- Chimera-users - RBVI Mailing Lists

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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Combining 2 electron density maps in 1
by Mazdak Radjainia 23 Feb '07

23 Feb '07

Hi, I would like to open two electron density maps in chimera and save/merge them together in one map. Both maps are activated in the "model panel" but I cannot select/save both at a time using the volume viewer. I appreciate your help! Kind regards Mazdak

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Chimera on 64-bit Windows
by Tom Goddard 21 Feb '07

21 Feb '07

Hi Christopher, I believe the 32-bit Windows Chimera distribution will run on 64-bit versions of Windows, such as Windows XP Pro x64 Edition. But I do not have a machine to try it on. It will certainly run on 32-bit Windows running on a 64-bit processor -- I've tried that with an AMD64 processor. Tom Christopher Akey wrote: > Steve and Tom- > > Will EMAN and Chimera run ok on a 64 bit machine running windows XP, > initially we plan to use it this way, then change over to Linux when > we have time. Or do we just install Linux right away? > > cheers C Akey

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Memory requirements for Chimera
by Tom Goddard 21 Feb '07

21 Feb '07

Hi Christopher, I think it starts making sense to use a 64-bit machine if you are loading data that requires >= 1 Gbyte. In general, 32-bit linux binaries will run on a 64-bit machine. Currently we only provide a 32-bit linux Chimera distribution though we plan on adding 64-bit Linux as a standard Chimera platform in the next 6 months. The 32-bit Chimera runs fine on 64-bit linux. The advantage of a 64-bit version is that it uses memory pointers that are 64 bits so they can address more than 4 Gbytes. On a 32-bit system the operating system and the many libraries that Chimera uses (~50) may occupy a significant portion of the 4 Gbyte address space. Even if you have less than 4 Gbytes of physical memory the operating system can and does use the full 32-bit 4 Gbyte address space and swap data to disk when there is not enough physical memory. But if a program asks for a 512 Mbyte block of memory and there is no available segment of that size in the address space then it will fail. Graphics drivers use the computer's main memory for data that will not fit on the card. Either 256 or 512 Mbytes on the graphics card should give good performance even for large systems. Unless you are using the volume "solid" rendering mode the rendering speed will slow to much less than 1 frame per second before you use up 256 Mbytes. For reference, the machines I currently use for developing Chimera and looking at large volume data sets are: 1) Mac dual G5 desktop with 1.5 Gbyte memory and 128 Mb ATI Radeon 9800 Pro graphics, and 2) MacBook Pro, Intel Core 2 duo, 2 Gbyte memory, 256 Mb ATI X1600 graphics. Thanks for the apoptosome papers -- interesting work. Tom Christopher Akey wrote: > Tom- > ok, I will keep notes on what is not working and send them to you, as > we go through making figures this week. > > Will chimera run fine on a 64 bit Linux box? The other option is 32 > bits, but if I buy a high end workstation it should probably be 64 bit > yes? > > Also, about making Chimera able to handle big sessions: is the rate > limiting factor the RAM or the memory on the Graphics Card. We have a > 512 Mb cache on our current graphics card and still have problems, so > I presume we are RAM limited. > > When buying a new machine, should I invest in a 512 Mb Nvidia card or > is 256 fine, as long as there is enough RAM? > > By the way, I am attaching two pdfs of papers published using Chimera > graphics. > > thanks. > > CWA > > > Tom Goddard wrote: >> Hi Christopher, >> >> I'm not sure what causes crashes in Chimera when you are working >> close to the available memory limit. If a memory allocation fails in >> C++ it should produce an error message in Chimera indicating that >> memory could not be allocated because we catch those exceptions. >> Memory allocations in C (not C++) libraries that Chimera uses are >> likely to cause a crash though. >> >> It would help us to know what Chimera is doing when the crashes >> occur. We may be able to put some safety checks in our C++ where C >> library allocations are known to fail. Do I understand correctly >> that crashes happen while you are saving an image (individual tiles >> being displayed on screen)? Chimera by default makes an image 3 >> times larger then requested to make a smoother image. That can take >> a good bit of memory. Are there other actions that cause crashes? >> >> Tom > >

