From meng at cgl.ucsf.edu Tue Nov 1 09:13:10 2005 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 1 Nov 2005 09:13:10 -0800 Subject: [Chimera-users] how to select multiple residues in multiple chains In-Reply-To: References: Message-ID: <11D058D9-64B2-47DC-AE6C-EBDB71232566@cgl.ucsf.edu> On Oct 28, 2005, at 9:50 AM, Eric Gillitzer wrote: > I work a lot with symmetrical, multi subunit structures and in > order to select say residue 45 in every subunit, I must one at a > time go in and in the sequence finder select the residue in each > chain and then color it. Is there a way to select all of the same > number residues (say number 45, might be an alanine) in the > structure displayed and color only those. If you select alanine, > it will select every single alanine in the structure. Chimera > seems to be a really powerful program, but I am pulling my hair out > trying to get it to do something productive in a timely fashion. > thanks, eric. > Hi Eric, It depends how the residues and chains are defined in the PDB file, but often it will be the same residue number but in different chains. In that case, it is fairly simple to select using a command. For example, in PDB 1e9i there are chains A-D, each comprising essentially the same sequence. To select residue 45 in all four chains: command: select :45.a-d or command: select :45.* Or, to select residue 45 in just chains A and D: command: select :45.a,45.d (To show the command line, choose Favorites... Command Line from the menu). 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 eric.dawson at vanderbilt.edu Tue Nov 1 09:37:21 2005 From: eric.dawson at vanderbilt.edu (Eric Dawson) Date: Tue, 1 Nov 2005 11:37:21 -0600 (CST) Subject: [Chimera-users] Display of qpack color output Message-ID: In the older UCSF MidasPlus incarnation of your software, there was a feature that allowed an interface with Gregort & Cohen's QPACK software for coloring according to molecular packing density using a sphere growth method. Per residue packing scores were applied with a color range after running qpack with the special option, '-m'. http://www.cmpharm.ucsf.edu/cohen/software/pages/qpack.html In the primary literature report of QPACK, it was suggested by the authors that they would work to make this feature available in UCSF MidasPlus and 'its successors'. Since this is a very fast and convenient way to evaluate the quality of models, I would like to recommend/request that this feature be enabled (or added) to Chimera. In MidasPlus, it was a command line option. The user simply entered qpack; there was a .midasrc file that contained the explicit local path to the qpack binary as well as a command line script to launch the package with the '-m' option. Thanks for your consideration of this suggestion. Best regards, Eric ______________________________________________________________________ Eric S. Dawson, Ph.D. CSB Computation, Education & Outreach Research Instructor, Biochemistry Center for Structural Biology (CSB) 5137 MRBIII Vanderbilt University Nashville, TN 37232-8755 Tel: (615)-936-5579 (MRB III) Tel: (615)-322-3303 (5119 SC) Fax: (615)-936-2211 "All that is gold does not glitter, not all those who wander are lost." J.R.R. Tolkien - Fellowship of the Ring From bshaanan at bgu.ac.il Tue Nov 1 09:48:17 2005 From: bshaanan at bgu.ac.il (Boaz Shaanan) Date: Tue, 1 Nov 2005 19:48:17 +0200 Subject: [Chimera-users] installing v1.2183 on XP & preserving preferences from previous version Message-ID: <20051101174424.506F533E62@smtp2.bgu.ac.il> Hi, For some reason I had problems installin 1.2183 under XP which I haven't had before. Only after un-installing the previous version it finally worked. Maybe something with the un-install script isn't quite working properly this time around ? I thought that by saving the preferences file and copying it back to the proper location (as it says under preferences/preferences) after installation, I would be able to continue with the same prerefences setting I had before. Apparently this didn't work. So what should I do in order to properly move the preference file from one version to the other ? Thanks for your help. Boaz From gregc at cgl.ucsf.edu Tue Nov 1 13:20:04 2005 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Tue, 1 Nov 2005 13:20:04 -0800 (PST) Subject: [Chimera-users] RGB->CMYK color conversion In-Reply-To: <3C6819A6-36B2-4F5C-8459-20B541A6B379@caltech.edu> References: <3C6819A6-36B2-4F5C-8459-20B541A6B379@caltech.edu> Message-ID: On Mon, 31 Oct 2005, James Puckett wrote: > I am writing to see if there are suggested methods for ensuring > good color conversion of rendered Chimera images from RGB to CMYK in > Photoshop (or other image editing programs). When printing to a > Tektronix Phaser 740 color laser, I am getting poor correlation > between screen colorings and the printed ones. I have heard that the > CMYK color space is basically a subset of the RGB color space. If > this is actually the case, is there a recommended way to pick RGB > colors that are relatively "safe" for conversion to a CMYK color space? Matching screen and print colors is getting easier. If you have Adobe PhotoShop, the best thing to do would be to read its help information on "Producing Consistent Color" and follow those recommendations. Microsoft has a website about "Color Management and Windows" that discusses many of the same issues. For Apple's Mac OS X, read about its ColorSync technology, . All of the above color management systems use ICC color profiles (). The basic idea is that you need a color profile for your screen and your printer and those profiles are used to match the colors. The color gamut of a screen and a printer vary greatly -- screens are much brighter than printers, but printers can produce colors that screens can't and are good at subtle differences in dark colors. Luckily, manufacturers usually provide an ICC color profile -- but to get the best results you'll need create your own using a colorimeter (e.g., ). For Windows, if you do not have a printing program that supports color profiles, you can use the free ICC Profile Conversion Software from Draw Creek Photo, . Good luck! Greg Couch UCSF Computer Graphics Lab gregc at cgl.ucsf.edu From pett at cgl.ucsf.edu Tue Nov 1 13:40:02 2005 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 1 Nov 2005 13:40:02 -0800 Subject: [Chimera-users] installing v1.2183 on XP & preserving preferences from previous version In-Reply-To: <20051101174424.506F533E62@smtp2.bgu.ac.il> References: <20051101174424.506F533E62@smtp2.bgu.ac.il> Message-ID: <60EC06FF-378A-4691-9D7B-0A5482CECB1C@cgl.ucsf.edu> On Nov 1, 2005, at 9:48 AM, Boaz Shaanan wrote: > Hi, > > For some reason I had problems installin 1.2183 under XP which I > haven't had before. Only after un-installing the previous version > it finally worked. Maybe something with the un-install script isn't > quite working properly this time around ? Hi Boaz, The new version should have worked without uninstalling the old version, unless you tried to install into the same location as the old version. Did you install into a separate location? > I thought that by saving the preferences file and copying it back > to the proper location (as it says under preferences/preferences) > after installation, I would be able to continue with the same > prerefences setting I had before. Apparently this didn't work. So > what should I do in order to properly move the preference file from > one version to the other ? You shouldn't have had to move your preferences file back and forth -- it's not removed by the de-installation process. If you moved your old preferences file into the location indicated by preferences/ preferences while Chimera was running, then there is a good chance that the file got overwritten without being used. For instance, if you opened a file then the directory and file name are written into preferences so you can easily get to the directory or open the file in your next session. At any rate, if you still have a good copy of the preferences you want, copy it into the preferences/preferences location when Chimera is not running. --Eric Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu From pett at cgl.ucsf.edu Tue Nov 1 13:54:05 2005 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 1 Nov 2005 13:54:05 -0800 Subject: [Chimera-users] Display of qpack color output In-Reply-To: References: Message-ID: On Nov 1, 2005, at 9:37 AM, Eric Dawson wrote: > In the older UCSF MidasPlus incarnation of your software, there was a > feature that allowed an interface with Gregort & Cohen's QPACK > software > for coloring according to molecular packing density using a sphere > growth > method. Per residue packing scores were applied with a color range > after > running qpack with the special option, '-m'. > > http://www.cmpharm.ucsf.edu/cohen/software/pages/qpack.html > > In the primary literature report of QPACK, it was suggested by the > authors > that they would work to make this feature available in UCSF > MidasPlus and > 'its successors'. Since this is a very fast and convenient way to > evaluate > the quality of models, I would like to recommend/request that this > feature > be enabled (or added) to Chimera. In MidasPlus, it was a command line > option. The user simply entered qpack; there was a .midasrc file that > contained the explicit local path to the qpack binary as well as a > command > line script to launch the package with the '-m' option. > > Thanks for your consideration of this suggestion. Good idea. We will work on it. --Eric Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu From pett at cgl.ucsf.edu Tue Nov 1 14:10:46 2005 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 1 Nov 2005 14:10:46 -0800 Subject: [Chimera-users] how to select multiple residues in multiple chains In-Reply-To: <11D058D9-64B2-47DC-AE6C-EBDB71232566@cgl.ucsf.edu> References: <11D058D9-64B2-47DC-AE6C-EBDB71232566@cgl.ucsf.edu> Message-ID: <02C0232C-EDED-4B9F-AEFC-23DD39698F63@cgl.ucsf.edu> Elaine's suggestions for using the command line are the easiest way to do what you want. However, if for some reason you prefer to use the menus, you can use the Select menu to change the "selection mode" to "append". This will allow you to build up selections since selecting new items won't deselect previous items. You can then do operations (like color) on the aggregate selection rather than having to do them separately. You can also save selections you've built up by using "Name Selection..." in the Select menu. If you save a session, named selections will be remembered in the session. --Eric Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu On Nov 1, 2005, at 9:13 AM, Elaine Meng wrote: > > On Oct 28, 2005, at 9:50 AM, Eric Gillitzer wrote: > >> I work a lot with symmetrical, multi subunit structures and in >> order to select say residue 45 in every subunit, I must one at a >> time go in and in the sequence finder select the residue in each >> chain and then color it. Is there a way to select all of the same >> number residues (say number 45, might be an alanine) in the >> structure displayed and color only those. If you select alanine, >> it will select every single alanine in the structure. Chimera >> seems to be a really powerful program, but I am pulling my hair out >> trying to get it to do something productive in a timely fashion. >> thanks, eric. >> > > Hi Eric, > It depends how the residues and chains are defined in the PDB file, > but often it will be the same residue number but in different > chains. In that case, it is fairly simple to select using a > command. For example, in PDB 1e9i there are chains A-D, each > comprising essentially the same sequence. To select residue 45 in all > four chains: > > command: select :45.a-d > or > command: select :45.