- Chimera-users - RBVI Mailing Lists

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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Re: [Chimera-users] Ubuntu 12.04 and Chimera 1.6.2
by Greg Couch 06 Nov '12

06 Nov '12

There are lots of things that could be wrong. To confirm that the X11/OpenGL GLX extension is missing, run the glxinfo program from the mesa-utils package (if you need to install mesa-utils, installing the associated dependencies might solve your problem) -- it should fail. Next examine /var/log/Xorg.0.log to see the error the X11 server has loading the GLX extension. Fix that error, restart the X11 server, and repeat until the glxinfo program works. Then Chimera should work too. Last bit of advice, a simple thing to try is to (re)install the graphics driver. If you have AMD/ATI or NVIDIA graphics, we strongly recommend that you install the proprietary driver that is installed with the Additional Drivers tool in the System Settings dialog. If you have Intel graphics and glxinfo works, but Chimera doesn't, then make sure you have all the Ubuntu patches installed. But even if you keep your system up-to-date, if you have Intel graphics, you should switch to newer versions of Ubuntu when they come out -- for instance, today, you should upgrade to 12.10, and I'd recommend 13.04 when it comes out, /ad infinitum/ or at least for the next 5 years, until the Intel graphics driver is much less buggy (it has drastically improved in the last couple of years, but there is much more being done). HTH, Greg On 11/06/2012 12:26 PM, sette(a)uniroma2.it wrote: > > Dear all, > > in Ubuntu 12.04, 32 bit, I have the following error message when > starting Chimera 1.6.2: > > "Error initializing OpenGL: X server is missing OpenGL GLX extension. > Couldn't configure togl widget". > > Do you know a solution for this problem? > > Thanks, > Marco > > > Dr.Marco Sette, Ph.D. > > Department of Chemical Sciences and Technology > University of Rome, "Tor Vergata" > via della Ricerca Scientifica, 00133, Rome, Italy > e-mail: sette(a)uniroma2.it > e-mail: m77it(a)yahoo.it > Tel.: +39-0672594424 > Fax: +39-0672594328 > > www.rete29aprile.it > > > ---------------------------------------------------------------- > Invito da parte dell'Ateneo: > Il tuo futuro e quello della Ricerca Scientifica hanno bisogno del > tuo aiuto. Dona il 5 x mille all'Universita' di Roma Tor Vergata > codice fiscale: 80213750583 http://5x1000.uniroma2.it

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Re: [Chimera-users] Problem with RMSD calculation
by Eric Pettersen 06 Nov '12

06 Nov '12

On Nov 2, 2012, at 1:33 AM, Aditi Gangopadhyay wrote: > Dear Sir/Madam, > > I've been using Chimera for the calculation of RMSD of two ligands associated with a protein. (In my specific case, it is the same ligand, one being associated with the usual protein, and the other with the protein bound to a small molecule). However, I have had a problem with this, since the RMSD values are differing when I select my concerned ligand using GUI and when I select using the ctrl+drag way. I would be very grateful if you would kindly tell me where I'm going wrong in my selection or somewhere else. Thank you so much in advance for your help! > > Regards, > Aditi. > -- > Aditi Gangopadhyay > > Junior Research Fellow > DBT Centre for Bioinformatics > Presidency University > Kolkata, India Hi Adit, I'm assuming you are using the "match" or "rmsd" command to measure the RMSD. The problem with using a selection as an argument to the command is that the atoms are matched in the same order as they were selected. This is fine if you selected the atoms one by one (with shift-control-click), but a control-drag adds the atoms to the selection in an arbitrary order. Probably the easiest way to specify your ligand in the match command, assuming there is only one instance of the ligand in each model and the models are #0 and #1 (and the ligand name is, say, "XYZ"): rmsd #0:xyz #1:xyz --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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MD analysis : get clusters
by Benjamin SCHWARZ 05 Nov '12

05 Nov '12

Hi list, I clustered a bunch of structures using the MD clustering tool, I am very happy with the result but I can't find how to download/save the result. Is there a way for instance to copy-paste the columns indicating the number of models as well as the index of the representative for each cluster; alternatively, is possible to sort out frames by clusters ? If there are command shortcuts to manipulate the clustering, I'd be happy to get them, or to get a link to it in the manual. Chimera is really a great tool, but the learning curve appears really steep ;) Ultimately, I wonder about the type of clustering used here. I suspect a complete linkage but I couldn't find the confirmation in the manual. Any info on that ? Thanks a lot for your extremely good work, and the fast answers on this mailing list --Ben

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occupancy calculations
by Benjamin SCHWARZ 02 Nov '12

