- Chimera-users - RBVI Mailing Lists

Chimera to visualize MOLDEN-generated VRML2.0 files
by Kalju Kahn 01 Feb '07

01 Feb '07

Dear Chimera users, I am looking for advice on how to make chimera work with VRML 2.0 files generated by MOLDEN. MOLDEN seems to generate valid VRML files (octagaplayer reads these in all right) but chimera crashes with Segmentation fault (core dumped) This happens both on 32-bit Suse 9 system and 64-bit recent Ubuntu system. Any ideas are appreciated! Kalju ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry University of California, Santa Barbara

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anyone using chimera on a an IBM T43p
by Jeff 01 Feb '07

01 Feb '07

hello, I have an IBM T43p (June '05 or so release) which has an ATI FireGL v3200 (Mobility). In XP, it isn't possible to try out drivers from the vendor, I am limited to drivers from IBM. In Linux, I have been able to install proprietary drivers from ATI, but there is no selection for the 'Mobility' version of the v3200 on ATI's website; the install has not complained though, and basic stuff appears to be fine (GUI is ok, glxgears, etc). In both XP and Linux, chimera will crash when attempting to use volume maps. It appears fine with pdb files, although I typically work with volume data so haven't rigorously tested that. I have been assuming that the FireGL v3200 (Mobility) is the same logic as the v3200, at least documentation I have been able to find seems to imply that. Does anyone know (or suggest) a chimera-stable driver version from ATI that I might test? I might at least be able to get it to work in Linux, as the driver suite downloaded from ATI appears to cover most late-generation cards. thanks for any suggestions, -Jeff

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Re: [Chimera-users] access to pdb parser
by Jean Didier Pie Marechal 01 Feb '07

01 Feb '07

Hi Eric, Well, the truth is that these are two good news. Most likely I didn't explain myself correctly. In reality, for practical reasons, I'd like to use only chimera for the teaching. So, I am planning to only use its internal python shell for python applications. Therefore the tips you gave me are perfect. Thanks a lot for the help! 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: +34.935814988 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: Eric Pettersen <pett(a)cgl.ucsf.edu> Data: Dimecres, Gener 31, 2007 10:31 pm Assumpte: Re: [Chimera-users] access to pdb parser > Hi JD, > I have good news and I have bad news. The good news it that using > > PDBio to do what you want is pretty easy. The bad news is that you > > can't use it in a generic Python shell, only in Chimera's own > Python > shell. This is because we use a modified version of Python so that > > the types we define in the C++ layer (Molecule, etc.) can have > attributes added to them in the Python layer -- otherwise they > would > behave like the built-in Python types (dict, list. etc.) that can't > > have arbitrary attributes added to them. We intend to improve our > own code to make modifying Python unnecessary, but haven't gotten > to > it so far. > Nonetheless, you can basically use Chimera in place of a Python > interpreter. "chimera --nogui script.py" will execute the Python > script named script.py without bringing up the Chimera interface. > Also, you can start Chimera normally and bring up the graphical > interface to its interactive Python shell, IDLE (under Tools- > >General > Controls) and type Python commands to that. > Here's a session of me using PDBio in IDLE. I've added some > comments. > >>> from chimera import PDBio # import PDBio > >>> pdbio = PDBio() # create a PDBio instance > >>> mols = pdbio.readPDBfile("/mol/pdb/gc/pdb1gcn.ent") # read a > PDB file given its file name > >>> m = mols[0] # readPDBfile() returned a list of models (NMR > can > have many) so get the model itself > >>> m.pdbHeaders["HEADER"] # each model will have a pdbHeaders > dictionary, keyed by the record type, the values will be a list of > strings -- the PDB records > ['HEADER HORMONE 17-OCT-77 > 1GCN 1GCN 3'] > >>> > > --Eric > > On Jan 31, 2007, at 12:42 PM, Jean Didier Pie Marechal wrote: > > > Hi Eric, > > > > Yes, that would be better to explain more what I'd like to do. > > > > I am planning to give a practical on computational (bio)chemistry > > > in my department next year. I'd stongly like to have the students > > > using chimera and python as their main tools (though both are > tools > > I am in process of learning :-)). > > > > One of the "simple things" I have in mind, is to obtain pdb infos > > > directly from the shell e.g list the SEQRES entry or access to > the > > resolution (REMARK 2), the crystallization conditions etc. The > > students will be chemists and I think that from a didactic point > of > > view, obtaining infos from the python shell would be better that > > reading the pdb files, especially if we want to compare different > > > structures e.g. Writing a comand that gives you ALL the > resolutions > > of the 10 structures you loaded would be interesting. I looked at > > > the PDBio, but I can see how to catch REMARKS infos. > > > > I'd really like to have this work going on, but as you can see, I > > > am a bit lost in where to begin. > > > > Any help to tell me where to start would be fantastic! > > > > 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: +34.935814988 > > e-mail: JeanDidier.Marechal(a)uab.es > > > > ----- Missatge original ----- > > De: Eric Pettersen <pett(a)cgl.ucsf.edu> > > Data: Dimarts, Gener 30, 2007 1:25 am > > Assumpte: Re: [Chimera-users] access to pdb parser > > > >> Hi JD, > >> Chimera does its PDB parsing in the C++ layer (the PDBio class in > >> > >> the Python layer). There is a file named PDB.py in the mmCIF- > >> parsing > >> module, but it's not for parsing PDB files. Perhaps if you > >> described > >> why you need Python PDB parsing I could suggest options -- using > >> PDBio possibly being one of them. > >> > >> --Eric > >> > >> Eric Pettersen > >> UCSF Computer Graphics Lab > >> pett(a)cgl.ucsf.edu > >> http://www.cgl.ucsf.edu > >> > >> On Jan 29, 2007, at 1:49 PM, Jean Didier Pie Marechal wrote: > >> > >>> Hello everyone, > >>> > >>> a short question. What is the right call for importing the > >>> pdbparser module in the chimera python shell? I found the PDB.py > >> > >>> module in the site-package mmlib, but I don't know how to import > >> it...> > >>> Thanks a lot, > >>> > >>> 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: +34.935814988 > >>> e-mail: JeanDidier.Marechal(a)uab.es > >>> > >>> > >>> _______________________________________________ > >>> Chimera-users mailing list > >>> Chimera-users(a)cgl.ucsf.edu > >>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > >> > >> > > > > > >

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TER Cards and Rainbow Colors
by Albion Baucom 31 Jan '07

31 Jan '07

Is there any way to introduce TER records between breaks in a chain, and still have N->C coloring continuous through a single chain? I have for instance a structure with missing loops that were not observed in density. Therefore there are breaks in the main chain. This is a very common occurrence. To prevent spuriously long bonds I have introduced TER records between the breaks. Then when I apply rainbow coloring from N->C terminus I get the spectral coloring between TER records rather than from the beginning of the chain to the end. I tried the card BREAK, but evidently that is not interpreted by Chimera. Coloring by chain, or by model in the Rainbow panel does not produce the desired effect. Thanks Albion

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Re: [Chimera-users] access to pdb parser
by Eric Pettersen 31 Jan '07

