- Chimera-users - RBVI Mailing Lists

surface display
by Markus Voehler 09 Mar '07

09 Mar '07

I have a PowerBook G4 and am not able to display surfaces on that laptop (it works fine on the SGI). I am running OSX 10.4.8 and chimera 1.2303 (1006/10/23). Does anybody have similar issues or know what to do about it. Other functionalities of chimera work just fine. Markus

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independent movement
by michel dedeo 09 Mar '07

09 Mar '07

I would like to use Chimera to make a movie in which multiple models or chains move in different directions simultaneously. The movie illustrating myosin thick filament analysis (http://www.cgl.ucsf.edu/chimera/animations/movies/myomovie.mov) is a good example. I am not sure if this post (http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-June/000843.html) on interpolated model motion is relevant, or if the 'movemodel' command imagined there actually exists in some patch that I do not have. If that proves too difficult (I have little programming experience) I would like to be able to hold one model or chain stationary while moving another. I can do this by using the model panel to make one model inactive while entering a movement command to move the active models, but I have not found a way to do this through the command line. Is there a command to activate/inactivate models, or another way to move some models/chains and not others? Thank you for your help. Michel Dedeo Francis Lab Department of Chemistry UC Berkeley

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Stereo using X11 versions
by Eduardo Sanz Garcia 08 Mar '07

08 Mar '07

I have had problems using the stereo capabilites of chimera using stereo glasses. I have two computers: * Mac G5 Quadro PPC + Nvidia FX 4000 with the latest drivers + Chimera X11 version 1.2304 * Fedora Enterprise 2 x Intel Xeon + Nvidia FX 3500 with the latest drivers + Chimera Linux 32-bit version 1.2349 The stereo hardware is correctly installed. I have other applications (X11 pymol) that display stereo nicely in both systems. On the mac, I have been able to display things in stereo but it crashes or displays weird stuff on the screen. On linux, I haven't been able to display things in stereo. Any suggestions? Thank you very much.

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savepos/reset problem with sessions and volumes
by Thomas Goddard 08 Mar '07

08 Mar '07

Hi Christopher, The problem is that Chimera does not preserve the model numbers of volume data sets when it restores a session. Restoring a saved position then moves the wrong models because it remembers the position associated with each model number. There are two Chimera bugs here. First the volume data restored from a session file should use the original model numbers. And secondly, even if the model numbers were to change, the savepos information should be updated to use the new model numbers. These problems exist in all versions of Chimera on all platforms. I'll work on fixing them and send you email if I get it working. I think I can fix the code so that your existing session files will restore correctly using the original model numbers. Tom Christopher Akey wrote: > Tom- > > I am using a build of Chimera from 11/08/2006 for windows. This version > is useful for us because the map to map correlation (fit map) and the > transform as both work nicely. > > However, I tried the savepos/reset within a session today. Set up a new > session that I would not be changing or if so, only by adding additional > files to the end of the listed files. The problem is that when I close > the session and recall it, then the reset commands invariably leave one > or two volumes out of alignment. The problem is that every time I open > the same session, the model list changes order, ie it does not seem to > be completely set in stone. If only one of your aligned images changes > order (actually 2 then), then all your previous commands are for naught, > unless you go ahead and realign them in the current session. Problem is > you don't realize they are misaligned until after you use reset and must > immediately undo move, or you are screwed. Also, you might have a > mixture of brix and mrc files, such that you might not always be able to > recover the right alignment for a file. > > Is this a windows version feature? I have noticed my files not behaving > properly before, but now have pinned it down. > > Do the models and their assoc numbers absolutely remain the same for ALL > MODELS in the linux version or in a newer windows version? > > The savepos/reset is great, you can theoretically recall you previous > figure positions and reshoot them after tweaking a color for a model or > whatever. > > cheers C Akey >

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Re: [Chimera-users] Red-cyan stereo
by Greg Couch 08 Mar '07

08 Mar '07

On March 7, Tom Goddard wrote: > I do not think Chimera produces red-green stereo, only red-cyan. Greg > Couch in our lab would know. I've sent your question to the Chimera > users groups so he can give a more definitive answer. Yes, for red-cyan stereo, chimera puts the left eye in the red channel and the right eye in the blue and green channels. This allows for stereo viewing of color images with red-cyan glasses, but there are many problems, such as red objects not having any stereo cues because they are in only one eye. You will get the best stereo effect with gray-scale images (shades of gray) and if you do use color, avoid saturated colors. You can see the red, green, and blue components of a color with chimera's Color Editor tool. The color name field can be set to any of the color names in the Actions Color menu. Other glasses, red-blue and red-green, will work well with gray-scale images, but will have greater problems with ghosting (ie., part of one eye's image appearing in the other's) in color images. Ghosting will always be present to some degree unless the glasses are perfectly matched to the frequencies of light emitted by the display. So the best advice is to color your data various shades of gray. Hope this helps, Greg Couch UCSF Computer Graphics Lab

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Re: [Chimera-users] copy cmd in nogui script
by Eric Pettersen 08 Mar '07