02 Nov '12

Hi list, I am using the MD->occupancy tool to produce occupancy densities of a very coarse grained model (I have a few spheres, with big radii : approximatively 10 spheres with 10A radius each). My problem is that the density is computed only for the center of each sphere, which tells me where the center stands. To have a better feeling of the space occupied by each sphere I'd rather like a density computed for the whole sphere (updating each cell of the grid by either incrementing if the cell is covered by the sphere, or why not with any type of kernel centered on the sphere and depending on the sphere's radius.). Can I do that with Chimera ? And if so, How ? thanks --Ben

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Re: [Chimera-users] Regarding Hydrogen Bond
by Elaine Meng 01 Nov '12

01 Nov '12

Dear Amit, You can identify hydrogen bonds with FindHBond (in menu under Tools... Structure Analysis). Click the Help button on that tool or see here for instructions: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbon…> If you want to analyze the environment around the metal and then add metal coordination bonds, you could use Metal Geometry (in menu under Tools... Structure Analysis): <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/metalgeom/metalgeo…> If you don't care about analysis and just want to draw a line between two atoms, you could do that using either of the following: (A) distance measurements, for example using the Distances tool (change label to "none" if you don't want to see the distance value) <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/stru…> (B) PseudoBond Reader <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.…> Please send Chimera questions to the chimera-users(a)cgl.ucsf.edu address so that everybody can benefit. You can search the manual using Help... Search Documentation in the Chimera menu, and you can search the chimera-users messages here: <http://www.cgl.ucsf.edu/chimera/docs/feedback.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 24, 2012, at 8:54 AM, Amit Jaiswal wrote: > Dear Dr.Meng, > Many thanks for your mail and suggestion for Metal fixation. I have done what you have advised. So, now my metal is near the catalytic site. So the next step is to form bond between Mg and Aspartic Acid residues. Now, I am confused. So I want to ask weather hydrogen bond and co-ordinate bond can be formed in Chimera? > Please do let me know. >

2 3

aligning multiple models in the same session
by m.sani＠nki.nl 30 Oct '12

30 Oct '12

Hi, I have 4 EM maps opened in one session and cant seem to get them all to align to a central map as origin. I have tried to fit them by hand onto one another and then move it translationally with “move” command to translates a specified model by a distance along a specified axis; in addition to a translational shift, the models also seems to be slightly rotated with respect to one another (see attach image). Can you help please? Musa Sani, PhD --------------------------------------------- Cell Biology II(B6) The Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital Plesmanlaan 121, 1066CX Amsterdam, the Netherlands, mobile: +31 625 498 194 Tel: +31 20 512 1008

2 1

Amber-style mol2 name
by Nikolay Igorovich Rodionov 26 Oct '12

26 Oct '12

Hi all, Simple Questions: To create mol2 files with naming compatible with Ambersuite programs I would have to save with non-sybyl hydrogen naming, yes? Also, after I save the files with the amber style naming scheme, which atom name column has the AMBER style naming (there are two)? Thanks! Nikolay Rodionov| MBA Candidate & B.S. Bioengineering 2015 Martin J. Whitman School of Management & L.C. Smith College of Engineering at Syracuse University Syracuse, New York 13244 Phone: 281.301.9401| Email: Nirodion(a)syr.edu

2 6

how to mask irregular shape in EM density map
by sy31802 25 Oct '12

25 Oct '12

Dear all, We want to color our EM density map , so we need mask different part of the map in order to distinguish them with different colors. Unfortunately, the sample is not irregular shape , we could not use "shape" to mask volume as usually. Could anyone give some suggestion? We also use Amira for 3D rendering. We think the rendering in amira is just the mask, so we want solve the problem the mask the irregular shape with amira , have anyone done with it? best regard 2012-10-25 sy31802

2 1

Re: [Chimera-users] segmentation fault
by Tim Richardson 25 Oct '12

25 Oct '12

Hi, I'm getting segmentation faults when using chimera. I tried to produce a backtrace, but got an error: [tim@nest ~]$ gdb chimera core.3777 GNU gdb (GDB) Fedora (7.4.50.20120120-50.fc17) Copyright (C) 2012 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html > This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Type "show copying" and "show warranty" for details. This GDB was configured as "i686-redhat-linux-gnu". For bug reporting instructions, please see: <http://www.gnu.org/software/gdb/bugs/>... "/usr/bin/chimera": not in executable format: File format not recognized [New LWP 3777] [New LWP 3787] Core was generated by `/opt/UCSF/Chimera-1.6.2/bin/python2.7 /opt/UCSF/Chimera-1.6.2/share/__main__.py'. Program terminated with signal 11, Segmentation fault. #0 0xb578ddc7 in ?? () (gdb) bt #0 0xb578ddc7 in ?? () #1 0x0963be90 in ?? () Backtrace stopped: previous frame inner to this frame (corrupt stack?) Could you advise how I might avoid a segmentation fault and what I'm doing wrong with the backtrace. Is there anything I can do short of installing a VM and running the windows version? Many thanks, Tim Richardson @timrich