31 Jan '07

Hi JD, I have good news and I have bad news. The good news it that using PDBio to do what you want is pretty easy. The bad news is that you can't use it in a generic Python shell, only in Chimera's own Python shell. This is because we use a modified version of Python so that the types we define in the C++ layer (Molecule, etc.) can have attributes added to them in the Python layer -- otherwise they would behave like the built-in Python types (dict, list. etc.) that can't have arbitrary attributes added to them. We intend to improve our own code to make modifying Python unnecessary, but haven't gotten to it so far. Nonetheless, you can basically use Chimera in place of a Python interpreter. "chimera --nogui script.py" will execute the Python script named script.py without bringing up the Chimera interface. Also, you can start Chimera normally and bring up the graphical interface to its interactive Python shell, IDLE (under Tools->General Controls) and type Python commands to that. Here's a session of me using PDBio in IDLE. I've added some comments. >>> from chimera import PDBio # import PDBio >>> pdbio = PDBio() # create a PDBio instance >>> mols = pdbio.readPDBfile("/mol/pdb/gc/pdb1gcn.ent") # read a PDB file given its file name >>> m = mols[0] # readPDBfile() returned a list of models (NMR can have many) so get the model itself >>> m.pdbHeaders["HEADER"] # each model will have a pdbHeaders dictionary, keyed by the record type, the values will be a list of strings -- the PDB records ['HEADER HORMONE 17-OCT-77 1GCN 1GCN 3'] >>> --Eric On Jan 31, 2007, at 12:42 PM, Jean Didier Pie Marechal wrote: > Hi Eric, > > Yes, that would be better to explain more what I'd like to do. > > I am planning to give a practical on computational (bio)chemistry > in my department next year. I'd stongly like to have the students > using chimera and python as their main tools (though both are tools > I am in process of learning :-)). > > One of the "simple things" I have in mind, is to obtain pdb infos > directly from the shell e.g list the SEQRES entry or access to the > resolution (REMARK 2), the crystallization conditions etc. The > students will be chemists and I think that from a didactic point of > view, obtaining infos from the python shell would be better that > reading the pdb files, especially if we want to compare different > structures e.g. Writing a comand that gives you ALL the resolutions > of the 10 structures you loaded would be interesting. I looked at > the PDBio, but I can see how to catch REMARKS infos. > > I'd really like to have this work going on, but as you can see, I > am a bit lost in where to begin. > > Any help to tell me where to start would be fantastic! > > 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: +34.935814988 > e-mail: JeanDidier.Marechal(a)uab.es > > ----- Missatge original ----- > De: Eric Pettersen <pett(a)cgl.ucsf.edu> > Data: Dimarts, Gener 30, 2007 1:25 am > Assumpte: Re: [Chimera-users] access to pdb parser > >> Hi JD, >> Chimera does its PDB parsing in the C++ layer (the PDBio class in >> >> the Python layer). There is a file named PDB.py in the mmCIF- >> parsing >> module, but it's not for parsing PDB files. Perhaps if you >> described >> why you need Python PDB parsing I could suggest options -- using >> PDBio possibly being one of them. >> >> --Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> pett(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu >> >> On Jan 29, 2007, at 1:49 PM, Jean Didier Pie Marechal wrote: >> >>> Hello everyone, >>> >>> a short question. What is the right call for importing the >>> pdbparser module in the chimera python shell? I found the PDB.py >> >>> module in the site-package mmlib, but I don't know how to import >> it...> >>> Thanks a lot, >>> >>> 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: +34.935814988 >>> e-mail: JeanDidier.Marechal(a)uab.es >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> > >

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Re: [Chimera-users] Update volume display without pressing show
by Thomas Goddard 31 Jan '07

31 Jan '07

Hi Jeff, I also wasn't able to reproduce this problem. There is probably a real problem but some step that causes it is missing. If you figure out that step let me know. Tom Jeff wrote: > sorry about the confusion, > > what I meant by 'does not work', is that once I have loaded the volume > planes tool, it appears to not allow me to select 'update display > without pressing show'. (the button is depressed in the dialog box, or > i unclick/reclick it, but it no longer toggles 'update....w/o press > show' on and off). 2318 build. > > sequence: > > 1) load map; display with solid rendering. default is 'update w/o > press show', and you can see the effect of playing with histogram > update in realtime. > > 2) start volume planes. now requires me to press 'show' to update the > display. this also includes other volumes that vol planes is not used > on, and 'update w/o show' no longer works in surface or solid mode. > > 3) close volume planes, or close session. problem persists. > > 4) restart chimera, now it allows 'update..w/o press show' again. > > so, this happened to me twice, and i figured it was just something to > do with the volume planes tool. As I am writing this, I just re-did > the sequence above, and now it works (volume plane tool updates, can > switch to surface). Because I can no longer replicate this, I should > probably be ignored. Also, I just loaded one of the sessions I was > having a problem with into a new launch of chimera, thinking there > might be some sort of 'system/state snapshot' I could send you, but > now it is working too. So, it appears to have been fixed by a restart > of chimera. Again, please ignore. > > -Jeff

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Re: [Chimera-users] Update volume display without pressing show
by Thomas Goddard 31 Jan '07

31 Jan '07

Hi Jeff, I tried the volume "update show" option in combination with volume planes and did not find an problem. Can you give me step by step instructions to produce the problem? Also I don't know what you mean by "does not work". Does it always update automatically, or never update automatically? What Chimera version? With the volume planes tool, the full map is still opened -- it is just display a subregion that is 1 plane high. Use Features / Region Bounds to see and change the subregion. Or use Features / Subregion Selection and press the Full button to get back to the full map. Also the volume planes dialog always acts on the volume displayed in the volume dialog. Perhaps it should have its own menu to choose the volume you want to show planes for. Tom Jeff wrote: > even if I close the volume planes tool, > > 'update display without pressing Show' no longer works (for instance, > adjusting the volume rendering histogram, or clicking 'surface' > rendering). if I close, then re-open the volume, it still doesn't > work. bug, or my version maybe? > > also, once you start 'volume planes tool', it only keeps track of the > plane it has pulled from the volume map - what used to be a > 100x100x100 volume is now 100x100x1; the volume viewer 'renames' the > map but does not save it out that way (which is good). is there a way > to be able to keep the full volume around, but not displayed? there > are reasons you might want to do that (well, I found myself trying to > do that), without having to re-open the volume. > > i did check to see if i could open 2 copies - one first to run 'volume > planes' on, and then one to subsample but have as a volume rendering, > for example. this works, as long as i don't accidentally touch the > 'volume planes' dialog when fooling with the second opened copy of the > volume. > > mainly just curious, not asking for additional functionality, just > wanted to let you know what I was trying and why. > > -Jeff > > > > Thomas Goddard wrote: >> Hi Jeff, >> >> The volume dialog data display option "Update display without >> pressing Show" only effect volume dialog features. It does not have >> any effect on the Volume Planes tool. The Volume Planes tool does >> not allow adjusting the plane number without updating the display. >> >> Tom >> >> >> Jeff wrote: >>> hi Tom, >>> >>> I have volume planes and precomputed subsamplings going, and the >>> 'update display without pressing Show' no longer works (keep >>> toggling on and off, but it doesn't have an effect) >>> >>> is there a way for me to 'refresh' the state of buttons like that? >>> >>> -Jeff >>

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Watershed segmentation of volumes
by Thomas Goddard 31 Jan '07

31 Jan '07

Hi Jeff, There is no watershed or flood-fill type of method in Chimera for segmenting volume data. This is on our (very long) list of features to develop though. Tom Jeff wrote: > tom, > > i hate to keep piling on questions, but how hard would it be to have a > feature where one places a chimera marker, and then has some sort of > algorithm expand to 'fill' the space, kind of an isosurface problem > (or does this already exist) > > i have 'voids' in some of my maps (stained sections) which i think > correspond to protein, like one sees in negative stain (the positive > values/density in the map correspond to stain; an enclosed void > (density more or less = 0 or close to it) is thought to represent the > actual protein, which was covered in stain, kind of like 'magic shell' > on ice cream - or think of dairy queen cone, dipped in chocolate that > then solidifies), and would like some way to 'grow' a blob in the void > (or at least try) > > does this already exist? i have a buddy who does level set methods who > is often looking for ways to use his library, but i thought i should > ask you first if there is some functionality like this > > -jeff

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Quadro FX 1400/3450 performance
by Thomas Goddard 31 Jan '07

31 Jan '07

Hi Maya, It must be exciting and alot of work to get your lab running. Glad to hear you are making Chimera converts. Graphics benchmark scores using Chimera with the quadro fx 1400 and quadro fx 3400 are shown here http://www.cgl.ucsf.edu/chimera/benchmarks.html We don't have any numbers for the fx 3450 and I don't know if it is similar to the 3400. The 1400 and 3400 have very similar Chimera scores. The Chimera scores indicate how big a test volume can be handled at 10 frames per second. Both these cards are very fast. The one difference I see is that on the Nvidia web site they say the 1400 has 128 Mbytes of memory while the 3450 has 256 Mbytes. http://www.nvidia.com/page/qfx_mr.html http://www.nvidia.com/page/quadrofx.html (fx 3400) Maybe that info is out of date -- maybe there is a choice of memory size. On the Chimera page the fx 1400 had 256 Mb. And 128 Mbytes is small by today's standards. 256 Mbytes is common, and 512 Mbytes is available with some cards. The amount of graphics memory is most noticable if you use the Chimera "solid" rendering mode because it tries to put red,green,blue 8-bit values for the entire volume on the card. For 256^3 volume that is 48 Mbytes, or if you use Chimera 2-D textures mode (the default) it take 3 times that (144 Mbytes). It can also make a difference for very large contour surfaces -- ones you might use for making a figure but would be too slow for interactive rotating (e.g. 10 million triangles at about 18 bytes per triangle = 180 Mbytes). Regarding stereo, I'm not sure if there are any flat panel displays that can work with the LCD glasses. They don't refresh fast enough so there is too much flicker. So you either need a CRT display or maybe some special high-end flat panel. See you at the EMAN workshop. Maya Topf wrote: > Hi Tom, > > How are you? > I am slowly settling down in the UK. Lots of work and collaborations. > A few people from the EM group at birkbeck started using chimera and > they really like it! > > I have a question about graphics cards and maybe you can help me. > I am thinking about buying either NVIDIA QUADRO FX 1400 (stereo) or FX > 3450 (stereo). > Do you think that there is a big difference when I want > to visualise large maps with chimera for example? > > thanks, > Maya > > I saw that you are coming to the eman workshop so I guess I will see > you there! > Tom

