This is true for all platforms > chimera runs on (Mac OS X, Windows, Linux, ...). For example, both > the > Quadro system and the HD 2600 systems mentioned had 2.8 Ghz CPU's and > Apple sells 3.0 and 3.2 Ghz systems for $800 and $1600 additional cost > respectively. I would expect the improvement to be roughly linear > with > the CPU speed change, so +7% and +14%. But we'll have to wait for > someone > to do the benchmarks to be sure. > > Being CPU limited is not a feature, but to fix it will take a > rewrite of > the chimera internals and we're still evaluating how best to do it. > > Greg Couch > UCSF Computer Graphics Lab > > On Tue, 4 Mar 2008, Tom Goddard wrote: > >> Here's a comparison of Chimera graphics benchmarks for the current >> standard PowerMac graphics versus the top-of-the-line graphics: >> >> Radeon HD 2600 - no additional cost >> Quadro FX 5600 - $2850 additional cost >> >> Surfaces and meshes: 1.8x faster >> >> Volume solid style: size 443**3 vs 325**3. Quadro system was >> limited >> 32-bit main memory address space. >> >> Molecule: Neglible difference for 34000 atom model in wire, stick, >> ball >> and stick, ribbon, sphere styles. >> >> The Quadro card has 1.5 Gbytes of memory and will probably have >> significantly higher performance on solid style volume rendering >> if the >> Chimera volume display code is optimized. Probably adding more main >> memory will not help because the limitation is the 32-bit address >> space >> (a limit of Mac OS graphical applications). >> >> The Quadro card did not correctly display volume data in solid style >> with 3d textures (solid rendering 2d texture option turned off) -- >> displayed a chessboard pattern. Did not test 3d textures on >> Radeon card. >> >> Tom > _______________________________________________ > 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 Mar 4 13:01:52 2008 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Tue, 04 Mar 2008 13:01:52 -0800 Subject: [Chimera-users] Graphics cards for Mac In-Reply-To: <6F6AF348-3C75-428B-8FD1-33028D9C882E@scripps.edu> References: <47CD8D1A.8070502@cgl.ucsf.edu> <6F6AF348-3C75-428B-8FD1-33028D9C882E@scripps.edu> Message-ID: <47CDB8C0.9090905@cgl.ucsf.edu> Hi Jeff, You are right, Leopard (Mac OS 10.5) allows for 64-bit graphical applications. I was not aware of this. We have not made a 64-bit Chimera version for the Mac and it could require significant work because 30 third-party packages Chimera uses will all have to build successfully in 64-bit mode. The Chimera developers have not yet discussed a time-line for achieving this. Tom From triffo at rice.edu Tue Mar 4 13:39:42 2008 From: triffo at rice.edu (William Jeffrey Triffo) Date: Tue, 04 Mar 2008 13:39:42 -0800 Subject: [Chimera-users] Graphics cards for Mac In-Reply-To: <47CDB8C0.9090905@cgl.ucsf.edu> References: <47CD8D1A.8070502@cgl.ucsf.edu> <6F6AF348-3C75-428B-8FD1-33028D9C882E@scripps.edu> <47CDB8C0.9090905@cgl.ucsf.edu> Message-ID: <47CDC19E.7070800@rice.edu> Tom, regarding 64-bit builds of various third-party packages, is there a way some of us Leopard users could help test / figure out if successful builds would be feasible? perhaps some of us who are knowledgeable with that kind of scut-work would be willing to help with that tedium (?) -Jeff (Triffo) Tom Goddard wrote: > Hi Jeff, > > You are right, Leopard (Mac OS 10.5) allows for 64-bit graphical > applications. I was not aware of this. We have not made a 64-bit > Chimera version for the Mac and it could require significant work > because 30 third-party packages Chimera uses will all have to build > successfully in 64-bit mode. The Chimera developers have not yet > discussed a time-line for achieving this. > > Tom > > _______________________________________________ > 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 Mar 4 14:02:02 2008 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Tue, 4 Mar 2008 14:02:02 -0800 (PST) Subject: [Chimera-users] Graphics cards for Mac In-Reply-To: <47CDC19E.7070800@rice.edu> References: <47CD8D1A.8070502@cgl.ucsf.edu> <6F6AF348-3C75-428B-8FD1-33028D9C882E@scripps.edu> <47CDB8C0.9090905@cgl.ucsf.edu> <47CDC19E.7070800@rice.edu> Message-ID: We have 64-bit builds on other platforms (e.g., Linux), so we know it's feasible. It's more of a resource issue, i.e., who is going to spend the time to do it, and how are we going to package it? Should we just make the OS X distribution fatter, and if we do, will it still run on 10.3? Does 10.5 let you run the 32-bit version to save memory when bundled with the 64-bit binary? Do we need to make 64-bit PPC version too? - Greg On Tue, 4 Mar 2008, William Jeffrey Triffo wrote: > Tom, > > regarding 64-bit builds of various third-party packages, is there a way > some of us Leopard users could help test / figure out if successful > builds would be feasible? perhaps some of us who are knowledgeable with > that kind of scut-work would be willing to help with that tedium (?) > > -Jeff (Triffo) > > > Tom Goddard wrote: >> Hi Jeff, >> >> You are right, Leopard (Mac OS 10.5) allows for 64-bit graphical >> applications. I was not aware of this. We have not made a 64-bit >> Chimera version for the Mac and it could require significant work >> because 30 third-party packages Chimera uses will all have to build >> successfully in 64-bit mode. The Chimera developers have not yet >> discussed a time-line for achieving this. >> >> Tom >> >> _______________________________________________ >> 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 kfurse at nd.edu Wed Mar 5 08:28:19 2008 From: kfurse at nd.edu (Kristina Furse) Date: Wed, 5 Mar 2008 11:28:19 -0500 Subject: [Chimera-users] Step through trajectory from command line? In-Reply-To: <8A96E46F-A904-42E3-8AF0-2BE5AA6C47DA@cgl.ucsf.edu> References: <1204309130.47c84c8aec55a@webmail.nd.edu> <8A96E46F-A904-42E3-8AF0-2BE5AA6C47DA@cgl.ucsf.edu> Message-ID: <1204734499.47ceca238b1b9@webmail.nd.edu> > There is no command for advancing trajectory frames. Perhaps you > can detail the scenario that you need this for and why the per-frame > scripting of the MD Movie tool doesn't cover your needs. Are you > trying to completely automate the production of a movie from a > trajectory or some such? Yes. > Even if there were a command to advance the trajectory, how would > you know when to stop? There are no "flow control" statements (if > statements/for loops/functions) in the Chimera command language. I > think you will have to use Python scripting for completely automating > trajectory-related scripting. I can provide assistance there. You are correct in your assessment--I don't know Python, but I do know Perl so I just wanted to use Perl to produce a line by line Chimera script that would do some zooms and rotations, writing POV files (actually x3d files that I'll translate into POV files in a later step), then flow straight into an MD movie, writing POV files for each frame. No worries--I'm sure I can figure out how to do a per-frame Python script that will write an x3d file with a unique name for each trajectory frame. It just made more sense to me the other way around. Thanks! Kristina -- Kristina Furse Postdoctoral Research Associate 262 Stepan Chemistry Hall Notre Dame, IN 46556 (574)631-3904 From pett at cgl.ucsf.edu Wed Mar 5 11:06:11 2008 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 5 Mar 2008 11:06:11 -0800 Subject: [Chimera-users] Step through trajectory from command line? In-Reply-To: <1204734499.47ceca238b1b9@webmail.nd.edu> References: <1204309130.47c84c8aec55a@webmail.nd.edu> <8A96E46F-A904-42E3-8AF0-2BE5AA6C47DA@cgl.ucsf.edu> <1204734499.47ceca238b1b9@webmail.nd.edu> Message-ID: <5CD8C777-A99E-4760-B0A8-60BCEF099968@cgl.ucsf.edu> On Mar 5, 2008, at 8:28 AM, Kristina Furse wrote: > You are correct in your assessment--I don't know Python, but I do > know Perl so I > just wanted to use Perl to produce a line by line Chimera script > that would do > some zooms and rotations, writing POV files (actually x3d files > that I'll > translate into POV files in a later step), then flow straight into > an MD movie, > writing POV files for each frame. No worries--I'm sure I can figure > out how to > do a per-frame Python script that will write an x3d file with a > unique name for > each trajectory frame. It just made more sense to me the other way > around. Unless you are going to process many trajectories, the easiest approach I think is for you to write your Perl script to handle the initial zoom/rotation part, then to switch to MD Movie's per-frame scripting for the rest. You don't have to use Python for the per- frame scripting, you can use regular Chimera commands. As mentioned in the per-frame dialog, the string "" in commands will be substituted with the current frame number, so it should be easy to produce uniquely-named files. --Eric -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Wed Mar 5 11:51:42 2008 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Wed, 05 Mar 2008 11:51:42 -0800 Subject: [Chimera-users] Unit cell coordinates, Python / Chimera In-Reply-To: <57075CCB-1A05-4025-AAC2-41CCAF4AA606@cgl.ucsf.edu> References: <47CDFA8C.8000707@jhu.edu> <57075CCB-1A05-4025-AAC2-41CCAF4AA606@cgl.ucsf.edu> Message-ID: <47CEF9CE.6070201@cgl.ucsf.edu> Hi Rachel, Attached is Python code that prints the unit cell axes of open PDB models to the reply log. You open the PDB models, then open this script, and the results appear in the reply log (menu Favorites / Reply Log), for example: 1a0m.pdb unit cell axes a axis = 44.400 0.000 0.000 b axis = 0.000 44.400 0.000 c axis = 0.000 0.000 23.500 I figured out the needed Chimera calls by looking at the Chimera Python code for the Unit Cell tool located in your Chimera distribution in chimera/share/UnitCell/__init__.py and I homed in on the show_outline_cb() function to quickly figure out the attached code. On the Mac this code is in Chimera.app/Contents/Resources/share/UnitCell/__init__.py and to look inside the Chimera.app folder click on its icon with the ctrl key held and select "Show Package Contents". Tom > *From: *Rachel Karchin > *Date: *March 4, 2008 5:42:36 PM PST > > Me again. Is there a way to get the coordinates of the unit cell > vertices or the plane equation from Chimera running through a python > script? > > Tx!! > > -- rk -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: cell.py URL: From matinhe at 163.com Thu Mar 6 07:52:53 2008 From: matinhe at 163.com (Martin) Date: Thu, 6 Mar 2008 23:52:53 +0800 (CST) Subject: [Chimera-users] one question about slicing Message-ID: <6616991.1260011204818773376.JavaMail.coremail@bj163app24.163.com> Hi, I write in this mail to ask your great help on the slicing of MRC files. I want to slice a map in MRC format in half and save it as a new MRC file which only contains the remaining half map. However, it seems that the "Per-Model Clipping" function of Chimera can only work on the visualization mode, without connection to the "Save map as" function to attain a new map file. I am wodering if there is any other method to realize my intention. Thank you very much! Sincerely yours, Jian -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Thu Mar 6 09:16:17 2008 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Thu, 06 Mar 2008 09:16:17 -0800 Subject: [Chimera-users] one question about slicing In-Reply-To: <6616991.1260011204818773376.JavaMail.coremail@bj163app24.163.com> References: <6616991.1260011204818773376.JavaMail.coremail@bj163app24.163.com> Message-ID: <47D026E1.9060102@cgl.ucsf.edu> Hi Jian, You are right that "Save map as..." ignores the per-model clip planes and near/far clip planes. The clip planes only effect what is displayed, not what is saved. To save a rectangular region of a map that may not be aligned with axes of the original map you need to interpolate the map on a new grid. The procedure for doing it is described in the Guide to Volume Data Display: http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#resample Tom From peter.hildebrand at charite.de Tue Mar 4 04:06:53 2008 From: peter.hildebrand at charite.de (Peter Hildebrand) Date: Tue, 04 Mar 2008 13:06:53 +0100 Subject: [Chimera-users] using EMAN/AIRS/SSEHunter Message-ID: <1204632413.30301.13.camel@trave.charite.de> Hallo there, we have installed the AIRS (EMAN 1.8) Package for Chimera (build 2470), but have difficulties to get it run. steps to reproduce: launch Chimera load .mrc file calling tools/AIRS/SSEHunter there is no file to select in the 'MRC file' selection box. If we provide parameters for Angstrom, Resolution and threshold and press 'Apply' we get this: ================================================================= UnboundLocalError Exception in Tk callback Function: (type: ) Args: () Traceback (innermost last): File "CHIMERA/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1747, in __call__ None File "CHIMERA/share/chimera/baseDialog.py", line 238, in command None File "/usr/local/EMAN/chimeraext/Airs/ssehunter.py", line 89, in Apply targetPath=airsIO.getPath(target) File "/usr/local/EMAN/chimeraext/Airs/airsIO.py", line 62, in getPath return path UnboundLocalError: local variable 'path' referenced before assignment ================================================================= Are we using this module in the wrong way (wrong parameters e.g.) or is it a bug (where?). Thanks in advance, jan and peter From goddard at cgl.ucsf.edu Thu Mar 6 10:00:01 2008 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Thu, 06 Mar 2008 10:00:01 -0800 Subject: [Chimera-users] using chimera on 3D EM map In-Reply-To: <47D026B5.70506@purdue.edu> References: <47D026B5.70506@purdue.edu> Message-ID: <47D03121.6080006@cgl.ucsf.edu> Hi Weimin, Thanks for explaining these problems. We intend to solve all of them (though it will take some time) and perhaps some already have solutions. 1) Volume eraser ball can't be made small enough. The ball can have any floating point radius value > 0. So you should be able to make it as small as you like. I've tried and had no trouble making it tiny. A radius value of 0 is not valid and the ball radius will be left at whatever it was prior to attempting to set it to zero. 2) There is no "undo" in volume eraser. Yes. This is a serious problem we plan on fixing. 