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An NMR Average Structure
by S W Simon Sham 21 Feb '07

21 Feb '07

Hi, I need to calculate an average structure from an emsembled structures in Chimera. Can we do it it Chimera? If yes, how? Thanks for any helps. Simon ------------------------------------------------------------------------ ----- Simon Sham, Ph.D. NMR Core Facility Comprehensive Cancer Center Univerisity of Alabama 933 South 19th Street CH19 B31 Birmingham, AL 35294 Office: (205) 934-5696 Fax : (205) 934-6475 Email : ssham44(a)uab.edu

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Create surface from markers
by Tom Goddard 20 Feb '07

20 Feb '07

Hi Jeff, Chimera cannot currently create a surface from markers placed with the volume path tracer tool. It would not be so hard to write some Python code to do this. Here is an example of Python code that creates a surface in Chimera: http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Reference/surface.html Tom Jeff wrote: > hi Tom, > > is there a way to use a marker file just to render a surface (a > series/group of dots, just needing to be connected by a mesh)? for > instance, to represent a membrane. > > -Jeff

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Saving full map when zoning
by Tom Goddard 20 Feb '07

20 Feb '07

Hi Jean-Francois, You can save a map with the original map size while using volume zone by first pressing the the "Full" button in the Features / Subregion Selection panel of the volume dialog. Then use the File / Save Map As button. You can see what region will be saved by looking at the Features / Region Bounds panel (and you could type in new bounds there and press the Enter key instead of pressing the Full button). The volume zone capability (Features / Zone) normally uses a smaller box of data so that it is faster. Even when part of the surface is hidden by the zoning the whole surface within the box being used is computed and that is sometimes slow. Tom jean-francois menetret wrote: > > Hi Thomas, > > when using the zone option in Chimera, is it possible to have the size > of the saved mrc file (after zoning) be the same as the original file ? > > Best wishes > > Jean-Francois

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Re: [Chimera-users] demo made under Linux has bland atoms in Windows
by Elaine Meng 17 Feb '07

17 Feb '07

On Feb 16, 2007, at 7:55 PM, Kenward Vaughan wrote: > For me, the byatom coloration is there to begin with under Linux. The > ach shows up colored properly, as does the acetylcholinesterase. > Aha!! Problem solved!! I am 99.99% sure the difference is your preferences file. The demo itself does not say to color by element when the structure is opened. However, there is a New Molecules section of the Preferences in which you can say structures should be colored that way when they are opened. Most likely you have this set on your home Linux machine, but not in the Chimera preferences used on the Windows machines. Months ago we discussed the need for some way to indicate that preferences should be bypassed at startup and/or when opening structures. This option would be appropriate for use with demos or scripts to be shared among multiple users each having some arbitrary set of preferences settings. However, this option hasn't been added (nor are we sure how best to implement it)... thanks for the additional motivation to revisit that issue! The demos included with Chimera were made in a directory with a default preferences file. It is likely, however, that some users with nondefault New Molecules preferences have played them back and gotten a result different than intended. > > I've noticed rotation is slow under Windows, but v. nice with Linux > (about 7 seconds total). > It depends on the graphics capabilities of the system. It is slow on our home desktop computer (>5 years old - you can almost hear gears grinding) but fast on my laptop (1-2 years old). Happy demoing and please do contact us with any problems or suggestions, 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

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demo made under Linux has bland atoms in Windows
by Kenward Vaughan 16 Feb '07

16 Feb '07

...in a fashion, that is. A demo I plan on using at school (a Windows fortress, it is) displays all atoms as grey--no color (by element). The demo was created on a Linux machine (at my home). :( Any thoughts? Kenward ps. both versions of Chimera are the latest production version (2304). -- In a completely rational society, the best of us would aspire to be _teachers_ and the rest of us would have to settle for something less, because passing civilization along from one generation to the next ought to be the highest honor and the highest responsibility anyone could have. - Lee Iacocca