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ViewDock descriptors problem
by "Воронков андрей" 31 Jan '07

31 Jan '07

Dear Chimera users, I have ranked database from DOCK. I need to see energies of these structures and their ranking. I open them by View Dock, but in the field Column menu I can see only name field. Why I don't have energy field there and how can I get it? Respectively yours, Andrew PS "Descriptors can be shown in or removed from the upper panel using the Column menu." -this is from manual, but I can;t make shown any descriptos but the name of the structure

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Re: [Chimera-users] using a marker file to zone a volume from python prompt
by Thomas Goddard 30 Jan '07

30 Jan '07

Hi Jeff, I added a user interface dialog for rotating and translating atom coordinates. Markers in Chimera are equivalent to atoms so it works on those. The rotation is specified in Euler angles. The new dialog, called Transform Molecule Coordinates, is available on the experimental features web page: http://www.cgl.ucsf.edu/chimera/experimental/experimental.html Tom Jeff wrote: > thanks Tom, > > much appreciated. how hard is it for me to write a dialog GUI to provide > 3 numerical inputs to the rotation script you forwarded me? (is it more > involved than a few lines? I am not familiar with Tkinter). > > don't want to bother you too much, if it is not a quick thing/response > feel free to punt, please. > > -jeff >

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Update volume display without pressing show
by Thomas Goddard 30 Jan '07

30 Jan '07

Hi Jeff, The volume dialog data display option "Update display without pressing Show" only effect volume dialog features. It does not have any effect on the Volume Planes tool. The Volume Planes tool does not allow adjusting the plane number without updating the display. Tom Jeff wrote: > hi Tom, > > I have volume planes and precomputed subsamplings going, and the 'update > display without pressing Show' no longer works (keep toggling on and > off, but it doesn't have an effect) > > is there a way for me to 'refresh' the state of buttons like that? > > -Jeff

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Re: [Chimera-users] Representation of volume data in memory
by Thomas Goddard 30 Jan '07

30 Jan '07

Hi Jeff, I suspect 2-byte integers are not faster to access or compute with then 4-byte floats on modern CPUs. But more of the map will fit into the CPUs cache which could improve bandwidth and could make computing a contour surface faster. But I don't think that will be significant. You would need to test it to know. Chimera keeps the native data type of the map to conserve memory when reading large maps. Tom Jeff wrote: > does this mean that a 2-byte integer format of a file will display > faster / render triangles faster than the equivalent sized 4-byte float > map? > > Thomas Goddard wrote: >> Hi Jeff, >> >> Chimera keeps volume data in memory using the same numeric value >> types that are present in the file, for example, 32-bit float, 16-bit >> integer, 8-bit integer. >> >> Volume data is copied only when necessary -- for instance, using the >> Gaussian Filter tool creates a floating point copy of the data since >> Gaussian convolution of integer data produces a floating point result. >> >> Tom >> >> >> Jeff wrote: >>> does chimera store all values as float internally (even if the >>> original map is in 2 byte integers), making the mode of the MRC file >>> irrelevant to chimera's performance? >>> >>> -jeff >>

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Re: [Chimera-users] zone tool and volume rendering
by Thomas Goddard 30 Jan '07

30 Jan '07

Hi Jeff, The Chimera handling of the MRC file origin position is done in Python code chimera/share/VolumeData/mrc/mrc_format.py In summary, if it is an MRC2000 file (ie has xorigin, yorigin, and zorigin header values) then (xorigin, yorigin, zorigin) is used as the xyz coordinates of the volume index (0,0,0) unless xorigin, yorigin and zorigin are all zero in which case the xyz position of the map index (0,0,0) is calculated using integer (ncstart, nrstart, nsstart) header values times the grid spacing (defined by (xlen/mx,ylen/my,zlen/mz)). It is never the case that both (ncstart,nrstart,nsstart) and (xorigin,yorigin,zorigin) are used in positioning the map. Tom Jeff wrote: > > I often use another tool to cut out subregions, that I then load into > chimera - until you told me recently, I did not know I could pre-load > subsampled maps, or be able to keep a 'subsampled overview' present > while selecting various regions > > when using other tools to cut out these smaller areas (either IMOD or > Priism), some tools record displacements, and some don't. the Priism > 'CopyRegion' tool appears to do this by adjusting the 'start pixel' > field in the MRC header. IMOD doesn't do this. the 'copyRegion' tool > also doesn't appear to transfer well to chimera, at least in my test > case the original and subvolume do not register properly. (I don't have > any expectation that it would work properly, but I would adapt if I knew > what chimera expects.) > > I am also not sure what entries chimera uses to keep track of > displacements when it cuts out volumes (I could do that experiment right > now), whether it uses 'start pixel' or 'origin', if 'origin' is recorded > in Angstroms or pixels, etc. Also, I don't know what chimera considers > the origin of a density map - if 'start pixel' is 10,10,10, the map is > 20x20x20 pixels in dim, and the origin is (0,0,0), is the origin at the > center of the map, or at the 0,0,0 pixel coordinate of the map? I have > been assuming that 'origin' has to refer to the map's origin location in > space, but this requires defining where the origin is in the volume map > (I think). if there is a 'start pixel' entry, does this effectively > shift the origin? As an example, if the pixel res is 10 A, will the map > example above now display starting at (10 A, 10 A, 10 A)? Or, is one > (or both) of these entries ignored? Finally, if there is already an > entry in one of these fields, does chimera respect that and just > increment, or does it clobber it with the relative displacement > calculated when excising a subvolume? (this slew of questions is > probably covered by a single answer, but I thought it would be good to > elaborate) > > If I knew, I could more appropriately jump between programs. As I am > writing this, I just got an email from David at Boulder telling me that > IMOD uses the origin entries in the header (but don't know yet what it > considers to be the origin, 'far left' corner or center or something else). > > -Jeff

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Precomputing subsampled map sizes
by Thomas Goddard 30 Jan '07

30 Jan '07

Hi Jeff, Yes, Chimera will complain and not allow precomputed volume subsamples if the size of the subsample grid is not what is expected. In the case you give (1434,1434,110) with subsample grid of size (358,358,26) the subsample grid size is not acceptable. Notice that 4 times the subsample size is (1432, 1432, 104) So a half size bins in the first two dimensions are left off (1434 - 1432 = 2) -- that is fine. But the third dimension is missing 1.5 bins (110 - 104 = 6). The subsample file should have size 27 in the third dimension, ie (358,358,27). I don't know why squeezevol from IMOD dropped off more than a whole bin in the third dimension. Chimera allows fractional bins to be dropped off, but does not allow whole bins to be missing. Tom Jeff wrote: > hi again, > > is there a problem with the precomputed subsamplings needing even > dimensions (I pre-cut my volume to even dimensions so that a binning of > 2 would result in a whole number for the subsampled dimensions, but it > can be hard to do this for a factor of 8 in advance). > > chimera is complaining to me about bad dimensions ('Data foo.mrc of size > (358,358,26) not a valid size for dubsamples of foo.mrc of size > (1434,1434,110). > > is there a program you use to bin / get around this problem? I use > 'squeezevol' from IMOD, I am not sure if it is completely transparent in > its output for what chimera would expect > > -j

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Representation of volume data in memory
by Thomas Goddard 30 Jan '07