* > > Or, to select residue 45 in just chains A and D: > > command: select :45.a,45.d > > (To show the command line, choose Favorites... Command Line from the > menu). > 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 > > > > > _______________________________________________ > 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 gregc at cgl.ucsf.edu Tue Nov 1 17:26:16 2005 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Tue, 1 Nov 2005 17:26:16 -0800 (PST) Subject: [Chimera-users] chimera and STRAP ? In-Reply-To: <62852.84.190.2.170.1130677633.squirrel@webmail.charite.de> References: <62852.84.190.2.170.1130677633.squirrel@webmail.charite.de> Message-ID: On Sun, 30 Oct 2005, Dr. Christoph Gille wrote: > I contact you because users of the program STRAP for protein > structures and sequences asked whether Chimera could be used within > STRAP for visualization. > > Currently Jmol and Pymol are used for visualiziation. For example the > results of 3D superpositions and the location of mutations can be > viewed. But some users apparently prefere Chimera. > > My question is whether Chimera could be linked to STRAP as well. The > most important point is, what mode of interprocess commmunication > exists in Chimera. > > For example Pymol and STRAP are linked via the stdin/stdout streams. > STRAP can send commands to Pymol and is notified when atoms are picked. > > STRAP uses the scripting language of Pymol to load proteins, create > selections and rotate proteins. > Could all this be done with Chimera in a similar way ? (Replies should be sent to chimera-dev at cgl.ucsf.edu) Sending commands and data to chimera can be done with the --send command line argument that was added for web browser support (it's not enabled by default except on Mac OS X, use Tools/Preferences Web Access to "Accept web data"). For bidirectional communication, you'll need to add some Python code -- python supports the same IPC that the underlying C library does, but the IPC should be integrated into the chimera event loop -- look at the socket code from CHIMERA/share/DBPuppet/tcl_sockets.py to see an example of integrating Internet sockets. Internet sockets are the general solution because standard input and output can only be used by one other appliction, but there are security issues. Chimera uses a shared key (read from the filesystem) security protocol to prevent hijacking of the web browser connection. I'd also recommend creating a chimera extension with all of the STRAP related code in it. For examples on how to do that, see the Chimera Programmer's Guide examples, . The examples also show how to use chimera selections pragrammatically. So the answer is yes, chimera could be linked to STRAP. I hope this answer gives you some ideas on how to proceed. I would be delighted to work with you to get the programs working together. Greg Couch UCSF Computer Graphics Lab gregc at cgl.ucsf.edu From bshaanan at bgu.ac.il Wed Nov 2 06:00:02 2005 From: bshaanan at bgu.ac.il (Boaz Shaanan) Date: Wed, 2 Nov 2005 16:00:02 +0200 Subject: [Chimera-users] 2D labels not saved ? Message-ID: <20051102135606.9B50C33E77@smtp2.bgu.ac.il> Hi, I used the 2D labels utility to make a few labels but when I save the image as tif I don't see them when I re-open the tif file. Is that possible ? Thanks, Boaz From goddard at cgl.ucsf.edu Wed Nov 2 09:20:31 2005 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Wed, 2 Nov 2005 09:20:31 -0800 (PST) Subject: [Chimera-users] RGB->CMYK color conversion In-Reply-To: <3C6819A6-36B2-4F5C-8459-20B541A6B379@caltech.edu> (message from James Puckett on Mon, 31 Oct 2005 21:20:48 -0800) References: <3C6819A6-36B2-4F5C-8459-20B541A6B379@caltech.edu> Message-ID: <200511021720.jA2HKV411931300@guanine.cgl.ucsf.edu> Hi James, The RGB and CMYK color spaces each contain colors that the other one cannot represent. But I do not think that is your problem. Computer monitors and printers and projectors vary wildly in the colors they produce. The easiest way to diagnose what device is contributing most to the color mismatch is to compare your Chimera image printed from two color printers, and on two or more different monitors. If the problem really is RGB versus CMYK color representations you might look at the figure in the middle of the following page: http://dx.sheridan.com/advisor/cmyk_color.html It shows the boundary in color space of the colors that can be reproduced by an RGB monitor and in CMYK printing. It suggests that the RGB monitor saturated blues and greens are outside the range of the CMYK gamut. Tom From pett at cgl.ucsf.edu Wed Nov 2 10:26:15 2005 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 2 Nov 2005 10:26:15 -0800 Subject: [Chimera-users] Mac OS X 10.4.3 update breaks Chimera Message-ID: <36745DB7-0826-43A9-ACA8-11055032F5D0@cgl.ucsf.edu> Hi, The 10.4.3 update to OS X breaks a significant amount of Chimera functionality. Attempts to use that functionality cause Chimera to exit. In particular, for structures that contain residues other than the standard amino/nucleic acids or water, anything that directly or indirectly makes Chimera determine atom types will cause the failure. Such things include adding hydrogens, finding hydrogen bonds, and going into ball-and-stick or sphere representation (the atom sizes are based on atom types) -- though stick-only mode is okay. We are working on a fix. Until we have one, you will have to weigh the improvements offered by 10.4.3 against the loss of Chimera functionality. I'll send mail to the list as soon as there are developments. --Eric Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Wed Nov 2 10:47:37 2005 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 2 Nov 2005 10:47:37 -0800 Subject: [Chimera-users] 2D labels not saved ? In-Reply-To: <20051102135606.9B50C33E77@smtp2.bgu.ac.il> References: <20051102135606.9B50C33E77@smtp2.bgu.ac.il> Message-ID: <505A5CF9-2EB7-4571-9E13-2751C68E6F69@cgl.ucsf.edu> Hi Boaz, This should not happen in the 1.2172 release and later (it was a "known problem" before then). What release are you using? --Eric Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu On Nov 2, 2005, at 6:00 AM, Boaz Shaanan wrote: > Hi, > > I used the 2D labels utility to make a few labels but when I save > the image as tif I don't see them when I re-open the tif file. Is > that possible ? > > Thanks, > > Boaz > > _______________________________________________ > 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 Wed Nov 2 14:20:23 2005 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 2 Nov 2005 14:20:23 -0800 Subject: [Chimera-users] 2D labels not saved ? In-Reply-To: <20051102135606.9B50C33E77@smtp2.bgu.ac.il> References: <20051102135606.9B50C33E77@smtp2.bgu.ac.il> Message-ID: Ah, we've reproduced this bug now. It happens when you ask for an image that is smaller (in pixels) than the Chimera window. If you ask for an image that is the same size or larger then the labels are okay. You can find out how many pixels the Chimera window is by using the "Get Pixels" button on the image-saving dialog. --Eric Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu On Nov 2, 2005, at 6:00 AM, Boaz Shaanan wrote: > Hi, > > I used the 2D labels utility to make a few labels but when I save > the image as tif I don't see them when I re-open the tif file. Is > that possible ? > > Thanks, > > Boaz > > _______________________________________________ > 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 gregc at cgl.ucsf.edu Wed Nov 2 16:23:29 2005 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Wed, 2 Nov 2005 16:23:29 -0800 (PST) Subject: [Chimera-users] RGB->CMYK color conversion In-Reply-To: <200511021720.jA2HKV411931300@guanine.cgl.ucsf.edu> References: <3C6819A6-36B2-4F5C-8459-20B541A6B379@caltech.edu> <200511021720.jA2HKV411931300@guanine.cgl.ucsf.edu> Message-ID: More information in a FAQ-style: Which CMYK profile should you use? If you know the printer, use its profile. The original question was about a Textronix Phaser 740. Tektronix paid to have that printer calibrated and the profile is available from . It is also available from the manufacturer (xerox.com since Xerox bought Tektronix's printer business a while ago). What if a journal requires CMYK and they don't provide a profile? If you want the colors printed in the journal to match what you submitted, you'll need to ask the publisher for a profile. If you're too shy, you can guess. For instance, many of the Elsevier publishing group's journals still require CMYK but the author instructions don't say which CMYK profile to use. Since they are European company and print on glossy paper, I'd recommend the "Europe ISO Coated FOGRA27" color profile from Adobe. Where can I get Adobe ICC color profiles? Adobe provides free ICC color profiles on their download page, . In that set of ICC color profiles there are 10 different CMYK profiles designed for different kinds of paper and standards (US, European, Japan). Those profiles are also provided in PhotoShop and some other Adobe products. When else would I want to use color profiles? If you're going to send your images to an online photo service, say for printing a holiday greeting card with a chimera image on it, then you'll want to use the printer profile provided by that service. For example, Costco.com provides printer profiles (the profile can make a huge difference, especially with wedding pictures). I'm using a printer color profile but the image changes color? The printer profile is used in conjuction with your monitor's profile to preview what will be printed. That set of colors is the common subset of the colors that the printer and the monitor can reproduce. It is the previewed colors that will match what is printed, not the original colors. The colors should be very close to the original colors, but slightly darker. How do I get my monitor's color profile? Any recent monitor should come with a color profile. Alternatively, you could use the standard sRGB color profile as an approximation. You also should calibrate your monitor to produce a full range of brightness (if there is too much light shining on your monitor, this is impossible). See for one possible method. If you google for "monitor calibration" you'll find more than you care for. Ideal monitor calibration uses a colorimeter to measure the color on the screen (but it's impossible to