08 Mar '07

On Mar 8, 2007, at 8:21 AM, Randy Heiland wrote: > Eric, > I just got around to trying this and am told: > “You need to accept the POV-Ray end-user license in GUI mode first” > > (using the 1.2352 snapshot). > Suggestions? > -Randy Hi Randy, You are required to accept the POV-Ray license. However, once you have accepted it, Chimera will remember that and won't keep asking you. So if you start up Chimera normally and save any kind of POV-Ray image and accept the license, you will then be able to run your script in nogui mode on the same machine without the licensing request halting the script. If this is still a problem for the way you want to use the script, let me know. We still intend to make it possible to save non-ray traced images in nogui mode, but prioritizing that would depend on whether POV-Ray images are going to work as a stopgap measure or not. --Eric > From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] > Sent: Friday, March 02, 2007 8:35 PM > To: Chimera BB > Cc: Randy Heiland > Subject: Re: [Chimera-users] copy cmd in nogui script > > With POVray in the latest snapshot, you can now use the "raytrace" > keyword of the copy command to get a ray-traced image in nogui mode. > > --Eric > > > On Feb 9, 2007, at 8:03 AM, Elaine Meng wrote: > > > Hi Randy, > It is my understanding that the GUI is used to render the image, thus > it is not possible to save images when in nogui mode. (Others, please > correct me if I've gotten this wrong!) > Best, > Elaine > > On Feb 9, 2007, at 7:46 AM, Randy Heiland wrote: > >> What cmd should I invoke in a --nogui script to copy the rendered >> image >> to a file? >> >>> From the interactive viewer cmd line, I can successfully execute >>> 'copy >> file foo.png png'; however, when trying to execute the following: >> >> % chimera --nogui cmd:dostuff >> where 'dostuff' is: >> open 1yc4 >> color byelement #0 >> copy file foo.png png >> >> I get: >> Fetching 1yc4 from web site www.rcsb.org >> Done fetching 1yc4; verifying... >> Opening 1yc4... >> 1 model opened >> Opened 1yc4 containing 1 model, 1890 atoms, and 427 residues >> Rendering high resolution image...Error while processing cmd:dostuff: >> AttributeError: '_chimera.NoGuiViewer' object has no attribute >> 'pilImages' >> (see reply log for Python traceback info) >> Traceback (most recent call last): >> File "/home/heiland/chimera/build/share/__main__.py", line 59, in ? >> value = chimeraInit.init(sys.argv) >> File "CHIMERA/share/chimeraInit.py", line 298, in init >> prefixableType=1) >> File "CHIMERA/share/chimera/__init__.py", line 1217, in open >> File "CHIMERA/share/Midas/ChimeraExtension.py", line 28, in func >> # lswdir = os.path.split(thisdir)[0] >> File "CHIMERA/share/Midas/midas_text.py", line 91, in >> processCommandFile >> File "CHIMERA/share/Midas/midas_text.py", line 60, in makeCommand >> File "CHIMERA/share/Midas/midas_text.py", line 542, in doCopy >> File "<string>", line 1, in ? >> File "CHIMERA/share/Midas/__init__.py", line 795, in copy >> File "CHIMERA/share/chimera/printer.py", line 705, in saveImage >> AttributeError: '_chimera.NoGuiViewer' object has no attribute >> 'pilImages' >> >> >> thanks, Randy >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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View scale and brix output
by Tom Goddard 08 Mar '07

08 Mar '07

Hi Christopher, If I understand your request you want to be able to easily return to a standard view magnification for making figures. There are 3 parameters that determine the apparent size of models seen in the Chimera window: the distance of the models from the eye position, the angular field of view, and the scale parameter which relates the screen pixels to physical units (Angstroms). With orthographic projection only the scale parameter matters. Chimera can use orthographic projection (activated in Camera tab of Side View dialog) but the default is perspective projection where all 3 parameters matter. Assuming you don't change the distance between the eye (i.e. camera) and the models, and you don't change the field of view then setting the scale alone would be sufficient to return to standard magnification settings. In the Side View dialog (menu entry Favorites / Side View) under the Camera tab there is an entry field for the scale factor. It gives the current absolute scale factor and can be changed to whatever value you like. It starts out as 1.0 in a new Chimera session. But if you open a session file it is set to whatever it was in the original session. If you open a session for a figure, then modify it, changing the scale as you go, then want to return to the original session scale factor you could use the command "reset session-start". This not only resets the scale but also the positions and orientations of all the models. Maybe that is not what you want because the new figure is perhaps showing the models from a different direction (e.g. rotated by 90 degrees). So perhaps you need a command like "resetscale session-start". That resetscale command does not exist but I could probably add it if you think it is what you need. Regarding writing BRIX map files, I agree it would be handy if Chimera could output more map formats. I think BRIX format is well enough documented that it could be done (writing files requires better understanding of the format than reading them). That format only saves unsigned 8-bit data values though. So going from float values in MRC to BRIX will lose information. Maybe Chimera would issue a warning about that. Tom Christopher Akey wrote: > Tom- > > A few more issues that have come up for user friendliness. > > 1. It would be useful to have a box where the user can specify the > absolute scale for the session, the first time it is opened, this > could be set at 1.0 for example after loading a ribosome map and the > atomics and putting them to a good size. > > Then the program should keep track of the changes made during the > session using the scale command (I guess you can't track changes made > with the mouse so one generally would avoid this, or even better one > should be able to turn off the mouse scale feature!). > > This way one could always look at the pull down for the current scale > value when you capture a particular view for a figure. > > One could then return to the original scale of 1.0 at the end of > session or write down the current scale value, which could be kept in > the ssesion. So upon reopening the session at a later date, one can > always get back to the correct scale to recapture a panel for a > figure. This is currently a real problem, as far as I can tell. > > 2. We often want to import a brix file with aligned pdbs, since we > dock and look at them in 'O', which is better in some ways for looking > at these maps, but not so good as Chimera for figure making > obviously....then in Chimera we may continue to trim or segment a map, > and then we want to take it back out, presumably as an MRC file, to be > converted into a brix by a conversion program (for us its SPIDER). > Then one can do another cycle of docking in 'O' using the > refined/cleaned up sub map from Chimera. > > While I can think of one way to do this without losing the relative > origins and thus, the map alignments, it is pretty tedious. If one > could write the zoned or volume erased brix volume back out as a new > brix file, with the correct dimensions and origin, relative to the > brix file brought into Chimera, this would allow you to cycle back and > forth using the best of both programs. > > > cheers C Akey >