30 Jan '07

Hi Jeff, Chimera keeps volume data in memory using the same numeric value types that are present in the file, for example, 32-bit float, 16-bit integer, 8-bit integer. Volume data is copied only when necessary -- for instance, using the Gaussian Filter tool creates a floating point copy of the data since Gaussian convolution of integer data produces a floating point result. Tom Jeff wrote: > does chimera store all values as float internally (even if the original > map is in 2 byte integers), making the mode of the MRC file irrelevant > to chimera's performance? > > -jeff

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Re: [Chimera-users] zone tool and volume rendering
by Thomas Goddard 30 Jan '07

30 Jan '07

Hi Jeff, I'll tell you my experience looking at a tomogram (2048 x 2048 x 76) of an immune synapse for a demonstration I gave last month at a cell tomography workshop. The file (mrc) is too large to conveninently display at full resolution. So I made binned versions 2x and 4x smaller along each axis (file size 8x or 64x smaller). Then I used the precomputed subsamples feature I described before. For some added convenience I then saved the map to a NetCDF file using Chimera because this saves the full matrix and binned versions in a single file (new in Chimera 1.2318). I use the volume dialog data display options to "Adjust step size to show at most 1 Mvoxels", or however many million voxels my computer can handle without getting too slow. Then I use the full view of the data to find regions I'm interested in, then use the subregion selection feature and Crop button to look at a smaller piece and the step size automatically is reduced. If I choose a small region I get full resolution. When doing this you have to keep in mind that once you manually change the step size at the top of the volume dialog it turns off the automatic step size adjustment. So I try to avoid that. Of course I also use the volume planes tool. I think you know all this and probably are using Chimera to the best of its current capabilities. You want to push it to use better compression (like resampling to have better aligned boxes) so you can see more data at full resolution. We don't have that yet. It is not hard to envision much fancier compression implementations that improve performance. Chandra Bajaj at U. Texas is very interested in this and may have software you can use. You might want to try his VolumeRover program. The Chimera EM capabilities were developed for single particle reconstructions. We have done little in Chimera to support work with EM tomograms which are very different in size and content (non-axis aligned structures, membranes, ...). We plan to develop tomogram capabilities and my volume planes tool created last month is a tiny step. But it will take years to implement the obvious stuff we can think of now. Your comments are helpful in guiding the priorities. I don't understand why you are "jotting down displacements" when saving subregions. Chimera puts that info into the MRC header. So why do you need to write it down? Tom Jeff wrote: > thanks Tom, > > with regards to the rotation/resampling, I was thinking mainly in > terms of visualizing large #'s of filaments and membrane, which in > themselves only constitute a small fraction of the actual volume they > traverse. even if re-sampling were done by cubic interpolation onto a > the same dimensioned grid, in some cases the loss in resolution would > be acceptable (definitely would be acceptable for some of my current > needs). i have problems with visualizing my whole maps unbinned but > was thinking that the savings such an approach would represent could > allow me to do that. for instance, this is already a problem for me > with trying to volume render a slab of membrane, which I think might > contain interesting features but I can't get the whole thing to go > unbinned; if it were rotated into the minimal enclosing volume, > interpolation artifacts or otherwise, my feeling was that I might > overcome that (there are also a bunch of filaments attached to the > membrane, and running underneath the membrane, so it is a real > difficulty for me to go back and forth between cutting out subvolumes > and binning them to be manageable, segment out filaments, or membrane, > etc, then try to put all the segmented items back into the same volume > and have a look-see). > > the volume planes tool has proven very helpful in segmenting out the > membranes, though. to get at the filaments that are attached to the > membrane, I was zoning out a region around the membrane (placed a > bunch of markers on the membrane using volume planes tool) about 400 A > in radius, but this proved difficult to render in the entire tomogram > b/c the zoned membrane still encompassed most of the original volume, > etc. so I was back to having to cut regions out of that segmented > membrane map to look further. (thus necessitating me jotting down the > displacements of each subregion, etc.) > > -jeff

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Re: [Chimera-users] using a marker file to zone a volume from python prompt
by Thomas Goddard 29 Jan '07

29 Jan '07

Hi Jeff, I forgot to mention that to run the volumezone.py script without display the Chimera user interface you would invoke it from a shell: % chimera --nogui volumezone.py The --nogui flag tells Chimera not to start any graphical user interface. Tom

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Re: [Chimera-users] zone tool and volume rendering
by Thomas Goddard 29 Jan '07

29 Jan '07

Hi Jeff, You are right that masking a filament that runs along the long diagonal of a box does not reduce the disk space or memory use any. (If you compressed the file then it would make a big difference. But you need to uncompress it to use it so that is of limited value.) So to achieve a space savings you need to resample the volume using a grid aligned with the axes of the filament. The resampling will degrade the data resolution some and it might be reasonable to do it on a grid with half the spacing (making the file 8x bigger). With such a resampled map the rotation and shift could be stored so that it can be placed in the original location in the full map. We don't support that now but when we add resampling we will store those rotation parameters in the map file header (maybe in the "labels" field for an MRC file). The time for Chimera to display a map depends on how large the volume grid is because it scans the entire grid in one pass when using the marching cubes algorithm to compute a contour surface. It also depends on how many triangles make up the contour surface. By eliminating the 99% of a masked file that is zeros using a new orientation and resampling it could compute contour surfaces faster. And the solid (volumetric) rendering should be faster directly proportional to the file size. That may be the more important case for your EM tomograms. I plan on supporting resampling on a rotated grid. But I think in many real uses it will not save much space because you will want to resample with finer grid spacing. But it could be convenient for exporting to analysis or visualization software that is limited to xy-planes. Tom Jeff wrote: > got it, > > what you say makes sense, I can definitely workaround, especially given > that the zone tool does a mask upon saving. > > I have been thinking about the problem I have with filaments (or > surfaces) spanning non-orthogonal regions of a volume, which means that > zoning out a long filament (or surface) that might take a much smaller > amount of space/memory once zoned actually takes up almost the same > amount currently, if I am thinking right. > > as an example, say you have a volume that is 100x100x100. inside the > volume, you have a filament, that takes up 10x10x244 voxels (effectively > spanning from one corner to the mirror/opposite corner of the volume). > in theory, zoning out that filament could take up ~1/40th the space, if > rotated to line up with one of the cartesian axes. I don't know how much > logic it would take to do this; I also don't know how chimera reads > origin information from an MRC file, or how much work it would take to > enable it to read (and use) an euler convention from an MRC file, for > displaying later. This would enable cutting a whole bunch of filaments > out of a volume, and then displaying them all concurrently without > running into the problem of loading in large rectangular prisms of space > that are mainly zeros (if this is currently happening, I don't know). I > guess at that point it makes sense to consider the geometric center of > such a rotated object at its origin, to reduce re-displaying the > object/filament properly in the original orientation to just storing a > shift and the rotation angles (6 parameters). > > the same holds true for membranes - right now, I have an entire membrane > that I segmented with markers, but it essentially runs along a hypotenuse. > > one question that probably negates the above paragraph would be 'does > the masked volume (with mostly zeros) display any faster / take less > resources than an equivalent volume without the zeros'? I have been > assuming this is not the case, that the zoned/masked volume still > entails reading in / accounting for that full rectangular prism, despite > the fact that it is mostly empty / full of zeros. > > thanks for you help, > > -Jeff

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Re: [Chimera-users] using a marker file to zone a volume from python prompt
by Thomas Goddard 29 Jan '07