be perfect, e.g., LCD monitors are brighter in the middle than on the sides). From meng at cgl.ucsf.edu Wed Nov 2 09:57:45 2005 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 2 Nov 2005 09:57:45 -0800 Subject: [Chimera-users] 2D labels not saved ? In-Reply-To: <20051102135606.9B50C33E77@smtp2.bgu.ac.il> References: <20051102135606.9B50C33E77@smtp2.bgu.ac.il> Message-ID: On Nov 2, 2005, at 6:00 AM, Boaz Shaanan wrote: > > I used the 2D labels utility to make a few labels but when I save the > image as tif I don't see them when I re-open the tif file. Is that > possible ? Hi Boaz, It has worked in our tests. For example, here's a tif I just saved from version 1.2183 on the mac. However, there may be something specific with your system. If you have more details and a saved session (2d labels are saved in sessions), please send them to us. Best, Elaine -------------- next part -------------- A non-text attachment was scrubbed... Name: test.tif Type: image/tif Size: 135561 bytes Desc: not available URL: -------------- next part -------------- From pett at cgl.ucsf.edu Thu Nov 3 20:15:22 2005 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 3 Nov 2005 20:15:22 -0800 Subject: [Chimera-users] Mac OS X 10.4.3 update breaks Chimera In-Reply-To: <36745DB7-0826-43A9-ACA8-11055032F5D0@cgl.ucsf.edu> References: <36745DB7-0826-43A9-ACA8-11055032F5D0@cgl.ucsf.edu> Message-ID: Okay, there is version available for download (1.2185) that works on all versions of 10.4 (only). Version 1.2184 runs on 10.2 through 10.4.2. The two versions are otherwise identical. Please let us know about any problems you find with these. Thanks! --Eric On Nov 2, 2005, at 10:26 AM, Eric Pettersen wrote: > Hi, > The 10.4.3 update to OS X breaks a significant amount of > Chimera functionality.? Attempts to use that functionality cause > Chimera to exit.? In particular, for structures that contain residues > other than the standard amino/nucleic acids or water, anything that > directly or indirectly makes Chimera determine atom types will cause > the failure.? Such things include adding hydrogens, finding hydrogen > bonds, and going into ball-and-stick or sphere representation (the > atom sizes are based on atom types) -- though stick-only mode is okay. > We are working on a fix.? Until we have one, you will have to weigh > the improvements offered by 10.4.3 against the loss of Chimera > functionality.? I'll send mail to the list as soon as there are > developments. > > --Eric > > ? ? ? ? ? ? ? ? ? ? ? ? Eric Pettersen > ? ? ? ? ? ? ? ? ? ? ? ? UCSF Computer Graphics Lab > ? ? ? ? ? ? ? ? ? ? ? ? pett at cgl.ucsf.edu > ? ? ? ? ? ? ? ? ? ? ? ? http://www.cgl.ucsf.edu > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1680 bytes Desc: not available URL: From cjamesgrant at earthlink.net Wed Nov 9 12:34:52 2005 From: cjamesgrant at earthlink.net (cjamesgrant at earthlink.net) Date: Wed, 9 Nov 2005 15:34:52 -0500 (GMT-05:00) Subject: [Chimera-users] chimera question Message-ID: <25713850.1131568493351.JavaMail.root@elwamui-rubis.atl.sa.earthlink.net> Does chimera have the capability of automatically connecting the elements of a protein to reveal its overall shape. I am trying to determine the amino acid sequence of the attached protein, but I am having a hard time visualizing how the elements are connected to each other. I am new to this program, so any help would be greatly appreciated. Thank you, C Grant -------------- next part -------------- ATOM 920 N PPP A 1 37.846 6.055 34.570 1.00 42.20 N TER ATOM 921 CA PPP A 2 37.192 7.356 34.616 1.00 40.07 C TER ATOM 922 C PPP A 3 35.704 7.337 34.250 1.00 35.67 C TER ATOM 923 O PPP A 4 34.880 7.955 34.918 1.00 32.56 O TER ATOM 924 CB PPP A 5 37.909 8.337 33.684 1.00 43.94 C TER ATOM 925 CG PPP A 6 39.411 8.466 33.893 1.00 50.01 C TER ATOM 926 CD PPP A 7 40.097 9.158 32.719 1.00 55.54 C TER ATOM 927 OE1 PPP A 8 39.539 10.155 32.205 1.00 56.27 O TER ATOM 928 OE2 PPP A 9 41.188 8.704 32.306 1.00 57.91 O TER ATOM 929 N PPP A 10 35.345 6.618 33.197 1.00 36.15 N TER ATOM 930 CA PPP A 11 33.949 6.643 32.772 1.00 31.67 C TER ATOM 931 C PPP A 12 32.890 6.034 33.686 1.00 28.79 C TER ATOM 932 O PPP A 13 31.728 6.442 33.631 1.00 26.56 O TER ATOM 933 CB PPP A 14 33.802 6.087 31.347 1.00 34.01 C TER ATOM 934 CG1 PPP A 15 34.203 4.617 31.296 1.00 35.31 C TER ATOM 935 CG2 PPP A 16 34.640 6.935 30.395 1.00 33.32 C TER ATOM 936 CD1 PPP A 17 33.857 3.955 29.978 1.00 35.84 C TER ATOM 937 N PPP A 18 33.261 5.091 34.543 1.00 29.17 N TER ATOM 938 CA PPP A 19 32.258 4.519 35.448 1.00 29.71 C TER ATOM 939 C PPP A 20 31.594 5.649 36.241 1.00 30.17 C TER ATOM 940 O PPP A 21 30.368 5.774 36.275 1.00 26.46 O TER ATOM 941 CB PPP A 22 32.903 3.529 36.424 1.00 30.98 C TER ATOM 942 CG PPP A 23 31.948 2.496 36.958 1.00 32.10 C TER ATOM 943 CD1 PPP A 24 31.126 2.783 38.048 1.00 33.90 C TER ATOM 944 CD2 PPP A 25 31.883 1.230 36.382 1.00 30.32 C TER ATOM 945 CE1 PPP A 26 30.243 1.815 38.561 1.00 32.72 C TER ATOM 946 CE2 PPP A 27 31.008 0.257 36.880 1.00 31.57 C TER ATOM 947 CZ PPP A 28 30.189 0.550 37.973 1.00 33.34 C TER ATOM 948 N PPP A 29 32.415 6.483 36.871 1.00 29.49 N TER ATOM 949 CA PPP A 30 31.893 7.587 37.661 1.00 32.03 C TER ATOM 950 C PPP A 31 31.133 8.593 36.806 1.00 28.94 C TER ATOM 951 O PPP A 32 30.155 9.177 37.256 1.00 31.27 O TER ATOM 952 CB PPP A 33 33.030 8.290 38.401 1.00 33.41 C TER ATOM 953 CG PPP A 34 33.455 7.547 39.655 1.00 39.39 C TER ATOM 954 OD1 PPP A 35 32.766 6.576 40.038 1.00 38.69 O TER ATOM 955 OD2 PPP A 36 34.479 7.936 40.256 1.00 39.54 O TER ATOM 956 N PPP A 37 31.584 8.795 35.572 1.00 30.23 N TER ATOM 957 CA PPP A 38 30.918 9.736 34.676 1.00 28.51 C TER ATOM 958 C PPP A 39 29.525 9.202 34.324 1.00 29.02 C TER ATOM 959 O PPP A 40 28.537 9.948 34.300 1.00 24.84 O TER ATOM 960 CB PPP A 41 31.743 9.912 33.408 1.00 27.00 C TER ATOM 961 CG PPP A 42 33.032 10.680 33.609 1.00 31.76 C TER ATOM 962 SD PPP A 43 33.960 10.787 32.076 1.00 34.88 S TER ATOM 963 CE PPP A 44 35.409 11.753 32.643 1.00 44.81 C TER ATOM 964 N PPP A 45 29.450 7.902 34.058 1.00 25.17 N TER ATOM 965 CA PPP A 46 28.172 7.292 33.730 1.00 27.57 C TER ATOM 966 C PPP A 47 27.210 7.411 34.916 1.00 29.58 C TER ATOM 967 O PPP A 48 26.042 7.742 34.744 1.00 26.50 O TER ATOM 968 CB PPP A 49 28.379 5.825 33.332 1.00 27.88 C TER ATOM 969 CG PPP A 50 29.039 5.683 31.957 1.00 26.58 C TER ATOM 970 CD1 PPP A 51 29.677 4.304 31.782 1.00 27.69 C TER ATOM 971 CD2 PPP A 52 27.993 5.928 30.894 1.00 25.60 C TER ATOM 972 N PPP A 53 27.701 7.146 36.126 1.00 30.29 N TER ATOM 973 CA PPP A 54 26.859 7.250 37.323 1.00 30.47 C TER ATOM 974 C PPP A 55 26.319 8.681 37.465 1.00 30.24 C TER ATOM 975 O PPP A 56 25.142 8.901 37.770 1.00 28.73 O TER ATOM 976 CB PPP A 57 27.675 6.883 38.571 1.00 31.65 C TER ATOM 977 CG PPP A 58 28.078 5.415 38.757 1.00 32.52 C TER ATOM 978 CD1 PPP A 59 28.960 5.263 39.995 1.00 31.41 C TER ATOM 979 CD2 PPP A 60 26.825 4.574 38.903 1.00 34.82 C TER ATOM 980 N PPP A 61 27.193 9.655 37.237 1.00 31.33 N TER ATOM 981 CA PPP A 62 26.807 11.058 37.332 1.00 29.99 C TER ATOM 982 C PPP A 63 25.696 11.387 36.344 1.00 30.92 C TER ATOM 983 O PPP A 64 24.754 12.107 36.674 1.00 30.72 O TER ATOM 984 CB PPP A 65 28.016 11.950 37.077 1.00 31.52 C TER ATOM 985 N PPP A 66 25.801 10.854 35.128 1.00 30.31 N TER ATOM 986 CA PPP A 67 24.786 11.106 34.112 1.00 28.70 C TER ATOM 987 C PPP A 68 23.462 10.481 34.530 1.00 29.28 C TER ATOM 988 O PPP A 69 22.402 11.099 34.397 1.00 25.59 O TER ATOM 989 CB PPP A 70 25.208 10.534 32.736 1.00 30.74 C TER ATOM 990 OG1 PPP A 71 26.570 10.894 32.465 1.00 32.00 O TER ATOM 991 CG2 PPP A 72 24.320 11.087 31.631 1.00 26.11 C TER ATOM 992 N PPP A 73 23.520 9.253 35.036 1.00 27.92 N TER ATOM 993 CA PPP A 74 22.308 8.574 35.480 1.00 29.79 C TER ATOM 994 C PPP A 75 21.651 9.400 36.587 1.00 31.28 C TER ATOM 995 O PPP A 76 20.433 9.578 36.611 1.00 29.75 O TER ATOM 996 CB PPP A 77 22.638 7.178 36.009 1.00 33.27 C TER ATOM 997 OG PPP A 78 21.453 6.414 36.137 1.00 37.05 O TER ATOM 998 N PPP A 79 22.477 9.902 37.495 0.75 31.93 N TER ATOM 1000 CA PPP A 81 22.002 10.714 38.605 0.75 35.66 C TER ATOM 1002 C PPP A 83 21.299 11.971 38.091 0.75 35.19 C TER ATOM 1004 O PPP A 85 20.257 12.374 38.613 0.75 35.25 O TER ATOM 1006 CB PPP A 87 23.184 11.097 39.502 0.75 37.53 C TER ATOM 1008 OG PPP A 89 22.823 12.091 40.442 0.75 44.47 O TER ATOM 1010 N PPP A 91 21.867 12.579 37.054 1.00 33.53 N TER ATOM 1011 CA PPP A 92 21.300 13.788 36.471 1.00 34.09 C TER ATOM 1012 C PPP A 93 19.936 13.491 35.872 1.00 33.57 C TER ATOM 1013 O PPP A 94 18.995 14.265 36.052 1.00 30.11 O TER ATOM 1014 CB PPP A 95 22.240 14.355 35.401 1.00 33.55 C TER ATOM 1015 CG PPP A 96 21.671 15.529 34.624 1.00 38.74 C TER ATOM 1016 CD PPP A 97 21.559 16.787 35.478 1.00 38.05 C TER ATOM 1017 NE PPP A 98 21.157 17.944 34.679 1.00 37.87 N TER ATOM 1018 CZ PPP A 99 20.487 18.995 35.149 1.00 41.41 C TER ATOM 1019 NH1 PPP A 100 20.134 19.050 36.428 1.00 40.50 N TER ATOM 1020 NH2 PPP A 101 20.175 19.998 34.338 1.00 38.62 N TER ATOM 1021 N PPP A 102 19.831 12.371 35.158 1.00 34.61 N TER ATOM 1022 CA PPP A 103 18.564 11.963 34.549 1.00 35.32 C TER ATOM 1023 C PPP A 104 17.527 11.780 35.657 1.00 35.66 C TER ATOM 1024 O PPP A 105 16.362 12.136 35.497 1.00 34.73 O TER ATOM 1025 CB PPP A 106 18.727 10.634 33.796 1.00 35.15 C TER ATOM 1026 CG PPP A 107 19.241 10.779 32.386 1.00 37.79 C TER ATOM 1027 CD1 PPP A 108 19.459 12.035 31.824 1.00 42.06 C TER ATOM 1028 CD2 PPP A 109 19.521 9.650 31.623 1.00 40.99 C TER ATOM 1029 CE1 PPP A 110 19.955 12.163 30.522 1.00 43.38 C TER ATOM 1030 CE2 PPP A 111 20.017 9.768 30.323 1.00 41.00 C TER ATOM 1031 CZ PPP A 112 20.233 11.029 29.775 1.00 40.56 C TER ATOM 1032 N PPP A 113 17.967 11.217 36.778 1.00 38.40 N TER ATOM 1033 CA PPP A 114 17.094 10.983 37.924 1.00 40.56 C TER ATOM 1034 C PPP A 115 16.577 12.302 38.493 1.00 40.49 C TER ATOM 1035 O PPP A 116 15.382 12.458 38.729 1.00 41.13 O TER ATOM 1036 CB PPP A 117 17.845 10.215 39.012 1.00 40.70 C TER ATOM 1037 CG PPP A 118 16.942 9.590 40.068 1.00 44.55 C TER ATOM 1038 CD PPP A 119 17.648 8.459 40.810 1.00 48.45 C TER ATOM 1039 NE PPP A 120 18.981 8.841 41.275 1.00 50.08 N TER ATOM 1040 CZ PPP A 121 20.119 8.362 40.776 1.00 51.91 C TER ATOM 1041 NH1 PPP A 122 20.099 7.472 39.790 1.00 49.18 N TER ATOM 1042 NH2 PPP A 123 21.283 8.770 41.266 1.00 51.82 N TER From meng at cgl.ucsf.edu Wed Nov 9 13:32:51 2005 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 9 Nov 2005 13:32:51 -0800 Subject: [Chimera-users] chimera question In-Reply-To: <25713850.1131568493351.JavaMail.root@elwamui-rubis.atl.sa.earthlink.net> References: <25713850.1131568493351.JavaMail.root@elwamui-rubis.atl.sa.earthlink.net> Message-ID: <21EF70AF-4569-4331-AF23-393ED424E868@cgl.ucsf.edu> On Nov 9, 2005, at 12:34 PM, cjamesgrant at earthlink.net wrote: > Does chimera have the capability of automatically connecting the > elements of a protein to reveal its overall shape. I am trying to > determine the amino acid sequence of the attached protein, but I am > having a hard time visualizing how the elements are connected to > each other. I am new to this program, so