3) No way to add density (as opposed to subtracting with volume eraser). I guess you mean you would like to use a 3d ball to mark the density you wish to keep instead of the density you want to erase. It might be easy to make a tool like this where you can paint the volume using a ball (like volume eraser). You could paint using one or more colors and then separate the different colored pieces into separate maps. The underlying code to do this is already in Chimera (color zone tool, and split map by color zone). It requires a way to place a marker that matches the painting ball -- basically just a "Color" button on the volume eraser dialog. Might be able to add this soon. I recently added plane by plane loop drawing for hand tracing surfaces that can be used with the new "mask" command to segment out the enclosed region (in current daily builds). But from what you say that is less useful in your high resolution case. 4) Statistical comparison of two maps. Chimera can report the correlation coefficient between two maps and it can optimize the position of one map within another. This tools was called "Fit Map in Map" in the current Chimera production release (version 1.2470) and is called "Fit in Map" (which also handles fitting models) in current Chimera daily builds. There is also a new option in "Fit in Map" that will update the correlation coefficient in real time as you move one map within the second map. Also there is a new "Fit in Map" option that will compute a simulated map from a PDB at a given resolution (like EMAN pdb2mrc) and will fit the simulated map and report its correlation in the experimental map. Are there other measures besides correlation coefficient that you want? From your example, maybe you want rotations in degrees between two different fits? Tom Weimin Wu wrote: > Dear Prof.: > > I am one postdoctoral in Prof. Wenjiang's group. We have employed > Chimera in our research and really appreciate it. However when our 3D > map goes beyond 5A (see Feb. 28, 2008 Nature paper) which enabled us > to see the boundaries among alpha helices and beta sheets, we meet > some problems in the segmentation which we do think you could help us > out. > > One problem is that the viewer eraser ball is too big even the radius > is set to zero. It prevented us from completely clearing the > neighboring signals. There is no undo option when using the eraser > function. Therefore we have to keep saving the intermediate maps. > > Another problem is that there is no 3D volume editor which can let us > add density in 3D EM map. Sometimes this is the most important for the > segmentation, because it is hard to tell which density should be > included if we go slice by slice, but it is much easier to tell > directly in 3D map with the stereo function. > > Another problem is that there is no statistical tool for analyzing the > slight difference between two 3D EM maps. Therefore it makes hard to > determine the fit quality of one map into the other, for example, when > fitting one subunit into the other, there is some conformation > difference between them, but we need quantitative values to evaluate > the difference and make a story. Something like in two PDBs, we can > fit one domain and check the difference of the other domain. > > If I don't explain the problems clearly, please let me know. Many thanks, > > weimin wu From goddard at cgl.ucsf.edu Thu Mar 6 10:07:28 2008 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Thu, 06 Mar 2008 10:07:28 -0800 Subject: [Chimera-users] using chimera on 3D EM map In-Reply-To: <47D03121.6080006@cgl.ucsf.edu> References: <47D026B5.70506@purdue.edu> <47D03121.6080006@cgl.ucsf.edu> Message-ID: <47D032E0.1080008@cgl.ucsf.edu> Hi Weimin, One more comment on the problem of making the volume eraser ball small enough. The slider that controls the ball radius in the volume eraser dialog only goes in discrete steps -- just because the smallest detectable slider motion is one screen pixel. You can resize the volume eraser window to make it wider, so the slider is longer and that will give finer slider steps. Or you can just type in whatever radius value you want and not use the slider at all. Tom From goddard at cgl.ucsf.edu Thu Mar 6 11:37:29 2008 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Thu, 06 Mar 2008 11:37:29 -0800 Subject: [Chimera-users] using EMAN/AIRS/SSEHunter In-Reply-To: <1204632413.30301.13.camel@trave.charite.de> References: <1204632413.30301.13.camel@trave.charite.de> Message-ID: <47D047F9.50303@cgl.ucsf.edu> Hi Jan and Peter, Matt Baker wrote the AIRs code that interfaces EMAN with Chimera. I'm not sure if he maintains the code and I don't think he reads the Chimera users mailing list. I'll send you his email address separately. The EMAN 1.8 Chimera extensions do not work with Chimera version 1.2470. That EMAN code is too old and not compatible with some changes made in newer Chimera versions. But EMAN 1.8 is the most recent stable version (of EMAN 1). One idea is to use an older Chimera version -- I recommend Chimera version 1.2422. Another approach is to get a newer EMAN -- a nightly build. I tried the EMAN nightly build for MacOS but it appears to date from April 2006 -- even older than EMAN 1.8. I tried the nightly EMAN source code. All of the Chimera extensions are written in Python (but the call the EMAN binaries) so they can be used from the source code copy (no compilation is needed). This has more recent AIRs code than EMAN 1.8. You can select the MRC map in the SSEHunter tool but it fails with another error message. I think you will have to use an older Chimera version or contact Matt Baker at NCMI to see if code that works with current Chimera versions is available. Tom From terry at lego.berkeley.edu Thu Mar 6 12:17:00 2008 From: terry at lego.berkeley.edu (Terry Lang) Date: Thu, 06 Mar 2008 12:17:00 -0800 Subject: [Chimera-users] pdb format and charges Message-ID: <47D0513C.309@lego.berkeley.edu> Hey Everyone, I would like to use Chimera to write charges for a pdb file in the b-factor column. I feel like this is possible but couldn't quite figure out how to do it. Sincerely, Terry -- P. Therese Lang Post Doc Alber Lab, UC Berkeley From meng at cgl.ucsf.edu Thu Mar 6 12:32:29 2008 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 6 Mar 2008 12:32:29 -0800 Subject: [Chimera-users] pdb format and charges In-Reply-To: <47D0513C.309@lego.berkeley.edu> References: <47D0513C.309@lego.berkeley.edu> Message-ID: Hi Terry, I am guessing this is to use as input to some other program? There are much better ways to save attribute values (charge, hydrophobicity, etc.) if you are going to be using them in Chimera. You can tell Chimera to change the bfactor to equal the charge, then save a PDB file (File... Save PDB or command "write"). However, the bfactor column only has 2 digits after the decimal and you lose a lot of the actual charge data. First add charge, then reset bfactor to equal them: - open Attribute Calculator (under Tools... Structure Analysis) http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/calculator/ calculator.html - in that tool, Calculate attribute bfactor for atoms with the Formula: atom.charge This is really twisting the intent of PDB saving in Chimera. We generate only standard PDB format, so you can't write the bfactor column with more digits. If you were saving the attribute values for later use in Chimera, you would instead save an attribute assignment file, which would preserve the entire values. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/ defineattrib.html#attrfile Names of several atom attributes are listed here: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ atom_spec.html#atprops 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 Mar 6, 2008, at 12:17 PM, Terry Lang wrote: > Hey Everyone, > > I would like to use Chimera to write charges for a pdb file in > the b-factor column. I feel like this is possible but couldn't quite > figure out how to do it. > > > Sincerely, > Terry > > -- > P. Therese Lang > Post Doc > Alber Lab, UC Berkeley > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From wu49 at purdue.edu Thu Mar 6 11:21:31 2008 From: wu49 at purdue.edu (Weimin Wu) Date: Thu, 06 Mar 2008 14:21:31 -0500 Subject: [Chimera-users] using chimera on 3D EM map In-Reply-To: <47D03121.6080006@cgl.ucsf.edu> References: <47D026B5.70506@purdue.edu> <47D03121.6080006@cgl.ucsf.edu> Message-ID: <47D0443B.4010100@purdue.edu> Tom Goddard wrote: > Hi Weimin, > > Thanks for explaining these problems. We intend to solve all of them > (though it will take some time) and perhaps some already have solutions. > > 1) Volume eraser ball can't be made small enough. The ball can have > any floating point radius value > 0. So you should be able to make it > as small as you like. I've tried and had no trouble making it tiny. > A radius value of 0 is not valid and the ball radius will be left at > whatever it was prior to attempting to set it to zero. > > 2) There is no "undo" in volume eraser. Yes. This is a serious > problem we plan on fixing. > > 3) No way to add density (as opposed to subtracting with volume > eraser). I guess you mean you would like to use a 3d ball to mark the > density you wish to keep instead of the density you want to erase. It > might be easy to make a tool like this where you can paint the volume > using a ball (like volume eraser). You could paint using one or more > colors and then separate the different colored pieces into separate > maps. The underlying code to do this is already in Chimera (color > zone tool, and split map by color zone). It requires a way to place a > marker that matches the painting ball -- basically just a "Color" > button on the volume eraser dialog. Might be able to add this soon. > I recently added plane by plane loop drawing for hand tracing surfaces > that can be used with the new "mask" command to segment out the > enclosed region (in current daily builds). But from what you say that > is less useful in your high resolution case. > > 4) Statistical comparison of two maps. Chimera can report the > correlation coefficient between two maps and it can optimize the > position of one map within another. This tools was called "Fit Map in > Map" in the current Chimera production release (version 1.2470) and is > called "Fit in Map" (which also handles fitting models) in current > Chimera daily builds. There is also a new option in "Fit in Map" that > will update the correlation coefficient in real time as you move one > map within the second map. Also there is a new "Fit in Map" option > that will compute a simulated map from a PDB at a given resolution > (like EMAN pdb2mrc) and will fit the simulated map and report its > correlation in the experimental map. Are there other measures besides > correlation coefficient that you want? From your example, maybe you > want rotations in degrees between two different fits? > > Tom > > Thanks for your reply. I will try the eraser ball again. To add the density, I really need something like 3D brush. I have tried a series of Markers and split by colors, however it is hard to choose marker position and choose color zone radius, because we need separate the signals within 4A distance, especially when two subunits cross over and one beta sheet is very close to the beta sheet on the other subunit. For statistical comparison of two maps, I need not only correlation, but also rotation degrees, translation, especially for the hinge region, something like rmsd in pdb comparison. Thanks, weimin From meng at cgl.ucsf.edu Mon Mar 10 09:50:43 2008 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 10 Mar 2008 09:50:43 -0700 Subject: [Chimera-users] using chimera on 3D EM map In-Reply-To: <47D0443B.4010100@purdue.edu> References: <47D026B5.70506@purdue.edu> <47D03121.6080006@cgl.ucsf.edu> <47D0443B.4010100@purdue.edu> Message-ID: <1C899C3F-01D5-40E9-8DA5-CD9FCF8AC42B@cgl.ucsf.edu> On Mar 6, 2008, at 11:21 AM, Weimin Wu wrote: > Thanks for your reply. I will try the eraser ball again. To add the > density, I really need something like 3D brush. I have tried a > series of > Markers and split by colors, however it is hard to choose marker > position and choose color zone radius, because we need separate the > signals within 4A distance, especially when two subunits cross over > and > one beta sheet is very close to the beta sheet on the other > subunit. For > statistical comparison of two maps, I need not only correlation, but > also rotation degrees, translation, especially for the hinge region, > something like rmsd in pdb comparison. > Hi Weimin, Another possibility is to make a surface, and then use the surface to divide the density map. This can be done with recent versions of Chimera. I don't know if this is a good way to work with your data, but if you want to try, here are more details: (a) in Volume Viewer, show a single density plane (Features... Planes in Volume Viewer menu) (b) use Volume Tracer to draw a line in that plane, actually a string of markers (Place markers on data planes and Place markers while dragging) http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ volumepathtracer/volumepathtracer.html#dragplace (c) repeat (a) and (b) for a stack of planes (d) use Volume Tracer to join the stack of lines into a surface (Features... Surfaces in Volume Tracer menu) http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ volumepathtracer/volumepathtracer.html#surfaces (e) use the command "mask" to use the surface to divide the data http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html Best, 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 From goddard at cgl.ucsf.edu Mon Mar 10 17:27:44 2008 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 10 Mar 2008 17:27:44 -0700 Subject: [Chimera-users] using chimera on 3D EM map In-Reply-To: <47D0443B.4010100@purdue.edu> References: <47D026B5.70506@purdue.edu> <47D03121.6080006@cgl.ucsf.edu> <47D0443B.4010100@purdue.edu> Message-ID: <47D5D200.1020905@cgl.ucsf.edu> Hi Weimin, I wonder if a 3d brush will be useful. The problem is you cannot see the depth in a 3d view of the data clearly. Amira provides a 2d brush which is much less trouble. The painting tool I suggested would have you push a button to paint within a sphere (maybe some other shape) and it would be a simple matter to allow you to drag it like a brush without the button press to test if that is useful. I'm not sure I understand the rotation and translation parameters you want. Is it that you have one map fit within another in 2 orientations and you want the rotation and translation relating those 2 orientations? Tom Weimin Wu wrote: > > Thanks for your reply. I will try the eraser ball again. To add the > density, I really need something like 3D brush. I have tried a series of > Markers and split by colors, however it is hard to choose marker > position and choose color zone radius, because we need separate the > signals within 4A distance, especially when two subunits cross over and > one beta sheet is very close to the beta sheet on the other subunit. For > statistical comparison of two maps, I need not only correlation, but > also rotation degrees, translation, especially for the hinge region, > something like rmsd in pdb comparison. > > Thanks, > weimin From lynnwuchao at gmail.com Tue Mar 11 04:29:21 2008 From: lynnwuchao at gmail.com (=?GB2312?B?zuKzrA==?=) Date: Tue, 11 Mar 2008 19:29:21 +0800 Subject: [Chimera-users] [chimera-users]torsional angle Message-ID: <6a4059ef0803110429x2d887fadgbe37ba104d237f5e@mail.gmail.com> Hi, folks! I have a problem about the measurement of torsional angle. In the chimera users' guide about the command angle, as follows, it says that if I select the atoms simultaneously, the order information will get lost. How can I keep the order information since I need it to calculate the angle I want exactly? For example, in the following command I originally want to calculate the n-ca-c-n(182) dihedral, angle :181.a at n,ca,c:182.a at n but in fact what chimera gave me was may be c-ca-n-n(182). I want to calculate a lot of diheral information so I can not click one by one in the gui mode, I wonder is there any way that I can get what I want . Thanks! Usage: *angle* *atom1 atom2 atom3* [ *atom4* ] *Angle* reports the bond angle for three specifiedatoms or the dihedral angle for four specifiedatoms. The order of specification is important, but atoms need not be connected. The angle value in degrees is reported in the status lineand *Reply Log*. The atoms can be specified collectively using the word *selected*, *sel*, or *picked* if the current selectioncontains only the three or four atoms of interest; the order in which the atoms were selected(most likely picked) is used. When order information is lacking (for example, the atoms were selected simultaneously), the angle actually measured may not be the one intended. There are no automatic updates if the angle changes. A new command must be issued to measure the changed angle. -- Chao Wu Currently: National Institute of Biological Sciences, Beijing Huang Niu's Lab http://www.nibs.ac.cn/ Tel: 80726688-8572 Address: Beijing ZhongGuanCun Life Science Park, NO.7 Science Park East Road, NIBS B427 Postcode: 102206 Life Science Honors Program, China Agricultural University PO.1055, NO.2 YuanMingYuan west road, Beingjing, 100094 P.R. China Tel: 86-10-62812484 E-mail: lynnwuchao at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Mar 11 09:42:32 2008 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 11 Mar 2008 09:42:32 -0700 Subject: [Chimera-users] [chimera-users]torsional angle In-Reply-To: <6a4059ef0803110429x2d887fadgbe37ba104d237f5e@mail.gmail.com> References: <6a4059ef0803110429x2d887fadgbe37ba104d237f5e@mail.gmail.com> Message-ID: <4E05078B-7F91-4DDF-A9C2-3984DF53DE28@cgl.ucsf.edu> Hi! Besides picking from the screen, you can just name the 4 atoms in order in the command, for example angle :181.a at n@ca at c:182.a at n When you use commas (,) the order is not necessarily preserved. Best, 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 Mar 11, 2008, at 4:29 AM, ?? wrote: > Hi, folks! > I have a problem about the measurement of torsional angle. > In the chimera users' guide about the command angle, as follows, it > says that if I select the atoms simultaneously, the order > information will get lost. > How can I keep the order information since I need it to calculate > the angle I want exactly? > For example, in the following command I originally want to calculate > the n-ca-c-n(182) dihedral, > angle :181.a at n,ca,c:182.a at n > but in fact what chimera gave me was may be c-ca-n-n(182). > > I want to calculate a lot of diheral