29 Jan '07

Hi Jeff, I've attached a script that opens a density map and a Chimera marker file and writes a new volume corresponding to a zone around the markers. It does not require showing the Chimera user interface to do this. Perhaps you don't need this now (I just got your follow-up email.) but perhaps you will find it useful in writing other scripts. Karin Gross at Max Planck Institute of Biochemistry has written a Chimera extension to slice tomograms at arbitrary angles. I saw it when I visited Munich in December. They also were planning on allowing marker placement on those planes. The volume planes tool could be made to average neighboring planes. Currently it simply displays a NxMx1 subvolume in solid rendering mode. Since there is no existing code in Chimera to support averaging adjacent planes that would have to be added. Probably the easiest solution is to add the adjacent planes in Python and create a new single plane volume on the fly. Tom Jeff wrote: > thanks Tom, > > I will try that. alongside that, is there a way for me to run a 'zone' > function and save a subregion from a python command line (no chimera > launched, just import a library?)? > > I have used the volume planes tool to generate a marker set of a > membrane, it was handy. But, it only handles orthogonal directions, it > can't provide an arbitrary interpolant (which is a large reason I rely > heavily on IMOD's slicer tool); this functionality would be very useful. > A second addition to the volume planes tool would simply be allowing > averaging several slices together (reduces noise) in the direction > normal to the planes, which may already be there (the documentation > online said something about this feature, but it wasn't clear to me) > > it the volume planes tool were able to handle an arbitrary > view/interpolant, then I wouldn't have to depend on the slicer tool, and > the previous request about rotating markers that was related to that > requirement (different features available in different slicer > orientations in IMOD, necessitating a rotation prior to visualization > with the volume planes tool in chimera, thus requiring old marker set > from original volume to be rotated to be used in new volume, etc) would > effectively be voided > > > -Jeff # ---------------------------------------------------------------------------- # Save a volume zone around a given set of markers as a new volume file. # def save_zone(volume_path, markers_path, radius, volume_out_path): # Read zone points atoms, bonds = marker_set_atoms_and_bonds(markers_path) from chimera import Xform xform = Xform() # Identity transform for marker points from SurfaceZone import path_points points = path_points(atoms, bonds, xform) from VolumeData import open_file_type vol = open_file_type(volume_path, 'mrc') # Get containing volume subregion ijk_min, ijk_max = containing_subregion(vol, points, radius) from VolumeData import Grid_Subregion subvol = Grid_Subregion(vol, ijk_min, ijk_max) # Make new volume with zeros outside radius from VolumeViewer import zone_masked_grid_data masked_vol = zone_masked_grid_data(subvol, points, radius) # Write new volume from VolumeData.mrc import write_mrc2000_grid_data write_mrc2000_grid_data(masked_vol, volume_out_path) # ---------------------------------------------------------------------------- # def marker_set_atoms_and_bonds(markers_path): from VolumePath.markerset import load_marker_set_xml msets = load_marker_set_xml(markers_path) atoms = [] bonds = [] for mset in msets: atoms.extend(map(lambda m: m.atom, mset.markers())) bonds.extend(map(lambda l: l.bond, mset.links())) return atoms, bonds # ---------------------------------------------------------------------------- # def containing_subregion(vol, points, radius): from VolumeViewer import points_ijk_bounds, clamp_region ijk_min, ijk_max = points_ijk_bounds(points, radius, vol) ijk_min, ijk_max = clamp_region((ijk_min, ijk_max, None), vol.size)[:2] from math import floor, ceil ijk_min = map(lambda x: int(floor(x)), ijk_min) ijk_max = map(lambda x: int(ceil(x)), ijk_max) return ijk_min, ijk_max # ---------------------------------------------------------------------------- # volume_path = '/usr/local/src/chimera-demos/volume/examples/tricorn_map.mrc' markers_path = '/usr/local/src/staff/goddard/chimera/devel/ZoneScript/test.cmm' radius = 5 volume_out_path = '/usr/local/src/staff/goddard/chimera/devel/ZoneScript/test.mrc' save_zone(volume_path, markers_path, radius, volume_out_path)

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access to pdb parser
by Jean Didier Pie Marechal 29 Jan '07

29 Jan '07

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Re: [Chimera-users] zone tool and volume rendering
by Thomas Goddard 29 Jan '07

29 Jan '07

Hi Jeff, The volume dialog "zone" feature does not work with solid (volumetric) rendering. The current implementation just hides surface triangles having vertices outside the given range so it only works on surfaces. When you use volume dialog File / Save map as... it makes a copy of the data with grid values set to zero outside the radius. Creating a copy of the map in memory or masking the map for use with solid rendering are not currently supported. We wish to add this in the future and it should not be hard to achieve although performance when changing the radius will be significantly worse than with the current surface zoning. The documentation does not mention this limitation and I will update the volume dialog description to describe it. Tom Jeff wrote: > hi Tom, > > is there a way to get the zone tool to operate when doing a solid/volume > rendering - in surface mode, if you set a zone radius, let's say 40 A, > you'll get a region that extends 40 A around the selected marker(s); > however, in 'solid' mode, it appears I get the entire orthogonal region > in the volume that encloses the markers plus that radius. thiis is > problematic if the markers span the hypotenuse of the volume; in that > case, zone with volume/'solid' appears to more or less display the > entire volume rather than just the surrounding region as in 'surface mode' > > do I have a buggy version? this is a recent release, but I've had this > happen with previous releases > > -jeff

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Re: [Chimera-users] chimera startup problem
by Greg Couch 29 Jan '07

29 Jan '07

Just a FYI to the list, the problem here was an ancient OpenGL graphics driver. Upgrading it made the problem disappear. I'll be adding an entry to our Graphics Driver bugs web page, <http://www.cgl.ucsf.edu/chimera/graphicsbugs.html> with a few more details. - Greg ---------- Forwarded message ---------- Date: Tue, 23 Jan 2007 12:25:41 -0500 From: Chen Xu <xuchen66(a)gmail.com> To: chimera-users(a)cgl.ucsf.edu Subject: [Chimera-users] chimera startup problem Dear List, after upgrading to 1.2304 (1.2303 freeze the computer after several minute loaded with a volume pdb file) , I have problem to start it up on (RedHat): agnieszka@raptor ~]$ chimera Error starting chimera: ValueError: attempt to create string with null pointer (see reply log for Python traceback info) Traceback (most recent call last): File "/sware/chimera/chimera-1.2304/share/__main__.py", line 59, in ? value = chimeraInit.init(sys.argv) File "CHIMERA/share/chimeraInit.py", line 255, in init tkgui.initializeGUI(exitonquit) File "CHIMERA/share/chimera/tkgui.py", line 2407, in initializeGUI File "CHIMERA/share/chimera/tkgui.py", line 2368, in createApp File "CHIMERA/share/chimera/tkgui.py", line 1784, in __init__ File "CHIMERA/share/chimera/tkgui.py", line 1811, in makeGraphicsWindow ValueError: attempt to create string with null pointer any help?

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Slow rendering in FC6
by Thomas Goddard 29 Jan '07

29 Jan '07

On Yifan's linux system a large molecule takes a second to redraw and gradually renders from one side to the other. Turned out he did not have the NVIDIA graphics driver installed, so MESA software rendering was being used. Determined this using linux "glxinfo" command. Solution was to install graphics driver. -------- Original Message -------- Subject: problem of running Chimera in FC6 Date: Sun, 28 Jan 2007 13:05:20 -0800 From: Yifan Cheng To: goddard(a)cgl.ucsf.edu Hi Tom, I have a question about running Chimera in Linux FC6 system and wondering if you could help me out? I have Linux boxes running FC6, with a Gigabyte GV-NX76G256D-RH Geforce 7600GS 256MB video card. But somehow the Chimera keep refreshing with any movement in the model or map I loaded into it. It runs this way in both thousands color mode as well as in millions color mode. This video card is not Quadro type and has no stereo function, but I thought this shouldn't matter. Do you have any idea what might be the problem? Thanks a lot for your help. best, Yifan

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Re: [Chimera-users] align different scale models
by Thomas Goddard 29 Jan '07

29 Jan '07

Hi Pu, The PDB file uses units of Angstroms. To specify the spacing between grid planes of your EM map, open it in Chimera, then use menu entry Features / Origin and Scale from the volume dialog. The "voxel size" values listed indicate the size of one grid cell in the density map which is equivalent to the grid spacing. You can change the values and press Return (or Enter) key and the map will be shown at the new scale. Enter the values in Angstroms. (Chimera does not know what units you are using but all data sets must use the same units if you want them to be displayed at the correct relative scales.) The map file is not modified. To save the new scale you either can save a Chimera session (File / Save session as... on the main Chimera window) or save a new copy of the map (File / Save map as... on the volume dialog). Tom P Qian wrote: > Hi Tom, > > I have question to ask you about alignment of PDB model and EM density map. > > When I open both EM density map and its corresponding PDB model, I found they > have different size. I think that is due to different scale they are using. My > question is: Is it possible for me to re-scale them individually so that they > can match each other. I cannot do it at the momemt because zoom function will > affect all data loaded, not only active data but also unactive one. I'm trying > to produce a EM density map which has same scale with PDB model to solve it, > but if Chimera could do it as well, it will be helpful. Thanks > > Best regards > > P. Qian > > Dr. Pu Qian > Physics Department > The University of Sheffield > Hicks Building > Hounsfield Road, S3 7RH > UK >