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saving map in different position
by Gabor Papai 16 Feb '07

16 Feb '07

Hi Tom, Is there a way to save a map with only transformation, or obtain the transformation matrix if I do a freehand transformation of an object? We would like to create a composite volume of several spheres. It would be the best to write a single map of several differently positioned spheres but I could also apply the transformation in IMAGIC if I would know the matrix. Thanks for helping! Regards, Gabor -- Gabor Papai IGBMC Department of Structural Biology and Genomics 1, rue Laurent Fries, BP 10142 67404 Illkirch, France phone +33-3-90244796 Fax +33-3-88653201 E-mail: papai(a)igbmc.u-strasbg.fr

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Re: [Chimera-users] making movies with MorphMap, exporting povray scenes, FitMapInMap
by Gatsogiannis, Christos 15 Feb '07

15 Feb '07

Hello Greg and Tom, povray: the assumed gamma-change was indeed the problem. Thank you very much! I´m waitin for the next snapshot release MorphMap: the updated version works correctly! Thanks! Do you maybe plan in the future on offering the possibility to save a density map also in different formats than mrc (situs, imagic .. etc) ? That would be very useful... Thanks again, Christos

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cavity cropped view
by Randy Heiland 15 Feb '07

15 Feb '07

What options exist in Chimera for letting me show only that portion of a protein that is "near" another smaller molecule? Specifically, I have a ligand in a cavity of a large protein and would like to eliminate the "clutter" of the protein away from the cavity of interest. Thanks, Randy

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making movies with MorphMap, exporting povray scenes, FitMapInMap
by Gatsogiannis, Christos 14 Feb '07

14 Feb '07

Dear Chimera users and developers, recently I used the new morph map tool and it worked very nice in my case. I encountered a problem while exporting the animation in any movie-format within Morphmap, I just get empty or very small files, which cannot be displayed in any media-player. I decided then to use the chimera-movie recorder utility to record the morphing animation and this worked fine (I´ve tested this with mpeg-2 format). At the moment I´m using the chimera-version 1.2309 in a SUSE LINUX 9.2 environment. Is this a version problem or a bug? Furthermore, I´ve exported some scenes in the povray format and I´ve noticed that the final images are of lower quality in comparison with images made some months ago with older chimera versions. I haven´t changed the povray-version, the rendering settings and the settings for the visualisation of my data in chimera (brightness etc...). The colors are too pale, I could send you some example-images if needed. I´ve tried also the Fit Map in Map tool recently and it worked perfectly (you sent this tool to a group-colleague some months ago). I´m wondering why you didn´t put this tool on the experimental site yet....and one more last question...after using Fit Map in Map, is there any possibility to save the "fitted" map with it´s new orientation? Thanks, Christos Christos Gatsogiannis Institute of Zoology Johannes Gutenberg University 55099 Mainz, Germany Tel: +49(0)6131-39-23091 email: gatsogia(a)uni-mainz.de

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Request for Chimera on CD
by Tom Goddard 13 Feb '07

13 Feb '07

Hi Zia, Our Chimera software can be downloaded from the web http://www.cgl.ucsf.edu/chimera/download.html We have never distributed it by CD. Perhaps we can do it. Our program needs about 512 Mbytes of computer memory. What operating system do you need it for? Windows? Linux? Mac OS X? Because almost all molecular structure and sequence data used in research is obtained from the web I suspect our software will be of limited use to you without internet access. Tom zia muhammad wrote: > Respected Dear Dr. > > I am teaching Bioinformatics at International Islamic University > Islamabad, Pakistan. I am teaching molecula Docking and Protein > Structure prediction, CHIMERA or HMMs methodology. I hvae done all > theoratical work but could not perform any practical due to lack of > softwares. I will thankful to you if you kindly provide me some basic > softwares in this respect. After basic knowledge and establishing > proper labs we will purchase relatd softwares but on initial basis we > need your help. I also could not download different softwares so can > you kindly send me on CD. > Your kind attention will be highly acknowledged. > > Please reply. > > Regards > > Zia > > > ******************************** > *Muhammad Zia* > *Room # 7, Hostel # 2* > *Quaid-i-Azam University,* > *Islamabad. Pakistan* > *45320* > *********************************ue

