- Chimera-users - RBVI Mailing Lists

Nutate or lemniscate program to scenes/animation?
by Hurt, Darrell (NIH/NIAID) [E] 19 Nov '12

19 Nov '12

Hi Chimera folks! I love, love, love the new scene-based animation! I know that it is still under development, but it is fantastic! And the "Animation" utility panel is easy to use and understand. I love the "Rock" and "Roll" "Actions" available in the Animation panel. That goes a long way to making movie-making a point-and-click affair! I would like to suggest or propose one more "Action" in addition to "Rock" and "Roll". It is "nutate" or "lemniscate". It is basically a "rock" in both the X and Y planes at the same time. I think that it can be coded relatively simply with a cosine function about the X axis concomitant to the sine function about the Y axis that is driving the current "Rock". You can see an example of what I'm talking about here: http://youtu.be/55_cmJLe3Is Also, if I could, I would also suggest or propose that the "Rock" and "Nutate/Lemniscate" have a single parameter to control the "width" of the rock or nutation/lemniscation — maybe choices of 15, 30, 45, and 60 degrees or a free-form entry. Thanks for everything you do! Best wishes, Darrell Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office 301-402-0095 Mobile 301-758-3559 http://bioinformatics.niaid.nih.gov (Within NIH) http://exon.niaid.nih.gov (Public) Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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Re: [Chimera-users] Using marker files to place oriented density maps inside a tomogram
by Tom Goddard 16 Nov '12