any help would be greatly > appreciated. > > Thank you, > > C Grant > Hi there, There are a lot of problems with that PDB file! Chimera will automatically connect atoms, except that this file has TER between each atom, forcing it to not include any bonds. Additional problems are that each atom is given a different residue number. It looks like these are normal amino acid residues, but instead of their usual names, the residue name throughout the file is PPP. I edited the whole file to be residue number 1 and removed all the TER lines, which is technically still very incorrect, but now you can visually tell the sequence of the peptide. The edited file is attached. To be technically correct you would have to name and number the residues correctly (looks like there are 14 of them). ----- 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 -------------- A non-text attachment was scrubbed... Name: temp.pdb Type: application/octet-stream Size: 9243 bytes Desc: not available URL: -------------- next part -------------- From cwmoad at gmail.com Thu Nov 10 12:06:31 2005 From: cwmoad at gmail.com (Charlie Moad) Date: Thu, 10 Nov 2005 15:06:31 -0500 Subject: [Chimera-users] Rotation callback Message-ID: <6382066a0511101206g6b370ay9b4cc0c72ad15949@mail.gmail.com> Is it possible to register a python callback for when a protein is rotated and get the rotation information? Thanks, Charlie From svozil at uochb.cas.cz Fri Nov 11 05:42:31 2005 From: svozil at uochb.cas.cz (Daniel Svozil) Date: Fri, 11 Nov 2005 14:42:31 +0100 Subject: [Chimera-users] Move atoms (selections) in Chimera Message-ID: <43749FC7.9020709@uochb.cas.cz> Hi, is there any possibility, how to move atoms (selections) in Chimera? If, e,g,, I want to make C-H bond a bit longer? move command seems to work only with model. Thanks Dan -- Daniel Svozil, PhD Institute of Organic Chemistry and Biochemistry Center for Biomolecules and Complex Molecular Systems http://www.molecular.cz/~svozil Czech Republic phone: +420-220 410 312 From sabuj.pattanayek at vanderbilt.edu Fri Nov 11 08:22:08 2005 From: sabuj.pattanayek at vanderbilt.edu (Sabuj Pattanayek) Date: Fri, 11 Nov 2005 10:22:08 -0600 Subject: [Chimera-users] v1.2184 - Is it possible to specify the color of the tube object (sugar-backbone) bond in nucleic acid models? Message-ID: <4374C530.40506@vanderbilt.edu> Hi, In v1.2184 is it possible to specify the color of the tube object connecting the sugar to the backbone in a nucleic acid model? Currently clicking apply in the nucleic acid depiction dialog changes its color to whatever the color of the base is set to. Thanks From meng at cgl.ucsf.edu Fri Nov 11 18:50:45 2005 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 11 Nov 2005 18:50:45 -0800 Subject: [Chimera-users] v1.2184 - Is it possible to specify the color of the tube object (sugar-backbone) bond in nucleic acid models? In-Reply-To: <4374C530.40506@vanderbilt.edu> References: <4374C530.40506@vanderbilt.edu> Message-ID: Hi Sabuj, According to my experiments, the tube gets the color of the C1' atom in the sugar. Thus first color the C1' atoms the desired tube color, e.g. with the command color hot pink @c1' or, for different colors for different residues color dodger blue :7.a at c1' (residue 7 in chain A) etc. and then use the Nucleotides tool to generate the representations with tubes. I hope this is what you had in mind. 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 Fri Nov 11 21:42:46 2005 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Fri, 11 Nov 2005 21:42:46 -0800 (PST) Subject: [Chimera-users] Move atoms (selections) in Chimera In-Reply-To: <43749FC7.9020709@uochb.cas.cz> (message from Daniel Svozil on Fri, 11 Nov 2005 14:42:31 +0100) References: <43749FC7.9020709@uochb.cas.cz> Message-ID: <200511120542.jAC5gk3f1752227@guanine.cgl.ucsf.edu> Hi Dan, There is currently no Chimera capability for moving atoms other than rotating about bonds. But I have been wanting to add mouse modes for moving and rotating sets of selected atoms around. Here is some Chimera code http://www.cgl.ucsf.edu/home/goddard/temp/moveselection.tar that adds a mouse mode to move selected atoms in the screen x and y directions with the mouse. The archive contains a directory called MoveSelection. Put it in your Chimera distribution in chimera/share or on Mac in Chimera.app/Contents/Resources/share Then when you start Chimera use menu entry Favorites / Preferences, and choose category "Mouse" from the preferences dialog. This shows the mouse modes table with the available modes along the top line. The last one is for moving selected atoms. Reassign a mouse button (say button 2) to this mode and you can move selected atoms. There is no undo. Tom From pett at cgl.ucsf.edu Fri Nov 11 22:16:59 2005 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Fri, 11 Nov 2005 22:16:59 -0800 Subject: [Chimera-users] Rotation callback In-Reply-To: <6382066a0511101206g6b370ay9b4cc0c72ad15949@mail.gmail.com> References: <6382066a0511101206g6b370ay9b4cc0c72ad15949@mail.gmail.com> Message-ID: Hi Charlie, The answer is: sort of. You can't get a callback for when a specific model moves, but you can get callbacks for when any models move and from there it's pretty easy to deduce if models you are interested in moved. There are two possible triggers you could use. The one most typically used is chimera.MOTION_STOP (mentioned in the Trigger Notifications programming example), which fires one second after models have stopped moving (the motion can be due to user interaction or programmatic repositioning). On the assumption that what you want to do in response to the trigger is somewhat heavyweight, this is the trigger you would want to use. The other trigger is 'OpenState', which will fire many times as a motion occurs. If you use this trigger, you could check to see if the trigger data's 'modified' attribute contains the OpenState instance of the model(s) you care about and whether the trigger data's 'reasons' attribute contains the string "transformation change". There is an OpenState instance for each model ID/subID pair. So some models share a single OpenState instance (e.g. a structure model and corresponding surface model). Models have an 'openState' attribute, and OpenState instances have an 'xform' attribute containing the transformation matrix. If you use the MOTION_STOP trigger, you would compare the transforms of the models you care about with previous ones that you'd saved to determine if the models had moved. UndoMove is an example of an extension that uses MOTION_STOP. --Eric Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu On Nov 10, 2005, at 12:06 PM, Charlie Moad wrote: > Is it possible to register a python callback for when a protein is > rotated and get the rotation information? > > Thanks, > Charlie > > _______________________________________________ > 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 svozil at uochb.cas.cz Sat Nov 12 00:12:32 2005 From: svozil at uochb.cas.cz (Daniel Svozil) Date: Sat, 12 Nov 2005 09:12:32 +0100 Subject: [Chimera-users] Move atoms (selections) in Chimera In-Reply-To: <200511120542.jAC5gk3f1752227@guanine.cgl.ucsf.edu> References: <43749FC7.9020709@uochb.cas.cz> <200511120542.jAC5gk3f1752227@guanine.cgl.ucsf.edu> Message-ID: <4375A3F0.7020509@uochb.cas.cz> Hi Tom, thanks for your help. It is really pleasant to see, tha Chimera is being actively developed, and the developers are so helpful. I wonder, if there are any plans for the future to add molecular building capabilities into Chimera. It would be very nice to have an open-source (or at least free of charge) molecular builder in spirit of Insight available (but with more modern interface), because IMHO this is a kind of software missing in the portfolio of free molecular modelling programs, though its unexceptionable usefulness. Chimera with its strong visualization capabilities seems to be an ideal candidate for this. Dan Thomas Goddard wrote: > Hi Dan, > > There is currently no Chimera capability for moving atoms other than > rotating about bonds. But I have been wanting to add mouse modes for > moving and rotating sets of selected atoms around. Here is some Chimera > code > > http://www.cgl.ucsf.edu/home/goddard/temp/moveselection.tar > > that adds a mouse mode to move selected atoms in the screen x and y > directions with the mouse. The archive contains a directory called > MoveSelection. Put it in your Chimera distribution in > > chimera/share > > or on Mac in > > Chimera.app/Contents/Resources/share > > Then when you start Chimera use menu entry Favorites / Preferences, > and choose category "Mouse" from the preferences dialog. This shows > the mouse modes table with the available modes along the top line. > The last one is for moving selected atoms. Reassign a mouse button > (say button 2) to this mode and you can move selected atoms. > > There is no undo. > > Tom > -- Daniel Svozil, PhD Institute of Organic Chemistry and Biochemistry Center for Biomolecules and Complex Molecular Systems http://www.molecular.cz/~svozil Czech Republic phone: +420-220 410 312 From peter.panizzi at Vanderbilt.Edu Sat Nov 12 19:34:25 2005 From: peter.panizzi at Vanderbilt.Edu (Panizzi, Peter) Date: Sat, 12 Nov 2005 21:34:25 -0600 Subject: [Chimera-users] export tiff... Message-ID: <20FFA924E225454E8943490F9B3B498B0716F5@mailbe02.mc.vanderbilt.edu> To whom it may concern, I have been using the chimera program and I cannot save or export a tiff or jpeg file is there some trick to doing this? Thanks, Pete -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Nov 14 09:24:24 2005 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 14 Nov 2005 09:24:24 -0800 Subject: [Chimera-users] export tiff... In-Reply-To: <20FFA924E225454E8943490F9B3B498B0716F5@mailbe02.mc.vanderbilt.edu> References: <20FFA924E225454E8943490F9B3B498B0716F5@mailbe02.mc.vanderbilt.edu> Message-ID: <4CC858DF-0D05-48E4-B1B8-7C834F4ED22C@cgl.ucsf.edu> Hi Pete, If you choose File... Save Image and (after adjusting parameters if you want) click "Save As," the image will be redrawn at the requested resolution. When that is done, another dialog for saving the image file will appear. On this second dialog, there are several choices for file type, including JPEG and TIFF. See the Save Image man page: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/print.html A second way is to use the "copy" command with the keyword for the desired format, as described in the man page: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/copy.html However, if you already got that far and still had trouble, let us know in more detail what happened. There is also a tutorial on making images for publication: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ frameimages.html Thanks, Elaine On Nov 12, 2005, at 7:34 PM, Panizzi, Peter wrote: > To whom it may concern, > > I have been using the chimera program and I cannot save or export a > tiff or jpeg file is there some trick to doing this? > > Thanks, > Pete > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users ----- 