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RMSD fit of an object to atom
by Navnit Kumar Mishra 08 Mar '07

08 Mar '07

Dear folks; Is there any simple way in chimera to do rmsd fitting of the object to the atom. I would like to measure the rmsd of an density peak with the atom. Could someone give the detail, how can I do it. And one another thing, how can I get rid of the problem with " At least four atoms should be selected", I am interested to do 'match' for two atoms. Thanks a lot, Navnit

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another snapshot
by Eric Pettersen 07 Mar '07

07 Mar '07

We just put out another snapshot (1.2352). It fixes some problems in the previous snapshot, including the scaling in the side-view window not matching the scaling in the main graphics window, and phylogeny support in Multalign Viewer not working. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Chimera to O and back again
by Tom Goddard 07 Mar '07

07 Mar '07

Hi Christopher, Ok, I see, you convert your MRC map to BRIX for working in O but then bring the PDB model that was adjusted in O back into Chimera and realign it with the original MRC. It sounds like the painful part of this process is that the BRIX map does not align with the original MRC map when viewed in Chimera. That is a problem with the SPIDER conversion from MRC to BRIX losing or interpreting differently the origin information. If the BRIX map actually had the correct origin so it aligned perfectly with the MRC map in Chimera then it would save you a bit of trouble. One solution is of course to have Chimera write out the BRIX file so it gets the positioning correct. I'm not sure when I would find time to write that code. Perhaps another solution is to figure out how the SPIDER conversion messes up the origin. That might allow choosing an MRC origin in Chimera such that the SPIDER BRIX map will align with the MRC map. My guess is that Chimera is using the MRC 2000 xorigin, yorigin, zorigin header fields while SPIDER is using the ncstart, nrstart, nsstart header values which Chimera sets to zero when it writes an MRC 2000 format file. If this theory is correct, the BRIX map might align with the MRC map if you change the MRC origin to (0,0,0) using the Chimera volume dialog Features / Origin and Scale panel. You could save this MRC map and work with it to avoid the BRIX/MRC misalignment problem. Tom Christopher Akey wrote: > Tom- > > As to our problem with getting files back into O without degradation of > information. Here is what we found that works. > > You have an original image in mrc format(1.mrc)=> convert to brix (we > use SPIDER) > > Then in O one can dock pdbs & do modeling etc. So now one has a brix > file and pdb modeled in approximately the right area. However, you want > to see if you can improve this difficult modeling. > > So you take the brix file and the pdb into Chimera. > > You write out the brix file as a new mrc file, ie 2.mrc, without any > transformations. > > You then read in the original (1.mrc) and move 2.mrc relative to 1.mrc > using local movements with mouse and then the the map vs map fitting. > > You then transform the fitted pdb file into the original 1.mrc using > "transform as" following the changes to the 2.mrc file. > > You can now do a zone or zone followed by a step of volume erase around > the pdb file using the 1.mrc file, they are in the same relative > orientation now. > > Finally, you write out a zoned/ve map, 1_zone_pdb.mrc, using the 1.mrc > map, so no loss of resolution here. > > Then you can convert 1_zone_pdb.mrc to a brix file and look at in O with > the pdb and it will now be docked in the correct way, ie one won't have > lost the correct origin/alignment of the pdb to the zoned map. > > ------ > > At this point in O, one can adjust the modeled pdb in the zoned density, > then bring the brix file and new modeled pdb files back into Chimera to > make a figure with a better fit of the modeled pdb file. > > This is obviously only needed when you have two structures interacting > and need to segment them vary carefully, to try and improve the local > fit of a loop or whatever. > > Did this make sense? > > It is a way to work in Chimera then transfer back > into O to visualize and work there and even to cycle between them. > > > cheers C Akey

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Re: [Chimera-users] View scale and brix output
by Eric Pettersen 07 Mar '07