2 1

Regarding Metal Fixing in Protein
by Amit Jaiswal 24 Oct '12

24 Oct '12

Dear Sir /Mam, I am new to Chimera and thus facing problems in inserting Metal in my protein. I am using the Build structure command in Chimera but I am unable to move the metal from one place to the other. Please guide me out in fixing the metal. -- Yours Sincerely, ~~~~~~~~~~~~~~~~~~~~~~~~ Amit Jaiswal, Department of Bioinformatics, School of Life Sciences, Pondicherry Central University, Kalapet, Pondicherry, Puducherry - 605 014. Phone No.: +91 8124954834. ~~~~~~~~~~~~~~~~~~~~~~~~~

3 3

pipes and planks
by Ishu Saraogi 23 Oct '12

23 Oct '12

Dear Chimera Users: I have been trying to makes pipes and planks in different colors for a co-crystal structure. I want each protein to be a certain color. The user manual says that I need to select "No colors" in the pipes and planks menu. However, this button is deactivated in my program. Has anyone else had that problem and is there a fix? I have tried using axes/planes command but it does not give me loops and sheets that I also need. Any advice will be greatly appreciated. Thanks! Ishu -- Ishu Saraogi, Ph.D. Postdoctoral Scholar California Institute of Technology 1200 E. California Blvd., MC 147-75 Pasadena, CA 91125-4100 USA Phone: (626)395 4071

2 1

Label help
by Hansen, Bryan (NIH/NIAID) [F] 23 Oct '12

23 Oct '12

Hi all, I was wondering how to increase the font size of the label of an amino acid? I'm guessing this is really simple and I'm just missing something, but any tips are appreciated. Bryan

2 2

scripting problem
by Strotz von Moos Dean 22 Oct '12

22 Oct '12

Hi, I have a question to the following code. I can not figure out why certain atom types are not understood (HG, QD etc). The atom types occur in the structure and I can select them through the terminal or add them as pseudo bonds through the pseudoBond reader. For a QD1 one for instance I get: KeyError: 'QD1' <module> grp.newPseudoBond(res[r1].atomsMap[A1][0],res[r2].atomsMap[A2][0]) Excerpt from the input file: 7 HA 7 H red #this is understood 7 H 7 QD1 yellow #error message for QD1 What is wrong with my code? The A1 = str(A1) ? How would I do it alternatively? All the best and many thanks Dean import chimera from chimera.colorTable import getColorByName from chimera.misc import getPseudoBondGroup from chimera import runCommand as rC # use 'rc' as shorthand for runCommand model = chimera.openModels.open('xxx.pdb') rC('show #0') rC('ribbon') rC('ribcolor gray') rC('background solid white') rC('unset depthCue') ins = open('pseudobondsToAdd.txt', "r" ) array = [] for line in ins: array.append(line) ins.close() for line in array: r1, A1, r2, A2, c = line.split() # Split the line on white space. r1 = int(r1) r2 = int(r2) A1 = str(A1) A2 = str(A2) c = str(c) res = model[0].residues grp = getPseudoBondGroup("mybonds", associateWith=model) grp.newPseudoBond(res[r1].atomsMap[A1][0],res[r2].atomsMap[A2][0]) grp.color = getColorByName(c) ETH Zürich Dean Strotz Laboratorium f. Physikalische Chemie HCI F 217 Wolfgang-Pauli-Str. 10 8093 Zürich E-Mail: dean.strotz(a)phys.chem.ethz.ch<mailto:dean.strotz@phys.chem.ethz.ch>

2 3

Show molecular surface for one chain only
by Hurt, Darrell (NIH/NIAID) [E] 22 Oct '12

22 Oct '12

Hi Chimera folks, I have a peptide bound to a protein. They are two separate chains in single PDB. I want to show the molecular surface for the protein, but not the peptide (to see the surface where the peptide binds to the protein). This is easy (the default, actually) for small molecules. But when I select the chain of the protein and display its surface, the surface is "broken" around the peptide and I cannot see what I want. The rest of the surface is OK, but in the area of interest, I cannot see the surface. I tried the "Intersurf" command and it sort of works, but I want an MSMS molecular surface of the protein with the peptide sitting in it. Is there some trick for this other than separating the peptide from the protein and putting it into a separate model? Thanks, 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.