information so I can not click > one by one in the gui mode, I wonder is there any way that I can > get what I want . > Thanks! > -- > Chao Wu > > Currently: > National Institute of Biological Sciences, Beijing > Huang Niu's Lab > http://www.nibs.ac.cn/ > Tel: 80726688-8572 > Address: Beijing ZhongGuanCun Life Science Park, NO.7 Science Park > East Road, NIBS B427 > Postcode: 102206 > > Life Science Honors Program, China Agricultural University > PO.1055, NO.2 YuanMingYuan west road, Beingjing, 100094 > P.R. China > Tel: 86-10-62812484 > E-mail: lynnwuchao at gmail.com From wu49 at purdue.edu Tue Mar 11 06:35:39 2008 From: wu49 at purdue.edu (Weimin Wu) Date: Tue, 11 Mar 2008 09:35:39 -0400 Subject: [Chimera-users] using chimera on 3D EM map In-Reply-To: <47D5D200.1020905@cgl.ucsf.edu> References: <47D026B5.70506@purdue.edu> <47D03121.6080006@cgl.ucsf.edu> <47D0443B.4010100@purdue.edu> <47D5D200.1020905@cgl.ucsf.edu> Message-ID: <47D68AAB.9010500@purdue.edu> My problem is that I have few subunits in the asymmetry unit. I fit one into the other subunit, and I try to figure out how good is the fit. Visually I can see they fit well, but there is some difference which I think it is due to conformation difference, however I need quantitative data to report the difference, or a tool as simple as rmsd in the PDB comparison. I once tried to convert the density map to pseudo PDB (vol2pdb in situs), but it is hard to open that PDB in chimera. weimin Thomas Goddard wrote: > Hi Weimin, > > I wonder if a 3d brush will be useful. The problem is you cannot > see the depth in a 3d view of the data clearly. Amira provides a 2d > brush which is much less trouble. The painting tool I suggested would > have you push a button to paint within a sphere (maybe some other > shape) and it would be a simple matter to allow you to drag it like a > brush without the button press to test if that is useful. > > I'm not sure I understand the rotation and translation parameters > you want. Is it that you have one map fit within another in 2 > orientations and you want the rotation and translation relating those > 2 orientations? > > Tom > From dimattia at ufl.edu Thu Mar 13 11:37:59 2008 From: dimattia at ufl.edu (Michael DiMattia) Date: Thu, 13 Mar 2008 14:37:59 -0400 Subject: [Chimera-users] segmentation fault - surface rendering Message-ID: <3af7f9360803131137h2a23f324iae90d929c435204d@mail.gmail.com> Hello, I am trying to surface render a few different proteins within the same Chimera session and I keep encountering a segmentation faullt. I imagine this is due to a memory limit being reached, although I do not know if it is a Chimera parameter that can be increased/overriden. Instead of having the different macromolecules in the same pdb, I have actually split it up into many pdbs and opened them one at a time, surface rendering one at a time. This worked for awhile but it seems I can't even get that far now. Any advice or tips on what I can do? I realize surface rendering is very computationally intensive but I would love to get this to work! Thanks Mike DiMattia -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Mar 13 15:43:35 2008 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 13 Mar 2008 15:43:35 -0700 Subject: [Chimera-users] segmentation fault - surface rendering In-Reply-To: <3af7f9360803131137h2a23f324iae90d929c435204d@mail.gmail.com> References: <3af7f9360803131137h2a23f324iae90d929c435204d@mail.gmail.com> Message-ID: Hi Mike, Rather than a memory issue, it is likely a failure of the surface calculation. Chimera uses MSMS for surface calculations, and we (and many bug reporters) have noted that it fails on a significant proportion of structures. The developers have been working very hard to write code to replace MSMS, but it is not yet available. The MSMS problems appear to be numerical instabilities sensitive to small changes in atomic radii, coordinates, surface vertex positions, and sometimes even the orientation of the molecule. Thus for each structure you can generally experiment and find some change(s) that will allow successful surface calculation. Unfortunately, there is no fix that necessarily works for all of the problem structures, and no way to tell beforehand which adjustment will be successful for a given structure! If the surface calculation is failing, here are a few things to try: (1) increase all atomic radii by some small amount, for example with the command: vdwdefine +0.01 http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html (2) change surface calculation parameters in the "New Surfaces" preferences (Favorites... Preferences, change to "New Surfaces" category). For example, in one recent case, it was necessary to increase the probe radius to 1.5 and set "show disjoint surfaces" to false. Remember to click Save if you want the settings to apply to your next use of Chimera. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New% 20Surfaces (3) add hydrogens (Tools... Structure Editing... AddH) or command "addh" - I prefer (1) or (2), however, as adding hydrogens will make the surface bumpier I don't know if you are calculating surfaces in some high-throughput fashion or concentrating on a few structures. If the latter and you are having trouble finding a tweak that will allow surface calculation, I could take a look at the structure for you (let me know the pdb ID, if any, or send the structure). I also don't know why splitting up your structure into multiple files might help, unless opening parts of the structure separately changed the surface geometry by making the surface enclose the individual parts rather than the entire thing (that can also be controlled with the "surfcat" command rather than splitting the file). Sorry for the difficulties. We are all looking forward to the new surface calculation code! 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 Mar 13, 2008, at 11:37 AM, Michael DiMattia wrote: > Hello, I am trying to surface render a few different proteins > within the same Chimera session and I keep encountering a > segmentation faullt. I imagine this is due to a memory limit being > reached, although I do not know if it is a Chimera parameter that > can be increased/overriden. Instead of having the different > macromolecules in the same pdb, I have actually split it up into > many pdbs and opened them one at a time, surface rendering one at a > time. This worked for awhile but it seems I can't even get that > far now. > > Any advice or tips on what I can do? > > I realize surface rendering is very computationally intensive but I > would love to get this to work! > > Thanks > > Mike DiMattia > _______________________________________________ > 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 Thu Mar 13 15:47:51 2008 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 13 Mar 2008 15:47:51 -0700 Subject: [Chimera-users] segmentation fault - surface rendering In-Reply-To: References: <3af7f9360803131137h2a23f324iae90d929c435204d@mail.gmail.com> Message-ID: <4C29F0E0-4E18-4497-BA40-16BA4CBC1DA2@cgl.ucsf.edu> One further caveat is that once surfacing fails in Chimera it won't work again in that Chimera -- you'll have to restart to try the workarounds. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Mar 13, 2008, at 3:43 PM, Elaine Meng wrote: > Hi Mike, > Rather than a memory issue, it is likely a failure of the surface > calculation. Chimera uses MSMS for surface calculations, and we (and > many bug reporters) have noted that it fails on a significant > proportion of structures. The developers have been working very hard > to write code to replace MSMS, but it is not yet available. > > The MSMS problems appear to be numerical instabilities sensitive to > small changes in atomic radii, coordinates, surface vertex positions, > and sometimes even the orientation of the molecule. Thus for each > structure you can generally experiment and find some change(s) that > will allow successful surface calculation. Unfortunately, there is > no fix that necessarily works for all of the problem structures, and > no way to tell beforehand which adjustment will be successful for a > given structure! > > If the surface calculation is failing, here are a few things to try: > > (1) increase all atomic radii by some small amount, for example with > the command: > vdwdefine +0.01 > > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html > > (2) change surface calculation parameters in the "New Surfaces" > preferences (Favorites... Preferences, change to "New Surfaces" > category). For example, in one recent case, it was necessary to > increase the probe radius to 1.5 and set "show disjoint surfaces" to > false. Remember to click Save if you want the settings to apply to > your next use of Chimera. > > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New% > 20Surfaces > > (3) add hydrogens (Tools... Structure Editing... AddH) or command > "addh" - I prefer (1) or (2), however, as adding hydrogens will make > the surface bumpier > > I don't know if you are calculating surfaces in some high-throughput > fashion or concentrating on a few structures. If the latter and you > are having trouble finding a tweak that will allow surface > calculation, I could take a look at the structure for you (let me > know the pdb ID, if any, or send the structure). > > I also don't know why splitting up your structure into multiple files > might help, unless opening parts of the structure separately changed > the surface geometry by making the surface enclose the individual > parts rather than the entire thing (that can also be controlled with > the "surfcat" command rather than splitting the file). > > Sorry for the difficulties. We are all looking forward to the new > surface calculation code! > 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 Mar 13, 2008, at 11:37 AM, Michael DiMattia wrote: > >> Hello, I am trying to surface render a few different proteins >> within the same Chimera session and I keep encountering a >> segmentation faullt. I imagine this is due to a memory limit being >> reached, although I do not know if it is a Chimera parameter that >> can be increased/overriden. Instead of having the different >> macromolecules in the same pdb, I have actually split it up into >> many pdbs and opened them one at a time, surface rendering one at a >> time. This worked for awhile but it seems I can't even get that >> far now. >> >> Any advice or tips on what I can do? >> >> I realize surface rendering is very computationally intensive but I >> would love to get this to work! >> >> Thanks >> >> Mike DiMattia >> _______________________________________________ >> 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Klaas.Decanniere at pandora.be Sat Mar 15 08:01:53 2008 From: Klaas.Decanniere at pandora.be (Klaas Decanniere) Date: Sat, 15 Mar 2008 16:01:53 +0100 Subject: [Chimera-users] preferences - povray - keep input files doesn't Message-ID: <47DBE4E1.3050307@pandora.be> For at least some versions of Chimera, the "keep pov-ray input files" option in the Favorites - Preferences- Pov-ray tab does not work ( .pov files are deleted after rendering during animation) This is true e.g for build 2491 2008/02/11 (Platform: linux2 windowing system x11). Is there a way to force this option? I would like to do some post processing on the .pov files before rendering. An option to generate an animation series .pov files without doing the actual rendering would be even better - how can I do that? Thanks for the help and kind regards, Klaas Decanniere From meng at cgl.ucsf.edu Sat Mar 15 12:53:20 2008 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sat, 15 Mar 2008 12:53:20 -0700 Subject: [Chimera-users] preferences - povray - keep input files doesn't In-Reply-To: <47DBE4E1.3050307@pandora.be> References: <47DBE4E1.3050307@pandora.be> Message-ID: <39A151A5-AD8D-4A62-9547-35F0F5861910@cgl.ucsf.edu> Hi Klaas, Movie recording overrides the "wait for POV-Ray" and "keep POV-Ray input files" options, as mentioned here: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#POV-Ray%20Options Our thinking was probably to prevent users from accidentally filling their disks with an avalanche of the very large *.pov files. However, obviously this prevents you from doing what you want. I can't think of any current "user interface" way to specify saving the files or not actually rendering them during movie recording (although we should probably discuss them as possible developments). I am hoping one of the programmers can suggest how to modify the Chimera Python code to do those things. If you are using the MD Movie tool, its per-frame script option can be used to export a file at each trajectory frame (more detail below). However, if there is not a 1-to-1 relationship between MD Movie trajectory frames and the frames you want in your movie, or if you are using Movie Recorder or the movie command (not MD Movie), I believe that modifying your copy of Chimera would be the more practical option. What you would put in a MD Movie per-frame script: The most recent versions of Chimera include an "export" command with a POV-Ray option (try the command "export list" just to see if your version has it, if not, get a newer daily build): http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/export.html Older versions have a similar command "x3dsave" but it only saves the X3D format, which could subsequently be converted to povray files with "x3d2pov" - the latter program is included with Chimera, as mentioned here: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/export.html Best, 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 Mar 15, 2008, at 8:01 AM, Klaas Decanniere wrote: > > For at least some versions of Chimera, the "keep pov-ray input files" > option in the Favorites - Preferences- Pov-ray tab does not work > ( .pov > files are deleted after rendering during animation) > > This is true e.g for build 2491 2008/02/11 (Platform: linux2 windowing > system x11). > > Is there a way to force this option? I would like to do some post > processing on the .pov files before rendering. > An option to generate an animation series .pov files without doing the > actual rendering would be even better - how can I do that? > > Thanks for the help and kind regards, > > Klaas Decanniere From francesco.malatesta at fastwebnet.it Mon Mar 17 09:56:17 2008 From: francesco.malatesta at fastwebnet.it (Francesco Malatesta) Date: Mon, 17 Mar 2008 17:56:17 +0100 Subject: [Chimera-users] interface residues Message-ID: <000601c8884f$d22a4a80$3d751417@nome80b5784770> Hello, could anyone help me out with this problem. I would like to exclusively colour interface residues in a dimeric protein represented as spheres or surface. Is this possible? Thank you very much Francesco Malatesta -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Mon Mar 17 11:00:55 2008 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 17 Mar 2008 11:00:55 -0700 Subject: [Chimera-users] preferences - povray - keep input files doesn't In-Reply-To: <47DBE4E1.3050307@pandora.be> References: <47DBE4E1.3050307@pandora.be> Message-ID: <47DEB1D7.8020809@cgl.ucsf.edu> Hi Klaas, You can make the Chimera movie recorder use your preference for keeping POVray files by editing file chimera/share/MovieRecorder/RecorderHandler.py changing line 120 from raytraceKeepInput = False, to # raytraceKeepInput = False, Then restart Chimera. Perhaps we should change the Chimera default for the "keep POVray input files" to false and have movie recorder respect the preference setting. Tom From pett at cgl.ucsf.edu Mon Mar 17 11:08:20 2008 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 17 Mar 2008 11:08:20 -0700 Subject: [Chimera-users] preferences - povray - keep input files doesn't In-Reply-To: <47DEB1D7.8020809@cgl.ucsf.edu> References: <47DBE4E1.3050307@pandora.be> <47DEB1D7.8020809@cgl.ucsf.edu> Message-ID: <43842C81-4FB1-42B4-A577-B78C8B1A41FE@cgl.ucsf.edu> We're thinking of adding some generic per-frame hook as a command so that you don't have to use Movie Recorder at all to generate a series of POVray files that you want to post-process before rendering (you would use the not-yet-documented "export" command to generate them). --Eric On Mar 17, 2008, at 11:00 AM, Thomas Goddard wrote: > Hi Klaas, > > You can make the Chimera movie recorder use your preference for > keeping POVray files by editing file > > chimera/share/MovieRecorder/RecorderHandler.py > > changing line 120 from > > raytraceKeepInput = False, > > to > > # raytraceKeepInput = False, > > Then restart Chimera. > > Perhaps we should change the Chimera default for the "keep POVray > input files" to false and have movie recorder respect the preference > setting. > > Tom > _______________________________________________ > 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 Mar 17 11:30:50 2008 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 17 Mar 2008 11:30:50 -0700 Subject: [Chimera-users] preferences - povray - keep input files doesn't In-Reply-To: <47DBE4E1.3050307@pandora.be> References: <47DBE4E1.3050307@pandora.be> Message-ID: <47DEB8DA.30309@cgl.ucsf.edu> Elaine Meng wrote: > Is there some similarly simple way to skip the rendering? I imagine > rendering is wasting a ton of time in his case... > Elaine Hi Elaine, Klaas, You can just generate the POVray scene file *.pov and options files *.ini and not do the rendering by editing Chimera (version 1.2499) file chimera/share/chimera/printer.py adding a line after line 1091 changing inifile.close() if raytraceKeepInput: to inifile.close() return if raytraceKeepInput: Then restart Chimera and use movie recorder to make the frames. As Eric pointed out this would be simpler if there was a way to execute a command on every Chimera frame. You could then use the new "export" command to create the *.pov file without rendering it. Tom From meng at cgl.ucsf.edu Mon Mar 17 15:27:02 2008 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 17 Mar 2008 15:27:02 -0700 Subject: [Chimera-users] interface residues In-Reply-To: <000601c8884f$d22a4a80$3d751417@nome80b5784770> References: <000601c8884f$d22a4a80$3d751417@nome80b5784770> Message-ID: On Mar 17, 2008, at 9:56 AM, Francesco Malatesta wrote: > Hello, > could anyone help me out with this problem. I would like to > exclusively colour interface residues in a dimeric protein > represented as spheres or surface. Is this possible? > Thank you very much > Francesco Malatesta > Hi Francesco, Of course - there are so many different ways you could do it, I'm not sure where to start! Also, I don't know if your structure is opened from two PDB files, or one PDB file with a different chain ID for each monomer. You could do it either way, but in my examples I will assume you have one file with protein chains A and B like structure 1tzz. My examples are commands, but the same things can be done with menus and/or graphical interfaces (it would just take a lot more words to describe). Possible ways to identify the residues: (a) with a simple distance cutoff (Select... Zone... or in commands) http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ atom_spec.html#zones command example: color red :.a & :.b za<5 - that would color atoms in chain A that are within 5 angstroms of any atom in chain B; you can include a distance limit in many other commands, such as "select" "display" "repr sphere" "surface" etc. The "za" means atom-based cutoff, whereas "z" or "zr" means residue- based (would color whole residues with any atom within that distance). You would then use a similar command for atoms in chain B close to atoms in chain A. (b) with Find Clashes/Contacts (under Tools... Structure Analysis) or command "findclash" http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/ findclash.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html command example: findclash :.a overlap -0.5 hb 0 makePseudobonds false select true ~select ~ :.b - the first command selects any atoms outside of chain A that are close to chain A (any atoms with VDW surfaces within 0.5 angstroms of the VDW surfaces of atoms in chain A). The second command deselects atoms NOT in chain B, so what you have left are just the atoms in B that are close to A. Then you can do what you want to the selected atoms with the Actions menu or other commands (including writing out a list of the atoms or residues). Next, use similar steps to get atoms in chain A that are close to the atoms in chain B. (c) with Intersurf (under Tools... Surface/Binding Analysis) or command "intersurf" http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/intersurf/ intersurf.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/intersurf.html command example: intersurf :.a :.b select true prune 10 That would select all the atoms from both chains found to form the interface. See the links above for the algorithm. The "prune" distance controls how far out to the sides the interface is computed and thus how many atoms will be selected. Intersurf creates a special interface surface and opens a dialog for recoloring it based on the distances between the subunits. If you don't want that surface, you can just close it. One other thing I should mention is that sometimes "surface" (display molecular surface, which is different than the special "intersurf" surfaces) will enclose multiple chains in the same surface when instead you wanted a separate surface for each chain. You can tell Chimera to make separate surfaces, as explained here: http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-February/ 002382.html 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 From jeandidier.marechal at uab.es Wed Mar 19 08:40:56 2008 From: jeandidier.marechal at uab.es (Jean-Didier =?ISO-8859-1?Q?Mar=E9chal?=) Date: Wed, 19 Mar 2008 16:40:56 +0100 Subject: [Chimera-users] Principal axis of inertia Message-ID: <1205941256.6758.5.camel@AMD3800> Hi everyone, I was wondering if there is a method available to calculate the principal axis of inertia of a protein (or a part of a protein) in chimera? If not what would be the easiest way to move forward? All the best, JD -- Dr. Jean-Didier Mar?chal Professor Lector Computational Bioorganic and Bioinorganic Chemistry @Transmet Office C7/018 Edifici C.n. Campus de Bellaterra Departament de Qu?mica Universitat Aut?noma de Barcelona 08193 Bellaterra, Catalunya, Spain Tel: (+34).935814936 Fax: (+34).935812920 e-mail: jeandidier.marechal at uab.es www: http://asklipio.qf.uab.es/cmc From meng at cgl.ucsf.edu Wed Mar 19 09:49:04 2008 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 19 Mar 2008 09:49:04 -0700 Subject: [Chimera-users] Principal axis of inertia In-Reply-To: <1205941256.6758.5.camel@AMD3800> References: <1205941256.6758.5.camel@AMD3800> Message-ID: <8D98E0C1-8119-4AA2-AEBD-3FDC5243C992@cgl.ucsf.edu> Hi JD, Take a look at the new Axes tool (under Tools... Structure Analysis in recent builds of Chimera): http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ structuremeas/structuremeas.html#axes It can show protein helix axes, but you can also calculate an axis for any set of selected atoms. Then you can perform other measurements such as distance to axis, crossing angle between two axes, etc. However, I am not sure whether this computed axis is what you need - it is not exactly an axis of inertia (doesn't depend on the atomic weights of the atoms, for example). Best, 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 Mar 19, 2008, at 8:40 AM, Jean-Didier Mar?chal wrote: > Hi everyone, > I was wondering if there is a method available to calculate the > principal axis of inertia of a protein (or a part of a protein) in > chimera? > > If not what would be the easiest way to move forward? > All the best, > JD From m945020003 at student.nsysu.edu.tw Thu Mar 13 00:15:10 2008 From: m945020003 at student.nsysu.edu.tw (Jason) Date: Thu, 13 Mar 2008 15:15:10 +0800 Subject: [Chimera-users] Data of Slice display Message-ID: <20080313063910.M30165@student.nsysu.edu.tw> Hi all I am using slice display to plot the profile of density map. That is the function that I want to exam the profile of virus density map without spherical average. Where can I get the data of each dot of profile, so I can plot profile at Excel for further use. Thank you for your help Kind regards Jason Chen -- Open WebMail Project (http://openwebmail.org) From bharatbioinformaticshau at gmail.com Wed Mar 19 04:23:11 2008 From: bharatbioinformaticshau at gmail.com (Bharat Yadav) Date: Wed, 19 Mar 2008 16:53:11 +0530 Subject: [Chimera-users] Requesting to solve my poblem Message-ID: Hello Sir / Madam Good Evening My name is Bharat Yadav and I am perusing Master's Degree in Bioinformatics from Chaudhary Charan Singh Haryana Agriculrual University - Hisar (India). I am working here on Molecular Modeling. With a long time I am using UCSF Chimera. It is the one of wonderful Molecular visiualization software haivng some very peculear features. Respected Sir / Madam, In my present work I am facing a bit problem. Hoping form you to help regarding this. My problem is as follows. I have generated five models of protein. when I open all these modles these were overlapping each other. I want to view all these five models in a single panel non overlapping. I mean I want to view these 3D models in panel as follows ----------------------------------------- | | | | | | | Model 1 | Model 2 | | | | ----------------------------------------- | | | | | | | Model 3 | Model 4 | | | | ----------------------------------------- | | | | | | | Model 5 | Model 6 | | | | ----------------------------------------- Hope that you now easily understand what actually I want. Please Help me regarding this and mail me its solution or steps or commands for this task. Please free to ask any question. Thanks in anticipation Warm regards from Bharat Yadav From meng at cgl.ucsf.edu Wed Mar 19 10:11:52 2008 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 19 Mar 2008 10:11:52 -0700 Subject: [Chimera-users] Requesting to solve my poblem In-Reply-To: References: Message-ID: <37BB555C-E967-43BB-B6EA-5CD8A75853FD@cgl.ucsf.edu> Hi Bharat, Thanks for your kind words! I think you just need to use "tile" in the Model Panel. Open Model Panel (Favorites... Model Panel). In there, choose all 5 models on the left side. Then, on the right, change the menu from "frequently used" to "infrequently used" - now there should be a "tile" button on the right - try using that. 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 Mar 19, 2008, at 4:23 AM, Bharat Yadav wrote: > Hello Sir / Madam > > Good Evening > My name is Bharat Yadav and I am perusing Master's Degree in > Bioinformatics from Chaudhary Charan Singh Haryana Agriculrual > University - Hisar (India). I am working here on Molecular Modeling. > With a long time I am using UCSF Chimera. It is the one of wonderful > Molecular visiualization software haivng some very peculear features. > Respected Sir / Madam, In my present work I am facing a bit problem. > Hoping form you to help regarding this. My problem is as follows. I > have generated five models of protein. when I open all these modles > these were overlapping each other. I want to view all these five > models in a single panel non overlapping. I mean I want to view these > 3D models in panel as follows > ----------------------------------------- > | | | > | | | > | Model 1 | Model 2 | > | | | > ----------------------------------------- > | | | > | | | > | Model 3 | Model 4 | > | | | > ----------------------------------------- > | | | > | | | > | Model 5 | Model 6 | > | | | > ----------------------------------------- > > Hope that you now easily understand what actually I want. Please Help > me regarding this and mail me its solution or steps or commands for > this task. Please free to ask any question. > > Thanks in anticipation > Warm regards from Bharat Yadav From goddard at cgl.ucsf.edu Wed Mar 19 10:48:05 2008 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Wed, 19 Mar 2008 10:48:05 -0700 Subject: [Chimera-users] Average slab thickness In-Reply-To: <47E0A534.5010201@rice.edu> References: <47E0A534.5010201@rice.edu> Message-ID: <47E151D5.4070105@cgl.ucsf.edu> Hi Jeff, The Chimera mask command code can be adapted to calculate the average thickness of a slab defined by two surfaces. I've attached the adapted Python code. You select the surfaces then open the script and it reports the mean thickness, standard deviation of thickness, min/max thickness and number of thickness samples used. The script contains a projection axis which should be perpendicular to the slab and a grid step which defines the grid spacing. The thickness is measured on a grid perpendicular to the axis and only grid points where the projection axis intersects the surfaces at least twice are used. You have to edit the script (at the bottom) to set the projection axis and grid step to appropriate values. Those values could be automatically set using the Python code of the inertia ellipsoid script I gave you earlier. Tested in Chimera version 1.2498 on a spherical surface. Tom Jeff wrote: > hi Tom, > > I'd like to compute the 'average distance' between two surfaces to > calculate the width of a cellular compartment (have attached an image, > the two surfaces delineating the compartment are colored blue). > > one way that has been suggested to me is to calculate the volume > between the two surfaces, and then just divide by a mean path length > along one of the surfaces. I know that chimera has a volume > calculation tool for an isosurface, and was wondering if I could use > the surfaces you see to do a volume calculation (and, if so, how I > would go about capping those surfaces to create a closed surface). If > able to calculate the volume that way, I could just use the path > length of a contour (which I have) that generated one of the two > surfaces to derive the "average width". > -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: thickness.py URL: From triffo at rice.edu Wed Mar 19 11:01:00 2008 From: triffo at rice.edu (William Jeffrey Triffo) Date: Wed, 19 Mar 2008 11:01:00 -0700 Subject: [Chimera-users] Average slab thickness In-Reply-To: <47E151D5.4070105@cgl.ucsf.edu> References: <47E0A534.5010201@rice.edu> <47E151D5.4070105@cgl.ucsf.edu> Message-ID: <47E154DC.2010902@rice.edu> Tom, much thanks! I have a (goofy) movie I made from some of my data, that shows what I was using your surface masking tools for. I can send it to you if you want to take a look; be forewarned that I am not much of a visual artist. -Jeff Tom Goddard wrote: > Hi Jeff, > > The Chimera mask command code can be adapted to calculate the average > thickness of a slab defined by two surfaces. I've attached the > adapted Python code. You select the surfaces then open the script and > it reports the mean thickness, standard deviation of thickness, > min/max thickness and number of thickness samples used. The script > contains a projection axis which should be perpendicular to the slab > and a grid step which defines the grid spacing. The thickness is > measured on a grid perpendicular to the axis and only grid points > where the projection axis intersects the surfaces at least twice are > used. You have to edit the script (at the bottom) to set the > projection axis and grid step to appropriate values. Those values > could be automatically set using the Python code of the inertia > ellipsoid script I gave you earlier. Tested in Chimera version 1.2498 > on a spherical surface. > > Tom > > > > Jeff wrote: >> hi Tom, >> >> I'd like to compute the 'average distance' between two surfaces to >> calculate the width of a cellular compartment (have attached an >> image, the two surfaces delineating the compartment are colored blue). >> >> one way that has been suggested to me is to calculate the volume >> between the two surfaces, and then just divide by a mean path length >> along one of the surfaces. I know that chimera has a volume >> calculation tool for an isosurface, and was wondering if I could use >> the surfaces you see to do a volume calculation (and, if so, how I >> would go about capping those surfaces to create a closed surface). If >> able to calculate the volume that way, I could just use the path >> length of a contour (which I have) that generated one of the two >> surfaces to derive the "average width". >> > -- ------------------------------------------------------------- Jeff Triffo Auer Group, Donner Lab, Lawrence Berkeley National Laboratory Raphael Group, Bioengineering Department, Rice University Medical Scientist Training Program (MSTP), Baylor College of Medicine phone (Berkeley): 510-486-7940 fax (Berkeley): 510-486-6488 From goddard at cgl.ucsf.edu Wed Mar 19 11:42:26 2008 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Wed, 19 Mar 2008 11:42:26 -0700 Subject: [Chimera-users] Principal axis of inertia In-Reply-To: <1205941256.6758.5.camel@AMD3800> References: <1205941256.6758.5.camel@AMD3800> Message-ID: <47E15E92.8030002@cgl.ucsf.edu> Hi JD, Attached is a script that computes the inertia axes of molecules. Open a molecule, then open the script. It will print the axes in the reply log and show an inertia ellipsoid. It is weighting the atoms by their atomic number, not by the average isotopic mass. Tested in Chimera 1.2498. Should work in older Chimera versions. Tom Jean-Didier Mar?chal wrote: > Hi everyone, > > I was wondering if there is a method available to calculate the > principal axis of inertia of a protein (or a part of a protein) in > chimera? > > If not what would be the easiest way to move forward? > > All the best, > > JD > > -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: inertiapdb.py URL: From pett at cgl.ucsf.edu Wed Mar 19 11:47:51 2008 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 19 Mar 2008 11:47:51 -0700 Subject: [Chimera-users] Principal axis of inertia In-Reply-To: <47E15E92.8030002@cgl.ucsf.edu> References: <1205941256.6758.5.camel@AMD3800> <47E15E92.8030002@cgl.ucsf.edu> Message-ID: Just wondering why you weighted by atomic number rather than mass (a.element.mass)? --Eric On Mar 19, 2008, at 11:42 AM, Tom Goddard wrote: > Hi JD, > > Attached is a script that computes the inertia axes of molecules. > Open a molecule, then open the script. It will print the axes in > the reply log and show an inertia ellipsoid. It is weighting the > atoms by their atomic number, not by the average isotopic mass. > Tested in Chimera 1.2498. Should work in older Chimera versions. > > Tom > > Jean-Didier Mar?chal wrote: >> Hi everyone, >> >> I was wondering if there is a method available to calculate the >> principal axis of inertia of a protein (or a part of a protein) in >> chimera? >> >> If not what would be the easiest way to move forward? >> >> All the best, >> >> JD >> >> > > > # > ---------------------------------------------------------------------- > ------- > # Compute inertia tensor principle axes for molecule. > # > def inertia_ellipsoid(m): > > atoms = m.atoms > n = len(atoms) > from _multiscale import get_atom_coordinates > xyz = get_atom_coordinates(atoms) > anum = [a.element.number for a in atoms] > from numpy import array, dot, outer, argsort, linalg > wxyz = array(anum).reshape((n,1)) * xyz > mass = sum(anum) > > c = wxyz.sum(axis = 0) / mass # Center of mass > v33 = dot(xyz.transpose(), wxyz) / mass - outer(c,c) > eval, evect = linalg.eigh(v33) > > # Sort by eigenvalue size. > order = argsort(eval) > seval = eval[order] > sevect = evect[:,order] > > return sevect, seval, c > > # > ---------------------------------------------------------------------- > ------- > # > def ellipsoid_surface(center, axes, lengths, color = (.7,.7,.7,1)): > > from Icosahedron import icosahedron_triangulation > varray, tarray = icosahedron_triangulation(subdivision_levels = 3, > sphere_factor = 1.0) > from numpy import dot, multiply > es = dot(varray, axes) > ee = multiply(es, lengths) > ev = dot(ee, axes.transpose()) > ev += center > > import _surface > sm = _surface.SurfaceModel() > sm.addPiece(ev, tarray, color) > return sm > > # > ---------------------------------------------------------------------- > ------- > # > def show_ellipsoid(axes, d2, center, model): > > from math import sqrt > d = [sqrt(e) for e in d2] > sm = ellipsoid_surface(center, axes, d) > sm.name = 'inertia ellipsoid for %s' % m.name > from chimera import openModels as om > om.add([sm], sameAs = model) > > # > ---------------------------------------------------------------------- > ------- > # > def print_axes(axes, d2, m): > > from math import sqrt > paxes = ['\tv%d = %6.3f %6.3f %6.3f d%d = %6.3f' % > (a+1, axes[a][0], axes[a][1], axes[a][2], a+1, sqrt(d2[a])) > for a in range(3)] > from chimera.replyobj import info > info('Inertia axes for %s\n%s\n' % (m.name, '\n'.join(paxes))) > from Accelerators.standard_accelerators import show_reply_log > show_reply_log() > > # > ---------------------------------------------------------------------- > ------- > # > from chimera import openModels as om, Molecule > mlist = om.list(modelTypes = [Molecule]) > for m in mlist: > axes, d2, center = inertia_ellipsoid(m) > print_axes(axes, d2, m) > show_ellipsoid(axes, d2, center, m) > _______________________________________________ > 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 Wed Mar 19 12:00:33 2008 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Wed, 19 Mar 2008 12:00:33 -0700 Subject: [Chimera-users] Principal axis of inertia In-Reply-To: References: <1205941256.6758.5.camel@AMD3800> <47E15E92.8030002@cgl.ucsf.edu> Message-ID: <47E162D1.5070108@cgl.ucsf.edu> Hi Eric, Just ignorance -- didn't know Chimera could tell me the atomic mass. Attached is the same script only using atomic mass instead of atomic number. Tom Eric Pettersen wrote: > Just wondering why you weighted by atomic number rather than mass > (a.element.mass)? > > --Eric > -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: inertiapdb.py URL: From jeandidier.marechal at uab.es Wed Mar 19 12:35:44 2008 From: jeandidier.marechal at uab.es (Jean-Didier =?ISO-8859-1?Q?Mar=E9chal?=) Date: Wed, 19 Mar 2008 20:35:44 +0100 Subject: [Chimera-users] problem with 17/03 build linux 64 In-Reply-To: References: Message-ID: <1205955344.6758.9.camel@AMD3800> Hi guys, thanks a lot for the different answers. I wanted to test Elaine's suggestion and I install the last linux 64 build. When running chimera I have: Traceback (most recent call last): File "/usr/local/chimera/share/__main__.py", line 65, in value = chimeraInit.init(sys.argv) File "/usr/local/chimera/share/chimeraInit.py", line 304, in init from chimera import tkgui File "CHIMERA/share/chimera/tkgui.py", line 80, in File "CHIMERA/share/chimera/printer.py", line 444, in AttributeError: 'module' object has no attribute 'No' Some problem in my installation ? All the best JD El mi?, 19-03-2008 a las 12:00 -0700, chimera-users-request at cgl.ucsf.edu escribi?: > Send Chimera-users mailing list submissions to > chimera-users at cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request at cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner at cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: Principal axis of inertia (Eric Pettersen) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 19 Mar 2008 11:47:51 -0700 > From: Eric Pettersen > Subject: Re: [Chimera-users] Principal axis of inertia > To: "'Chimera BB'" > Message-ID: > Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed > > Just wondering why you weighted by atomic number rather than mass > (a.element.mass)? > > --Eric > > On Mar 19, 2008, at 11:42 AM, Tom Goddard wrote: > > > Hi JD, > > > > Attached is a script that computes the inertia axes of molecules. > > Open a molecule, then open the script. It will print the axes in > > the reply log and show an inertia ellipsoid. It is weighting the > > atoms by their atomic number, not by the average isotopic mass. > > Tested in Chimera 1.2498. Should work in older Chimera versions. > > > > Tom > > > > Jean-Didier Mar?chal wrote: > >> Hi everyone, > >> > >> I was wondering if there is a method available to calculate the > >> principal axis of inertia of a protein (or a part of a protein) in > >> chimera? > >> > >> If not what would be the easiest way to move forward? > >> > >> All the best, > >> > >> JD > >> > >> > > > > > > # > > ---------------------------------------------------------------------- > > ------- > > # Compute inertia tensor principle axes for molecule. > > # > > def inertia_ellipsoid(m): > > > > atoms = m.atoms > > n = len(atoms) > > from _multiscale import get_atom_coordinates > > xyz = get_atom_coordinates(atoms) > > anum = [a.element.number for a in atoms] > > from numpy import array, dot, outer, argsort, linalg > > wxyz = array(anum).reshape((n,1)) * xyz > > mass = sum(anum) > > > > c = wxyz.sum(axis = 0) / mass # Center of mass > > v33 = dot(xyz.transpose(), wxyz) / mass - outer(c,c) > > eval, evect = linalg.eigh(v33) > > > > # Sort by eigenvalue size. > > order = argsort(eval) > > seval = eval[order] > > sevect = evect[:,order] > > > > return sevect, seval, c > > > > # > > ---------------------------------------------------------------------- > > ------- > > # > > def ellipsoid_surface(center, axes, lengths, color = (.7,.7,.7,1)): > > > > from Icosahedron import icosahedron_triangulation > > varray, tarray = icosahedron_triangulation(subdivision_levels = 3, > > sphere_factor = 1.0) > > from numpy import dot, multiply > > es = dot(varray, axes) > > ee = multiply(es, lengths) > > ev = dot(ee, axes.transpose()) > > ev += center > > > > import _surface > > sm = _surface.SurfaceModel() > > sm.addPiece(ev, tarray, color) > > return sm > > > > # > > ---------------------------------------------------------------------- > > ------- > > # > > def show_ellipsoid(axes, d2, center, model): > > > > from math import sqrt > > d = [sqrt(e) for e in d2] > > sm = ellipsoid_surface(center, axes, d) > > sm.name = 'inertia ellipsoid for %s' % m.name > > from chimera import openModels as om > > om.add([sm], sameAs = model) > > > > # > > ---------------------------------------------------------------------- > > ------- > > # > > def print_axes(axes, d2, m): > > > > from math import sqrt > > paxes = ['\tv%d = %6.3f %6.3f %6.3f d%d = %6.3f' % > > (a+1, axes[a][0], axes[a][1], axes[a][2], a+1, sqrt(d2[a])) > > for a in range(3)] > > from chimera.replyobj import info > > info('Inertia axes for %s\n%s\n' % (m.name, '\n'.join(paxes))) > > from Accelerators.standard_accelerators import show_reply_log > > show_reply_log() > > > > # > > ---------------------------------------------------------------------- > > ------- > > # > > from chimera import openModels as om, Molecule > > mlist = om.list(modelTypes = [Molecule]) > > for m in mlist: > > axes, d2, center = inertia_ellipsoid(m) > > print_axes(axes, d2, m) > > show_ellipsoid(axes, d2, center, m) > > _______________________________________________ > > 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 > > > End of Chimera-users Digest, Vol 59, Issue 18 > ********************************************* From jnettle at emory.edu Wed Mar 19 12:43:34 2008 From: jnettle at emory.edu (Jim Nettles) Date: Wed, 19 Mar 2008 15:43:34 -0400 Subject: [Chimera-users] Un-tile In-Reply-To: References: Message-ID: <5464F6BF-1FA4-4DC6-B676-AEC6CCCBA3CF@emory.edu> Thanks that is a useful function I hadn't explored. However, how to you un-tile to go back to a previously aligned system? Thanks, Jim > > Message: 4 > Date: Wed, 19 Mar 2008 16:53:11 +0530 > From: "Bharat Yadav" > Subject: [Chimera-users] Requesting to solve my poblem > To: chimera-users at cgl.ucsf.edu > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1 > > Hello Sir / Madam > > Good Evening > > My name is Bharat Yadav and I am perusing Master's Degree in > Bioinformatics from Chaudhary Charan Singh Haryana Agriculrual > University - Hisar (India). I am working here on Molecular Modeling. > With a long time I am using UCSF Chimera. It is the one of wonderful > Molecular visiualization software haivng some very peculear features. > Respected Sir / Madam, In my present work I am facing a bit problem. > Hoping form you to help regarding this. My problem is as follows. I > have generated five models of protein. when I open all these modles > these were overlapping each other. I want to view all these five > models in a single panel non overlapping. I mean I want to view these > 3D models in panel as follows > ----------------------------------------- > | | | > | | | > | Model 1 | Model 2 | > | | | > ----------------------------------------- > | | | > | | | > | Model 3 | Model 4 | > | | | > ----------------------------------------- > | | | > | | | > | Model 5 | Model 6 | > | | | > ----------------------------------------- > > Hope that you now easily understand what actually I want. Please Help > me regarding this and mail me its solution or steps or commands for > this task. Please free to ask any question. > > Thanks in anticipation > > Warm regards from Bharat Yadav > > > ------------------------------ > > Message: 5 > Date: Wed, 19 Mar 2008 10:11:52 -0700 > From: Elaine Meng > Subject: Re: [Chimera-users] Requesting to solve my poblem > To: "Bharat Yadav" > Cc: chimera-users at cgl.ucsf.edu > Message-ID: <37BB555C-E967-43BB-B6EA-5CD8A75853FD at cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > Hi Bharat, > > Thanks for your kind words! I think you just need to use "tile" in > the Model Panel. Open Model Panel (Favorites... Model Panel). In > there, choose all 5 models on the left side. Then, on the right, > change the menu from "frequently used" to "infrequently used" - now > there should be a "tile" button on the right - try using that. > > 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 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Wed Mar 19 12:52:13 2008 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Wed, 19 Mar 2008 12:52:13 -0700 Subject: [Chimera-users] Data of Slice display In-Reply-To: <20080313063910.M30165@student.nsysu.edu.tw> References: <20080313063910.M30165@student.nsysu.edu.tw> Message-ID: <47E16EED.7000806@cgl.ucsf.edu> Hi Jason, You can have Chimera print out the density map values used for the slice display in the volume tracer dialog by adding a line to the Python code. Edit file chimera/share/VolumePath/gui.py to add "print values" after the interpolated_values() call: values = data_region.interpolated_values(xyz_list, vertex_xform, use_subregion = True) print values Use the same indentation for the "print values" line as the preceding one since that is important in Python. If you restart Chimera and place a marker on your virus map it will output the array of values to the reply log which you can display with menu entry Favorites / Reply Log. You can copy and paste the values from there. If you just want slices along the x, y or z axes you could get the exact values from the map (no interpolation) by setting the volume region bounds (volume menu Features / Region bounds) to just include a 1 dimensional slice (for example x range 83 83 1, y range 97 97 1 -- ranges are ) then open the attached Python script that will print the values for just that region. Tom -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: printvolume.py URL: From meng at cgl.ucsf.edu Wed Mar 19 12:54:34 2008 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 19 Mar 2008 12:54:34 -0700 Subject: [Chimera-users] Un-tile In-Reply-To: <5464F6BF-1FA4-4DC6-B676-AEC6CCCBA3CF@emory.edu> References: <5464F6BF-1FA4-4DC6-B676-AEC6CCCBA3CF@emory.edu> Message-ID: <0C46DD3F-CBD7-435A-B5B3-908CE7419566@cgl.ucsf.edu> Hi Jim, It is not exactly the same as "untile," but I use the command "reset" - that puts all models in their untransformed state. However, if you had previously matched the models or gotten them in your favorite orientation, you might not want to use reset. Other possibilities are (a) (requiring foresight) use the "savepos position-name" before tiling and then "reset-position-name" afterward (b) use Undo Move (under Tools... Movement) - I recommend this last because although it puts the models back on top of each other, it did not restore the pre-existing scale and translation when I tried it just now... 