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Re: [Chimera-users] using a marker file to zone a volume from python prompt
by Thomas Goddard 29 Jan '07

29 Jan '07

Hi Jeff, I understand your problem. I think you can handle the large data sets interactively using the "precomputed subsample" feature of the volume dialog. As you mentioned you need to create smaller binned versions of your data. Then you open your full size map in Chimera but do not display it. Then you use Features / Precomputed Subsamples and add the binned file (ie. subsampled data). Then when you display the data with step sizes larger than 1 where it can use the binned data it will use the binned data. In this way Chimera never needs to open the full data if you only display at binned step sizes. You can then use the zone or subregion box tools to specify a smaller piece of the map and then use the volume dialog "File / Save map as" menu entry. That always says at full resolution, so the needed part of the full size map will be read when you do that. There is a Chimera script for creating the binned data (chimera/share/VolumeProcessing/downsize.py) described in the Volume Viewer documentation in the Chimera User's Guide: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volum… Another useful tool for handling tomograms that are too large to display in Chimera at full resolution is the Volume Planes module that can be downloaded from the Chimera experimental features page http://www.cgl.ucsf.edu/chimera/experimental/experimental.html When you display just one plane at a time, Chimera only loads that plane from the map file (for most map file formats, e.g. MRC). This can allow you to flip through the planes at full resolution while having just a limited amount of data in memory at any one time. Tom ---- Date: Jan 29, 2007 hi Tom, is it possible for me to use a (previously generated) chimera marker file to zone and save a region from a volume map from a python prompt, without launching chimera? A lot of volumes I use are simply too big to handle in chimera, and if I chop up large volumes, I might have filaments running across the borders that I cut, etc. When I have done such 'chopping out' of subvolumes, it is often difficult for me to figure out which filaments I care about (or where they are ...) a priori. One solution I was thinking of is to use a several-times binned file to generate a marker file using chimera, and then to use the zone tool from a python prompt on the unbinned volume, without having to launch chimera and try to actually visualize the full, unsegmented volume. can I do this? (or, does this question make sense?) thanks, -Jeff

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Color using Beta factor
by Batsal Devkota 24 Jan '07

24 Jan '07

Hi, Is it possible to color the atoms according to their beta factor? Also, is there anyway I can search "the chimera-user archives"? batsal. -------------------------------------------------- Batsal Devkota Graduate Student, School of Biology GeorgiaInstitute ofTechnology Atlanta, GA 30332-0400

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Re: [Chimera-users] defining rotation of a chimera markers file
by Thomas Goddard 24 Jan '07

24 Jan '07

Hi Jeff, Attached is a Python script to rotate Chimera markers about the origin using specified Euler angles. You open the script with Chimera menu entry File/Open... to apply the rotation which is specified at the end of the script. Tom Jeff wrote on Wed, Jan 24, 2007: thanks Tom (and Elaine), did not have the chance to reply yet. I have not done a whole lot w/ Euler angles in general but do know there are several conventions - seems like one for each package... As for a convention, the reason this came up is b/c the slicer tool in the IMOD viewer allows the user to rotate the volume according to the angles listed in the slider tool window. I use IMOD quite a bit to look plane by plane in various orientations in a reconstruction, and I'd like to be able to go back and forth with chimera (the IMOD extension in chimera only cycles through z; for an arbitrary plane, one would have to rotate the volume and reload into chimera). So, the convention used by IMOD would be preferred by me, for practical reasons. Here's the manpage for 'rotatevol' in IMOD, which mentions the convention: http://bio3d.colorado.edu/imod/doc/man/rotatevol.html 15 lines of code is fine; I might actually be able to dissect something that size and use it to learn. If I had a script I could do it through a python prompt, which would get me started. A command in chimera would be nicer, but not required (same goes for a graphical interface). You know, if I knew how to import the marker positions into an array in python, I could probably play with this myself - I guess I would also have to know how to write out the file too, and I'd have to brush up on my rotations. I have scanned through the contents of a marker file (`cat foo.cmm | less`, for example) and realize it is text, but I don't have enough familiarity with python to parse it into something useful. If you were to write a simple script, for basic I/O of a marker file (or tell me how to go about that) and a rotation matrix / execution as an example, I could probably run with that. For instance, if I do some things in EMAN or SPIDER, I might be able to adjust the convention when needed without further assistance. At some point, I'd like to know enough to make extensions for chimera, but lack the time to plug away at it. -Jeff # ------------------------------------------------------------------------------ # Rotate all markers in the active path tracer marker set. # def rotate_markers(xform): from VolumePath import volume_path_dialog d = volume_path_dialog() if d == None: return # No marker sets exist. ms = d.active_marker_set if ms == None: return # No marker set chosen in dialog. from chimera import Point for m in ms.markers(): xyz = m.xyz() # Python tuple txyz = xform.apply(Point(*xyz)).data() m.set_xyz(txyz) # ------------------------------------------------------------------------------ # Convert Euler angles to an equivalent Chimera transformation matrix. # # Angles must be in degrees, not radians. # # Uses the most common Euler angle convention (the chi-convention) described at # # http://mathworld.wolfram.com/EulerAngles.html # def euler_transform(phi, theta, psi): from chimera import Xform, Vector xf1 = Xform.rotation(Vector(0,0,1), phi) # Rotate about z-axis xp = xf1.apply(Vector(1,0,0)) # New x-axis xf2 = Xform.rotation(xp, theta) # Rotate about new x-axis zp = xf2.apply(Vector(0,0,1)) # New z-axis xf3 = Xform.rotation(zp, psi) # Rotate about new z-axis xf = Xform() xf.premultiply(xf1) xf.premultiply(xf2) xf.premultiply(xf3) return xf # ------------------------------------------------------------------------------ # xf = euler_transform(30, 60, 45) rotate_markers(xf)

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Problem loading trajectories ....
by sharada 23 Jan '07

23 Jan '07

Dear Chimera-users, Hello, I am a brand new entry into this forum. I have started using chimera recently. I use Gromacs for my molecular modeling work. Till I become friendly with chimera I need your valuable suggestions and cooperations. I request you to kindly bear with my very silly doubts and questions. Let me explain my problem. I have a protein of 35 residues and have simulated in a box of water for 10ns. My protein has charge so in order to neutralize it I have added counterions randomly placed them in the solvent(water). The counter ions that I am adding are Cl- ions. I have created a *.trr file of the tracjectory for this 10ns. I would like to visulaize this trajectory using chimera. I am using Tools /MD/Ensemble Analysis /MD Movie to load the trr file. when I do so I am getting the following error: Unknown molecule type: CL- TypeError: __len__() should return an int (see reply log for Python traceback info) Traceback (most recent call last): File "/usr/local/chimera/share/__main__.py", line 59, in ? value = chimeraInit.init(sys.argv) File "CHIMERA/share/chimeraInit.py", line 318, in init tkgui.eventLoop() File "CHIMERA/share/chimera/tkgui.py", line 2675, in eventLoop File "CHIMERA/lib/python2.4/lib-tk/Tkinter.py", line 965, in mainloop self.tk.mainloop(n) File "CHIMERA/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1751, in __call__ File "CHIMERA/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1814, in _reporterror File "CHIMERA/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1377, in displayerror File "CHIMERA/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1747, in __call__ File "CHIMERA/share/chimera/baseDialog.py", line 231, in <lambda> File "CHIMERA/share/chimera/baseDialog.py", line 473, in OK File "CHIMERA/share/Trajectory/EnsembleLoader.py", line 87, in Apply File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line 56, in loadEnsemble File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line 67, in loadEnsemble File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 30, in __init__ File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 218, in __init__ File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 229, in _readHeader File "CHIMERA/lib/python2.4/xdrlib.py", line 194, in unpack_fstring if j > len(self.__buf): TypeError: __len__() should return an int What exactly is the problem ? How to solve it ?

4 3

File open
by Bill altenberger 23 Jan '07

23 Jan '07

We are considering using the program in a general lab environment. However, when we do a file open we are able to browse the contents of our C drive even though we have it restricted with windows group policies. Is there a way to force the program to open to a specific location and not over ride windows group policies? Thanks.

