- 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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Error inizializing OpenGL
by Francesco Pietra 01 Oct '12

01 Oct '12

Hello: Following and upgrading of Debian GNU-Linux i386 testing (= wheezy) of my old PC francesco@deb32:~$ lspci | grep VGA 01:00.0 VGA compatible controller: NVIDIA Corporation NV11DDR [GeForce2 MX200] (rev b2) francesco@deb32:~$ with modern kernel francesco@deb32:~$ uname -r 3.2.0-3-686-pae francesco@deb32:~$ chimera francesco@deb32:~$ chimera --version chimera production version 1.6.1 (build 35849) 2012-03-13 22:24:07 UTC francesco@deb32:~$ does not start anymore: Error inizializing OpenGl. Couldn't configure togl widget. Before I go messing the system, may be I can get advice on where to put the hands. libgotl is not installed, but the same occurs with my GTX-680 amd64 system, where chimera works fine. Thanks francesco pietra

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Re: [Chimera-users] [chimera-dev] The style of Ribbon in alpha 1.7 version
by Elaine Meng 29 Sep '12

29 Sep '12

Hi Cheng, Actually the ribbon shape has not changed, but a bug in the lighting that made the ribbon look rounder than it really was has been fixed. (see release notes "general changes" http://www.cgl.ucsf.edu/chimera/docs/relnotes/snapshot.html#general ) You could use Ribbon Style Editor to make something that looks more similar to the old ribbon. I tried making a ribbon style shaped like a football (named "football") and combined that with a ribbon scaling with larger height for helix, sheet, and arrow base (named "fat"). I wasn't very careful drawing the football so you could probably make it better by drawing it more carefully. I attached a file you could use as your preferences file (although you would then lose your own earlier preferences), or you could text-edit to insert all of the lines in the attached file *except* the top and bottom lines into your existing preferences file. Either way, you should save a copy of your existing preferences file first so you don't lose your settings. Or, you could just make a fatter scaling and football-shaped cross section (style) in Ribbon Style Editor yourself, without using the attached file. If you do use the attached file, you could apply everything with commands: ribscale fat ribrepr football Chimera-dev is for programming questions - I'll CC the chimera-users email address since that is more appropriate for this issue, and others on the list may be interested. 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 Sep 29, 2012, at 3:17 PM, Cheng Wang wrote: > Dear Chimera Team, > Hi. > The ribbon style in 1.6 version is a little round for helix, while it is really flat in 1.7 version. I want to use v1.7 since several commands are really good for movie making eg. format option and transparency. However the ribbon style for helix is not as nice as it in 1.6. I am wondering how could I change the style of ribbon in 1.7 to be the same as in 1.6 since the ribbon style seams the same in the panel for both versions. > Many thanks. > Best, > Cheng

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Specifying colour of surface cap when surface coloured by electrostatic potential
by Ashley Pike 28 Sep '12

28 Sep '12

Hi - Can't find answer to this question in manual. Is it possible to assign a uniform solid colour to a surface cap when the (clipped) surface is coloured by electrostatic potential (using external .dx file)? I know such capping can be done when the surface is coloured by some other attribute but have not found a way to specify in the above case. Any hints gratefully received. Many thanks, Ashley -- Dr. Ashley Pike Membrane Protein Crystallography | Structural Genomics Consortium | University of Oxford

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Silhouette color change
by vamsee 27 Sep '12

27 Sep '12

Hi Elaine, I need to change the silhouette color of individual models and if possible for individual representations (ribbon, surface or atoms). Is there a command line option that I could use? (maybe set?) Thanks in advance Vamsee

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Measuring angles between atoms pairs
by Yasser Almeida Hernandez 26 Sep '12

26 Sep '12

Dear Chimerians... I'm running an analysis about H-bonds geometries in several models. I need to measure the distance of a H-bond and the angle formed with a third atom bonded to one of the H-bond atoms. How could I do that in a python IDLE/script? In a more general way, how could I measure the angle between three atoms linked by a bond o pseudobond? Thanks in advance Yasser -- Yasser Almeida Hernández, BSc. Center of Molecular Immunology (CIM) Tumor Biology Department 216 St.& 15th Ave, Siboney, Playa P.O.Box 16040, Havana 11600 CUBA Phone: (+53-7) 214-3178 almeida(a)cim.sld.cu<mailto:almeida@cim.sld.cu>

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E. coli cells
by Victor Padilla-Sanchez 24 Sep '12

24 Sep '12

Dear UCSF Chimera, Could you tell me where to find chimera maps of E. coli cell(s) ? Or could you send me some maps ? Thank you very much Victor Padilla-Sanchez

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drawing circles
by Bala subramanian 24 Sep '12