16 Nov '12

Hi Daniel, Probably you can modify your script and make Chimera open the copies much faster. The python script should also achieve that. The trick with your command script is that between each command Chimera draws a frame and may update the volume dialog histograms. One way to avoid this is put all the commands on one line separated by semicolons. Maybe another better method is have one open command and one transform setting command open template.em template.em template.em ... (repeat for as many copies as you need) matrixset transforms.txt I believe the matrixset command can have the positions for as many models as you want with the model id number specified before the transform. See the Chimera manual or try matrixget to write an example file with several models being displayed to see the precise format when you have multiple transforms. A Python script could be faster still because it wouldn't need to open the same map file over and over. It could create all the map copies from the first. As an example making 100 translated copies of an open 100**3 volume took 3 seconds with the following Python from VolumeViewer import active_volume v = active_volume() from chimera import Xform for i in range(100): c = v.copy() c.openState.localXform(Xform.translation(i*20,0,0)) c.show() Tom > Hi Tom, > > > Yes, both methods that you describe work nicely. In particular, I was > not aware of the possibility of changing the level of a set of models > with a single command line operation: that does help a lot. > > The only actual annoyance that remains in my implementation for the > manipulation of sets of volumes is the loading of the volumes?. I > suspect the way I do it is too rudimentary, as I just open Chimera > passing as argument a .cmd command file that loads the same file again > and again, placing it each time in a different location, i.e: > > open 0 template.em > matrixset transform_0.cmd > open 1 template.em > matrixset transform_1.cmd > > ? and so on for hundreds of models, so that the user basically sees > the Volume Viewer getting updated with a new model and then a new one > for several minutes. I guess with the .py script that you send me I > will be able to load the volumes in a less messy manner than this one. > > Thanks for all the info! > Daniel > > >> Hi Daniel, >> >> I see. You'd like to control the contour level, color, >> surface/mesh style, step size... of all the copies as if they were >> one model instead of 100 different models, each a copy of the same >> map. For making hundreds of copies of an atomic model, the >> multiscale dialog in Chimera does this using a single model. But >> that doesn't currently work with maps. One disadvantage of having a >> single model for all the copies of a map is that the maps will all >> have to have the same color, same step size, same contour level >> because all those properties are stored with the model. Maybe that >> restriction is fine for your use. I would like to make that possible >> by allowing Chimera to place identical copies of any type of model by >> just specifying the list of positioning matrices. The model would >> just remember the list of matrices for the different placements. >> >> For now using a hundred different models of the same map is >> workable. You can't adjust all of them at the same time with the >> volume dialog. But you can adjust one to figure out the contour >> level you like and then use one volume command to set the level for >> all the copies, for example, "volume #1-100 level 1.24 color yellow >> step 2". >> >> Another approach is to make a single map by adding your hundred >> placed copies on a single grid (e.g. the tomogram grid). Then you >> open that one map and all the copies appear. The drawback is that you >> may want finer grid spacing on the individual copies then you have >> with the tomogram, and that would make the map to large and slow to >> work with (and mostly empty). If you are interested in trying this >> approach though you can use a command like "vop add #1-100 onGrid #0" >> to produce such a map after placing the hundred separate models with >> your current script. Then save that new map and use it in the future >> instead of the 100 copies. >> >> Tom >> >> >> -------- Original Message -------- >> Subject: Re: [Chimera-users] Using marker files to place oriented >> density maps inside a tomogram >> From: Daniel Castano Diez >> To: Tom Goddard >> Date: 11/15/12 7:12 AM >>> Hi Tom, >>> >>> thanks for the helpful explanation. The extension that you mention >>> you've been working on seems interesting. I guess that will allow >>> the user to change the isosurface level in one single model to >>> change it in all the models simultaneously, am I right? This would >>> solve another problem I'm having with my scripts, as they fed each >>> copy of the map into Chimera as a different model. So, I'm looking >>> forwards to trying it when it becomes available. >>> >>> best, >>> Daniel >>> >>> >>> >>>> Hi Daniel, >>>> >>>> You can use a Chimera marker file but that only knows how to place >>>> spheres. If you wanted to make use of the "map" and "matrix" >>>> attributes you added to the markers then that would require some >>>> extra Python script. That could be done -- it is just a different >>>> format of input from the script I sent you. >>>> >>>> If you can't display hundreds of copies of the map due to slow >>>> graphics then it doesn't matter how you input the data. Having >>>> hundreds of copies of the same map open doesn't load the map data >>>> more than once. So you shouldn't run out of memory. But the >>>> surface for each map might have a million triangles and it does >>>> make a separate surface copy for each copy you place in your >>>> tomogram. Of course you won't see the detail in a tiny map put >>>> into a tomogram so the solution would be to display a very coarse >>>> image of the map that is being placed many times in the tomogram. >>>> I've worked recently on making Chimera display multiple copies of >>>> identical objects without making copies of the surface in memory -- >>>> just reuse the same surface. But it is not in Chimera yet. And >>>> your graphics speed will still become unusable if you try to >>>> display too many copies with too much detail. So the main need is >>>> to show an appropriate low level of detail for all or most of your >>>> hundreds of copies. >>>> >>>> Tom >>>> >>>> >>>> -------- Original Message -------- >>>> Subject: Re: [Chimera-users] Using marker files to place oriented >>>> density maps inside a tomogram >>>> From: Daniel Castano Diez >>>> To: Tom Goddard >>>> Date: 11/14/12 1:28 PM >>>>> Hi Tom, >>>>> >>>>> thanks for the answer. Actually I already wrote some scripts for >>>>> placing each different copy of the density map as an individual >>>>> model, but this is not practical for placing hundreds of copies >>>>> (as it's the case with tomograms). I will try your python script. >>>>> >>>>> >>>>> I was under the impression that a .cmm markerfile was a better >>>>> approach, as I though that one could define a marker with more >>>>> attributes as in the example: >>>>> >>>>> <marker id="1" x="-6.1267" y="17.44" z="-3.1338" radius="0.35217"/> >>>>> >>>>> I mean, something like: >>>>> >>>>> <marker id="1" x="-6.1267" y="17.44" z="-3.1338" map >>>>> ="my_map.em" matrix = "my_matrix.txt" /> >>>>> >>>>> or similar with quaternions or euler angles... but I guess that >>>>> was wrong? That'll be a pitty, as I am interfacing Chimera with >>>>> the subtomogram averaging package Dynamo and the most stable way >>>>> seemes to be having Dynamo converting its "table" files (lists of >>>>> positions and angles) into .cmm files that could then be directly >>>>> fed into Chimera. >>>>> >>>>> Thanks! >>>>> >>>>> Daniel >>>>> >>>>> >>>>> >>>>> >>>>>> Hi Daniel, >>>>>> >>>>>> Take a look at the placem.py script which can place copies of >>>>>> maps or molecules at specified positions. >>>>>> >>>>>> http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts >>>>>> >>>>>> It specifies the rotation as a quaternion which is close to a >>>>>> rotation axis and angle description. I could show you how to >>>>>> adapt it to use Euler angles or a 3x3 rotation matrix if you like. >>>>>> >>>>>> Tom >>>>>> >>>>>> >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> I'd like to use a Chimera marker file to place multiple copies >>>>>>> of a density map in different spatial positions inside a >>>>>>> tomogram. My input is thus a single map file a set of 3d >>>>>>> locations, each attached to an euler triplet (or a rotation matrix) >>>>>>> >>>>>>> With the documentation I could find >>>>>>> >>>>>>> http://www.cgl.ucsf.edu/chimera/1.2065/docs/ContributedSoftware/volumepatht… >>>>>>> it is explained how to place spheres without orientation in a >>>>>>> volume, but I was not able to figure out how to place a density >>>>>>> map at those locations, and also how to impart a different >>>>>>> orientation to the density map located at each position. >>>>>>> >>>>>>> My question is: where could I find a description of the marker >>>>>>> file syntax that describes this functionality? >>>>>>> >>>>>>> thanks, >>>>>>> Daniel >>>>>>> >>>>>>> >>>>>>> ---------------------------------------------------------------- >>>>>>> This message was sent using IMP, the Internet Messaging Program. >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Chimera-users mailing list >>>>>>> Chimera-users(a)cgl.ucsf.edu >>>>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>>> ---------------------------------------------------------------- >>>>> This message was sent using IMP, the Internet Messaging Program. >>>>> >>>>> >>>> >>>> >>> >>> >>> >>> ---------------------------------------------------------------- >>> This message was sent using IMP, the Internet Messaging Program. >>> >>> >> >> > > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > >

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delay updating to Ubuntu 12.10
by Greg Couch 15 Nov '12

15 Nov '12

Something happened in Ubuntu 12.10 that breaks Chimera's SideView tool, even if you have the proprietary graphics driver installed. So we recommend waiting until this bug is resolved. I plan to retest Ubuntu 12.10 every two or three weeks, but if anyone finds out that it is fixed earlier, please let me know. HTH, Greg

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Re: [Chimera-users] Using marker files to place oriented density maps inside a tomogram
by Tom Goddard 15 Nov '12

15 Nov '12

Hi Daniel, I see. You'd like to control the contour level, color, surface/mesh style, step size... of all the copies as if they were one model instead of 100 different models, each a copy of the same map. For making hundreds of copies of an atomic model, the multiscale dialog in Chimera does this using a single model. But that doesn't currently work with maps. One disadvantage of having a single model for all the copies of a map is that the maps will all have to have the same color, same step size, same contour level because all those properties are stored with the model. Maybe that restriction is fine for your use. I would like to make that possible by allowing Chimera to place identical copies of any type of model by just specifying the list of positioning matrices. The model would just remember the list of matrices for the different placements. For now using a hundred different models of the same map is workable. You can't adjust all of them at the same time with the volume dialog. But you can adjust one to figure out the contour level you like and then use one volume command to set the level for all the copies, for example, "volume #1-100 level 1.24 color yellow step 2". Another approach is to make a single map by adding your hundred placed copies on a single grid (e.g. the tomogram grid). Then you open that one map and all the copies appear. The drawback is that you may want finer grid spacing on the individual copies then you have with the tomogram, and that would make the map to large and slow to work with (and mostly empty). If you are interested in trying this approach though you can use a command like "vop add #1-100 onGrid #0" to produce such a map after placing the hundred separate models with your current script. Then save that new map and use it in the future instead of the 100 copies. Tom -------- Original Message -------- Subject: Re: [Chimera-users] Using marker files to place oriented density maps inside a tomogram From: Daniel Castano Diez To: Tom Goddard Date: 11/15/12 7:12 AM > Hi Tom, > > thanks for the helpful explanation. The extension that you mention > you've been working on seems interesting. I guess that will allow the > user to change the isosurface level in one single model to change it > in all the models simultaneously, am I right? This would solve another > problem I'm having with my scripts, as they fed each copy of the map > into Chimera as a different model. So, I'm looking forwards to trying > it when it becomes available. > > best, > Daniel > > > >> Hi Daniel, >> >> You can use a Chimera marker file but that only knows how to place >> spheres. If you wanted to make use of the "map" and "matrix" >> attributes you added to the markers then that would require some >> extra Python script. That could be done -- it is just a different >> format of input from the script I sent you. >> >> If you can't display hundreds of copies of the map due to slow >> graphics then it doesn't matter how you input the data. Having >> hundreds of copies of the same map open doesn't load the map data >> more than once. So you shouldn't run out of memory. But the surface >> for each map might have a million triangles and it does make a >> separate surface copy for each copy you place in your tomogram. Of >> course you won't see the detail in a tiny map put into a tomogram so >> the solution would be to display a very coarse image of the map that >> is being placed many times in the tomogram. I've worked recently on >> making Chimera display multiple copies of identical objects without >> making copies of the surface in memory -- just reuse the same >> surface. But it is not in Chimera yet. And your graphics speed will >> still become unusable if you try to display too many copies with too >> much detail. So the main need is to show an appropriate low level of >> detail for all or most of your hundreds of copies. >> >> Tom >> >> >> -------- Original Message -------- >> Subject: Re: [Chimera-users] Using marker files to place oriented >> density maps inside a tomogram >> From: Daniel Castano Diez >> To: Tom Goddard >> Date: 11/14/12 1:28 PM >>> Hi Tom, >>> >>> thanks for the answer. Actually I already wrote some scripts for >>> placing each different copy of the density map as an individual >>> model, but this is not practical for placing hundreds of copies (as >>> it's the case with tomograms). I will try your python script. >>> >>> >>> I was under the impression that a .cmm markerfile was a better >>> approach, as I though that one could define a marker with more >>> attributes as in the example: >>> >>> <marker id="1" x="-6.1267" y="17.44" z="-3.1338" radius="0.35217"/> >>> >>> I mean, something like: >>> >>> <marker id="1" x="-6.1267" y="17.44" z="-3.1338" map ="my_map.em" >>> matrix = "my_matrix.txt" /> >>> >>> or similar with quaternions or euler angles... but I guess that was >>> wrong? That'll be a pitty, as I am interfacing Chimera with the >>> subtomogram averaging package Dynamo and the most stable way seemes >>> to be having Dynamo converting its "table" files (lists of positions >>> and angles) into .cmm files that could then be directly fed into >>> Chimera. >>> >>> Thanks! >>> >>> Daniel >>> >>> >>> >>> >>>> Hi Daniel, >>>> >>>> Take a look at the placem.py script which can place copies of maps >>>> or molecules at specified positions. >>>> >>>> http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts >>>> >>>> It specifies the rotation as a quaternion which is close to a >>>> rotation axis and angle description. I could show you how to adapt >>>> it to use Euler angles or a 3x3 rotation matrix if you like. >>>> >>>> Tom >>>> >>>> >>>> >>>>> Hi, >>>>> >>>>> I'd like to use a Chimera marker file to place multiple copies of >>>>> a density map in different spatial positions inside a tomogram. My >>>>> input is thus a single map file a set of 3d locations, each >>>>> attached to an euler triplet (or a rotation matrix) >>>>> >>>>> With the documentation I could find >>>>> >>>>> http://www.cgl.ucsf.edu/chimera/1.2065/docs/ContributedSoftware/volumepatht… >>>>> it is explained how to place spheres without orientation in a >>>>> volume, but I was not able to figure out how to place a density >>>>> map at those locations, and also how to impart a different >>>>> orientation to the density map located at each position. >>>>> >>>>> My question is: where could I find a description of the marker >>>>> file syntax that describes this functionality? >>>>> >>>>> thanks, >>>>> Daniel >>>>> >>>>> >>>>> ---------------------------------------------------------------- >>>>> This message was sent using IMP, the Internet Messaging Program. >>>>> >>>>> >>>>> _______________________________________________ >>>>> Chimera-users mailing list >>>>> Chimera-users(a)cgl.ucsf.edu >>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>>> >>>> >>>> >>> >>> >>> >>> ---------------------------------------------------------------- >>> This message was sent using IMP, the Internet Messaging Program. >>> >>> >> >> > > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > >

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Using marker files to place oriented density maps inside a tomogram
by Daniel Castano Diez 14 Nov '12

14 Nov '12

Hi, I'd like to use a Chimera marker file to place multiple copies of a density map in different spatial positions inside a tomogram. My input is thus a single map file a set of 3d locations, each attached to an euler triplet (or a rotation matrix) With the documentation I could find http://www.cgl.ucsf.edu/chimera/1.2065/docs/ContributedSoftware/volumepatht… it is explained how to place spheres without orientation in a volume, but I was not able to figure out how to place a density map at those locations, and also how to impart a different orientation to the density map located at each position. My question is: where could I find a description of the marker file syntax that describes this functionality? thanks, Daniel ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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Re: [Chimera-users] Fussy density around the particle
by Elaine Meng 14 Nov '12

14 Nov '12

On Nov 14, 2012, at 4:04 AM, Mohit Kumar wrote: > Hi Elaine, > Can you please tell me how to remove the fussy density from the plane of a > particle? > I went to Volume Viewer>Features>Planes>One to make a plane of the particle. > I can see a fussy density around the particle at the entire boundary. > How can I deactivate it ?? > Thanks in advance. > Best, > Mohit > Hi Mohit, Please send chimera questions to chimera-users(a)cgl.ucsf.edu rather than to me directly -- it allows other people to answer if I cannot, and allows other users to benefit from the information. In this case, I may not understand the question. You could (a) adjust the thresholds for density display using the Volume Viewer dialog <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/frame…> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volum…> (b) filter your map using Volume Filter (in menu under Tools... Volume Data) <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/gauss…> (c) erase parts of a map using Volume Eraser (d) segment using Segment Map etc... see "volume tour" <http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html> Best, Elaine

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lib64bz2, question, running and installing chimera
by Sai Tong 14 Nov '12

14 Nov '12

I tried to install alpha version of chimera today in a linux machine running fedora core 14 chimera-alpha-linux_x86_64.bin after installation, running chimera gives the following Traceback (most recent call last): File "/opt/UCSF/Chimera64-2012-11-14/share/__main__.py", line 69, in <module> value = chimeraInit.init(sys.argv) File "/opt/UCSF/Chimera64-2012-11-14/share/chimeraInit.py", line 594, in init import chimera File "/opt/UCSF/Chimera64-2012-11-14/share/chimera/__init__.py", line 16, in <module> from _chimera import BBox, Camera, Color, ColorGroup, DirectionalLight, LODControl, Lens, LensViewer, Light, Material, MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, PositionalLight, Selectable, SharedState, SpotLight, Sphere, Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, Xform ImportError: libbz2.so.1.0: cannot open shared object file: No such file or directory The lib64 directory contains the following: lrwxrwxrwx. /lib64/libbz2.so.1 -> libbz2.so.1.0.6 -rwxr-xr-x. /lib64/libbz2.so.1.0.6 If I install the current production release version, running chimera from this production installation would be without problem. Should I temporarily link libbz2.so.1.0.6 to libbz2.so.1.0 in /lib64 in order to make the alpha version of chimera run?