2 1

chimera startup problem
by Chen Xu 23 Jan '07

23 Jan '07

Dear List, after upgrading to 1.2304 (1.2303 freeze the computer after several minute loaded with a volume pdb file) , I have problem to start it up on (RedHat): agnieszka@raptor ~]$ chimera Error starting chimera: ValueError: attempt to create string with null pointer (see reply log for Python traceback info) Traceback (most recent call last): File "/sware/chimera/chimera-1.2304/share/__main__.py", line 59, in ? value = chimeraInit.init(sys.argv) File "CHIMERA/share/chimeraInit.py", line 255, in init tkgui.initializeGUI(exitonquit) File "CHIMERA/share/chimera/tkgui.py", line 2407, in initializeGUI File "CHIMERA/share/chimera/tkgui.py", line 2368, in createApp File "CHIMERA/share/chimera/tkgui.py", line 1784, in __init__ File "CHIMERA/share/chimera/tkgui.py", line 1811, in makeGraphicsWindow ValueError: attempt to create string with null pointer any help? -- Chen Xu Brandeis University Rosenstiel Center, MS029 Waltham, MA 02454 phone: +1 781 736 2469 fax: +1 781 736 2419

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defining rotation of a chimera markers file
by Jeff 22 Jan '07

22 Jan '07

hello, is there a way to rotate a chimera markers file in a defined way, for instance by providing a sequence of euler angles? The context is in the case of defining a marker set in a a particular volume map, say volume A, and then doing additional processing of volume A outside of chimera, perhaps just a simple series of rotations, creating volume B. now, I would like to use the same marker set in a precise way on volume B (without just visually rotating it into place by hand). is there a way to apply the same rotations to the marker set? thanks, -Jeff

2 1

Experimental features
by Edmond Alexander 22 Jan '07

22 Jan '07

Good Morning, I have attempted to load some of the Chimera "Experimental Features" following the installation instructions: > On Macintosh computers put it in > > Chimera.app/Contents/Resources/share > > > On the Mac you will need to use Finder menu entry Go / Go to Folder... > to see inside the Chimera.app folder. > > When Chimera.app/Contents/Resources/share is typed into the Go To Folder I get a message that the "Folder can not be found". Subsequent searches show only the Chimera application. I am running a Mac G4 running Mac OS 10.3.9 and iMac (Mac Intel) running Mac OS 10.4.8 My Chimera version is 1.2303 Am I missing something? Your help will be greatly appreciated. Thanks in Advance, Edmond Alexander Alexander & Turner Medical Illustration Studio

2 2

hbonds and addh geometry
by Jim Procter 22 Jan '07

22 Jan '07

Hi all. Has anyone noticed and/or fixed the slight problem with applying the hbonds command (without 'sloppy' bond geometry allowed) after adding hydrogens to a structure with addh ? The identified hbonds are marked between donor and acceptor, but the donor's proton seems often seems to lie some way off the hbond vector by a seemingly consistent amount, suggesting a systematic error in the addh protonation geometry. As an aside to this, it would be very nice to be able to re-connect the detected hydrogen bonds so that the bond vector lies between the proton and the acceptor, rather than between the heavy atoms. Does anyone have a script to do this ? thanks in advance! Jim Procter -- ------------------------------------------------------------------- J. B. Procter (VAMSAS Project) Barton Bioinformatics Research Group Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk

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Using 3dconnexion 6DOF controller with Chimera
by Shi Jiye (ROC) 22 Jan '07

22 Jan '07

Hello, Does Chimera support 6DOF controllers such as SpaceExplorer from 3dconnexion? It would be nice to have this feature. Thanks, Jiye Shi **************************************************************************** Legal Notice: This electronic mail and its attachments are intended solely for the person(s) to whom they are addressed and contain information which is confidential or otherwise protected from disclosure, except for the purpose for which they are intended. Dissemination, distribution, or reproduction by anyone other than the intended recipients is prohibited and may be illegal. If you are not an intended recipient, please immediately inform the sender and return the electronic mail and its attachments and destroy any copies which may be in your possession. UCB screens electronic mails for viruses but does not warrant that this electronic mail is free of any viruses. UCB accepts no liability for any damage caused by any virus transmitted by this electronic mail.

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AA and DNA base-pair substitutions
by David Segal 22 Jan '07

22 Jan '07

Dear Chimera-users, I would often like to take a pdb of a protein-DNA complex and just change one aa or one base pair. Can Chimera do this? If not, does anyone know of free software that can (for example, Swiss-PDB Viewer can mutate an aa, but not a base). Thanks in advance. - Dave Segal -------- David J. Segal, Ph.D. University of California, Davis Genome Center/Pharmacology 4513 GBSF 451 E. Health Sciences Dr. Davis, CA 95616 Tel: 530-754-9134 Fax: 530-754-9658 Email: djsegal(a)ucdavis.edu Web: www.genomecenter.ucdavis.edu/segal/ NOTICE: This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message

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save mol2 command
by Huang, Shengyou 22 Jan '07

22 Jan '07

Hi, Does anybody know a COMMAND which can save a mol2 format file in Chimera? Thanks! Shengyou Huang

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yet another chimera question...
by Jeff 19 Jan '07

19 Jan '07

good morning Tom, there isn't by chance a way to output the orientation/location of a given model (or, likewise, its corresponding per-model clipping plane) so that I can write down particular views that are useful, without having to re-save chimera sessions with unique IDs (my kludge as of right now). and a related follow-up - if so, how do I re-input the orientations by command line in chimera (if possible?) thanks, -jeff

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clarification regarding the application of chimera...
by harini senthil 19 Jan '07

19 Jan '07

I am a final year b.tech industrial biotech student working on docking studies between a polymer and membrane proteins of e.coli. I would like to know whether chimera can be utilised for performing polymer protein docking studies. Thanking you --------------------------------- Heres a new way to find what you're looking for - Yahoo! Answers

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Re: [Chimera-users] chimera to rebuild crystal
by Elaine Meng 18 Jan '07

18 Jan '07

Maybe a more integrated solution would be to put the additional option(s) in Unit Cell - easy for me to say, however! 8-) Elaine On Jan 12, 2007, at 2:15 PM, Thomas Goddard wrote: > Hi Elaine, > > Brady Bernard wanted to output multiple unit cells, more than 3x3x3 > in > fact (which is what multiscale can do). The script lets you set the > number > of unit cells along each axis. That isn't supported in Unit Cell. > > Sorry the Brady email wasn't posted to chimera-users. Nag Eric about > that since the original email went directly to him. Of course, I too > now > have personal email messages from Brady that should have gone to > chimera-users. > I am still figuring out how to forward the mail and have the original > sender's name appear in the chimera-users archive summary. > > Tom

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Re: [Chimera-users] Export idatmType
by Eric Pettersen 18 Jan '07

18 Jan '07

On Jan 17, 2007, at 10:47 PM, Brady Bernard wrote: > is there a way to do this with --nogui so that i can automate it in > a script? > > thanks, > brady It's pretty easy to make a Python script that opens a file, loops through open molecules and then their atoms, and prints our the atom identifier and IDATM type to that file. Here's an example: import chimera f = open("types.txt", "w") for m in chimera.openModels.list(modelTypes=[chimera.Molecule]): for a in m.atoms: print>>f, a, a.idatmType f.close() If you save the above into a file with a ".py" suffix (e.g. types.py), then you could save all the types of 1gcn with "chimera -- nogui pdb:1gcn types.py", which would create a file named "types.txt" (in the same folder as types.py) with the types listed. BTW, you need to preserve the indentation of the Python code above -- it matters to Python. If you're automating this in a shell script, it may be simpler to just print the info to standard output and redirect that into a file, rather than open the file in the Python script. The command would then be "chimera --nogui --nostatus pdb:1gcn types.py > 1gcn_types.txt" (note the "--nostatus" flag so that status messages don't get mixed into the output). The Python script becomes: import chimera for m in chimera.openModels.list(modelTypes=[chimera.Molecule]): for a in m.atoms: print a, a.idatmType --Eric > ----- Original Message ----- > From: Eric Pettersen > To: Brady Bernard > Cc: Thomas Goddard ; Elaine Meng > Sent: Tuesday, January 16, 2007 4:40 PM > Subject: Re: Export idatmType > > Hi Brady, > Tom forwarded your mail to me. There almost is a way. In the > 1.2318 snapshot, the Render By Attribute tool allows you to save > attribute values to a file using that tool's "File->Save > Attributes..." menu item (saved in the format that Define Attribute > accepts). So, why "almost"? The idatmType attribute is screened > out of the list of available attributes since it can be expensive > to compute the values -- and since you could already select by > IDATM type using the regular selection menu. But now that save > exists I will have to improve Render By Attribute so that it can > know that idatmType values are strings ahead of time (so it doesn't > have to ask for any values to figure that out). > Anyway, for your purposes it is not too hard to force Render By > Attribute to show you idatmType. First, get the 1.2318 release. > Then edit the file <your Chimera>/share/ShowAttr/__init__.py (on a > Mac: Chimera.app/Contents/Resources/share/ShowAttr/__init__.py) > and edit line 24. It will look like this: > > 'name': False, 'idatmType': False, 'idatmIsExplicit': False, > > change it to: > > 'name': False, 'idatmIsExplicit': False, > > Save the file and thereafter Render By Attribute should show you > the idatmType attribute. > > --Eric > >> hi tom - is there a quick way to save the atom types from >> idatmType to a text/log file along with the atom name or number? > >