2 2

Feature request: changing default color for H-bonds
by Miguel Ortiz Lombardía 21 Oct '12

21 Oct '12

Hi, I think the subject of the message is explicit enough... Perhaps the option of having a default color different than cyan for hydrogen bonds already exists, but I have failed to find it. I have this line in my .chimera/preferences file: 'FindHBonds': {'line width': 2.0}, So I tried to include something like 'color: (0.0, 0.0, 0.0, 1.0)' (or bond color or H-bond color...) in the FindHBonds dictionary, alas without success. Let me give some rationale: I prefer having a white background, against which cyan is not really very visible when the structure gets complex. Not to me eyes at least. Thank you! Best regards, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR7257) CNRS, Aix-Marseille Université Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombardia@afmb.univ-mrs.fr http://w2.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

2 2

coloring 3D maps according to local cross-correlation fit of docked PDB structures
by Jean-Francois Menetret 19 Oct '12

19 Oct '12

Dear users, we would like to color a Cryo-EM map according to the cross-correlation fit of docked PDB structures. Is that possible in Chimera ? Best wishes J-F Menetret

2 3

H-bonds - molecules selection questions
by Marek Maly 18 Oct '12

18 Oct '12

Hello all, #1 I am just curious if it is in Chimera implemented possibility to select all the molecules which are connected via H-bonds with previously selected ("primary") molecule. If it is not implemented I would vote for putting it in the developers queue as it would allow to show easily and clearly (after action command "show selected only") just all the molecules from the given solution directly interacting with previously selected "primary" molecule and it would be a nice and useful feature I think. Perhaps the optimal solution would be to add into "H-bond Parameters" table an additional "clik choice" which would ensure (if marked) that together with visualizing of all H-bonds (defined in the table) will be also selected all molecules which are connected by that H-bonds. (as the supplementary option might be eventually selection of end residues only (not whole molecules) which might be also useful in some cases) #2 Similarly would be cool to have in menu-table "Select -> Zone..." except "Select all atoms/bonds of any residue in selection zone" also possibility like: "Select all atoms/bonds of any MOLECULE having at least one atom in selection zone". Then again using the action "show selected only" one might have quick and nice picture only of all and WHOLE molecules which are in the defined neighbourhood of the initially selected "primary" molecule. #3 Perhaps is it shame :)) but until now I was not able to find the right button to clear/delete previously visualized H-bonds. So my solution (probably not so much elegant) is that I simply select one atom (which is really not the candidate for H-bond ) like C atom and then I ask to visualize all H-bonds which has this atom as the one end. So naturally no H-bond is found and if I do not mark "Retain currently displayed H-bonds" also the previously visualized H-bonds are deleted. But perhaps there is more elegant solution, if not button so at least some command ? Thanks in advance ! Best wishes, Marek

4 5

Three-dimensional surface trace
by Larsson, Per (pl6n) 18 Oct '12

18 Oct '12

Dear Chimera-users I have a problem that I'm not sure can be solved in Chimera, but I thought I'd put the questions out there. Have search the archives, but couldn't turn up anything really relevant. I have a set of pdb-structures (snapshots of the same protein from a molecular dynamics simulation). The protein sits in a membrane and has a bunch of floppy loops that protrude into the solvent region. My aim is to be able to make a plot (in 3D) of the space explored by these loops over the entire simulation, essentially to see if some regions of space are preferred over others. What I thought of doing was to calculate the surface regions traced out by the loops projected on the half-sphere formed by the membrane in the x-y-plane and z>0. I hope that makes sense! Is something like this even possible in Chimera, or should I look elsewhere for a solution (perhaps inventing my own method?) Thanks /Per Larsson, University of Virginia

2 1

Re: [Chimera-users] multialign
by Tom Goddard 17 Oct '12

17 Oct '12

Hi Ed, I don't know if more than one chain can be associated with a sequence in Multalign Viewer. The documentation says " A structure (even if it has multiple chains) cannot be associated with more than one sequence, but a single sequence can be associated with more than one structure." http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mu… That doesn't really say whether multiple chains of a single structure can associate with a sequence, only that multiple structures (different PDB models) can associate with the same sequence. So I tried it as I'm sure you did and I was not able to make it associate more than one chain (I used groel 1grl) with the same sequence in a multiple alignment. When I load the structure it associates chain A but not any of the other chains. Then if I use MultAlign Viewer menu Structure / Associations... to associate chain B with the same sequence then it seems to lose the association of chain A. At least when I select residues on the sequence, only chain B on the structure has residues selected. I'm forwarding this to the Chimera list since Elaine Meng or Eric Pettersen will have a better answer. Tom > Hi, > I am wondering if this is a bug or limitation in Chimera, or if I am > missing something. I have a molecular model of F-actin, with many > identical chains. Using the Multialign Viewer, it appears that I can > only do a 1 to 1 mapping of a single chain to a single sequence. How > can I map 10 identical chains to one sequence? > Regards, > Ed > -- > > <imap://goddard@imap.sonic.net:993/fetch%3EUID%3E.INBOX%3E23891?header=quotebody&part=1.2.3&filename=signature.html> > > Edward H. Egelman, Ph.D. > > Professor > > Dept. of Biochemistry and Molecular Genetics > University of Virginia >