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 puckett at caltech.edu Mon Nov 14 09:25:00 2005 From: puckett at caltech.edu (James Puckett) Date: Mon, 14 Nov 2005 09:25:00 -0800 Subject: [Chimera-users] export tiff... In-Reply-To: <20FFA924E225454E8943490F9B3B498B0716F5@mailbe02.mc.vanderbilt.edu> References: <20FFA924E225454E8943490F9B3B498B0716F5@mailbe02.mc.vanderbilt.edu> Message-ID: <92440263-C7CD-4612-AB9A-3D53BD0A2162@caltech.edu> The Chimera Users Guide description may be of use to you: http:// www.cgl.ucsf.edu/chimera/docs/UsersGuide/print.html If this does not help, feel free to e-mail. --Jim On Nov 12, 2005, at 7:34 PM, Panizzi, Peter wrote: > To whom it may concern, > > I have been using the chimera program and I cannot save or export a > tiff or jpeg file is there some trick to doing this? > > Thanks, > Pete > _______________________________________________ > 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 Nov 14 10:08:15 2005 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 14 Nov 2005 10:08:15 -0800 (PST) Subject: [Chimera-users] Move atoms (selections) in Chimera In-Reply-To: <4375A3F0.7020509@uochb.cas.cz> (message from Daniel Svozil on Sat, 12 Nov 2005 09:12:32 +0100) References: <43749FC7.9020709@uochb.cas.cz> <200511120542.jAC5gk3f1752227@guanine.cgl.ucsf.edu> <4375A3F0.7020509@uochb.cas.cz> Message-ID: <200511141808.jAEI8FuJ2070241@guanine.cgl.ucsf.edu> Hi Dan, The only model building capabilities current in Chimera are commands addaa and swapaa which add and swap amino acids, and bond rotation capabilities. We think creating capabilities for building models into density maps like the program O is too big a project. Building models without reference to maps may be easier but I suspect molecular dynamics capabilities or at least energy minimization are needed to make that useful. Chimera does not do MD calculations or energy minimization and again that is a big project we have been reluctant to take on so far. If you think specific new model building capabilities would be helpful given the above limitations, explain them and we will be happy to consider them. Tom From eric.dawson at vanderbilt.edu Mon Nov 14 10:17:39 2005 From: eric.dawson at vanderbilt.edu (Eric Dawson) Date: Mon, 14 Nov 2005 12:17:39 -0600 (CST) Subject: [Chimera-users] Move atoms (selections) in Chimera In-Reply-To: <200511141808.jAEI8FuJ2070241@guanine.cgl.ucsf.edu> References: <43749FC7.9020709@uochb.cas.cz> <200511120542.jAC5gk3f1752227@guanine.cgl.ucsf.edu> <4375A3F0.7020509@uochb.cas.cz> <200511141808.jAEI8FuJ2070241@guanine.cgl.ucsf.edu> Message-ID: On Mon, 14 Nov 2005, Thomas Goddard wrote: > Hi Dan, > > The only model building capabilities current in Chimera are commands > addaa and swapaa which add and swap amino acids, and bond rotation > capabilities. We think creating capabilities for building models into > density maps like the program O is too big a project. Building models > without reference to maps may be easier but I suspect molecular > dynamics capabilities or at least energy minimization are needed to > make that useful. Chimera does not do MD calculations or energy > minimization and again that is a big project we have been reluctant to > take on so far. > > If you think specific new model building capabilities would be helpful > given the above limitations, explain them and we will be happy to consider > them. > > Tom > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users Tom, You guys might get away with just a 'quick & dirty' energy evaluation that includes a 'soft' steric repulsive term. This could be implemented in a manner similar to the 'scuplting' feature in Pymol. Just a suggestion. This type of feature would be quite useful to our users at Vanderbilt in the Medical Center. Thanks for your consideration. Eric ______________________________________________________________________ Eric S. Dawson, Ph.D. CSB Computation, Education & Outreach Research Instructor, Biochemistry Center for Structural Biology (CSB) 5137 MRBIII Vanderbilt University From pett at cgl.ucsf.edu Mon Nov 14 10:26:50 2005 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 14 Nov 2005 10:26:50 -0800 Subject: [Chimera-users] export tiff... In-Reply-To: <20FFA924E225454E8943490F9B3B498B0716F5@mailbe02.mc.vanderbilt.edu> References: <20FFA924E225454E8943490F9B3B498B0716F5@mailbe02.mc.vanderbilt.edu> Message-ID: <95A8F9E4-6514-465B-97C9-5494A30A4A1E@cgl.ucsf.edu> Hi Pete, If you are using Windows, there was a bug in there for a while where you could not save non-PNG images successfully. If that's happening for you, you should download the 1.2184 release which includes a fix for that. --Eric Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu On Nov 12, 2005, at 7:34 PM, Panizzi, Peter wrote: > To whom it may concern, > > I have been using the chimera program and I cannot save or export a > tiff or jpeg file is there some trick to doing this? > > Thanks, > Pete > _______________________________________________ > 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 cyberworm_upm at yahoo.com Wed Nov 16 22:08:19 2005 From: cyberworm_upm at yahoo.com (Reiner Villavicencio) Date: Thu, 17 Nov 2005 06:08:19 +0000 (GMT) Subject: [Chimera-users] Reference Manual In-Reply-To: Message-ID: <20051117060819.8258.qmail@web31613.mail.mud.yahoo.com> Dear all, Is an offline reference manual (*.pdf) available for Chimera? I realized that under the documentation section of the website, that only online references are present. Having an offline user guide would be more convenient because there is no need to go online everytime a problem is encountered. Thank you and good day Reiner Villavicencio BS Biochemistry Dept. of Physical Sciences and Mathematics College of Arts and Sciences University of the Philippines, Manila "Its hard to hold on to something that can never be yours in anyway you want... something that wasn?t really yours to begin with... you just have to go on and accept the fact that while good things never last some don?t even start...." Send instant messages to your online friends http://uk.messenger.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Nov 17 12:27:33 2005 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 17 Nov 2005 12:27:33 -0800 Subject: [Chimera-users] Reference Manual In-Reply-To: <20051117060819.8258.qmail@web31613.mail.mud.yahoo.com> References: <20051117060819.8258.qmail@web31613.mail.mud.yahoo.com> Message-ID: <517BA305-CA99-48C3-915F-0AC346651A1B@cgl.ucsf.edu> Hi Reiner, A complete copy of the documentation is included with your download, so it's not necessary to have internet access to use it. The documentation opened with the Help menu in Chimera is your local copy. You can even search this local copy with Help... Search Documentation. We have looked at generating a PDF file, but the User's Guide is very nonlinear and the results were unsatisfactory. With the local copy, you can still follow all the links and benefit from the interconnections without having access to the internet. Best, Elaine On Nov 16, 2005, at 10:08 PM, Reiner Villavicencio wrote: > > Dear all, > > Is an offline reference manual (*.pdf) available for Chimera? > I realized that under the documentation section of the website, > that only online references are present. Having an offline user > guide would be more convenient because there is no need to go > online everytime a problem is encountered. > Thank you and good day > > Reiner Villavicencio > BS Biochemistry > Dept. of Physical Sciences and Mathematics > College of Arts and Sciences > University of the Philippines, Manila > > > "Its hard to hold on to something that can never be yours in anyway > you want... something that wasn?t really yours to begin with... you > just have to go on and accept the fact that while good things never > last some don?t even start...." > Send instant messages to your online friends http:// > uk.messenger.yahoo.com > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users ----- 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 svozil at uochb.cas.cz Fri Nov 18 06:58:17 2005 From: svozil at uochb.cas.cz (Daniel Svozil) Date: Fri, 18 Nov 2005 15:58:17 +0100 Subject: [Chimera-users] Move atoms (selections) in Chimera In-Reply-To: <200511141808.jAEI8FuJ2070241@guanine.cgl.ucsf.edu> References: <43749FC7.9020709@uochb.cas.cz> <200511120542.jAC5gk3f1752227@guanine.cgl.ucsf.edu> <4375A3F0.7020509@uochb.cas.cz> <200511141808.jAEI8FuJ2070241@guanine.cgl.ucsf.edu> Message-ID: <437DEC09.7080508@uochb.cas.cz> Hi Tom, > If you think specific new model building capabilities would be helpful > given the above limitations, explain them and we will be happy to consider > them. For the beginning, I think the following "model building" capabilities would make Chimera even more useful (some of them are maybe already implemented, I do not know Chimera so well yet): 1) Move atom, move selection of atoms, delete selection/atom. Add atoms. 2) Change atom to another one. 3) Add/attach functional groups from library 4) I work in the field of nucleic acids, it would be nice one could build the "ideal" structure (B-DNA, A-DNA, Z-DNA) from sequence (if needed, I can provide a references to papers publishing geometry parameters). Possibly change of pseudorotation angle in deoxyribose and ribose. I am sure other Chimera users would take a benefit if them too. Of course you're right more sophisticated capabilities would probably require force field implementation, and I understand this is (unfortunately) not the direction Chimera is heading to. Regards Dan -- Daniel Svozil, PhD Institute of Organic Chemistry and Biochemistry Center for Biomolecules and Complex Molecular Systems http://www.molecular.cz/~svozil Czech Republic phone: +420-220 410 312 From sasmith1313 at yahoo.com Fri Nov 18 10:48:16 2005 From: sasmith1313 at yahoo.com (Stephen A. Smith) Date: Fri, 18 Nov 2005 10:48:16 -0800 (PST) Subject: [Chimera-users] creating cubes and other 3D shapes Message-ID: <20051118184817.94657.qmail@web60213.mail.yahoo.com> Hi I want to create a cube (box; 1?^3, 2?^3, etc.) at specific grid points and color them as needed. Is this possible in Chimera? It is easy to do with spheres by specifying an atom at the desired location and then defining its VDW radius. I would like to create cubes and rectangles of various sizes, related to regions of my protein, to denote specific atomic / residue features. Any help would be greatly appreciated. Thanks Steve __________________________________ Yahoo! Mail - PC Magazine Editors' Choice 2005 http://mail.yahoo.com From meng at cgl.ucsf.edu Fri Nov 18 12:22:18 2005 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 18 Nov 2005 12:22:18 -0800 Subject: [Chimera-users] creating cubes and other 3D shapes In-Reply-To: <20051118184817.94657.qmail@web60213.mail.yahoo.com> References: <20051118184817.94657.qmail@web60213.mail.yahoo.com> Message-ID: Hi Stephen, A recent addition to Chimera (version 1.2184 and later) is that it can read BILD format, a very simple text format for specifying lines, arrows, spheres, boxes, cones, and cylinders. This sounds like what you are looking for. The format description can be viewed at: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html In release 1.2184 and snapshot 1.2186, there is a problem with transformations (translate, rotate, and scale commands in this format), but that is fixed in our working version, and thus in future releases. It sounds like you may not want to use transformations anyway, just use the coordinate system of your protein. I've attached an example file that does not include any transformations. This file can simply be opened in Chimera, for example with File... Open. Best, Elaine On Nov 18, 2005, at 10:48 AM, Stephen A. Smith wrote: > Hi > I want to create a cube (box; 1?