07 Mar '07

Just to clarify some of the things that Elaine was unsure of: if a model gets closed that was involved in saved positions then it will simply be ignored when the position is restored. If some new model gets the same ID and sub-ID # as the closed model then that model will be positioned as if it were the closed model (except for per-model clip planes). --Eric On Mar 7, 2007, at 12:24 PM, Elaine Meng wrote: > Hi Christopher, > As long as you save the session after using savepos the positions > should be there. However, as you suspected the model numbers are > important - the individual transformations for the models are restored > based on those model numbers. I think it will restore the positions > of whichever models are there, despite complaining that some are > missing (it's been a while, I'd have to try it to make sure). If you > closed model 0 and opened a new model 0 it might try to put it in the > position the old model 0 was in. Also not sure about that one. When > I use saved positions for my own work, I don't delete/add models > between saving and restoring the positions. > > I can't really envision how positions could be saved without using the > model numbers. The only other thing I can think of is data file name, > but frequently one will have the same data file opened as more than > one model at a time, with different transformations. > ----- > Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu > UCSF Computer Graphics Lab and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > > > On Mar 7, 2007, at 12:15 PM, Christopher Akey wrote: > > Elaine - > > yeah,that does seem to work nicely within a session, lets see what > happens when I close and reopen it. However, is the savepos option > sensitive to things like deleting one object from the session before > closing, then opening and adding a new object (now the numbering of > the objects may vary and this seems to screw up matrices that are > saved cause they depend on the numbers). I would hope that savepos > doesn't depend on numbered objects? > > cwa > > > Meng wrote: >> Hi Christopher, >> Tom did mention "reset," but I thought I'd expand on that topic a >> bit. You can actually save multiple named positions, which will >> then be included in a single saved session. When I make a set of >> figures that differ in view and scale but with basically the same >> display/coloring setup, I use the "savepos" command to save the >> position for each figure, and then save the session. It doesn't >> matter what position everything is in when you save the session, >> because you will still be able to get back to any of those saved >> positions with "reset." >> The saved positions include scale. If you really only want to >> restore scale, currently you could note the value shown in the >> Camera tool (as mentioned by Tom), and later type that into the >> Camera tool to restore it. >> more about savepos and reset: >> http://www.cgl.ucsf.edu/chimera/1.2304/docs/UsersGuide/midas/ >> savepos.html >> http://www.cgl.ucsf.edu/chimera/1.2304/docs/UsersGuide/midas/ >> reset.html >> Elaine >> ----- >> Elaine C. Meng, Ph.D. meng(a)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 >> Christopher Akey wrote: >>> Tom- >>> >>> A few more issues that have come up for user friendliness. >>> >>> 1. It would be useful to have a box where the user can specify the >>> absolute scale for the session, the first time it is opened, this >>> could be set at 1.0 for example after loading a ribosome map and the >>> atomics and putting them to a good size. >>> >>> Then the program should keep track of the changes made during the >>> session using the scale command (I guess you can't track changes made >>> with the mouse so one generally would avoid this, or even better one >>> should be able to turn off the mouse scale feature!). >>> >>> This way one could always look at the pull down for the current scale >>> value when you capture a particular view for a figure. >>> >>> One could then return to the original scale of 1.0 at the end of >>> session or write down the current scale value, which could be kept in >>> the ssesion. So upon reopening the session at a later date, one can >>> always get back to the correct scale to recapture a panel for a >>> figure. This is currently a real problem, as far as I can tell. >>> >>> 2. We often want to import a brix file with aligned pdbs, since we >>> dock and look at them in 'O', which is better in some ways for >>> looking >>> at these maps, but not so good as Chimera for figure making >>> obviously....then in Chimera we may continue to trim or segment a >>> map, >>> and then we want to take it back out, presumably as an MRC file, to >>> be >>> converted into a brix by a conversion program (for us its SPIDER). >>> Then one can do another cycle of docking in 'O' using the >>> refined/cleaned up sub map from Chimera. >>> >>> While I can think of one way to do this without losing the relative >>> origins and thus, the map alignments, it is pretty tedious. If one >>> could write the zoned or volume erased brix volume back out as a new >>> brix file, with the correct dimensions and origin, relative to the >>> brix file brought into Chimera, this would allow you to cycle back >>> and >>> forth using the best of both programs. >>> >>> >>> cheers C Akey >>> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > -- > cheers C Akey > > ------------------------------------------------------------------ > STRUCTURAL ELECTRON MICROSCOPY & CRYSTALLOGRAPHY GROUP > ------------------------------------------------------------------ > Christopher W. Akey, Professor > Physiology & Biophysics > Boston Univ. School of Medicine > 700 Albany St. > Boston, Mass. 02118-2526 > > off: 617 638 4051 lab: 617 638 4088 > fax: 617 638 4041 > cakey(a)bu.edu > http://biophysics.bumc.bu.edu/faculty/akey/index.html > ------------------------------------------------------------------ >

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Re: [Chimera-users] Red-cyan stereo
by Tom Goddard 07 Mar '07