3 2

(no subject)
by Ondřej Holas 17 Oct '12

17 Oct '12

Greetings, I have encountered this problem with energy minimization of pyrazinamidase molecule. This molecule contains within its structure iron atom which Chimera does not support. Therefore I cannot find the way to overcome this problem. Is there any way to add iron to supported elements or any other way to solve this? Best regards -- Ondrej Holas Ph.D. Department of Pharmaceutical Chemistry and Drug Control Faculty of Pharmacy Heyrovského 1203 500 05 Hradec Kralove Czech Republic

2 1

Need Information
by wisdom＠sanbi.ac.za 16 Oct '12

16 Oct '12

Hi, I am Wisdom, an MSc Bioinformatics student of the University of the Western Cape, South Africa. I wish to understand the meaning of the colouring of the individual amino acids in the sequence window of multiple sequence alignment as per the attached. I one see that all the Rs indicated by the black arrow are all red while the blue arrow has black Rs and orange Gs in the same column. There are other similar coloring all over the alignment. What does each (green, black, blue, orange, purple,red ) colour represent? Thanks Wisdom

2 1

density maps & sub-region selection.
by Hernando J Sosa 16 Oct '12

16 Oct '12

Hi, I am trying to select subregions in two density maps using the subregion selection option in the volume viewer. When selecting the same subregion different sub-volumes in the two maps are selected (there is a displacement between the ROIs along the Z axis) even though the two maps are aligned to each other (or appear to be aligned in the display window). Both maps are in the MRC format and both have a voxel size of 2A/pix. ? Ideally what I want to do is to select equivalent regions of the two maps and then save them as new density maps. How can I best do this? Thanks Hernando. UCSF Chimera version alpha 1.7 (build 36659) on Windows 7 64b

3 2

Trajectories, movies and multi-scale models
by Evan Kantrowitz 15 Oct '12

15 Oct '12

Hi I have a series of pdb files corresponding to a quaternary conformational change involving 12 chains. I can read these pdb files into Chimera via the MD movie, and I can view the conformational change. What I would like to do is to convert the movie into one using multiscale models with one surface for each chain. If I go into multiscale I can convert the initial pdb to multiscale, but it does not carry over to the other pdb files corresponding to the conformational change. Any suggestions would be appreciated. Evan Kantrowitz ------------------------------------------------------------------- Evan R. Kantrowitz, Ph.D evan.kantrowitz(a)bc.edu Boston College Tel. 617-552-4558 Department of Chemistry FAX 617-552-2705 Merkert Chemistry Center, Rm 239 www2.bc.edu/~kantrow Chestnut Hill, MA 02467 -------------------------------------------------------------------

2 1

Re: [Chimera-users] Any option for terminating minimization without losing prior iterations?
by Elaine Meng 12 Oct '12

12 Oct '12

On Oct 11, 2012, at 5:42 PM, Thomas W. Sturgill wrote: > Dear Elaine, > Is there a way to interrupt minimization run without losing everything? > Is this running on the laptop or at a computer at UCSF? > Any link to list of your prior answers to questions on the minimization? > Thank you, > Tom Sturgill Hi Thomas, There is no "restart" if you interrupt the minimization, but you will still have the coordinates of the last update (you don't lose everything). The calculation runs on your own computer. You can see the minimization help by clicking the Help button on the GUI, or using command "help minimize". <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.…> Please send Chimera questions to chimera-users(a)cgl.ucsf.edu instead of to me personally -- the chimera-users messages can be searched (for example, for "minimization"): <http://www.cgl.ucsf.edu/chimera/docs/feedback.html> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

2 2

Depicting buried surfaces
by Tom Goddard 12 Oct '12

12 Oct '12

> Hi Tom, > I have a non-EM density question! > Is there a way to display the buried surface between two PDB chains in Chimera? Something like what GRASP does: > http://www.csb.yale.edu/poststructure/grasp/grasp2.html > > I know I can measure the area with: > "measure buriedArea :.A :.B" > but is there a way to display the buried surfaces? > Thanks! > -gabe > > Hi Gabe, The measure buriedArea command sets a value for each atom giving the area buried (square Angstroms). So you can use measure buriedArea :.A :.B surfcat a :.A surfcat b :.B color pink :.A color lightblue :.B surface @/buriedSESArea>1 The surfcat command just defines chains A and B as two different objects for surfacing and the surface command show the surface patches associated with all atoms having buried solvent excluded surface area greater than 1 square Angstrom. It shows the entire patch of area for those atoms, not just the part that is buried. So it is pretty ugly and a bigger surface then just the buried part. For a much prettier picture but a slightly different measurement you might try instead split #0 surface measure contactArea #0.1 #0.2 2 slab 0.5 The split puts chains A and B in two models #0.1 and #0.2. The "surface" makes surfaces on each. And the "measure contactArea..." finds all points on one surface within 2 Angstroms of any point on the other surface and displays a pretty looking slab depicting the surface (attached picture). This is a different definition of buried area but might do. http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/measure.html#… Tom