^3, 2?^3, etc.) at specific grid > points > and color them as needed. Is this possible in Chimera? It is easy to > do with spheres by specifying an atom at the desired location and then > defining its VDW radius. I would like to create cubes and rectangles > of various sizes, related to regions of my protein, to denote specific > atomic / residue features. Any help would be greatly appreciated. > Thanks > Steve ----- 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 -------------- A non-text attachment was scrubbed... Name: example.bild Type: application/octet-stream Size: 559 bytes Desc: not available URL: -------------- next part -------------- From goddard at cgl.ucsf.edu Fri Nov 18 20:22:47 2005 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Fri, 18 Nov 2005 20:22:47 -0800 (PST) Subject: [Chimera-users] Move atoms (selections) in Chimera In-Reply-To: <437DEC09.7080508@uochb.cas.cz> (message from Daniel Svozil on Fri, 18 Nov 2005 15:58:17 +0100) References: <43749FC7.9020709@uochb.cas.cz> <200511120542.jAC5gk3f1752227@guanine.cgl.ucsf.edu> <4375A3F0.7020509@uochb.cas.cz> <200511141808.jAEI8FuJ2070241@guanine.cgl.ucsf.edu> <437DEC09.7080508@uochb.cas.cz> Message-ID: <200511190422.jAJ4MllJ1902989@guanine.cgl.ucsf.edu> Hi Dan, Those are good specific suggestions. Eric Pettersen is the most likely Chimera developer to work on this. I focus on Chimera tools for large molecular assemblies (viruses) and density maps. Eric's to-do list is very long but many people have expressed interest in model building tools including participants at a 2-day Chimera workshop that ended today. So Eric will be evaluating the priority relative to other Chimera feature enhancements, and your input helps. Thanks, Tom From goddard at cgl.ucsf.edu Fri Nov 18 20:38:58 2005 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Fri, 18 Nov 2005 20:38:58 -0800 (PST) Subject: [Chimera-users] creating cubes and other 3D shapes In-Reply-To: <20051118184817.94657.qmail@web60213.mail.yahoo.com> (sasmith1313@yahoo.com) References: <20051118184817.94657.qmail@web60213.mail.yahoo.com> Message-ID: <200511190438.jAJ4cwTe1903843@guanine.cgl.ucsf.edu> Hi Steve, The Chimera volume path tracer tool can place markers which are spheres and connect them with cylinders. The spheres and cylinders can be made of small radius to make the outline of a cube. Below is an example XML file that makes a cube positioned at the origin with side length 1. You can change the x, y, z values to put it where you want it. When you open it in Chimera it will create a molecule model (it is implemented as atoms and bonds) and you can adjust its color, or move it relative to other models as you like. Tom --- File cube.cmm follows. Use the ".cmm" suffix so it is recognized by Chimera. From cyberworm_upm at yahoo.com Sun Nov 20 05:44:39 2005 From: cyberworm_upm at yahoo.com (Reiner Villavicencio) Date: Sun, 20 Nov 2005 13:44:39 +0000 (GMT) Subject: [Chimera-users] Selecting Protein portions In-Reply-To: Message-ID: <20051120134439.2420.qmail@web31604.mail.mud.yahoo.com> Dear all, I have read a couple of literature which uses the Chimera program. Before performing a docking run, most of them selects only the relevant residues within a certain region (for example in a 20 angstrom core). May I ask how is this done in Chimera? I mean do the "unrelevant" portions get deleted? Thank you and good day - RV "Its hard to hold on to something that can never be yours in anyway you want... something that wasn?t really yours to begin with... you just have to go on and accept the fact that while good things never last some don?t even start...." Send instant messages to your online friends http://uk.messenger.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Sun Nov 20 12:03:03 2005 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sun, 20 Nov 2005 12:03:03 -0800 Subject: [Chimera-users] Selecting Protein portions In-Reply-To: <20051120134439.2420.qmail@web31604.mail.mud.yahoo.com> References: <20051120134439.2420.qmail@web31604.mail.mud.yahoo.com> Message-ID: Dear Reiner, Chimera does not do any automated docking. Instead, it provides a tool (ViewDock) for viewing your results from the separate program DOCK. For information about DOCK, see http://dock.compbio.ucsf.edu/ The DOCK people also have mailing lists for questions and discussion about their program, see http://dock.compbio.ucsf.edu/contact_info/index.htm More generally, different docking programs handle the problem differently, so it will depend on what you decide to use. 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 Nov 20, 2005, at 5:44 AM, Reiner Villavicencio wrote: > Dear all, > ? > ???? I have read a couple of literature which uses the Chimera > program. Before performing a docking run, most of them selects only > the relevant residues within a certain region (for example in a 20 > angstrom core). May I ask how is this done in Chimera? I mean do the > "unrelevant" portions get deleted? > ???? Thank you and good day > ? > ????????????????????????????????????????????????????????????????? - RV > > >> "Its hard to hold on to something that can never be yours in anyway >> you want... something that wasn?t really yours to begin with... you >> just have to go on and accept the fact that while good things never >> last some don?t even start...."Send instant messages to your online >> friends >> http:// >> uk.messenger.yahoo.com_______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 2071 bytes Desc: not available URL: From pett at cgl.ucsf.edu Sun Nov 20 19:48:01 2005 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Sun, 20 Nov 2005 19:48:01 -0800 Subject: [Chimera-users] Move atoms (selections) in Chimera In-Reply-To: <200511190422.jAJ4MllJ1902989@guanine.cgl.ucsf.edu> References: <43749FC7.9020709@uochb.cas.cz> <200511120542.jAC5gk3f1752227@guanine.cgl.ucsf.edu> <4375A3F0.7020509@uochb.cas.cz> <200511141808.jAEI8FuJ2070241@guanine.cgl.ucsf.edu> <437DEC09.7080508@uochb.cas.cz> <200511190422.jAJ4MllJ1902989@guanine.cgl.ucsf.edu> Message-ID: <19934008ff4c372e146349cd4da777f2@cgl.ucsf.edu> Yes, we have gotten a lot of requests for structure-building features, so we will put some effort into that in the near term. Certainly the simple geometry-based features would come first, but even the more sophisticated force-field type features are becoming more feasible. We already include MMTK under the hood in Chimera for its NetCDF trajectory-reading capabilities, and with some effort we could leverage its minimization features (most effort being getting charges onto atoms and getting Chimera's molecule data into and out of MMTK format). One simple thing requested at the workshop was the ability to change a bond's length. That's really easy and I'll be doing that first, so if anyone else would want that then let me know and I'll send you the code when it's ready. --Eric On Nov 18, 2005, at 8:22 PM, Thomas Goddard wrote: > Hi Dan, > > Those are good specific suggestions. Eric Pettersen is the most > likely > Chimera developer to work on this. I focus on Chimera tools for large > molecular assemblies (viruses) and density maps. Eric's to-do list is > very long but many people have expressed interest in model building > tools > including participants at a 2-day Chimera workshop that ended today. > So > Eric will be evaluating the priority relative to other Chimera feature > enhancements, and your input helps. > > Thanks, > > Tom > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From dekonerding at lbl.gov Mon Nov 21 11:28:02 2005 From: dekonerding at lbl.gov (David E. Konerding) Date: Mon, 21 Nov 2005 11:28:02 -0800 Subject: [Chimera-users] Move atoms (selections) in Chimera In-Reply-To: <200511141808.jAEI8FuJ2070241@guanine.cgl.ucsf.edu> References: <43749FC7.9020709@uochb.cas.cz> <200511120542.jAC5gk3f1752227@guanine.cgl.ucsf.edu> <4375A3F0.7020509@uochb.cas.cz> <200511141808.jAEI8FuJ2070241@guanine.cgl.ucsf.edu> Message-ID: <43821FC2.20904@lbl.gov> Thomas Goddard wrote: >Hi Dan, > > The only model building capabilities current in Chimera are commands >addaa and swapaa which add and swap amino acids, and bond rotation >capabilities. We think creating capabilities for building models into >density maps like the program O is too big a project. Building models >without reference to maps may be easier but I suspect molecular >dynamics capabilities or at least energy minimization are needed to >make that useful. Chimera does not do MD calculations or energy >minimization and again that is a big project we have been reluctant to >take on so far. > > No, it would be sufficient to have a "sprout atom by type" which would only involve bond length, bond angle, and torsion terms, all of which are already available. The idealized geometry is already available from the AMBER force field. I've developed a C++ code which implements the AMBER force field (and have been working on some Python wrappings, but it's a very low priority project). It doesn't do minimization or dynamics (I planned to use the Gnu Scientific Library for that but it's also low priority). I'd be happy to make this code available under a reasonable (IE BSD) license so that it could be included in Chimera. It would be acceptably fast for minimizing models built using sprouting. Dave From dekonerding at lbl.gov Mon Nov 21 11:32:18 2005 From: dekonerding at lbl.gov (David E. Konerding) Date: Mon, 21 Nov 2005 11:32:18 -0800 Subject: [Chimera-users] Move atoms (selections) in Chimera In-Reply-To: <437DEC09.7080508@uochb.cas.cz> References: <43749FC7.9020709@uochb.cas.cz> <200511120542.jAC5gk3f1752227@guanine.cgl.ucsf.edu> <4375A3F0.7020509@uochb.cas.cz> <200511141808.jAEI8FuJ2070241@guanine.cgl.ucsf.edu> <437DEC09.7080508@uochb.cas.cz> Message-ID: <438220C2.4070006@lbl.gov> Daniel Svozil wrote: >Hi Tom, > > > >> If you think specific new model building capabilities would be helpful >>given the above limitations, explain them and we will be happy to consider >>them. >> >> > >For the beginning, I think the following "model building" capabilities >would make Chimera even more useful (some of them are maybe already >implemented, I do not know Chimera so well yet): > >1) Move atom, move selection of atoms, delete selection/atom. Add atoms. >2) Change atom to another one. >3) Add/attach functional groups from library >4) I work in the field of nucleic acids, it would be nice one