07 Mar '07

Hi Jean-Francois, I do not think Chimera produces red-green stereo, only red-cyan. Greg Couch in our lab would know. I've sent your question to the Chimera users groups so he can give a more definitive answer. Tom jean-francois menetret wrote: > > Hi Thomas, > > I have tried the red-cyan stereo option of Chimera with red-green glasses > (I couldn't find red-cyan glasses). One gets the stereo effect but > there is a > shadow from the cyan image that the red filter doesn't stop completely. > Is it possible to change the cyan to green ? > > Jean-Francois

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Re: [Chimera-users] md movie amber issue
by Elaine Meng 05 Mar '07

05 Mar '07

Hi Tom, Recording a movie uses the screen resolution. In contrast, image saving uses "supersampling": a bigger image is saved initially and then sampled back down to the requested size, and that gets rid of jagged edges. Currently, movie recording cannot save the image frames with supersampling, but we plan to add that in the future. If you are recording a trajectory in MD Movie, use the "recording" feature in MD Movie. There is no advantage to using Movie Recorder (under Utilities) or the command "movie" because they use exactly the same underlying mechanism to save frames and assemble them into a movie, and are subject to identical resolution issues. All the same flags that can be used with the "movie" command can be entered in the recording dialog called from MD Movie. The difference is (as you noted) the Movie Recorder is not synchronized well with trajectory playback. See http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/ movie.html#recording and the "encode" options in: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html In neither case would you have to assemble the individual frames yourself (unless you wanted to for some reason) - on Movie Recorder, clicking the "Make movie" button encodes the saved frames into a movie file. Settings that affect the final movie appearance are Chimera window size (adjust this before saving image frames) and the encoding options mentioned above. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Mar 4, 2007, at 4:20 AM, Thomas Caulfield wrote: > Hi again Elaine, > > (I) > So I have a MD movie trajectory working (NAMD style, not AMBER), but > my question now goes to rendering a movie. I noticed that under the > MD trajectory window (which plays the frames), that the net resolution > afterward is pretty low (whether I choose MPEG-1/2/4 or > quicktime.mov). But when I do renderings of images the quality is > amazing. > (II) > I also went to Utilities under tools and movie recording, where it > seems some preferences are listed (like resolution etc.), but when I > hit record under that option the trajectory doesn't play, so It starts > taking high-resolution screenshots into a folder with the name > qui*blah-1,2,3,4,... and so on. If this were to play the trajectory > that would be fine, because I could use graphic converter to make a > movie of that. When I tried to do it manually and the make the movie, > it was better resolution, but jerky skipping tons of frames at a time. > > Is there an easier way to do it in (I) and set some preference to the > desired resolution (it looked all bitmappy and fuzzy by the end), > rather than trying to take 1000+screeshots from method (II)? > > Thanks again. > > -Tom > > PS I will try getting this to that other email you gave before thanks. > > On Mar 3, 2007, at 1:26 PM, Elaine Meng wrote: > >> Hi Tom, >> For some reason the mail came to me and not Eric! It may be because >> his address was typed with a one instead of an ell (should be cgl not >> cg1) - but no harm, I've forwarded it to him. He will have to address >> the first question, but I'll tackle the other. >> >> In single-PDB input, the frames should be indicated with MODEL and >> ENDMDL records. For an example, see any NMR structure in the PDB >> that has more than one set of coordinates (1plx is a nice small >> example). >> Best, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu >> UCSF Computer Graphics Lab and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> http://www.cgl.ucsf.edu/home/meng/index.html >> >> >> >> >> On Mar 3, 2007, at 1:06 AM, Thomas Caulfield wrote: >> >>> Hi Eric, >>> >>> I wanted to know about using Amber prmtop with Chimera movie md >>> traj. I used it and my initlal frame looks fine, but then it starts >>> bouncing out of camera and back, and my final molecule looks a mess. >>> But in VMD it looks just fine. I'd rather use Chimera for >>> rendering since everything looks so nice in it, however I don't know >>> why it is doing this. >>> >>> I also tried using a series of PDBs instead (to circumvent this >>> issue), but I cannot load it as a single PDB (with multiple frames >>> in it), since the program complains there is only 1 structure in the >>> file. I removed all END and added numbers between the files to try >>> and get it to realize there were frames. >>> >>> What can I do to fix this? >>> >>> Thanks a bunch! >>> >>> -Tom >>> >>> _____________________________ >>> Tom Caulfield, Ph.D. Candidate >>> School of Chemistry & Biochemistry >>> Cherry Emerson Bldg., RM 329 >>> Georgia Institute >>> of Technology >>> Atlanta, GA 30332-0400 >>> Harvey Laboratory: >>> http://rumour.biology.gatech.edu >>> _____________________________ >>> >>> >>> >> > >

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copy cmd in nogui script
by Randy Heiland 02 Mar '07