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Re: [Chimera-users] Movie resolution
by Zoghbi, Maria 18 Jan '07

18 Jan '07

Now it works perfectly! Thanks Maria Elena Zoghbi UMass Medical School Maria.Zoghbi(a)umassmed.edu -----Original Message----- From: Thomas Goddard [mailto:goddard@cgl.ucsf.edu] Sent: Wednesday, January 17, 2007 5:04 PM To: Zoghbi, Maria Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] Movie resolution Hi Maria, Sorry the code I suggested was not correct. The new lines should have images = ... instead of image = ... Otherwise your change looks correct. Tom

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For Chimera mac users
by Eduardo Sanz-Garcia 17 Jan '07

17 Jan '07

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Re: [Chimera-users] Movie resolution
by Zoghbi, Maria 17 Jan '07

17 Jan '07

I made the change (please, see document attached to be sure I did it right). When I restarted Chimera and tried to record a movie there was an error message (see reply log attached). Maria Elena Zoghbi UMass Medical School Maria.Zoghbi(a)umassmed.edu -----Original Message----- From: Thomas Goddard [mailto:goddard@cgl.ucsf.edu] Sent: Wednesday, January 17, 2007 4:16 PM To: Zoghbi, Maria Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] Movie resolution Hi Maria, Ok, so the bug is not fixed in Chimera version 1.2304. I made a note of that in our bug database. Here is a suggestion from the original bug report that solved the problem in that case: Edit the file in you Chimera 1.2304 distribution chimera/share/MovieRecorder/RecorderHandler.py using any text editor to change line 97 from image = chimera.viewer.pilImages() to width, height = chimera.viewer.windowSize image = chimera.viewer.pilImages(width, height, supersample = 1, opacity = False) Make sure to use the same indentation as the original code since this is important in the Python language. Then restart Chimera and try movie recorder again. Let me know if that fixes the problem. Tom

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Re: [Chimera-users] Movie resolution
by Zoghbi, Maria 17 Jan '07

17 Jan '07

I see. Thanks. I am using the version 1.2304, and the platform is Windows XP. Maria Elena Zoghbi UMass Medical School Maria.Zoghbi(a)umassmed.edu -----Original Message----- From: Thomas Goddard [mailto:goddard@cgl.ucsf.edu] Sent: Wednesday, January 17, 2007 1:45 PM To: Zoghbi, Maria Subject: Re: [Chimera-users] Movie resolution Hi Maria, This is a bug. The movie capture should work for any window size without artifacts. This Chimera bug was reported earlier: http://www.cgl.ucsf.edu/cgi-bin/gnatsweb.pl?cmd=view&pr=3151&database=ch imera Pressing the "view audit trail" button on that bug report page gives more info -- more than you want to konw. Supposedly that bug was fixed in Chimera version 1.2297. If you are using a newer version of Chimera than that and you still have this problem, then send me email with your Chimera version number and platform (Windows, Linux, Mac). Tom

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bond rotation buglet
by Eric Pettersen 17 Jan '07

17 Jan '07

I just found out that the current release has a bug where it sometimes claims that a bond is terminal (and therefore won't let you rotate it) when it isn't. This occurs when there is already an active bond rotation adjacent to the desired new rotation, and the atom in common would have all its bonds in rotations. You can work around the problem by deactivating the other rotation (in the panel showing the rotations, click on the label for the rotation (under "Bond") which brings up a menu of actions, one of which is Deactivate). I also have a code fix that I could send to people that need it -- just drop me an email. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Movie resolution
by Zoghbi, Maria 17 Jan '07

17 Jan '07

Hello, I'm trying to make a movie, but the only format that I have been able to make work is the VCD (Video Compact Disc), which produces a low resolution movie (457x240). As soon as I change to a different standard format the recorded images are totally wrong (rotated, shifted, wear lines, etc). I have tried to choose my own resolution and the only one that has worked is when high=3/2width, but only when high ≤ 300. Are these restrictions for the resolution of the movies normal or am I doing something wrong? How can a make a higher resolution movie? I appreciate any help. Thanks Maria Elena Zoghbi UMass Medical School Maria.Zoghbi(a)umassmed.edu

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Re: [Chimera-users] Export idatmType
by Eric Pettersen 16 Jan '07

16 Jan '07

Hi Brady, Tom forwarded your mail to me. There almost is a way. In the 1.2318 snapshot, the Render By Attribute tool allows you to save attribute values to a file using that tool's "File->Save Attributes..." menu item (saved in the format that Define Attribute accepts). So, why "almost"? The idatmType attribute is screened out of the list of available attributes since it can be expensive to compute the values -- and since you could already select by IDATM type using the regular selection menu. But now that save exists I will have to improve Render By Attribute so that it can know that idatmType values are strings ahead of time (so it doesn't have to ask for any values to figure that out). Anyway, for your purposes it is not too hard to force Render By Attribute to show you idatmType. First, get the 1.2318 release. Then edit the file <your Chimera>/share/ShowAttr/__init__.py (on a Mac: Chimera.app/Contents/Resources/share/ShowAttr/__init__.py) and edit line 24. It will look like this: 'name': False, 'idatmType': False, 'idatmIsExplicit': False, change it to: 'name': False, 'idatmIsExplicit': False, Save the file and thereafter Render By Attribute should show you the idatmType attribute. --Eric > hi tom - is there a quick way to save the atom types from idatmType > to a text/log file along with the atom name or number?

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Fwd: chimera to rebuild crystal
by Eric Pettersen 16 Jan '07

16 Jan '07

Hi Tom, Brady's question below seems more up your alley somehow. It also seems like one of those things that should be cross-posted to the chimera-users or -dev lists for "community building" purposes, though I'll leave that up to your discretion. --Eric Begin forwarded message: > From: "Brady Bernard" <bradyb(a)u.washington.edu> > Date: January 11, 2007 5:06:21 PM PST > To: "Eric Pettersen" <pett(a)cgl.ucsf.edu> > Subject: chimera to rebuild crystal > > hi, > > i am interested in using distance-dependent statistics in a scoring > function and i would like more than the default 3x3x3 repeating units > to rebuild a crystal using cryst1 data in pdb files. how can i do > this with chimera? i will need to do this for thousands of files and > am familiar with scripting and using the -nogui option with cmd files, > etc. > > thanks in advance for your help, > > brady bernard > uw bioengineering

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Chimera doesn't display AMBER molecular dynamics trajectories with periodic boundary condition.
by juyong Lee 16 Jan '07

16 Jan '07

Hi, I'm using chimera 1.2309 version. And I found out that MD movie module in chimera doesn't display AMBER trajectory file with periodic condition correctly. I works well only with non-periodic condition trajectory file. Another visualization program, VMD, has two seperated options for AMBER trajectory file: with periodic condition and not. I prefer display style of chimera. So, I really hope to see my AMBER trajectory with Chimera. Do you have any tips for this problem? or have plan to add the format, with periodic boundary condition. :-) Thanks again for your great program and have a nice day! ============================================= Lee, juyong Ph.D student, Department of chemistry, Seoul National University, Korea. drfaust23(a)gmail.com

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