2 1

Sybyl - Amber atom type dictionary
by Nikolay Igorovich Rodionov 12 Oct '12

12 Oct '12

Hi all, I was wondering if there is a text editor readable dictionary file that shows Sybyl atom types and their complementary Amber/GAFF atom types names inside the Chimera program contents folder. Thanks, Nikolay Rodionov Nikolay Rodionov| MBA Candidate & B.S. Bioengineering 2015 Martin J. Whitman School of Management & L.C. Smith College of Engineering at Syracuse University Syracuse, New York 13244 Phone: 281.301.9401| Email: Nirodion(a)syr.edu

2 1

Re: [Chimera-users] APBS interface in Chimera
by Elaine Meng 11 Oct '12

11 Oct '12

Hi Boaz, It is brand new, so you have not at all been negligent! I only documented it a few days ago. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html> Currently it does not have the option to use a locally installed APBS -- it uses an APBS web service provided by the National Biomedical Computation Resource. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 8, 2012, at 9:24 AM, Boaz Shaanan wrote: > Hi, > Totally due to my negligence I've only just discovered the long sought APBS interface in the daily build (the one I'm using is from 25/9). Well done Chimera and APBS teams! > > Practical question: I don't see on the APBS pull-down menu where I define the location of the executable (I'm talking about the Windows version right now, soon I'll try the linux version too). Is it clever enough to find it wherever APBS is installed or have I missed something? > > Cheers, > Boaz

4 3

How to change the font for residue label
by Jean Didier Pie Marechal 11 Oct '12

11 Oct '12

Hi, I would like labels to appear bigger like with a bold font. How is that possible? Best JD Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://asklipio.qf.uab.es ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Dimecres, Octubre 10, 2012 9:00 pm Assumpte: Chimera-users Digest, Vol 114, Issue 11 > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: Coloring nucleic acid ladder with opacity. Possible bug? > (Tom Goddard) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Wed, 10 Oct 2012 10:04:13 -0700 > From: Tom Goddard <goddard(a)sonic.net> > To: Rebecca Swett <rswett(a)chem.wayne.edu> > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] Coloring nucleic acid ladder with > opacity. Possible bug? > Message-ID: <5075AA8D.5050304(a)sonic.net> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Rebecca, > > I put in a fix so that nucleotide ladder transparency looks right > in > tonight's daily builds. The fix applies to all Chimera VRML models > when > single-layer transparency is used. If multi-layer transparency is > used > then the opacity times the red,green,blue values of all transparent > layers are added together without regard to which layers are in > front of > which other layers, and that will still produce overly bright and > incorrect transparency. That is hard to fix. The single-layer > transparency mode is the default in Chimera 1.6 and later. > > Tom > > -------- Original Message -------- > Subject: Re: [Chimera-users] Coloring nucleic acid ladder with > opacity. > Possible bug? > From: Tom Goddard > To: Rebecca Swett > Date: 10/9/12 6:11 PM > > Hi Rebecca, > > > > Transparency does not work well with Chimera's nucleotide > > representations (slabs, ladder). Here's a technical explanation > that > > may help you understand why you see what you see. The > transparent > > nucleotide ladder is shown by multiplying the red, green, blue > color > > components (range 0 to 1) by the opacity (= 1 - transparency) and > > those color values are simply added to the image. Even in > > single-layer transparency mode both the back and the front of the > > cylinders are being added which makes the colors twice as bright > as > > they should be and can make it appear entirely white if rgb > values all > > end up greater than 1. > > > > This is a defective way to show something transparent. > Nucleotides > > are drawn as "VRML" models and all such Chimera models have this > > deficiency. Normal surfaces and molecules in Chimera do not have > this > > problem with transparency. It may be possible to fix the VRML > > transparency so it respects the "single-layer transparency" > option and > > that would make it much better since front and back side colors > would > > not get added creating an overly bright (sometimes white) > appearance.> > > Tom > > > > > > -------- Original Message -------- > > Subject: Re: [Chimera-users] Coloring nucleic acid ladder with > > opacity. Possible bug? > > From: Greg Couch > > To: Rebecca Swett > > Date: 10/9/12 5:31 PM > >> It's not a feature. :-) For me, transparency for ladder rungs > kinda > >> works -- the rungs are transparent, but not enough. And I only > see > >> opaque white when the ladder rungs are facing the key light. You > >> could mitigate the opaque white by moving the model or the key > >> light. If you are seeing different results or if you're > interested > >> in being notified after the bug is fixed, please file a bug report. > >> > >> FYI, in the Chimera daily build (available tomorrow), I've > eliminated > >> the extra cylinder caps that are exposed when you make the > ladder > >> transparent, so you can get a slightly better picture. > >> > >> HTH, > >> > >> Greg > >> > >> On 10/07/2012 07:01 PM, Rebecca Swett wrote: > >>> Hey all, quick question on coloring here. I'm handling a > structure > >>> that has nucleic acids and protein. I'd like to represent the > >>> nucleic acids with the ladder representation and then have them > at a > >>> lower opacity to bring focus to the protein structure. When I > try > >>> coloring the ladder with opacity, the ribbons color just fine, > but > >>> the rungs go opaque white. Is this a bug, or has anyone gotten > this > >>> to work? I just updated to 1.6.2. Thanks for any help. > >>> ~Rebecca > >>> > >>> Rebecca Swett > >>> Wayne State University > >>> 357 Chemistry > >>> Detroit, MI 48201 > >>> > >>> Lab Phone 313-577-0552 > >>> Cell Phone 906-235-0768 > >> > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 114, Issue 11 > ********************************************** >