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 Mar 19, 2008, at 12:43 PM, Jim Nettles wrote: > Thanks that is a useful function I hadn't explored. > However, how to you un-tile to go back to a previously aligned system? > Thanks, > Jim From meng at cgl.ucsf.edu Wed Mar 19 12:58:51 2008 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 19 Mar 2008 12:58:51 -0700 Subject: [Chimera-users] Un-tile In-Reply-To: <0C46DD3F-CBD7-435A-B5B3-908CE7419566@cgl.ucsf.edu> References: <5464F6BF-1FA4-4DC6-B676-AEC6CCCBA3CF@emory.edu> <0C46DD3F-CBD7-435A-B5B3-908CE7419566@cgl.ucsf.edu> Message-ID: <411661CF-F58D-470D-92D7-2C93FCC62E53@cgl.ucsf.edu> Me again, too much rushing led to typing errors: On Mar 19, 2008, at 12:54 PM, Elaine Meng wrote: > It is not exactly the same as "untile," but I use the command "reset" > - that puts all models in their untransformed state. However, if you > had previously matched the models or gotten them in your favorite > orientation, you might not want to use reset. I should have said "you might not want to reset to the default positions." > > (a) (requiring foresight) use the "savepos position-name" before > tiling and then "reset-position-name" afterward the *command* "savepos position-name" and then the command "reset position-name" (no hyphen after "reset"). Sorry about that! Elaine From gregc at cgl.ucsf.edu Wed Mar 19 13:11:13 2008 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Wed, 19 Mar 2008 13:11:13 -0700 (PDT) Subject: [Chimera-users] problem with 17/03 build linux 64 In-Reply-To: <1205955344.6758.9.camel@AMD3800> References: <1205955344.6758.9.camel@AMD3800> Message-ID: That should have been fixed in yesterday's daily build, but another bug prevented the daily build from building, so we rebuilt it today and right now there is a fixed daily build on the website!! Greg Couch On Wed, 19 Mar 2008, Jean-Didier Mar?chal wrote: > From: "Jean-Didier [ISO-8859-1] Mar?chal" > Sender: chimera-users-bounces at cgl.ucsf.edu > To: chimera-users at cgl.ucsf.edu > Date: Wed, 19 Mar 2008 20:35:44 +0100 > Subject: [Chimera-users] problem with 17/03 build linux 64 > Received-SPF: pass (cgl.ucsf.edu: 169.230.27.3 is authenticated by a trusted > mechanism) > Received-SPF: pass (cgl.ucsf.edu: domain of jeandidier.marechal at uab.es > designates 158.109.168.135 as permitted sender) > > Hi guys, thanks a lot for the different answers. I wanted to test Elaine's suggestion and I install the last linux 64 build. When running chimera I have: Traceback (most recent call last): File "/usr/local/chimera/share/__main__.py", line 65, in value = chimeraInit.init(sys.argv) File "/usr/local/chimera/share/chimeraInit.py", line 304, in init from chimera import tkgui File "CHIMERA/share/chimera/tkgui.py", line 80, in File "CHIMERA/share/chimera/printer.py", line 444, in AttributeError: 'module' object has no attribute 'No' Some problem in my installation ? All the best JD El mi??, 19-03-2008 a las 12:00 -0700, chimera-users-request at cgl.ucsf.edu escribi??: > Send Chimera-users mailing list submissions to > chimera-users at cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request at cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner at cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: Principal axis of inertia (Eric Pettersen) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 19 Mar 2008 11:47:51 -0700 > From: Eric Pettersen > Subject: Re: [Chimera-users] Principal axis of inertia > To: "'Chimera BB'" > Message-ID: > Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed > > Just wondering why you weighted by atomic number rather than mass > (a.element.mass)? > > --Eric > > On Mar 19, 2008, at 11:42 AM, Tom Goddard wrote: > > > Hi JD, > > > > Attached is a script that computes the inertia axes of molecules. > > Open a molecule, then open the script. It will print the axes in > > the reply log and show an inertia ellipsoid. It is weighting the > > atoms by their atomic number, not by the average isotopic mass. > > Tested in Chimera 1.2498. Should work in older Chimera versions. > > > > Tom > > > > Jean-Didier Mar?chal wrote: > >> Hi everyone, > >> > >> I was wondering if there is a method available to calculate the > >> principal axis of inertia of a protein (or a part of a protein) in > >> chimera? > >> > >> If not what would be the easiest way to move forward? > >> > >> All the best, > >> > >> JD > >> > >> > > > > > > # > > ---------------------------------------------------------------------- > > ------- > > # Compute inertia tensor principle axes for molecule. > > # > > def inertia_ellipsoid(m): > > > > atoms = m.atoms > > n = len(atoms) > > from _multiscale import get_atom_coordinates > > xyz = get_atom_coordinates(atoms) > > anum = [a.element.number for a in atoms] > > from numpy import array, dot, outer, argsort, linalg > > wxyz = array(anum).reshape((n,1)) * xyz > > mass = sum(anum) > > > > c = wxyz.sum(axis = 0) / mass # Center of mass > > v33 = dot(xyz.transpose(), wxyz) / mass - outer(c,c) > > eval, evect = linalg.eigh(v33) > > > > # Sort by eigenvalue size. > > order = argsort(eval) > > seval = eval[order] > > sevect = evect[:,order] > > > > return sevect, seval, c > > > > # > > ---------------------------------------------------------------------- > > ------- > > # > > def ellipsoid_surface(center, axes, lengths, color = (.7,.7,.7,1)): > > > > from Icosahedron import icosahedron_triangulation > > varray, tarray = icosahedron_triangulation(subdivision_levels = 3, > > sphere_factor = 1.0) > > from numpy import dot, multiply > > es = dot(varray, axes) > > ee = multiply(es, lengths) > > ev = dot(ee, axes.transpose()) > > ev += center > > > > import _surface > > sm = _surface.SurfaceModel() > > sm.addPiece(ev, tarray, color) > > return sm > > > > # > > ---------------------------------------------------------------------- > > ------- > > # > > def show_ellipsoid(axes, d2, center, model): > > > > from math import sqrt > > d = [sqrt(e) for e in d2] > > sm = ellipsoid_surface(center, axes, d) > > sm.name = 'inertia ellipsoid for %s' % m.name > > from chimera import openModels as om > > om.add([sm], sameAs = model) > > > > # > > ---------------------------------------------------------------------- > > ------- > > # > > def print_axes(axes, d2, m): > > > > from math import sqrt > > paxes = ['\tv%d = %6.3f %6.3f %6.3f d%d = %6.3f' % > > (a+1, axes[a][0], axes[a][1], axes[a][2], a+1, sqrt(d2[a])) > > for a in range(3)] > > from chimera.replyobj import info > > info('Inertia axes for %s\n%s\n' % (m.name, '\n'.join(paxes))) > > from Accelerators.standard_accelerators import show_reply_log > > show_reply_log() > > > > # > > ---------------------------------------------------------------------- > > ------- > > # > > from chimera import openModels as om, Molecule > > mlist = om.list(modelTypes = [Molecule]) > > for m in mlist: > > axes, d2, center = inertia_ellipsoid(m) > > print_axes(axes, d2, m) > > show_ellipsoid(axes, d2, center, m) > > _______________________________________________ > > 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 > > > End of Chimera-users Digest, Vol 59, Issue 18 > ********************************************* _______________________________________________ Chimera-users mailing list Chimera-users at cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From heiland at indiana.edu Thu Mar 20 12:24:19 2008 From: heiland at indiana.edu (Randy Heiland) Date: Thu, 20 Mar 2008 15:24:19 -0400 Subject: [Chimera-users] source headers, release Message-ID: Before I attempt to rebuild a plugin, can someone tell me if the 1.2349 headers that you currently provide: http://www.cgl.ucsf.edu/ chimera/sourcecode.html will play nice with the current, 1.2470, release? thanks, Randy From triffo at rice.edu Thu Mar 20 12:59:48 2008 From: triffo at rice.edu (William Jeffrey Triffo) Date: Thu, 20 Mar 2008 12:59:48 -0700 Subject: [Chimera-users] BILD object question Message-ID: <47E2C234.1030202@rice.edu> hello, I have been writing simple .bild files for BILD objects (arrows, spheres) that I then load into Chimera. what would the commands be in a python script to generate a BILD model within the current session, so that I don't have to keep hand-writing and re-loading the .bild file (the contents of the .bild file are often outputted coordinates from such a script, that I then copy into a text file and load)? thanks, -Jeff From goddard at cgl.ucsf.edu Thu Mar 20 13:33:33 2008 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Thu, 20 Mar 2008 13:33:33 -0700 Subject: [Chimera-users] source headers, release In-Reply-To: References: Message-ID: <47E2CA1D.1070302@cgl.ucsf.edu> Hi Randy, The Chimera C++ headers are included in Chimera version 1.2470 and later versions in chimera/include or on the Mac in Chimera.app/Contents/Resources/include The 1.2439 headers on the web are very unlikely to work with Chimera 1.2470. Tom From bshaanan at bgu.ac.il Fri Mar 21 10:25:01 2008 From: bshaanan at bgu.ac.il (Boaz Shaanan) Date: Fri, 21 Mar 2008 17:25:01 GMT Subject: [Chimera-users] turning off PipesAndPlanks or Axes Message-ID: Hi, How do I turn off PipesAndPlanks once they're depicted ? The same holds for Axes. (build 2492). ?Thanks, ???????????? Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan? -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Mar 21 10:59:24 2008 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 21 Mar 2008 10:59:24 -0700 Subject: [Chimera-users] turning off PipesAndPlanks or Axes In-Reply-To: References: Message-ID: Hi Boaz, Axes is brand new and changing rapidly - unfortunately, there is no way to get rid of the axis depictions right now other than deleting or closing the corresponding atoms. Some way of deleting them independently will be added soon! PipesAndPlanks makes a separate model that can be closed. For example, show the Model Panel (Favorites... Model Panel), click the line for the pipes-planks model on the left, and use the close button on the right (*not* the Close button on the bottom... I occasionally do that by mistake!) Best, 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 Mar 21, 2008, at 5:25 PM, Boaz Shaanan wrote: > Hi, > How do I turn off PipesAndPlanks once they're depicted ? The same > holds for Axes. (build 2492). > Thanks, > Boaz From pett at cgl.ucsf.edu Fri Mar 21 14:47:04 2008 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Fri, 21 Mar 2008 14:47:04 -0700 Subject: [Chimera-users] BILD object question In-Reply-To: <47E2C234.1030202@rice.edu> References: <47E2C234.1030202@rice.edu> Message-ID: Hi Jeff, The Axis class in share/StructMeasure/Axes.py does this since it builds its axes depictions using BILD objects. Basically, it uses a StringIO object to emulate a file that it can then hand off to chimera.openModels.open(). Here is the pertinent code: from StringIO import StringIO if isinstance(color, basestring): colorPart = ".color " + color else: if hasattr(color, "rgba"): rgb = color.rgba()[:3] else: rgb = color[:3] colorPart = ".color %g %g %g" % tuple(rgb) end1 = center + vec * ext1 end2 = center + vec * ext2 bild = StringIO("%s\n.cylinder %g %g %g %g %g %g %g\n" % (colorPart, end1[0], end1[1], end1 [2], end2[0], end2[1], end2[2], radius)) self.model = chimera.openModels.open(bild, type="Bild", sameAs=sameAs, hidden=True, identifyAs=name)[0] # allow balloon help to give informative string... self.model.oslIdent = lambda *args: self.name --Eric On Mar 20, 2008, at 12:59 PM, William Jeffrey Triffo wrote: > hello, > > I have been writing simple .bild files for BILD objects (arrows, > spheres) that I then load into Chimera. > > what would the commands be in a python script to generate a BILD model > within the current session, so that I don't have to keep hand-writing > and re-loading the .bild file (the contents of the .bild file are > often > outputted coordinates from such a script, that I then copy into a text > file and load)? > > thanks, > > -Jeff > _______________________________________________ > 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 Fri Mar 21 23:55:22 2008 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Fri, 21 Mar 2008 23:55:22 -0700 Subject: [Chimera-users] Principal axis of inertia In-Reply-To: <47E162D1.5070108@cgl.ucsf.edu> References: <1205941256.6758.5.camel@AMD3800> <47E15E92.8030002@cgl.ucsf.edu> <47E162D1.5070108@cgl.ucsf.edu> Message-ID: <47E4AD5A.10605@cgl.ucsf.edu> Oops. That script I posted for calculating the inertia of a molecule had some problems. The printed matrix of axes was transposed though the correct axes were used for the displayed ellipsoid. Also I was using inertia matrix I_ij = sum_over_k(m_k*r_ki*r_kj) omitting the diagonal term. Should have been I_ij = sum_over_k(m_k*(|r_k| - r_ki*r_kj)). And finally I incorrectly computed the ellipsoid size along each axis. Everything was a little bit wrong. Here's the fixed version. Tested in Chimera version 1.2500 but should work with earlier versions. Tom -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: inertiapdb.py URL: From goddard at cgl.ucsf.edu Mon Mar 24 09:06:48 2008 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Mon, 24 Mar 2008 09:06:48 -0700 Subject: [Chimera-users] Displaying volumes with negative densities In-Reply-To: <20080322150810.kha0v6qlmsk8oss0@webmail.biochem.mpg.de> References: <1097683522.e5b1fa099de6c@webmail.biochem.mpg.de> <200410131754.i9DHsjZu1931344@guanine.cgl.ucsf.edu> <1130527304.e6e1830efe186@webmail.biochem.mpg.de> <200510281935.j9SJZJk72027020@guanine.cgl.ucsf.edu> <1130543928.2c25ae47d086d@webmail.biochem.mpg.de> <200510290045.j9T0j9ZH1976407@guanine.cgl.ucsf.edu> <20080322150810.kha0v6qlmsk8oss0@webmail.biochem.mpg.de> Message-ID: <47E7D198.8050404@cgl.ucsf.edu> Hi Julio, If you are creating volume contour surfaces where the objects of interest have more negative data values then you should turn off the "cap high values at box faces" option in the volume dialog surface and mesh options panel. Since you view these inverted density maps often you probably want to save that setting using volume dialog menu entry "Features / Save default dialog settings" so Chimera will use it in future sessions. Tom Dr .Julio Ortiz wrote: > Dear Thomas, > > I noticed that when displaying volumes as isosurfaces we can not > visualize negative densities. The volumes turns a solid cube bellow > cero. I can imagine that with volumes coming from some programs of > SPA like in EMAN, this is not a matter, because they use > protein=white. But we are always using protein=black. > > I wanted to ask you if there is a simple way to correct that, because > I love to use chimera for fast check of my volumes and it will be not > fun to change the contrast each time. > > Just for your info: the last version that works for me was: > chimera-1.2422-win32 > > Greetings, > Julio From triffo at rice.edu Mon Mar 24 20:56:21 2008 From: triffo at rice.edu (Jeff Triffo) Date: Mon, 24 Mar 2008 20:56:21 -0700 Subject: [Chimera-users] pdb to density map function Message-ID: <47E877E5.4020501@rice.edu> hi, I think I recall seeing information about a pdb -> density map function (like an MRC density map). is this currently implemented/contained within Chimera? I can use an outside program to do this, but if it is already in Chimera I would prefer to do that. thanks, -Jeff From meng at cgl.ucsf.edu Tue Mar 25 09:03:29 2008 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 25 Mar 2008 09:03:29 -0700 Subject: [Chimera-users] pdb to density map function In-Reply-To: <47E877E5.4020501@rice.edu> References: <47E877E5.4020501@rice.edu> Message-ID: <638CF385-92E5-4E11-8875-C5D9682073F5@cgl.ucsf.edu> On Mar 24, 2008, at 8:56 PM, Jeff Triffo wrote: > hi, > I think I recall seeing information about a pdb -> density map > function > (like an MRC density map). is this currently implemented/contained > within Chimera? I can use an outside program to do this, but if it is > already in Chimera I would prefer to do that. > thanks, > -Jeff > Hi Jeff, Yes, there is a "molmap" command in recent versions: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html In addition, the "Fit in Map" tool can use the same functionality to simulate a map from atomic coordinates and then use map-in-map fitting: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/ fitmaps.html These features were added after the November production release but are available in recent daily builds: http://www.cgl.ucsf.edu/chimera/alpha-downloads.html Best, 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 From bgurda at ufl.edu Tue Mar 25 04:47:44 2008 From: bgurda at ufl.edu (Brittney L. Gurda) Date: Tue, 25 Mar 2008 07:47:44 -0400 Subject: [Chimera-users] Chimera_v1.2470 Message-ID: <200803251147.m2PBlfZu024890@smtp.ufl.edu> Hello, I have a general question about opening files in the new version. Upon opening my EM maps (in .pif format), my structure is in a solid box which makes viewing difficult. Has anyone encountered this problem before? The older version that I had (not sure which one) never had this issue. Currently I am converting the .pif to a .map file and that seems to work just fine, but I am still curious about where the box is coming from and how I can get rid of it...artificial unit cell perhaps? Thanks, Brittney L. Gurda From wu49 at purdue.edu Tue Mar 25 12:38:33 2008 From: wu49 at purdue.edu (Weimin Wu) Date: Tue, 25 Mar 2008 15:38:33 -0400 Subject: [Chimera-users] using chimera on 3D EM map In-Reply-To: <47D032E0.1080008@cgl.ucsf.edu> References: <47D026B5.70506@purdue.edu> <47D03121.6080006@cgl.ucsf.edu> <47D032E0.1080008@cgl.ucsf.edu> Message-ID: <47E954B9.5050506@purdue.edu> Tom Goddard wrote: > Hi Weimin, > > One more comment