02 Mar '07

What cmd should I invoke in a --nogui script to copy the rendered image to a file? >From the interactive viewer cmd line, I can successfully execute 'copy file foo.png png'; however, when trying to execute the following: % chimera --nogui cmd:dostuff where 'dostuff' is: open 1yc4 color byelement #0 copy file foo.png png I get: Fetching 1yc4 from web site www.rcsb.org Done fetching 1yc4; verifying... Opening 1yc4... 1 model opened Opened 1yc4 containing 1 model, 1890 atoms, and 427 residues Rendering high resolution image...Error while processing cmd:dostuff: AttributeError: '_chimera.NoGuiViewer' object has no attribute 'pilImages' (see reply log for Python traceback info) Traceback (most recent call last): File "/home/heiland/chimera/build/share/__main__.py", line 59, in ? value = chimeraInit.init(sys.argv) File "CHIMERA/share/chimeraInit.py", line 298, in init prefixableType=1) File "CHIMERA/share/chimera/__init__.py", line 1217, in open File "CHIMERA/share/Midas/ChimeraExtension.py", line 28, in func # lswdir = os.path.split(thisdir)[0] File "CHIMERA/share/Midas/midas_text.py", line 91, in processCommandFile File "CHIMERA/share/Midas/midas_text.py", line 60, in makeCommand File "CHIMERA/share/Midas/midas_text.py", line 542, in doCopy File "<string>", line 1, in ? File "CHIMERA/share/Midas/__init__.py", line 795, in copy File "CHIMERA/share/chimera/printer.py", line 705, in saveImage AttributeError: '_chimera.NoGuiViewer' object has no attribute 'pilImages' thanks, Randy

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snapshot release source
by Randy Heiland 02 Mar '07

02 Mar '07

Would it be possible for the dev team to post the source headers for the 1.234*/numpy snapshot release? -Randy

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Virus map density versus radius
by Tom Goddard 02 Mar '07

02 Mar '07

Hi Padma, I added a Chimera keyboard shortcut "rd" that prints out average map density versus radius. https://www.cgl.ucsf.edu/cgi-bin/chimera-get.py?file=experimental/radialden… This zip file contains a directory RadialDensity that you put in chimera/share. You enable keyboard shortcuts with Tools / General Controls / Accelerators On, open your VIPER map and type shortcut "rd". A table of radius and average density values is displayed in the Chimera reply log. You can copy and paste it to a plotting program. I've attached an example image for em_1sva. I used the following plotting program on the Mac. http://www.apple.com/downloads/macosx/math_science/plot.html The calculation is very slow because it is done in Python. For em_1sva (size 72^3) it took 12 seconds on my intel Mac and for em_1011 (size 256^3) it took 10 minutes. It could be 100 to 1000 times faster in C++ but that would require more code. I tested with Chimera 1.2343. I will be at the Biophysical Society meeting Sunday through Tuesday and probably not answering email. Tom Padmaja Natarajan wrote: > Tom, > > I was also wondering if it is possible to get "max. radius" value for > every entry by > radially averaging the density values for radii going in steps of the > pixel size of that map. > Then we do not have to give the radius value in the input text file > and also will be able to produce a text > file with "radius vs. average density" for each entry. Just a thought. > > Thanks > Padma >

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Fitting and measuring lengths in volume data
by Tom Goddard 02 Mar '07

02 Mar '07

Hi Mazdak, To fit a PDB model in a map in Chimera you can hand place the model in roughly the right location and then do a computational optimization that maximizes the density at the atom positions. Here are instructions: http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#fitmod… Your map grid plane spacing has to be set correctly in Angstroms since the PDB model coordinates are in Angstroms. Adjust the map grid plane spacing using the volume dialog menu entry Features / Origin and Scale and change the Voxel Size entry fields and press the Enter key to use those new values. Voxel size is the same as grid plane spacing. You can measure the length between two markers. Just select the link (ctrl click on it with the left mouse button) and use keyboard shortcut "pl". You first have to turn on keyboard shortcuts using menu entry Tools / General Controls / Accelerators On. Here are more details http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#pathle… For more info on volume data capabilities look at the Guide to Volume Data Display http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html I will look at map merging today if I have time. So far I have been busy all week. Tom Mazdak Radjainia wrote: > Hi Tom, > > There are actually two more tasks where I was hoping that chimera could help > me. > > 1. I would like to fit high resolution data from a coordinate file in a > low-electron density map. Can chimera perform such a docking/fitting? I > tried to do it manually but I couldn't resize the opened pdb file towards my > .mrc electron density map. > > 2. Is it possible to measure the length of a link between two markers? I > tried to use the experimental "distance to surface" feature. But it never > measures the distance between two markers which I hoped it could do. > > I really appreciate that you are already helping me out with map-merging > feature which I hope doesn't cause too much trouble. It's just great to know > if I could do the entire molecular visualization and structure analysis in > chimera? > > Cheers > Mazdak >

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Re: [Chimera-users] yet another chimera question...
by Eric Pettersen 01 Mar '07

01 Mar '07

> On Jan 19, 2007, at 11:13 AM, Elaine Meng wrote: > > > One other thing you might not know is that you can save multiple > > positions in a single session (i.e. you don't have to save a session > > for each position). Positions are named/saved with the command > > "savepos" and reapplied with "reset": > > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/savepos.html > > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html > > > > These positions definitely include the global clipping plane > > positions. > > I'm not sure about the per-model clipping plane positions. > > They unfortunately do not contain the per-model clip planes yet. > > --Eric I have just added the saving of per-model clipping settings in positions, so it will be in the next snapshot release. A consequence of this improvement is that you will be able to use the 'reset' command to smoothly interpolate per-model clipping in scripts. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Re: [Chimera-users] 2d labels in chimera
by Elaine Meng 01 Mar '07