2 1

(no subject)
by Francesco Pietra 10 Oct '12

10 Oct '12

Hello: chimera production version 1.6.2 (build 36855) 2012-07-06 17:55:00 UTC is unable to restore *.py files saved with chimera alpha version 1.7 (build 36726) 2012-06-21 01:06:17 UTC on another computer. Both computers running GNU-Linux Debian amd64 wheezy.. Error message "cannot open session that was saved in a newer version of Chimera; update your version" Does "alpha version" override date and stable compilations? The unable version has a more recent date. Then, I have installed the latest stable version of chimera, and the error was the same. Thanks for advice francesco pietra

3 2

distance dash line thickness in rendering
by Andrew Waight 10 Oct '12

10 Oct '12

Howdy everyone, I love this program! Anyway I'm trying to make some figures with distance dashes included. I can obviously change the line thickness (pseudobond display options) in the program, but when I save a high resolution image (no pov ray) the line thickness in has no effect. What to do? Thanks for your help. Drew Waight Stroud Lab Genentech Hall S414

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Met CH3 and NH3+ hydrogen optimization
by Visvaldas K. 09 Oct '12

09 Oct '12

Dear colleagues, Regarding H addition to protein structures, there are indications that hydrogens of NH3+ groups of lysine or N-termini, and side chain methyls of methionines need a rotational optimization (Richardson & Richardson, Chapter 15 in "Structural Bioinformatics", 2nd ed., 2009, p. 380) . I think this problem is not too common, but I did encounter it at least once when I had to rotate manually a Methionine methyl to remove a clash with the ligand. I think Chimera doesn't perform this optimization, or does it? If it doesn't, perhaps this could be put on a list of future improvements:) Best regards, Vis Kairys Institute of Biotechnology Vilnius University

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surface texture export
by Laura Lynn Gonzalez 09 Oct '12

09 Oct '12

Hi. Is there any way to export Coloumbic colored surfaces as JPG textures when you export geometry (obj, vrml, etc)? Or get the 3D texture data in some other format? I'm trying to import my Coulombic-colored protein into a 3D program. -Laura Lynn

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Re: [Chimera-users] APBS interface in Chimera
by Baker, Nathan 08 Oct '12

08 Oct '12

Hi Boaz -- That was news to me as well; thanks for making me aware of this! Best, -- Nathan Baker Pacific Northwest National Laboratory Tel: +1-509-375-3997 http://nabaker.me From: Boaz Shaanan <bshaanan(a)exchange.bgu.ac.il<mailto:bshaanan@exchange.bgu.ac.il>> Date: Monday, October 8, 2012 11:24 AM To: "chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>" <chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Cc: Nathan Baker <nathan.baker(a)pnnl.gov<mailto:nathan.baker@pnnl.gov>> Subject: APBS interface in Chimera Hi, Totally due to my negligence I've only just discovered the long sought APBS interface in the daily build (the one I'm using is from 25/9). Well done Chimera and APBS teams! Practical question: I don't see on the APBS pull-down menu where I define the location of the executable (I'm talking about the Windows version right now, soon I'll try the linux version too). Is it clever enough to find it wherever APBS is installed or have I missed something? Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il<mailto:bshaanan@bgu.ac.il> Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

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Re: [Chimera-users] using modeller through chimera
by Elaine Meng 08 Oct '12

08 Oct '12

On Oct 8, 2012, at 2:21 AM, Taufiq Rahman wrote: > Just wonder whether in using modeller through Chimera interface, we can use our own alignment file or not. Hi Taufiq, Yes, you can definitely use your own alignment file -- just open it in Chimera. To run Modeller using the Chimera interface, all you need is a sequence alignment of target and template (and if it has additional sequences, that is fine) plus the template structure, both opened in Chimera. There are several ways of obtaining these inputs, outlined here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mu…> See the third one, "using a pre-existing target-template sequence alignment" Regards, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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НА: Chimera --send on MacOS
by Sp 07 Oct '12

07 Oct '12

Отправлено с моего коммуникатора HTC

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Re: [Chimera-users] Chimera-users Digest, Vol 114, Issue 2
by Pu Qian 05 Oct '12