on the problem of making the volume eraser ball > small enough. The slider that controls the ball radius in the volume > eraser dialog only goes in discrete steps -- just because the smallest > detectable slider motion is one screen pixel. You can resize the > volume eraser window to make it wider, so the slider is longer and > that will give finer slider steps. Or you can just type in whatever > radius value you want and not use the slider at all. > > Tom > Another problem when using volume eraser is that the keyboard accelerator "es" doesn't work. My system is Linux x86_64. weimin From Nicholas.Horelik at tufts.edu Wed Mar 26 00:17:14 2008 From: Nicholas.Horelik at tufts.edu (Nick Horelik) Date: Wed, 26 Mar 2008 03:17:14 -0400 Subject: [Chimera-users] copy cmd in nogui script Message-ID: Hi, This (http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-March/001396.html) answered most of my questions, but I have one more followup question. Is there any way for me to accept the POV-Ray Liscence in nogui mode? I don't have the capability to use the gui at this time. Thanks, Nick -- Tufts University 508.527.9625 -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Wed Mar 26 10:01:47 2008 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Wed, 26 Mar 2008 10:01:47 -0700 Subject: [Chimera-users] Chimera_v1.2470 In-Reply-To: <200803251147.m2PBlfZu024890@smtp.ufl.edu> References: <200803251147.m2PBlfZu024890@smtp.ufl.edu> Message-ID: <47EA817B.6080302@cgl.ucsf.edu> Hi Brittney, The solid box you see when opening some maps I suspect is caused by the new option to "cap high values at box faces" that is in the volume dialog Surface and Mesh options panel. This means that if the contouring level is lower than the volume data values at a face of the volume box then the box face appears solid. You can turn this option off then make that the default using volume dialog menu entry Features / Save Default Dialog Settings. This is particularly a problem if your map is inverted -- that is, high density corresponds to negative data values. I guess when you say you solve the problem by converting from PIF format to MRC you also invert the map values (v -> -v). The file format has no effect on how the data appears, only the data values matter. Tom From goddard at cgl.ucsf.edu Wed Mar 26 10:11:51 2008 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Wed, 26 Mar 2008 10:11:51 -0700 Subject: [Chimera-users] [chimera-dev] fit map in map -- also fit a/pix at the same time ? In-Reply-To: <50626.213.64.26.148.1206174927.squirrel@webmail.umu.se> References: <50626.213.64.26.148.1206174927.squirrel@webmail.umu.se> Message-ID: <47EA83D7.6000506@cgl.ucsf.edu> Hi Stefan, Chimera cannot optimize the volume grid spacing when fitting a molecule model. I agree that would be useful. I'll add it to our requested features list. http://www.cgl.ucsf.edu/chimera/plans.html You can do this scale optimization by hand using the volume dialog Coordinates panel to change the voxel size (press the return key after you change the number), then press the Fit button on the Fit in Map dialog. With small scale changes the fit should converge each time and you can quickly try several different scales. The newer Chimera releases (Jan 31, 2008, 1.2492) available on the daily builds page can make a simulated map for your molecule at the desired resolution and report correlation coefficients which is probably better than average map values for this scale optimization. Tom From goddard at cgl.ucsf.edu Wed Mar 26 10:22:30 2008 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Wed, 26 Mar 2008 10:22:30 -0700 Subject: [Chimera-users] using chimera on 3D EM map In-Reply-To: <47E954B9.5050506@purdue.edu> References: <47D026B5.70506@purdue.edu> <47D03121.6080006@cgl.ucsf.edu> <47D032E0.1080008@cgl.ucsf.edu> <47E954B9.5050506@purdue.edu> Message-ID: <47EA8656.4060704@cgl.ucsf.edu> Hi Weimin, To use the "es" keyboard shortcut with volume eraser you have to turn on keyboard shortcuts using menu entry Tools / General Controls / Accelerators On. They are not enabled by default. I should add an "enable shortcuts" button to the volume eraser dialog or automatically enable them when you show that dialog. One reason for not enabling shortcuts by default is that accidentally typing in the Chimera window can do many unexpected things as there are more than a hundred shortcuts. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/alist.html Tom From jeandidier.marechal at uab.es Wed Mar 26 11:12:30 2008 From: jeandidier.marechal at uab.es (Jean-Didier =?ISO-8859-1?Q?Mar=E9chal?=) Date: Wed, 26 Mar 2008 19:12:30 +0100 Subject: [Chimera-users] Splitting surfnet surfaces and calculate enclosed volume. In-Reply-To: References: Message-ID: <1206555151.13081.68.camel@asklipio> Hi everyone, I would like to calculate the volume of the main pocket provided by a surfnet calculation performed on a given selection. The resulting calculation returns me different pockets of variable sizes. And I have two small questions: 1. Is there a way to split the resulting surfaces in individual size ranked entities so that I can calculate the volume of each of them? 2. What would be the easiest way to call the mv accelerator function from the python shell (whether by a command emulation or a directly importing a module)? Cheers, JD On Tue, 2008-03-25 at 12:00 -0700, chimera-users-request at cgl.ucsf.edu wrote: > Send Chimera-users mailing list submissions to > chimera-users at cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request at cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner at cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. pdb to density map function (Jeff Triffo) > 2. Re: pdb to density map function (Elaine Meng) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 24 Mar 2008 20:56:21 -0700 > From: Jeff Triffo > Subject: [Chimera-users] pdb to density map function > To: chimera-users at cgl.ucsf.edu > Message-ID: <47E877E5.4020501 at rice.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > hi, > > I think I recall seeing information about a pdb -> density map function > (like an MRC density map). is this currently implemented/contained > within Chimera? I can use an outside program to do this, but if it is > already in Chimera I would prefer to do that. > > thanks, > > -Jeff > > > > ------------------------------ > > Message: 2 > Date: Tue, 25 Mar 2008 09:03:29 -0700 > From: Elaine Meng > Subject: Re: [Chimera-users] pdb to density map function > To: Jeff Triffo > Cc: chimera-users at cgl.ucsf.edu > Message-ID: <638CF385-92E5-4E11-8875-C5D9682073F5 at cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > > > On Mar 24, 2008, at 8:56 PM, Jeff Triffo wrote: > > hi, > > I think I recall seeing information about a pdb -> density map > > function > > (like an MRC density map). is this currently implemented/contained > > within Chimera? I can use an outside program to do this, but if it is > > already in Chimera I would prefer to do that. > > thanks, > > -Jeff > > > > Hi Jeff, > Yes, there is a "molmap" command in recent versions: > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html > > In addition, the "Fit in Map" tool can use the same functionality to > simulate a map from atomic coordinates and then use map-in-map fitting: > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/ > fitmaps.html > > These features were added after the November production release but > are available in recent daily builds: > http://www.cgl.ucsf.edu/chimera/alpha-downloads.html > > Best, > 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 > > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 59, Issue 24 > ********************************************* From meng at cgl.ucsf.edu Wed Mar 26 11:49:05 2008 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 26 Mar 2008 11:49:05 -0700 Subject: [Chimera-users] Splitting surfnet surfaces and calculate enclosed volume. In-Reply-To: <1206555151.13081.68.camel@asklipio> References: <1206555151.13081.68.camel@asklipio> Message-ID: <82F00553-F36D-4259-8C84-0CDFF9ECE909@cgl.ucsf.edu> On Mar 26, 2008, at 11:12 AM, Jean-Didier Mar?chal wrote: > Hi everyone, > I would like to calculate the volume of the main pocket provided by a > surfnet calculation performed on a given selection. The resulting > calculation returns me different pockets of variable sizes. And I have > two small questions: > > 1. Is there a way to split the resulting surfaces in individual size > ranked entities so that I can calculate the volume of each of them? > 2. What would be the easiest way to call the mv accelerator function > from the python shell (whether by a command emulation or a directly > importing a module)? > Cheers, > JD Hi JD, In recent versions of Chimera (newer than the production release in November 2007... get a daily build), you can measure the surface area and enclosed volume of each separate "blob" with "Measure and Color Blobs": http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pickblobs/ pickblobs.html It doesn't give you a ranked list, however; you just have to click on each blob you want to measure. The surface area and volume are computed directly from the surface triangle positions. I should mention the new "CASTp fetch" capability: it looks up a structure in the CASTp database and brings up a table of all the pockets, their surface areas and volumes, and pocket mouth measurements. It is most excellent, the main limitation being that not all PDBs are in that database. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/castp.html You can fetch from CASTp with File... Fetch by ID, or with a command such as: open castp:4enl open castp:2gsh.A (the latter showing how to get results for just a particular chain). I will have to leave question #2 to someone else! 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 From goddard at cgl.ucsf.edu Wed Mar 26 12:04:25 2008 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Wed, 26 Mar 2008 12:04:25 -0700 Subject: [Chimera-users] Splitting surfnet surfaces and calculate enclosed volume. In-Reply-To: <1206555151.13081.68.camel@asklipio> References: <1206555151.13081.68.camel@asklipio> Message-ID: <47EA9E39.1070309@cgl.ucsf.edu> Hi JD, You can split the surfnet surface into separate selectable pieces by selecting the whole surface (ctrl-left-button) then using keyboard shortcut "Sc" (split connected pieces). You have to enable keyboard shortcuts with menu entry Tools / General Controls / Accelerators On. After this you can select individual pieces and measure their volumes with the "mv" shortcut. You can select all of the pieces and use "mv" to get a list of volumes for all the pieces. "ma" lists areas. Each piece is numbered and you that number will be shown in a pop-up if you the mouse over it. You can run the measure volumes shortcut (mv) from Python code using: import MeasureVolume MeasureVolume.report_selected_volumes() This code is in your Chimera distribution in chimera/share/MeasureVolume/__init__.py. Tom From gregc at cgl.ucsf.edu Wed Mar 26 12:40:06 2008 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Wed, 26 Mar 2008 12:40:06 -0700 (PDT) Subject: [Chimera-users] copy cmd in nogui script In-Reply-To: References: Message-ID: On Wed, 26 Mar 2008, Nick Horelik wrote: > Hi, > > This (http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-March/001396.html) > answered most of my questions, but I have one more followup question. > > Is there any way for me to accept the POV-Ray Liscence in nogui mode? I > don't have the capability to use the gui at this time. > > Thanks, > > Nick Actually, even if you could accept the POV-Ray license in nogui mode, the copy command (and the new export command) still won't work. This limitation is bug 3678 and fixing it requires a rewrite of the chimera internals. That said, we have an experimental version of chimera, that is always in nogui mode, where the copy command does work. You can get from the chimera daily builds web page and it is the "Linux 64-bit Off-screen OpenGL" version, but get it tomorrow because I've fixed it so it will ask for the POV-Ray license in nogui mode (and fixed a few other nogui mode bugs too). Of course, if you don't need raytracing, a regular copy works too. We are planning to have a 32-bit linux version as well as the 64-bit version in the daily builds sometime soon. Other platforms are unlikely unless there is enough demand. Attached is the output from the following chimera command script and the experimental version of chimera: windowsize 640 480 open 3fx2 preset apply int 3 turn y 180 focus ligand copy file 3fx2 png raytrace Hope this helps, Greg Couch UCSF Computer Graphics Lab -------------- next part -------------- A non-text attachment was scrubbed... Name: 3fx2.png Type: application/octet-stream Size: 265656 bytes Desc: URL: From hiltonlds at gmail.com Wed Mar 26 15:32:48 2008 From: hiltonlds at gmail.com (Robert Hilton) Date: Wed, 26 Mar 2008 16:32:48 -0600 Subject: [Chimera-users] Chimera Message-ID: When using Chimera, I want to be able to use XY translation. In the help menu, I found that if I hold down the middle mouse button, I can control XY translation. However, I have a mac, and so have no middle mouse button. How can I control XY translation using a mac? Thanks, Rob Hilton hiltonlds at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From aurelien.grosdidier at gmail.com Thu Mar 27 04:17:56 2008 From: aurelien.grosdidier at gmail.com (Aurelien Grosdidier) Date: Thu, 27 Mar 2008 12:17:56 +0100 Subject: [Chimera-users] Collaboratory tool removed ? Message-ID: <200803271217.57039.aurelien.grosdidier@gmail.com> Hello, I recently noticed that the current production version of Chimera (v1 build 2470) does not have the "Collaboratory tool" anymore. I wanted to give it a try and I am quite disappointed. From a previous changelog (http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2417.html), I read that "Collaboratory removed (use version 1.2309 for this tool)". My question is: can we expect this feature to be back one day, or should I look for an alternative ? Thanks, Aur?lien. From meng at cgl.ucsf.edu Thu Mar 27 10:26:03 2008 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 27 Mar 2008 10:26:03 -0700 Subject: [Chimera-users] Chimera In-Reply-To: References: Message-ID: <7CC0839A-4CEF-47B1-8AFB-E0050EC466AC@cgl.ucsf.edu> Hi Rob, On a Mac with a one-button mouse, buttons 2 and 3 can be emulated with the option and apple (clover) keys, respectively. For example, click-dragging with the option key pressed performs XY-translation (assuming default Mouse preferences). However, in Mac OS Leopard (10.5), this emulation of a 3-button mouse is off by default; you have to turn it on in the Input section of the X11 preferences. Here are the relevant man pages, although I think I summarized everything above. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#2button http://www.cgl.ucsf.edu/chimera/1.2492/osx_x11.html 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 Mar 26, 2008, at 3:32 PM, Robert Hilton wrote: > When using Chimera, I want to be able to use XY translation. In the > help menu, I found that if I hold down the middle mouse button, I > can control XY translation. However, I have a mac, and so have no > middle mouse button. How can I control XY translation using a mac? > Thanks, > Rob Hilton > hiltonlds at gmail.com > From jeandidier.marechal at uab.es Thu Mar 27 10:34:42 2008 From: jeandidier.marechal at uab.es (Jean-Didier =?ISO-8859-1?Q?Mar=E9chal?=) Date: Thu, 27 Mar 2008 18:34:42 +0100 Subject: [Chimera-users] Splitting surfnet surfaces and calculate enclosedvolume. In-Reply-To: <47EA9E39.1070309@cgl.ucsf.edu> References: <"120655 5151.13081.68.camel"@asklipio> <47EA9E39.1070309@cgl.ucsf.edu> Message-ID: <1206639282.18318.11.camel@asklipio> Great! Both answers have been useful! Just two small questions: 1. Is it possible to call for an accelerator from the python shell using runCommand? 