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display two volumes alternatively
by Montserrat Samso 13 Feb '07

13 Feb '07

Hi, I am trying to compare two cryoEM density maps of the same protein, the only difference between them is a conformational change. Is there a way to switch directly from one volume to the other without having to display both of them together in between? Thanks, Montserrat ------------------------------------------------------- Montserrat Samso, Ph.D. Assistant Professor Department of Anesthesia Research Brigham and Women's Hospital Harvard Medical School 75 Francis St. Boston, MA 02115 Tel: 617 7328107 Fax: 617 7326927 E-mail: msamso(a)zeus.bwh.harvard.edu -------------------------------------------------------- CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s). The information contained in this message may be private and confidential, and may also be subject to the work product doctrine. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

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programmatic representation
by Randy Heiland 12 Feb '07

12 Feb '07

I'd like to be able to set the representation (wire, stick, bs, cpk) of a model programmatically, in this case, from a plugin. I was trying the following, but the newly displayed model would always be displayed in wire: self.model = ReadSDF.readSDF(tmpfile.name) chimera.openModels.add(self.model) #Midas.represent('stick', self.model) Midas.represent('cpk', self.model) Suggestions? thanks, Randy

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Re: [Chimera-users] opacity for stick representation in chimera
by Elaine Meng 12 Feb '07

12 Feb '07

Hi Jerome, First make a transparent color and then use it on the atoms/bonds - there are a handful of routes. You can make the transparent color using the Color Editor (under Tools... Utilities; click the Opacity to get a slider for that, then adjust the red/green/blue/opacity sliders as desired). This color can be used on atoms/bonds, ribbons, whatever (depending on the current target setting under Actions.. Color) by choosing "Actions... Color... from editor" or it can be used in coloring commands using the color name "fromeditor" Color Editor description: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/colortool.html Alternatively, you can make the transparent color with the command "colordef" and give it whatever name you want. The new color name can then be used in coloring commands. Color definitions are saved in sessions. Or, if you don't want to save sessions, just make a command file with all of your favorite color definitions and read it in whenever you want those colors defined. "colordef" man page: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/colordef.html I hope this makes sense - feel free to write back if it doesn't! Best, E ----- 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 Feb 11, 2007, at 5:14 PM, Jerome Nilmeier wrote: > Hi Elaine: > > I was wondering: can you adjust the opacity of the stick > representation in chimera? > > best, J

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xforms, cpk scale
by Randy Heiland 08 Feb '07

08 Feb '07

Is there a command to scale sphere of a CPK rep? Is there a command to save the current viewing transformation to a file and then read it back/apply it at a later time? Thanks, Randy

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Drawing Artifacts
by Albion Baucom 08 Feb '07

08 Feb '07

Using the latest stable current production release of Chimera, 1.2304, I have begun to experience some drawing problems that I never had in previous versions. Specifically I frequently get a thin wireframe rendering of my protein structure when I draw the structure as a ribbon with a volume open at the same time. This wire frame persists even when I turn the display of the molecule off in the model panel, and it also does not rotate or translate if the protein is selected as the only active object. In effect it leaves behind a ghost image. Curiously this representation alternates from a light gray/white color to black when I open dialog boxes. The artifact toggles on and off with the volume in some instances. My processing and graphics hardware have not changed recently, nor has operating system (Linux). I do not experience this behavior with my last version of Chimera, 1.2199; it never renders this artifact. I have a nVidia Geforce 6800GT graphics card with the nVidia Linux drivers 1.0-9746. My X11 server is version 6.8.2. Here is a screen image of this phenomenon http://msg.ucsf.edu:8100/~baucom/images/chimera_image.jpg I have rotate the model slightly to show that the thin wireframe stays behind. It is not a separate object in the model panel. Thanks Albion