05 Oct '12

Hi, I'm working on a big protein complex with MW ~500 kD. It contains a cave inside of the protein. Now I would like to high light this cave so that I can show the room that is big enough for a quinone molecule to move. Question is: is there a function in Chimera which allows users to produce such cave inside of the protein based on PDB file of the protein. If is, where can I find it and how to use it. It would be a great appreciated if anyone here could give me advices. Thanks. Best regards Dr. Pu Qian Department of Molecular Biology The University of Sheffield Sheffield, S10 2TN UK

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Chimera --send on MacOS
by François Stricher 04 Oct '12

04 Oct '12

Hi all, I want to be able to interact with Chimera from another program, sending commands and all. I tried the chimera --send my_file.com to test it under MacOS 10.7. Each time I do this, it opens a new instance (instead of reusing the previous one) and doesn't process my_file.com at all. When I open my_file.com from inside chimera, it operates the commands inside it without any problem. Any idea? Francois

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Global and per-user preference files?
by mike _ 03 Oct '12

03 Oct '12

I wish to deploy a Chimera installation across multiple machines for multiple users. For obvious reasons the users will not have write permission on the application directory. In this scenario Chimera's default behaviour of regularly checking for updates is unhelpful so I wish to disable it. Having read http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Preferences I assumed I could disable the update checking by putting a suitable preferences file in the application directory and then having users invoke Chimera in such a way that preferences file is found. That works, but generates a warning that the preferences file is read-only (which it is, it's in the application directory) and Chimera seems to only want to use the one preferences file. So the result is that users can't save any preferences. Is there any way to make Chimera read a global preferences file that contains some useful defaults and also allow each user to have their own preferences file? thanks, mike

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Re: [Chimera-users] using modeller through chimera
by Elaine Meng 03 Oct '12

03 Oct '12

Hi Taufiq, As you mentioned, the models will appear automatically in the Chimera main window, and there will be an additional dialog, Modeller results (a list of the homology models and other information). For example, the two bottom figures in the Comparative Modeling tutorial show this dialog: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.html> I don't understand what you are clicking... it should not be necessary to click anything. More details about the Modeller results dialog: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modbase.html#modellist> Best, Elaine On Oct 3, 2012, at 6:16 AM, Taufiq Rahman wrote: > Dear Elaine, Many thanks for the reply. It was very helpful and I can now do it. The only fresh problem is: whenever Modeller seems to complete the job (I assume), I can't click on 'modeller results' - its there but clicking on it doesn't open up anything, whilst in the 3d space, I can see the modelled structure as well as the templates. > Any advice? > Regards, > taufiq > > On Oct 3 2012, Elaine Meng wrote: > >> Hi Taufiq, It is probably disabled because you are viewing a single sequence rather than an alignment of 2 or more sequences. In Chimera, there are several ways to get the needed inputs for Modeller, which include the sequence alignment and a structure to use as the template. Some ways are outlined here: >> >> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mu…> >> >> Once you have the inputs, you can run Modeller either via web service or via your local installation. If you haven't already, you would also need to obtain a Modeller license key before running (even if you are going to use the web service). >> >> I would also recommend that you get a newer version of Chimera (at least 1.6.2). The Modeller interface is improved in that version compared to older versions. The sequence window menu will then include both "Structure... Modeller (homology)" and "... Modeller (loops/refinement)" instead of a single "...Modeller Tools" entry. >> >> This documentation is for 1.6.2: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mo…> >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> On Oct 2, 2012, at 7:49 AM, Taufiq Rahman wrote: >> >>> Hello, I want to use modeller through Chimera's interface. I have seen the video and read about the way to do it. My problem is my 'modeller tool' option in the structure menu remains disabled. I have installed modeller locally but don't know how to integrate it into chimera. >>> any suggestion? >>> taufiq >> >> > > -- > Taufiq Rahman > MSc(Manchester), PhD (Cantab) > Royal Society University Research Fellow > University of Cambridge > Cambridge > CB2 1PD > UK >

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using modeller through chimera
by Taufiq Rahman 03 Oct '12

03 Oct '12

Hello, I want to use modeller through Chimera's interface. I have seen the video and read about the way to do it. My problem is my 'modeller tool' option in the structure menu remains disabled. I have installed modeller locally but don't know how to integrate it into chimera. any suggestion? taufiq

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crystal structure reconstruction
by rainy908＠yahoo.com 01 Oct '12

01 Oct '12

Hi, I am new to Chimera. I have a PDB of a protein comprising of a loop region that appears to have slight alpha-helical behavior when visualized in Pymol. However, I doubt that this region is actually structured, and that this alpha-helical behavior is actually an artifact from experimental conditions. To double-check the validity of this loop, I was broadly advised that "crystal structure reconstruction" can be performed in Chimera. I suspect this is either the 'molmap' or "Fit in Map" feature? Sincerely, Lili

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