could >build the "ideal" structure (B-DNA, A-DNA, Z-DNA) from sequence (if >needed, I can provide a references to papers publishing geometry >parameters). Possibly change of pseudorotation angle in deoxyribose and >ribose. > For nucleotide polymers, I've wrapped most of X3DNA in Python in my Ensemble.Legacy library. It's highly alpha code, but I've been able to use it to generate X3DNA parameters from PDB files, and adding support for building nucleotide structures with arbitrary X3DNA parameters wouldn't be hard (you give it twist, tilt, roll, etc, and it gives you a PDB structure consistent with those parameters). If I had an infinite number of monkeys, I could probably wrap all that into a Chimera extension that let you build arbitrary structures for DNA/RNA, etc with a nice interface. However, I don't, so all I can do is make the code available on a subversion repository and provide minimal advice on how to build onto it. Dave From cyberworm_upm at yahoo.com Wed Nov 16 21:54:33 2005 From: cyberworm_upm at yahoo.com (Reiner Villavicencio) Date: Thu, 17 Nov 2005 05:54:33 +0000 (GMT) Subject: [Chimera-users] Reference Manual Message-ID: <20051117055433.59304.qmail@web31614.mail.mud.yahoo.com> Dear all, Is an offline reference manual (*.pdf) available for Chimera? It woulb be more convenient, because its hard to go online whenever you have a problem. Thank you and good day Reiner Villavicencio BS Biochemistry Dept. of Physical Science and Mathematics College of Arts and Sciences University of the Philippines, Manila "Its hard to hold on to something that can never be yours in anyway you want... something that wasn?t really yours to begin with... you just have to go on and accept the fact that while good things never last some don?t even start...." Send instant messages to your online friends http://uk.messenger.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From Johan.Borjesson at biokem.lu.se Thu Nov 17 08:05:37 2005 From: Johan.Borjesson at biokem.lu.se (=?windows-1252?Q?Johan_B=F6rjesson?=) Date: Thu, 17 Nov 2005 17:05:37 +0100 Subject: [Chimera-users] Chimera failed abnormally Message-ID: <6a5b866a2d45.6a2d456a5b86@net.lu.se> Hi I have downloaded the chimera-1.2184-win32.exe version of Chimera and installed it on my laptop running on an Celeron M 370 processor. The operation system is Windows XP. The problem is that I get an error message when I try to run the program. Chimera failed abnormally; the exit code was: 1. use the --debug command line option for the full error message. Hope that you can tell what the problem is and what I can do about it. Best regards Johan B?rjesson Dept. of Biochemistry Lund University, Sweden From fgimble at purdue.edu Fri Nov 18 07:23:37 2005 From: fgimble at purdue.edu (Frederick Gimble) Date: Fri, 18 Nov 2005 10:23:37 -0500 Subject: [Chimera-users] Question about connectivity Message-ID: <2DC15DF6-9C32-4752-8404-90CCDAF25E7F@purdue.edu> I have just begun using Chimera on my Mac, and find that it will be able to produce the graphics that I need for publication and display purposes. I recently opened a pdb file of a protein that we study bound to DNA and used the depiction, nucleotides tool to render the DNA backbone as ribbons with the bases shown as slabs. I noticed a discontinuity in one of the DNA strands, which may be caused by the severe distortion of the DNA. I think that this also happened with a previous program that I used called SPOCK that I used to draw the DNA strands as worms. In that case I could repair the break by changing the settings for the connectivity distances. How would I repair the break in Chimera? Thanks for your help. Sincerely, Fred Gimble Frederick S. Gimble, Ph. D. Associate Professor Department of Biochemistry BCHM 315 175 S. University St. Purdue University West Lafayette, IN 47906 Telephone: (765) 494-1653 Fax: (765) 494-7897 Email: fgimble at purdue.edu From pett at cgl.ucsf.edu Tue Nov 22 14:36:17 2005 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 22 Nov 2005 14:36:17 -0800 Subject: [Chimera-users] Chimera failed abnormally In-Reply-To: <6a5b866a2d45.6a2d456a5b86@net.lu.se> References: <6a5b866a2d45.6a2d456a5b86@net.lu.se> Message-ID: Hi Johan, Just FYI, problems reports should be sent to chimera- bugs at cgl.ucsf.edu. I am going to open an entry in our bug database for your problem and will be sending you mail off-list shortly asking for some more information about your system. --Eric Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu On Nov 17, 2005, at 8:05 AM, Johan B?rjesson wrote: > Hi I have downloaded the chimera-1.2184-win32.exe version of > Chimera and installed it on my laptop running on an Celeron M 370 > processor. The operation system is Windows XP. The problem is that > I get an error message when I try to run the program. > > Chimera failed abnormally; the exit code was: 1. > use the --debug command line option for the full error message. > > Hope that you can tell what the problem is and what I can do about it. > > Best regards > > Johan B?rjesson > Dept. of Biochemistry > Lund University, Sweden From gregc at cgl.ucsf.edu Tue Nov 22 14:49:14 2005 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Tue, 22 Nov 2005 14:49:14 -0800 (PST) Subject: [Chimera-users] Question about connectivity In-Reply-To: <2DC15DF6-9C32-4752-8404-90CCDAF25E7F@purdue.edu> References: <2DC15DF6-9C32-4752-8404-90CCDAF25E7F@purdue.edu> Message-ID: Replied to off-list due to lack of data. From meng at cgl.ucsf.edu Tue Nov 22 14:50:32 2005 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 22 Nov 2005 14:50:32 -0800 Subject: [Chimera-users] Question about connectivity In-Reply-To: <2DC15DF6-9C32-4752-8404-90CCDAF25E7F@purdue.edu> References: <2DC15DF6-9C32-4752-8404-90CCDAF25E7F@purdue.edu> Message-ID: <11DD17E6-DB8D-43CB-B365-9C4AC5527376@cgl.ucsf.edu> Hello Dr. Gimble, Is this a publicly available PDB file? We may be better able to answer the question if we can take a look at what causes the break. Without that knowledge, however, the most relevant tool is probably the Ribbon Style Editor. With that tool you can define different "ribbon residue classes" - these are defined by which atom is used to guide the ribbon path, which is used to set the ribbon orientation, and which atoms are considered part of the mainchain or backbone. There is no distance parameter, however. By default, the built-in "nucleic acid" class will be used for your DNA. You could experiment with defining a new class and using that. It is possible to select part of the structure and apply the new class to only that part; however, that might introduce discontinuities where the different classes are used. It is hard to tell without some experimentation. Man page for Ribbon Style Editor http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ ribbonstyle.html (the bottom section deals with residue classes) This approach is via the user interface. Others may have suggestions that involve Python or other code. Elaine On Nov 18, 2005, at 7:23 AM, Frederick Gimble wrote: > I have just begun using Chimera on my Mac, and find that it will be > able to produce the graphics that I need for publication and display > purposes. I recently opened a pdb file of a protein that we study > bound to DNA and used the depiction, nucleotides tool to render the > DNA backbone as ribbons with the bases shown as slabs. I noticed a > discontinuity in one of the DNA strands, which may be caused by the > severe distortion of the DNA. I think that this also happened with a > previous program that I used called SPOCK that I used to draw the DNA > strands as worms. In that case I could repair the break by changing > the settings for the connectivity distances. How would I repair the > break in Chimera? > > Thanks for your help. > > Sincerely, > > Fred Gimble > > > Frederick S. Gimble, Ph. D. > Associate Professor > Department of Biochemistry > BCHM 315 > 175 S. University St. > Purdue University > West Lafayette, IN 47906 > > Telephone: (765) 494-1653 > Fax: (765) 494-7897 > Email: fgimble at purdue.edu > > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users ----- 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 cwmoad at gmail.com Mon Nov 28 06:47:16 2005 From: cwmoad at gmail.com (Charlie Moad) Date: Mon, 28 Nov 2005 09:47:16 -0500 Subject: [Chimera-users] Feature Request: Expose rotation to python Message-ID: <6382066a0511280647ka6dd4c8k4071517fa56f0d99@mail.gmail.com> The repr of an xform shows the opengl rotation matrix. I want to get this efficiently in python, but I don't believe it is exposed. Could a getter please be added returning a 4x4 tuple, so a Numeric array can be trivial/efficiently made from it? If there is a current approach please let me know. Thanks, Charlie From goddard at cgl.ucsf.edu Mon Nov 28 09:56:15 2005 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 28 Nov 2005 09:56:15 -0800 (PST) Subject: [Chimera-users] Feature Request: Expose rotation to python In-Reply-To: <6382066a0511280647ka6dd4c8k4071517fa56f0d99@mail.gmail.com> (message from Charlie Moad on Mon, 28 Nov 2005 09:47:16 -0500) References: <6382066a0511280647ka6dd4c8k4071517fa56f0d99@mail.gmail.com> Message-ID: <200511281756.jASHuFT71681414@guanine.cgl.ucsf.edu> Hi Charlie, I second your request for having a Xform.getMatrix() method that provides 3x4 Numeric array or tuple of tuples. I use this a good bit. My solution is to use the Chimera PDBmatrices.matrices module which deals with 3x4 matrices where the first 3 columns are the rotation and the last column is the translation. It's been in Chimera for the last couple years (with ocassional changes). Look at Python code chimera/share/PDBmatrices/matrices.py to see what is there. Example, >>> xf = chimera.Xform.zRotation(30) >>> from PDBmatrices import matrices >>> m = matrices.xform_matrix(xf) >>> print m ((0.866025, -0.5, 0.0, 0.0), (0.5, 0.866025, 0.0, 0.0), (0.0, 0.0, 1.0, 0.0)) There is a chimera_xform() routine to go from matrix to Xform, and other routines to apply 3x4 matrices to points, or vectors, invert matrices, multiply matrices, .... Tom From cwmoad at gmail.com Mon Nov 28 10:48:57 2005 From: cwmoad at gmail.com (Charlie Moad) Date: Mon, 28 Nov 2005 13:48:57 -0500 Subject: [Chimera-users] Feature Request: Expose rotation to python In-Reply-To: <200511281756.jASHuFT71681414@guanine.cgl.ucsf.edu> References: <6382066a0511280647ka6dd4c8k4071517fa56f0d99@mail.gmail.com> <200511281756.jASHuFT71681414@guanine.cgl.ucsf.edu> Message-ID: <6382066a0511281048r36dba9abxac7daed85cc37528@mail.gmail.com> Then would this be a practical solution: matrices.xform_matrix(chimera.openModels.list()[0].openState.xform) On 11/28/05, Thomas Goddard wrote: > Hi Charlie, > > I second your request for having a Xform.getMatrix() method that > provides 3x4 Numeric array or tuple of tuples. > > I use this a good bit. My solution is to use the Chimera > PDBmatrices.matrices module which deals with 3x4 matrices where the > first 3 columns are the rotation and the last column is the > translation. It's been in Chimera for the last couple years > (with ocassional