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Morph Map
by Tom Goddard 07 Feb '07

07 Feb '07

I've added a Chimera extension called Morph Map http://www.cgl.ucsf.edu/chimera/experimental/morph_map/morphmap.html to the experimental features web page: http://www.cgl.ucsf.edu/chimera/experimental/experimental.html It interpolates between two volume data sets and makes animations. The original version of this tool was written by Wei Zhang in Pawel Penczek's lab. Tom

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Re: [Chimera-users] Map Orientation for Symmetry Plug-in
by Tom Goddard 07 Feb '07

07 Feb '07

Hi Albion, Ok, I made the "fit map in map" tool print out a point on the rotation axis. The new code for use with Chimera 1.2318 is here: https://www.cgl.ucsf.edu/cgi-bin/chimera-get.py?file=experimental/fitmap231… The zip file contains a directory FitMap that you put in your Chimera distribution under chimera/share or on Mac Chimera.app/Contents/Resources/share For more installation details see http://www.cgl.ucsf.edu/chimera/experimental/install.html This FitMap directory replaces your existing one. After restarting Chimera you can fit a helically symmetric map in a rotated copy of itself then get the axis point (shown in Favorites / Reply Log) and adjust the map origin (volume dialog Features / Origin and Scale) to put the axis point at (0,0,0). I described this in more detail in my previous message: http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-February/001313.html The output of the axis point will be included in the next Chimera snapshot due out in one to three weeks. The matrix you sent me had no rotation, just a translation by 52 along z. You will need to rotate the map copy before fitting to get a meaningful rotation axis point. In fact I suspect the accuracy will be increased for rotations near 180 degrees rather than small rotations (e.g. 30 degrees). Tom Albion Baucom wrote: > Thanks Tom. > > OK, here is my rotation matrix after following your instructions > > 0.99944468 -0.03326699 0.00190528 -0.09024247 > 0.03326443 0.99944566 0.00136109 0.10539160 > -0.00194951 -0.00129696 0.99999726 52.82194789 > > Sorry, I forgot how to compute the rotation axis vector from this > matrix ... its been awhile since I had to do that manually ... its > pretty simple if I remember right. > > Any code to automate this would be greatly appreciated. > > Thanks again! > > Albion

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colorzone tool
by Jeff 06 Feb '07

06 Feb '07

would it be possible to allow 'color zone' to go past 30 A radius? -Jeff

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Hiding part of a marker set
by Tom Goddard 06 Feb '07

06 Feb '07

Hi Jeff, You can hide part of a marker set by selecting the markers you want to show (maybe using the select connected shortcut "sc" as described earlier) then use invert selection (main window menu Select / Invert, or shortcut "is"), then use path tracer menu entry Actions / Hide markers (or shortcut "ha" for hide atoms). Tom Jeff wrote: > I don't suppose there's a way to hide only a portion of a marker set > (just keep one filament visible out of 10, for instance) > > -Jeff

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Mac laptop benchmark
by Tom Goddard 06 Feb '07

06 Feb '07

Hi Jeff, I ran the Chimera benchmark tool on my new MacBook Pro and got scores: surface 543 mesh 545 contour 183 solid 256 recolor 132 But running hand tests I see the real surface/mesh scores should be 380. It appears the benchmark no longer is reporting correct scores either because a graphics driver optimization is speeding things up because the test image is not actually displayed, or Chimera code has changed (perhaps no longer guaranteeing the OpenGL buffers are swapped). Probably other scores on the Chimera benchmark web page are likewise inaccurate. This will have to be investigated. At any rate, actual surface rendering is about 65% faster than my Dell Precision M50. A test on a GeForce Go 7400 (aka Quadro NVS 120M) in a new Dell Lattitude D820 also gave erroneous scores, but hand testing gave surface rendering score 420 and horrible mesh (110) and solid (<20) numbers. Tom Jeff wrote: > could you run the benchmark on your mac? (I have run it on my > workstation, but forgot the scores; will do again and compare) > > -jeff

