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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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