- Chimera-users - RBVI Mailing Lists

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

05 Feb '07

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

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

05 Feb '07

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

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rotation by a set angle
by Eva Vanamee 05 Feb '07

05 Feb '07

Hi, I am trying to make a figure of my EM fit at different orientations. Is it possible to rotate the molecule/map by a certain angle so I know exactly the rotation between views? Thanks in advance, - Eva

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Re: [Chimera-users] not able to 'transfer markers'
by Thomas Goddard 05 Feb '07

05 Feb '07

Hi Jeff, Menu entry "Actions / Transfer selected markers to current set" in the path tracer dialog moves the markers to the marker set chosen on the first line of the path tracer dialog. That should be the same as the one chosen in the marker set scrolling list (Features / Marker set list) unless that list has multiple sets selected. The error message "Markers in one set cannot link to markers in a different set" means you tried to transfer some markers to the current set but they were connected by at least one link to markers in another set. That is not supported. There is a command, keyboard shortcut "sc" that extends the current selection to all markers connected to currently selected ones. You'll need to turn on keyboard shortcuts with main window menu entry Tools / General Controls / Accelerators On. You can have them turned on by default every time you start Chimera using the Preferences dialog (menu Favorites / Preferences) category Tools and clicking the check button in the autostart column next to "Accelerators On". One possible confusion about hiding/showing markers is that if you have any markers selected then the Actions / Show & Hide menu entries act on those selected ones no matter what marker set they belong to. If there are no markers selected then those same menu entries act on all markers in the current marker set, that is the one chosen at the top of the path tracer dialog. The marker set scrolled list is used for closing multiple marker sets and for saving multiple marker sets. This may have been the problem when you could not close a marker set. It closed the one selected in the scrolled list which was different from the "current marker set" shown at the top of the path tracer dialog. When you change the current marker set menu it unfortunately does not clear the selected marker sets in the scrolled list. That is a bug. Let me know if you can reproduce the problem hiding/showing markers. Tom Jeff wrote: > hi Tom, > > using build 2318, if I select a series of markers, and then click > 'actions -> transfer selected markers to current set', it gives the > error 'Markers not transfered. Markers in one set cannot link to markers > in a different set.' when I did this, I assumed that the 'current set' > meant the one selected in the 'marker sets' dialog box in the volume > path tracer. > > is there a way for me to get around this? I had traced out a series of > actin filaments in one set, and for practical reasons want to be able to > show/hide each marker path that corresponds to a filament; the only way > I could think of doing this was to have each filament be a separate > marker file, unless there is a command that allows me to select a single > marker and then just 'display markers connected to selected marker' > (preferred, actually), as opposed to using the up-arrow, which selects > the entire set. > > after performing the 'transfer markers' request, I was no longer able to > show/unshow the marker sets. Also, when I closed a marker set, it was > still displayed. I shut down the session and recreated it from scratch. > I'll let you know if this show/unshow/close marker file issue occurs > again and under what circumstances; it would be hard for me to claim > that it was correlated to the 'transfer markers' command, I just know > that after that point in the session I could no longer show/unshow/close > the markers. > > thanks, > > -Jeff >

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PDB file format for movie
by Mingfeng Yang 05 Feb '07

05 Feb '07

Dear Chimera users and developers, I'd like to use chimera to view the motions of a protein. If all the snapshots are to be saved in a single PDB file, what's the correct format for them? I tried the following, but chimera complained that a single structure is included only. Thanks, Mingfeng ------------------ MODEL 1 ATOM 1 N ALA 1 -4.564 -7.956 -6.531 1.00 0.00 N ATOM 2 CA ALA 1 -5.237 -8.746 -5.532 1.00 0.00 C ATOM 3 C ALA 1 -4.360 -9.172 -4.378 1.00 0.00 C ... ATOM 81 HN ALA 10 0.195 11.398 3.736 1.00 0.00 H END MODEL 2 ATOM 1 N ALA 1 -5.031 -8.234 -5.174 1.00 0.00 N .... END