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NumPy in Chimera
by Tom Goddard 06 Feb '07

06 Feb '07

Hi Chimera Extension Writers, If you have written Chimera extensions that use Numeric Python you will need to convert them to instead use NumPy to work with future versions of Chimera. NumPy provides almost all the same routines as Numeric but some function and module names have changed. We are switching Chimera over from Numeric Python to NumPy and will have a Chimera snapshot out in one to three weeks that uses NumPy. We envision having a Chimera production release that uses NumPy in perhaps 3 months. The change was necessary because Numeric is no longer maintained. Numeric will no longer be included with Chimera because dynamic library name space collisions with NumPy occur on the Mac because of certain Chimera compilation options. The conversion of Chimera code was not much trouble, but we had to also convert third party packages that are included with Chimera (PyOpenGL, MMTK, Scientific (for netcdf file reading), MSMS molecular surfaces) and that took some work. Thanks for your patience. Tom

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Re: [Chimera-users] question about mac laptops / workstations and chimera stability
by Tom Goddard 06 Feb '07

06 Feb '07

Hi Jeff, I just got my MacBook Pro with 2 Gb memory and 160 Gb hard-drive yesterday. It's been working well with Chimera volume display, surface and solid. Performance is roughly a factor of two better than my 4 year old Dell Precision M50 with Quadro 4 GoGL 500 graphics (a very heavy machine, ~10lb). I just took a look at a 2k by 2k by 76 tomogram and performance was as expected. 2 Gb memory is adequate for my uses. I went for the 160 Gb harddrive instead of the 120 Gb since volume data and video can take some space. The 200 Gb option was a 4200 rpm drive which I suspect would be slower than the smaller 5200 rpm models so I avoided it. If you'd like to try my laptop before you order you are welcome to come over to my house in SF. Tom Jeff wrote: > Tom, > > is the base 2 GB memory sufficient, and do you have any reservations > regarding transfer speed from the harddrive? > > I am going to place an order, wanted to check with you first about > those 2 things before going ahead. > > (I figure, if you are developing on it, this is not a bad idea.) > > -Jeff

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Map Orientation for Symmetry Plug-in
by Albion Baucom 05 Feb '07

05 Feb '07

I am using the Symmetric Molecule Copies plug-in with Chimera. I am wondering if there is a preferred way to orient an EM volume so that it is centered around the z-axis at the origin. From my experience with this plug-in, symmetry related molecules are generated around z-axis at the origin of the viewing area. I am finding that my maps tend to be close, but not exactly oriented around the z-axis for a helical volume. Molecules fit into a portion of the map then tend to have slightly askew symmetry mates relative to the volume (presumably because the z-axis of the map is not exactly oriented along the origin of the symmetry z-axis). After playing around with various map tools (MAPMAN, Priism), I am still not satisfied with my orientation protocol and wonder if anyone can suggest a tried and true method for this. Thanks Albion

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Re: [Chimera-users] volume/3586 problem zoning out volume
by Thomas Goddard 05 Feb '07

05 Feb '07

Hi Jeff, To check the memory limits set by a bash shell use shell command "ulimit -a". For a csh use "limit". Here's an example on my Mac (no memory limit). Tom $ ulimit -a core file size (blocks, -c) 0 data seg size (kbytes, -d) 6144 file size (blocks, -f) unlimited max locked memory (kbytes, -l) unlimited max memory size (kbytes, -m) unlimited open files (-n) 256 pipe size (512 bytes, -p) 1 stack size (kbytes, -s) 8192 cpu time (seconds, -t) unlimited max user processes (-u) 100 virtual memory (kbytes, -v) unlimited Jeff wrote: > I had forgotten about 4-byte floats versus 2-byte integers, > > you are right in that this is most likely a machine limitation, I was > surprised to get a fault and error about an allocation call. is there a > specific environment variable I should check to see if the shell is > limiting chimera's memory requests, I will change that if possible (?). > > -Jeff >

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