2. Could I rename the individual surfaces? Cheers! JD On Wed, 2008-03-26 at 12:04 -0700, Tom Goddard wrote: > Hi JD, > > You can split the surfnet surface into separate selectable pieces by > selecting the whole surface (ctrl-left-button) then using keyboard > shortcut "Sc" (split connected pieces). You have to enable keyboard > shortcuts with menu entry Tools / General Controls / Accelerators On. > After this you can select individual pieces and measure their volumes > with the "mv" shortcut. You can select all of the pieces and use "mv" > to get a list of volumes for all the pieces. "ma" lists areas. Each > piece is numbered and you that number will be shown in a pop-up if you > the mouse over it. > > You can run the measure volumes shortcut (mv) from Python code using: > > import MeasureVolume > MeasureVolume.report_selected_volumes() > > This code is in your Chimera distribution in > chimera/share/MeasureVolume/__init__.py. > > Tom > From meng at cgl.ucsf.edu Thu Mar 27 10:42:36 2008 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 27 Mar 2008 10:42:36 -0700 Subject: [Chimera-users] Collaboratory tool removed ? In-Reply-To: <200803271217.57039.aurelien.grosdidier@gmail.com> References: <200803271217.57039.aurelien.grosdidier@gmail.com> Message-ID: <03562788-6FDF-4827-8855-499AFD8C3212@cgl.ucsf.edu> Hi Aurelien, We do not plan to add this feature back. However, you can still download version 1.2309 if you want to try it (scroll down a bit): http://www.cgl.ucsf.edu/chimera/olddownload.html Best, 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 Mar 27, 2008, at 4:17 AM, Aurelien Grosdidier wrote: > Hello, > I recently noticed that the current production version of Chimera > (v1 build > 2470) does not have the "Collaboratory tool" anymore. I wanted to > give it a > try and I am quite disappointed. From a previous changelog > (http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2417.html), I read > that "Collaboratory removed (use version 1.2309 for this tool)". > > My question is: can we expect this feature to be back one day, or > should I > look for an alternative ? > Thanks, > Aur?lien. > From goddard at cgl.ucsf.edu Thu Mar 27 11:26:35 2008 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Thu, 27 Mar 2008 11:26:35 -0700 Subject: [Chimera-users] Collaboratory tool removed ? In-Reply-To: <200803271217.57039.aurelien.grosdidier@gmail.com> References: <200803271217.57039.aurelien.grosdidier@gmail.com> Message-ID: <47EBE6DB.3080406@cgl.ucsf.edu> Hi Aurelien, We removed the Collaboratory (remote Chimera sharing) capability because it did not support mirroring most of the Chimera tools. With increased network bandwidth from 5 years ago it is quite reasonable to use a desktop sharing program such as VNC. Using a general desktop sharing program to mirror the display of Chimera is what we recommend for using Chimera with remote collaborators. Tom From goddard at cgl.ucsf.edu Thu Mar 27 11:45:57 2008 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Thu, 27 Mar 2008 11:45:57 -0700 Subject: [Chimera-users] Splitting surfnet surfaces and calculate enclosedvolume. In-Reply-To: <1206639282.18318.11.camel@asklipio> References: <"120655 5151.13081.68.camel"@asklipio> <47EA9E39.1070309@cgl.ucsf.edu> <1206639282.18318.11.camel@asklipio> Message-ID: <47EBEB65.60202@cgl.ucsf.edu> Hi JD, There is no Chimera command to run an accelerator. Would be handy. I'll add that to the requested feature list. There is no user interface to rename surface pieces. You can do it from Python with code like: plist = m.surfacePieces plist[0].oslName = 'filament 3' Here m is a SurfaceModel object and plist is the list of SurfacePiece objects. Setting the oslName changes the name shown in the popup balloon when the mouse is over that surface piece. There isn't any other code that uses surface piece names (e.g. no dialog that lists the surface piece names to allow you to select them, and no way to select a piece using its name). So the names are currently not too useful. Also there is no file format for saving the surface pieces. Lots of limitations. Tom From pintilie at mit.edu Thu Mar 27 13:57:28 2008 From: pintilie at mit.edu (Greg Pintilie) Date: Thu, 27 Mar 2008 16:57:28 -0400 Subject: [Chimera-users] origin of volume data Message-ID: A question about data origin in densiy maps... I open a map using the python script (in IDLE): >>> import VolumeData >>> gd = VolumeData.mrc.open ( "MRC map file" )[0] looking at the origin of this map: >>> gd.origin (-135.679992676, -135.679992676, -135.679992676) It is different than the origin reported if I open the same map file in Volume Viewer; pasted from the Volume Viewer dialog: -136.75 -136.75 -136.75 Why the difference? As to why I care, it's because if I open the map as in the python script above and then subsequently use it to compute average density values for certain structures, they are different than the average density values reported in the 'Fit Model in Map' dialog. It would give me more peace of mind if they matched... Now to start speculating on why the difference, I've seen that, internally, MRC maps define the origin in terms of a grid value, for example -64,-64,-64 in a 128x128x128 map. So the first value for the origin, as in the script method above, is calculated as if the origin is at the _center_ of the first grid point: origin[0] = -64 * step + step/2 (where step is 2.13669279804), while the second value (showing up in Volume Viewer) is simply calculated right on the grid point: origin[0] = -64 * step What's the right way to think about this? In the worst case, it's really a pretty small offset so not a big deal. Greg -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Thu Mar 27 16:04:11 2008 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Thu, 27 Mar 2008 16:04:11 -0700 Subject: [Chimera-users] origin of volume data In-Reply-To: References: Message-ID: <47EC27EB.10504@cgl.ucsf.edu> Hi Greg, Perhaps a very old version of Chimera changed the origin by half a voxel size. Tests on a current Chimera (1.2500) show no difference between the origin obtained with VolumeData.mrc.open() versus opening with Volume Viewer. What version of Chimera are you using? If it is relatively recent (< 6 months old) could you send me a map that has this problem? Otherwise try a newer Chimera. Tom From bala at igib.res.in Mon Mar 31 02:42:18 2008 From: bala at igib.res.in (bala) Date: Mon, 31 Mar 2008 15:12:18 +0530 Subject: [Chimera-users] trajectory analysis Message-ID: <91F147390CA53D44BFADECB36C489D13026AB4@n1ex> Dear Chimerians, I have an amber trajectory. I want to use gromacs to do some analysis. Is it possible in chimera to i) convert amber traj to gromacs traj format ii) convert amber topo file to gromacs topo format Thanks, Bala -------------- next part -------------- An HTML attachment was scrubbed... URL: From zhaojunwei2004 at 126.com Fri Mar 28 01:17:23 2008 From: zhaojunwei2004 at 126.com (zhaojunwei) Date: Fri, 28 Mar 2008 16:17:23 +0800 (CST) Subject: [Chimera-users] Criteras about hydrogen bonds in chimera Message-ID: <14064083.370651206692243461.JavaMail.coremail@bj126app80.126.com> Hi, all I have a question about the hbond. What is the definition about hydrogen bond in chimera? As we know, there're different criterias among softwares, I'm wondering the distence between donor atom and acceptor atom, and the angle of donor-hydrogen-acceptor in chimera. Any reply will be deeply appreciated! It'll be kind if you can send the reply to my address, cause I'm not in the mailing list. Junwei Zhao -------------- next part -------------- An HTML attachment was scrubbed... URL: From hjoseph at brandeis.edu Mon Mar 31 10:14:15 2008 From: hjoseph at brandeis.edu (hjoseph at brandeis.edu) Date: Mon, 31 Mar 2008 13:14:15 -0400 Subject: [Chimera-users] selecting one water molecule Message-ID: <20080331131415.wgmuj6w50kckwkow@webmail.brandeis.edu> Hi Everyone, I want to select one water molecule but every time I try to do that, all the molecules get selected. Could some one tell me the command line instruction for selecting water 241. Thanks, Helen Josephine From goddard at cgl.ucsf.edu Mon Mar 31 10:39:04 2008 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Mon, 31 Mar 2008 10:39:04 -0700 Subject: [Chimera-users] [chimera-dev] Wrapping Chimera in a Java program In-Reply-To: References: Message-ID: <47F121B8.7050406@cgl.ucsf.edu> Hi Fabrice, I do not think Chimera could run using Jython because Chimera uses dozens of compiled C/Python modules. You can communicate with Chimera via a pipe. One approach is to start Chimera with a popen() system call and send commands to Chimera's stdin using the ReadStdin capability: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/readstdin/readstdin.html It is also possible to talk to an already running instance of Chimera using the "chimera --send " shell command. This is used to have a web browser helper application directly send files to Chimera. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/webdata/webdata.html The implementation uses a socket that Chimera is listening on but it is somewhat tricky to find the right port number. It is saved on the local machine in a file as a security measure to prevent network connections. The details of that implementation are in your Chimera distribution chimera/share/send_to_chimera.py Scooter Morris in our lab has written code to communicate with Chimera from a Java application called Cytoscape. He might be able to provide more advice. Tom Fabrice Jossinet wrote: > Dear developers, > > I would like to launch Chimera from my Java program. I would like to > send messages to Chimera to highlight in its own display selections I > do in my Java program's display. I already did that with PyMOL using a > pipe communication. > > So, several questions: > - is it possible to start Chimera from a classical python distribution > (not the embedded python of Chimera)? One of my ideas is to start > Chimera from Jython, a Java implementation of Python > - is it possible to communicate with Chimera using a pipe ? > - and the most general question: is it possible to communicate with > Chimera from the outside? > > Thank you for your answers > > Fabrice > > From pett at cgl.ucsf.edu Mon Mar 31 11:26:21 2008 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 31 Mar 2008 11:26:21 -0700 Subject: [Chimera-users] selecting one water molecule In-Reply-To: <20080331131415.wgmuj6w50kckwkow@webmail.brandeis.edu> References: <20080331131415.wgmuj6w50kckwkow@webmail.brandeis.edu> Message-ID: <02DA75A9-AC84-4E71-BFF8-8A1E14AEB7FB@cgl.ucsf.edu> Hi Helen, This specifier: :241.water should select just water 241. Another trick you can use is to type a '+' in the command (separated by spaces from the rest of the command) and then control-click on an atom in the residue you want. The '+' will be replaced by the specifier for that atom, in your case probably something like: :241.water at O You would then just delete the "@O" part. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Mar 31, 2008, at 10:14 AM, hjoseph at brandeis.edu wrote: > Hi Everyone, > I want to select one water molecule but every time I try to > do that, all the molecules get selected. Could some one tell me the > command line instruction for selecting water 241. > > Thanks, > Helen Josephine > > _______________________________________________ > 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 pett at cgl.ucsf.edu Mon Mar 31 12:01:42 2008 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 31 Mar 2008 12:01:42 -0700 Subject: [Chimera-users] trajectory analysis In-Reply-To: <91F147390CA53D44BFADECB36C489D13026AB4@n1ex> References: <91F147390CA53D44BFADECB36C489D13026AB4@n1ex> Message-ID: Hi Bala, Chimera doesn't write any trajectory formats, so the answer is clearly no. VMD might be able to do this, though I'm guessing it doesn't write the GROMACS .trj file format. There does seem to be a standalone script that does exactly what you want though. It's here: http://chemistry.csulb.edu/ffamber/tools.html --Eric On Mar 31, 2008, at 2:42 AM, bala wrote: > Dear Chimerians, > > I have an amber trajectory. I want to use gromacs to do some > analysis. Is it possible in chimera to > i) convert amber traj to gromacs traj format > ii) convert amber topo file to gromacs topo format > > Thanks, > Bala > > _______________________________________________ > 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 meng at cgl.ucsf.edu Mon Mar 31 16:00:53 2008 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 31 Mar 2008 16:00:53 -0700 Subject: [Chimera-users] Criteras about hydrogen bonds in chimera In-Reply-To: <14064083.370651206692243461.JavaMail.coremail@bj126app80.126.com> References: <14064083.370651206692243461.JavaMail.coremail@bj126app80.126.com> Message-ID: <29EB6289-FE93-41C3-85A5-FFE1D6926937@cgl.ucsf.edu> Hi Junwei, FindHBond (and command "findhbond" or "hbonds") uses detailed criteria that depend on the atom types. There isn't just one distance or angle, but different ones for different combinations of donor and acceptor types. As mentioned here, http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/ findhbond.html#criteria the cutoffs are from a paper based on very-high-resolution small molecule crystal structures: J.E.J. Mills and P.M. Dean, "Three-dimensional hydrogen-bond geometry and probability information from a crystal survey" J Comput-Aided Mol Des 10: 607 (1996). The cutoffs are in Tables 5-8. Depending on the atom types, there may be two or three angle criteria, and donor-acceptor distance criteria are mostly near 3.0-3.4, although they range from 2.87 (protonated carboxylic acid donor) to 3.73 (thiocarbonyl acceptor). In addition, because structures in the PDB are generally lower resolution than those small molecules, the values from the paper are relaxed by 0.4 angstroms and 20 degrees (by default; you can change those amounts). Best, 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 Mar 28, 2008, at 1:17 AM, zhaojunwei wrote: > Hi, all > I have a question about the hbond. What is the definition about > hydrogen bond in chimera? > As we know, there're different criterias among softwares, I'm > wondering the distence between donor atom and acceptor atom, and > the angle of donor-hydrogen-acceptor in chimera. > > Any reply will be deeply appreciated! > It'll be kind if you can send the reply to my address, cause I'm > not in the mailing list. > > Junwei Zhao From ercanselami at gmail.com Mon Mar 31 10:28:21 2008 From: ercanselami at gmail.com (Selami ERCAN) Date: Mon, 31 Mar 2008 20:28:21 +0300 Subject: [Chimera-users] chimera segmentation fault Message-ID: <1206984501.17437.16.camel@shabut12.dicle.edu.tr> hi. i'm using chimera-1.2470-linux_x86_64.exe on suse 10.3. in addition to this my graphic card is nvidia geforce 8600m gt 512 mb and also i have installed mesa and xorg softwares. and here is problem: using 1EP4.pdb from rcsb.org causes problem.whenever i select structure-->main, then action-->surface-->show it crashes. and it gives the report shown below. Copyright M.F. Sanner (March 2000) Compilation flags WARNING: class_arete2: warning hole in a reentrant face 17081 WARNING: class_arete2: warning hole in a reentrant face 22603 WARNING: classe_aretes1: No cycle in face 25771 (nba=-4) WARNING: classe_aretes1: No cycle in face 25772 (nba=-1) WARNING: classe_aretes1: No cycle in face 25774 (nba=-1) WARNING: classe_aretes1: No cycle in face 25776 (nba=-3) WARNING: classe_aretes1: No cycle in face 25779 (nba=-1) WARNING: classe_aretes1: No cycle in face 25781 (nba=-1) WARNING: classe_aretes1: No cycle in face 25783 (nba=-1) WARNING: classe_aretes1: No cycle in face 25785 (nba=-1) WARNING: classe_aretes1: No cycle in face 25787 (nba=-1) WARNING: classe_aretes1: No cycle in face 25789 (nba=-1) RESTART FROM SES: 1 radius of atom 2855 goes from 1.760000 to 1.860000 radius of atom 2857 goes from 1.640000 to 1.740000 radius of atom 2858 goes from 1.760000 to 1.860000 radius of atom 2871 goes from 1.880000 to 1.980000 radius of atom 6942 goes from 1.880000 to 1.980000 radius of atom 6945 goes from 1.760000 to 1.860000 radius of atom 6946 goes from 1.760000 to 1.860000 radius of atom 6947 goes from 1.760000 to 1.860000 radius of atom 6948 goes from 1.760000 to 1.860000 radius of atom 6987 goes from 1.460000 to 1.560000 radius of atom 6988 goes from 1.760000 to 1.860000 Partial mode Segmentation fault From parsonsl at upstate.edu Mon Mar 31 12:05:04 2008 From: parsonsl at upstate.edu (Lee Parsons) Date: Mon, 31 Mar 2008 15:05:04 -0400 Subject: [Chimera-users] Chimera with 3d (6-axis) mouse? Message-ID: <47F0FDA0020000220001CD74@gwmta2.upstate.edu> Hello I was wondering if there is any support for using a 3d mouse with chimera. In particular, I have a 3dconnexion space explorer, and it does not seem to work in chimera for windows. I have not found anything in the archives pertaining to this, or even its logitech ancestor the "magellan". thank you