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Re: [Chimera-users] occupancy calculations
by Benjamin SCHWARZ 12 Nov '12

12 Nov '12

Hi Tom, Not sure I understand you well, my problem doesn't seem to be merely connected with threshold settings. Please have a look at the attached screenshot. I generated the red map with the occupancy tool, values range from 0 to 213. Then I saved it, changed the name, reopened it, and got that yellowish map with values from -128 to 127. It looks like a certain range of values was somehow shifted somewhere in the process… --Ben Le 10 nov. 2012 à 19:46, Tom Goddard a écrit : > Hi Ben, > > You have to set the contour level for the surface after you open the occupancy map. This is set with the volume dialog by moving the bar on the histogram or using the level entry field, or you can use the volume command (volume #0 level 0.123). The displayed level when you first created the map was apparently much lower than the level that is automatically chosen when you open the saved map file. > > Tom > > > On Nov 9, 2012, at 10:24 PM, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > >> Hi Ben, >> The save and restore of the volume map isn't the part of Chimera I work on. I'm forwarding your message to Tom Goddard, who programs the vast majority of Chimera's volumetric capabilities, and hopefully he'll get back to you with a solution soon. >> >> --Eric >> >> Begin forwarded message: >> >>> From: Benjamin SCHWARZ <schwarz.ben(a)gmail.com> >>> Date: November 9, 2012 8:29:56 AM PST >>> To: Eric Pettersen <pett(a)cgl.ucsf.edu> >>> Subject: Re: [Chimera-users] occupancy calculations >>> >>> Hi Eric, >>> >>> Creation of the map works fine, but I have issues opening it when saved. You'll find attached a picture of the map as it is computed and rendered on my screen (good), ad of what happen to it when I save it and reload it from the file. Hopes this helps. >>> >>> <image--bug-visu---good.png> >>> >>> <image--bug-visu---bad.png> >>> >>> >>>> Hi Ben, >>>> I just added an option to MD Movie to allow atomic radii to be factored in. The two options (other than the previous behavior which is also available) is to increment all grid cells within the atomic radii uniformly, or to increment those closer to the atomic center more. The latter is a very simple scheme in that the "outermost" cells are incremented by 1, the next layer by 2, the next by 3, etc. with the center cell getting the highest increment. >>>> >>>> --Eric >>> >> --- Benjamin SCHWARZ Email : schwarz(a)igbmc.fr Voice : +33 (0)3 68 85 47 30 FAX : +33 (0)3 68 85 47 18 Biocomputing group -- Integrated Structural Biology -- IGBMC 1 rue Laurent Fries, BP 10142 F - 67404 Illkirch CEDEX FRANCE

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save axes coordinates?
by esserlo＠helix.nih.gov 09 Nov '12

09 Nov '12

Hi, I'd like to write out the coordinates of helix axes and I know that this can be done in "Structure Measurements" gui window with "Save". However, I would like to be able to use a script. So how can I activate this "Save" function from a script (.com) ? Ah, there is one more thing, when I calculate the angle beween 2 helix axes the result is printed in the "Reply log" - useful but can I also automatically write this on out to keep a record? Thanks, Lothar P.S. I am currently using chimera-1.7-alpha 11/9/12 on 64 bit Linux.

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icosahedral reconstruction volume color
by Reginald McNulty 08 Nov '12

08 Nov '12

Dear Users, I've done a symmetric reconstruction utilizing Viper (I1) icosahedral symmetry with XMIPP. Is there a way to color my recon.vol file surface according to symmetry? Kind regards, Reggie -- Reginald McNulty, Ph.D. Postdoctoral Research Associate The Scripps Research Institute Johnson Lab Department of Molecular Biology La Jolla, California 92037 Email: rmcnulty(a)scripps.edu

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