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Re: [Chimera-users] question about mac laptops / workstations and chimera stability
by Thomas Goddard 05 Feb '07

05 Feb '07

Hi Jeff, I have not seen any graphics driver bug reports with the MacBook Pro with X1600 graphics. I just ordered this machine to replace my four year old Dell with Quadro 4 graphics -- I am confident it will work well using volume data in Chimera. Here is our graphics driver bug page of problems observed with Chimera http://www.cgl.ucsf.edu/chimera/graphicsbugs.html It only has about 1/3 of the driver bugs and I will be adding more from our Chimera bug tracking system when I have time. Tom

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volume path tracer / render surface with marker set
by Jeff 02 Feb '07

02 Feb '07

hello, is there a way to render a surface of arbitrary thickness using a marker set? as in, fit some sort of spline to a marker set, with the constraint being that the algorithm assumes they all lie on the same surface? this would be useful for modeling membranes, perhaps it is already implemented and I am not seeing it in the dialogs. thanks, -J

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Copying volume settings to a second data set
by Thomas Goddard 02 Feb '07

02 Feb '07

Hi Jeff, There is no capability to copy settings (thresholds, colors, brightness, display style, rendering options) that are specific to each volume data set to another data set. That would be useful and I'll add it to the feature request list. Here are some hacks to achieve this. I don't think they are worth the trouble to use but you can decide. If you save a Chimera session with a volume having settings you want to reuse you can edit the session file changing the line: 'path': 'F:\\cygwin\\home\\Tom\\work\\volume\\emd\\emd_1282.map', to 'path': 'F:\\cygwin\\home\\Tom\\work\\volume\\emd\\XXX.map', Then when you reopen that session Chimera will say it cannot find the map file and ask you to select a new map file with a file open dialog. You can choose some other map. The settings from the original map will then be applied to this newly opened map. Another hack is to use the Volume Series tool available on the experimental features web page: http://www.cgl.ucsf.edu/chimera/experimental/experimental.html You can open your maps that you want to use the same settings for as a "volume series". That tool copies settings when you use it to flip between volume in a series. It can even adjust thresholds so they have the same rank position on the histogram (e.g. greater than 94% of voxel values). Tom Jeff wrote: > thanks Tom, > > is there a way to save the thresholds (and color settings) in the > volume viewer, so that when I close a map and reopen a > similar/filtered one, I don't have to re-do all the settings > (brightness and transparency too, for instance) > > i realize the histrogram changes for each map, but even if it saved > how many control points (and their colors) were there, that would > work. is there a 'save volume viewer state' button? I could not find one. > > -Jeff >

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Question on how to represent only chain A of Chimera
by nsomboon＠berkeley.edu 02 Feb '07

02 Feb '07

Hi, I need help. I received the modeling structures of my query (black) and the best representative 1qopB (magenta) through MODWEB, and used Chimera to visualize them (please see attached file). However, the magenta structure also contains 1qopA, in which I only want the 1qopB and don't want the 1qopA. I read through tutorials but cannot find a way to get rid of the chain A of the 1qop. Hence, could you please direct me of how to cut out chain A of 1qop in this attached file? Thank you very much. Sincerely yours, Nara

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Saving modified PDB files
by Bernard Heymann 02 Feb '07

02 Feb '07

I have a problem saving PDB files relative to density maps in recent versions of Chimera. When I load a PDB file and move it relative to a density map, and then try to save it relative to the density map, it does not apply the transformation to the PDB coordinates. This used to work in older versions. My workaround is to have another molecule open and save the transformed one relative to that. However, I would prefer to be able to save a transformed molecule relative to a density map. Can this be fixed? Bernard Heymann, Research Fellow Rm 1515, 50 South Dr., MSC 8025, NIAMS, NIH Bethesda MD 20892-8025 Tel. 301-451-8241, Fax. 301-480-7629

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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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