changes). > > Look at Python code > > chimera/share/PDBmatrices/matrices.py > > to see what is there. > > > Example, > > >>> xf = chimera.Xform.zRotation(30) > >>> from PDBmatrices import matrices > >>> m = matrices.xform_matrix(xf) > >>> print m > ((0.866025, -0.5, 0.0, 0.0), > (0.5, 0.866025, 0.0, 0.0), > (0.0, 0.0, 1.0, 0.0)) > > There is a chimera_xform() routine to go from matrix to Xform, and > other routines to apply 3x4 matrices to points, or vectors, invert matrices, > multiply matrices, .... > > Tom > > > From sabuj.pattanayek at Vanderbilt.Edu Mon Nov 28 11:08:52 2005 From: sabuj.pattanayek at Vanderbilt.Edu (Pattanayek, Sabuj) Date: Mon, 28 Nov 2005 13:08:52 -0600 Subject: [Chimera-users] estimaded standard deviation (sigma levels) for electron densities in volume viewer Message-ID: <1133204932.438b55c4d616e@vuwebmail.vanderbilt.edu> Hi, Is it possible to specify the estimated standard deviation (sigma level) for electron densities in the volume viewer? Currently, I have to eyeball the distribution of the volume data and place the bar accordingly. Thanks, Sabuj Pattanayek From goddard at cgl.ucsf.edu Mon Nov 28 12:33:11 2005 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 28 Nov 2005 12:33:11 -0800 (PST) Subject: [Chimera-users] Feature Request: Expose rotation to python In-Reply-To: <6382066a0511281048r36dba9abxac7daed85cc37528@mail.gmail.com> (message from Charlie Moad on Mon, 28 Nov 2005 13:48:57 -0500) References: <6382066a0511280647ka6dd4c8k4071517fa56f0d99@mail.gmail.com> <200511281756.jASHuFT71681414@guanine.cgl.ucsf.edu> <6382066a0511281048r36dba9abxac7daed85cc37528@mail.gmail.com> Message-ID: <200511282033.jASKXB6a1724252@guanine.cgl.ucsf.edu> Hi Charlie, Yeah, you can apply matrices.xform_matrix() to m.openState.xform to get the 3 by 4 matrix. Tom From goddard at cgl.ucsf.edu Mon Nov 28 13:27:26 2005 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 28 Nov 2005 13:27:26 -0800 (PST) Subject: [Chimera-users] estimaded standard deviation (sigma levels) for electron densities in volume viewer In-Reply-To: <1133204932.438b55c4d616e@vuwebmail.vanderbilt.edu> (sabuj.pattanayek@vanderbilt.edu) References: <1133204932.438b55c4d616e@vuwebmail.vanderbilt.edu> Message-ID: <200511282127.jASLRQ6I1738091@guanine.cgl.ucsf.edu> Hi Sabuj, Chimera currently has no capability to display standard deviation values for volume data. It would be useful if the volume viewer dialog had an option to use sigma units. Could you tell me what crystallographers define "1 sigma" to be for a density map? Is it the root mean square density value over the entire map? For now here is a Chimera tool to report mean, root mean square, and standard deviation values for a volume data set. http://www.cgl.ucsf.edu/home/goddard/temp/volumestats.tar This archive contains a directory VolumeStatistics that you put in your Chimera distribution in chimera/share or on the Mac in Chimera.app/Contents/Resources/share Then when you start Chimera you will have a new menu entry Tools -> Volume Data -> Volume Statistics that reports the values for the current volume viewer data set, printing them in the Chimera reply log (menu entry Favorites / Reply Log). Tom From goddard at cgl.ucsf.edu Mon Nov 28 15:09:14 2005 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 28 Nov 2005 15:09:14 -0800 (PST) Subject: [Chimera-users] estimaded standard deviation (sigma levels) for electron densities in volume viewer In-Reply-To: <1133204932.438b55c4d616e@vuwebmail.vanderbilt.edu> (sabuj.pattanayek@vanderbilt.edu) References: <1133204932.438b55c4d616e@vuwebmail.vanderbilt.edu> Message-ID: <200511282309.jASN9EHT1752937@guanine.cgl.ucsf.edu> Hi Sabuj, When setting volume data threshold levels based on the appearance of the volume viewer histogram it is important to know that the heights of the histogram bars are the logarithm of the number grid points in the density range (bin) represented by that histogram bar. So if one histogram bin contains 10 volume grid points and another contains 1000, then the larger one will be 3 times higher than the smaller (not 100 times higher). So the bars for high density values appear much taller than if they directly represented the number of density values. It is done this way so useful information can be seen in the histogram outside of the noise density range. Tom From gregc at cgl.ucsf.edu Mon Nov 28 17:18:18 2005 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Mon, 28 Nov 2005 17:18:18 -0800 (PST) Subject: [Chimera-users] Feature Request: Expose rotation to python In-Reply-To: <6382066a0511280647ka6dd4c8k4071517fa56f0d99@mail.gmail.com> References: <6382066a0511280647ka6dd4c8k4071517fa56f0d99@mail.gmail.com> Message-ID: On Mon, 28 Nov 2005, Charlie Moad wrote: > The repr of an xform shows the opengl rotation matrix. I want to > get this efficiently in python, but I don't believe it is exposed. > Could a getter please be added returning a 4x4 tuple, so a Numeric > array can be trivial/efficiently made from it? If there is a current > approach please let me know. The new and improved method is to use the getCoordFrame method :-) and the coorresponding Xform.coordFrame constructor. I agree that it would be better for Python to have a method that returned a Numeric array. Example: >>> xf = chimera.Xform.zRotation(30) >>> x, y, z, o = xf.getCoordFrame() >>> print "x: %s, y: %s, z: %s, o: %s" % (x, y, z, o) x: 0.866025 0.5 0, y: -0.5 0.866025 0, z: 0 0 1, o: 0 0 0 Using getCoordFrame would simplify PDBmatrices.matrices.xform_matrix to be: rx, ry, rz, t = xform.getCoordFrame() return ((rx[0], ry[0], rz[0], t[0]), (rx[1], ry[1], rz[1], t[1]), (rx[2], ry[2], rz[2], t[2])) You could do something similar to construct a Numeric array. Xforms have improved in the latest release. Now you can easily make copies of matrices using the constructor: xformprime = chimera.Xform(xform) or: import copy xformprime = copy.copy(xform) Type: help(chimera.Xform) to see all of the methods and static methods. Hope this helps, Greg Couch UCSF Computer Graphics Lab gregc at cgl.ucsf.edu From cwmoad at gmail.com Tue Nov 29 07:01:49 2005 From: cwmoad at gmail.com (Charlie Moad) Date: Tue, 29 Nov 2005 10:01:49 -0500 Subject: [Chimera-users] Feature Request: Expose rotation to python In-Reply-To: References: <6382066a0511280647ka6dd4c8k4071517fa56f0d99@mail.gmail.com> Message-ID: <6382066a0511290701s386cf200yfb6f607363c37c67@mail.gmail.com> Thanks for all this. It is working great! Now comes the inverse question which should hopefully be easy. How do I apply an xform to a structure to update the viewer? Applying rotations to the model.openState.xform seems to have no effect. I would like to be able to reset to the original view by doing something like, model.openState.xform.multiply(model.openState.xform.inverse()). Thanks, Charlie On 11/28/05, Greg Couch wrote: > On Mon, 28 Nov 2005, Charlie Moad wrote: > > > The repr of an xform shows the opengl rotation matrix. I want to > > get this efficiently in python, but I don't believe it is exposed. > > Could a getter please be added returning a 4x4 tuple, so a Numeric > > array can be trivial/efficiently made from it? If there is a current > > approach please let me know. > > The new and improved method is to use the getCoordFrame method :-) and > the coorresponding Xform.coordFrame constructor. I agree that it would be > better for Python to have a method that returned a Numeric array. > > Example: > > >>> xf = chimera.Xform.zRotation(30) > >>> x, y, z, o = xf.getCoordFrame() > >>> print "x: %s, y: %s, z: %s, o: %s" % (x, y, z, o) > x: 0.866025 0.5 0, y: -0.5 0.866025 0, z: 0 0 1, o: 0 0 0 > > Using getCoordFrame would simplify PDBmatrices.matrices.xform_matrix to > be: > > rx, ry, rz, t = xform.getCoordFrame() > return ((rx[0], ry[0], rz[0], t[0]), > (rx[1], ry[1], rz[1], t[1]), > (rx[2], ry[2], rz[2], t[2])) > > You could do something similar to construct a Numeric array. > > Xforms have improved in the latest release. Now you can easily make > copies of matrices using the constructor: > > xformprime = chimera.Xform(xform) > > or: > > import copy > xformprime = copy.copy(xform) > > Type: > > help(chimera.Xform) > > to see all of the methods and static methods. > > Hope this helps, > > Greg Couch > UCSF Computer Graphics Lab > gregc at cgl.ucsf.edu > > From goddard at cgl.ucsf.edu Tue Nov 29 10:11:30 2005 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Tue, 29 Nov 2005 10:11:30 -0800 (PST) Subject: [Chimera-users] Feature Request: Expose rotation to python In-Reply-To: <6382066a0511290701s386cf200yfb6f607363c37c67@mail.gmail.com> (message from Charlie Moad on Tue, 29 Nov 2005 10:01:49 -0500) References: <6382066a0511280647ka6dd4c8k4071517fa56f0d99@mail.gmail.com> <6382066a0511290701s386cf200yfb6f607363c37c67@mail.gmail.com> Message-ID: <200511291811.jATIBUb32006416@guanine.cgl.ucsf.edu> Hi Charlie, To set a model's transformation to the identity: identity = chimera.Xform() model.openState.xform = identity This may throw the model out of view. To apply a rotation about the z-axis in the model's coordinate system: zrot = chimera.Xform.zRotation(30) # rotation by 30 degrees model.openState.localXform(zrot) To apply a rotation about the screen z-axis: zrot = chimera.Xform.zRotation(30) # rotation by 30 degrees model.openState.globalXform(zrot) The localXform() and globalXform() methods just multiply the current transformation by the given one (on the right or left) and set the model's transformation to the result. The model transformation maps a point in the model coordinate system to the screen coordinate system (x horizontal, y vertical, z out of screen) controlling where the model appears on the screen. When you use localXform(xf) the xf gets applied first, and then the current transformation. When you use globalXform(xf) the current transform is applied first and then xf. Some more examples are given in the Programmer's Guide FAQ: http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q4 Getting the transformation math right can be tricky. Tom From pett at cgl.ucsf.edu Tue Nov 29 10:25:31 2005 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 29 Nov 2005 10:25:31 -0800 Subject: [Chimera-users] Feature Request: Expose rotation to python In-Reply-To: <200511291811.jATIBUb32006416@guanine.cgl.ucsf.edu> References: <6382066a0511280647ka6dd4c8k4071517fa56f0d99@mail.gmail.com> <6382066a0511290701s386cf200yfb6f607363c37c67@mail.gmail.com> <200511291811.jATIBUb32006416@guanine.cgl.ucsf.edu> Message-ID: <685B92C7-7BFC-4DB9-A798-2D7CCB93079F@cgl.ucsf.edu> On Nov 29, 2005, at 10:11 AM, Thomas Goddard wrote: > Hi Charlie, > > To set a model's transformation to the identity: > > identity = chimera.Xform() > model.openState.xform = identity The key thing to realize is that in a statement like: x = model.openState.xform x is now a _copy_ of the transformation matrix -- making changes to this copy doesn't affect the actual transformation matrix. To make the changes take effect you need to: model.openState.xform = x --Eric Eric Pettersen UCSF Computer Graphics Lab pett at cgl.ucsf.edu http://www.cgl.ucsf.edu