01 Mar '07

Hi Eman, We were able to restore your session and save images that included the labels (nice figure, by the way!). I will send you the resulting images in a separate message. It is now sounding like an issue with your graphics hardware and/or drivers. We would like to get information on your graphics setup - the easiest way is to choose Help... Report a Bug from the Chimera menu, which will fill in that information automatically, and send us a bug report. Since we've been trading mails, you don't need to put a lot of additional information in there, maybe just your e-mail address and something like "2d labels not included in saved image". If it is a graphics driver issue, there is not much we can do, but you may be able to improve performance by updating it. Also, we could add the information to our list of known graphics driver bugs. Thanks and sorry for the difficulties, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Mar 1, 2007, at 5:50 AM, Eman Ghanem wrote: > Hi Elaine: > I e-mailed you last night and mentioned that the chimera 2d labels > are fine now. After that, I started working on a different file and > the I had the same problem (2dlabels not showing in the image > file). I am not sure where the problem is. I hope this is OK, but > I am attaching the session file including the labels Would you > please try to save is and see you have the same problem? Also, you > asked if I tried different image formats; I tried but the file type > does not make a different. Thank you. > Regards, > > Eman

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2d labels in chimera
by Eman Ghanem 28 Feb '07

28 Feb '07

Hi: I am not able to save an image that contains 2d labels as a Tiff file. Every time I save it, the labels don't show up on the image. I read on your web site that this only happens if I am trying to save an image that is smaller than the original pixels of the chimera window. However, I tried saving it without changing any specifications. Any idea what I can do?? thanks, EG --------------------------------- Don't get soaked. Take a quick peak at the forecast with theYahoo! Search weather shortcut.

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64-bit Linux chimera snapshot available
by Greg Couch 27 Feb '07

27 Feb '07

If you are running a 64-bit version of Linux with an AMD64, Opteron, or Intel Xeon processors, then please try out our new snapshot at <http://www.cgl.ucsf.edu/chimera/download.html>. This platform is now supported and will have future snapshot and production releases. Greg Couch UCSF Computer Graphics Lab

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Re: [Chimera-users] Saving model positions
by Tom Goddard 27 Feb '07

27 Feb '07

Hi Christopher, If you have 10 models open in a Chimera session and you close model number 7, the session should still save correctly. If it doesn't please report it as a bug. Unfortunately restoring the session file uses different model numbers for the density maps (the lowest available numbers). That is a bug that I need to fix. It should use all of the original model numbers even if there are gaps. Even though the model numbers will change, the orientations of all the models 1-6 and 8-10 will all be correct in the restored session. I sent your earlier email to our Chimera users mailing list. That is why your reply to me went to that mailing list. I like to post the questions to the mailing list so others can benefit from the answer and I remove any confidential information (email, phone, signature line, research details). Let me know if you want to keep your questions off of the Chimera mailing list. Here's the message where I posted your original question and my reply. http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-February/001366.html Tom Christopher Akey wrote: > > Thomas - > > This went via reply to some kinda list, sorry. > > I will try some of these approaches. However, there is a question. If > you have 10 objects in a session, and decide to delete number 7, then > sometimes you cannot get the session to save properly with a missing > number. > > In theory, if one could get the session to save, then a matrix for the > first 6 objects would still work? > > > cheers C Akey

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New chimera development snapshot available
by Greg Couch 26 Feb '07

26 Feb '07

See <http://www.cgl.ucsf.edu/chimera/docs/relnotes/snapshot.html> for details (this will be accurate for the next few days, after that read the release notes that are bundled into the chimera snapshot). The snapshot uses NumPy instead of Numeric python, so some third-party extensions may break (eg., parts of EMAN). Other highlights include intial support for PDB 3.0 (remediated PDB) format and built-in POV-Ray raytraced image support. Enjoy, Greg Couch UCSF Computer Graphics Lab

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Saving model positions
by Thomas Goddard 26 Feb '07

26 Feb '07

Hi Christopher, The problem you have with the Chimera matrixget and matrixset commands is that the matrix file lists the model number (0.0, 1.0, 2.0, ...) with each matrix. For example, Model 0.0 -0.0635922 -0.740419 0.66913 247.807 -0.979146 -0.0833402 -0.185275 540.192 0.192946 -0.666958 -0.719679 472.752 Model 1.0 0.233245 -0.923975 -0.303095 418.621 0.970522 0.201738 0.131868 -125.304 -0.0606967 -0.324918 0.943792 100.98 When you open maps and PDB files in a different order they get different numbers. Chimera assigns the lowest available number (starting at 0) each time you open a data set. Then when you use matrixset <filename> to get your standard orientation it applies the matrices to the wrong models because of the different numbering. The easiest remedy for this is to open your data sets in a fixed order (first large ribosomal map (#0), then small ribosomal map (#1), ...). This can be inconvenient. If you save a single positioning matrix in a file there is no current command to say to apply that matrix to a model that you specify as a command argument (e.g. no command like "matrixset <matrix-file> <model-number>" exists). There are some other approaches to the problem of getting standard orientations. One method is to save your ribosome large and small subunit map positions in a Chimera session. Then if you want to use different maps, open the reference session, then open the new maps and use the "matrixcopy" command http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matrixcopy.html to position the new maps to match the reference map positions. Instead of using matrixcopy you could use the equivalent Model Panel dialog "Transform As" button to apply the positioning matrix of one map to a second map. Another command that may be helpful is "savepos <name>". http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/savepos.html It remembers the positions of all currently opened data sets and gives a name to that set of positions. You can later restore those positions with the command "reset <name>". These named positions are saved in Chimera session files. The trouble is that there is not an immediate way to apply those positioning matrices to different maps or PDB models. But that could be achieved with the matrixcopy command or Model Panel / Transform As button. If this set of capabilities does not let you easily do what you want could you describe an exact scenario (how many maps, how many models, how are they related) and if possible propose a new command that would help you. I think it would be great if density map file formats supported saving multiple named positioning matrices in their header. For example, you might want to save how a piece of a map is positioned in the full source map, and also how a piece of a map fits into different map (e.g. at various locations in a tomogram), and your case of just a standard orientation ("front view", "top view"). I do not believe any of the commonly used density map formats allow this although it may be possible to put that info into header comment fields in some map files. Tom Christopher Akey wrote: > Tom - > > ... > > Chimera is very good, but there are still problems. A new workstation > will help and will be here in a few weeks. > > However, one thing is really annoying. It is important to set a > particular view for your structure, for example a side-by-side frontal > view of the ribosome with regards to the small and large subunits. > > Once you have this in one session it would be useful to be able to > recreate this easily in other sessions. (For logistical reasons, it is > ofter easier to keep a session for each Figure so that they don't get to > crowded.) > > Right now, if you save a matrix (matrixget) and then make a change in > the session, ie delete or add a file, you get unpredictable results, but > usually, the matrix no longer works or it only works for one volume in > the session. This is not good when you have separate vols for the small > and large subunits in proper registration, you get a matrix for the > front view, and then at a later time, only one subunit will be realigned > properly! > > It would be great if you could set a matrix for a particular map as a > benchmark, then when you read that map into any other session, you could > recreate this orientation using the matrix. I don't understand why this > won't work. > > The feature of being able to bring in other maps and align them in > CHimera is great and works very well (its in our older test version that > we are using, and its very useful as we often have 3 or more structures > of the same basic object with minor diffs). > > I hope this makes sense. > > cheers C Akey >

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many days after...another question Re: Select atom by serial number.
by Jean Didier Pie Marechal 26 Feb '07

26 Feb '07

Hi everybody, I'd like to select a series of atoms by their serial number (again!!!) (e.g. from atom number 1 to atom number 10). the sel @/serialNumber=1-10 doesn't seem to be the right syntax. Is it possible to do this kind of selection? If yes, what is the right syntax please. Cheers, JD Dr. Jean-Didier Maréchal Professor Lector Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdonyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: Elaine Meng <meng(a)cgl.ucsf.edu> Data: Dijous, Gener 11, 2007 8:59 pm Assumpte: Re: [Chimera-users] Select atom by serial number. > > Hi JD, > We also tested Chimera 1.2309 on Windows, and these specifications > > work correctly. Example: > Command: sel @/serialNumber=232 > will select NZ of Lys 27 in chain A of the PDB entry 1zik. The > only > other thing I can think of (besides what was in the previous > message) > is to check if your PDB file is correctly formatted. The > ATOM/HETATM > serial number is supposed to be in columns 7-11 and right-justified. > Best, > Elaine > > On Jan 11, 2007, at 11:39 AM, Elaine Meng wrote: > > > Hi JD, > > You are using the correct specifications - both of your examples > > > should work. I tested both approaches in Chimera 1.2304 on Mac > OSX > > and they worked correctly. We'll have to look into your > specific > > version/platform and get back to you. If you want, you could > send > > me the PDB file you are using so I could test if there is some > > issue specific to that structure. To be clear: the serial > number > > is the number shown in the column after ATOM (or HETATM) in the > PDB > > file, regardless of what order the atoms are really in. That > is, > > if the first ATOM has 2 in that column, its serial number is 2 > and > > not 1. > > Best, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu > > UCSF Computer Graphics Lab and Babbitt Lab > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > http://www.cgl.ucsf.edu/home/meng/index.html > > > > > > > > > > On Jan 11, 2007, at 10:47 AM, Jean-Didier Maréchal wrote: > > > >> Hi Everyone, > >> > >> > >> > >> > >> > >> I am desperately trying to select an atom of my pdb by its > serial > >> number. > >> > >> Looking at the archives, it seems that I should put something > like > >> @/serialNumber=525 > >> > >> I tried “sel #0@/serialNumber=525” in the commandl ine and “@/ > >> serialNumber=525” in the Atom Specifier. None of these > selections > >> worked. Can someone tell me the right way to do this, please ? > >> > >> > >> > >> Cheers > >> > >> JD > >> > >> > >> > >> Current running chimera: version 1 build 2309 > >> > >> OS: windows > >> > >> > >> > >> _______________________________________________ > >> Chimera-users mailing list > >> Chimera-users(a)cgl.ucsf.edu > >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > >

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