24 Sep '12

Friends, I want to draw concentric circles of increasing sizes around the protein. To achieve this, i used the 'define plane' option to draw disk choosing I three reference atoms and drew the disks of increasing sizes and choose two different color for the inner and outer disk. Since the reference atoms are the same. If i change the color of the bigger disk, i get a weird appearance of the inner disk. I dnt know how to resolve this problem. I would like to know if i can do something like making the disk transparent/removing the fill color of the disk. thanks, Bala -- C. Balasubramanian

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"No MMTK name for atom "H" in standard residue "G" "
by Nikolay Igorovich Rodionov 22 Sep '12

22 Sep '12

Hi could someone help me with this error: No MMTK name for atom "H" in standard residue "G" I get this error when running the minimize structure function. Does anyone know a work around or how I can fix the problem? 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

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Potential Energy Calculations
by Nikolay Igorovich Rodionov 22 Sep '12

22 Sep '12

Hi all, I was wondering the there is a tool in chimera that can find the net interaction potential energy between models, something like Lennard Jones Potential. Specifically, I need to measure the interaction potential between a protein and water in a solvated system. 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

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Calculation of SASA with probe size of 0.8Å
by Amy Davenport 21 Sep '12

21 Sep '12

Hi all, I am trying to calculate the solvent accessible surface area of my protein. I would like to use a probe radius of 0.8Å to do so, but do not see a way to alter the probe size past what the selectable values are in the structools menu. Additionally, I need all atoms to be included, which means hydrogens as well. Any help would be greatly appreciated. Thank you, Amy Davenport Migliori UCSD

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Estimated RMSD after using Modeller feature
by Claudia Fernandes 21 Sep '12

21 Sep '12

I used Modeller function in Chimera to make some comparative models and then used the estimated RMSD function. I used two querys for different modeling jobs. The original query that was similar to the target I choose and a query that has an extra 26 N-terminus aminoacids than the target I choose. Using the same tamplate, shouldn't the estimated RMSD be the same for the original query and the longer query (with the extra Nterminus aminoacids)? As it isn't, how is it being calculated? I found that the calculation was carried out with TSVMod, but I couldn't find anything about how i does it. Any help would be welcome. Regards, Cláudia Fernandes

2 1

Modeller-Chimera interface
by James Valdes 21 Sep '12

21 Sep '12

Hello Chimera, I'm using the Modeller interface via Chimera and I was wondering if the models produced takes into account multiple templates (e.g., selecting all) from a multiple alignment produced by MAFFT (http://mafft.cbrc.jp/alignment/software/) I appreciate any insight you may provide. Cheers, James Jason Valdés, Ph.D.

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arrow heads for pipes and planks
by Evan Kantrowitz 20 Sep '12

20 Sep '12

Hi, Probably a dumb question, but I cannot figure out how to show arrow heads on pipes and planks. I found this info Show arrow on helix and Show arrow on strand (both default true) place arrowheads on the C-terminal ends of secondary structure elements to indicate N→C directionality. These are not on the pipes and planks tool. What is the format on the command line to use this commands I tried Show arrow on helix Show arrow on helix true Thanks Evan ------------------------------------------------------------------- Evan R. Kantrowitz, Ph.D evan.kantrowitz(a)bc.edu<mailto:evan.kantrowitz@bc.edu> Boston College Tel. 617-552-4558 Department of Chemistry FAX 617-552-2705 Merkert Chemistry Center, Rm 239 www2.bc.edu/~kantrow<http://www2.bc.edu/~kantrow> Chestnut Hill, MA 02467 -------------------------------------------------------------------

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saving a rotated map
by Filip Van Petegem 20 Sep '12

20 Sep '12

Dear chimera users, I have a problem with saving a cryoEM map after rotating/translating it. I've used the 'fit in map' option to superpose 2 maps (in ccp4 format) This seems to work fine, but when I save the reoriented map (in any of the available formats), and try to open it, it is back to the original position. Is there any way to save the reoriented map file? Best regards, Filip Van Petegem -- Filip Van Petegem, PhD Associate Professor The University of British Columbia Dept. of Biochemistry and Molecular Biology 2350 Health Sciences Mall - Rm 2.356 Vancouver, V6T 1Z3 phone: +1 604 827 4267 email: filip.vanpetegem(a)gmail.com http://crg.ubc.ca/VanPetegem/

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solvation box transformed
by Visvaldas K. 20 Sep '12

20 Sep '12

Dear Users, I have some difficulties with reference frames when solvating a protein. The essence of my problem as follows. Chimera solvates a box using _untransformed_ coordinates, but if I try to write out the inpcrd/prmtop, it writes out the _transformed_ coordinates, thus the box planes become no longer parallel to xyz axes, which does not allow to transfer the inpcrd coordinates to another program (NAMD). Of course, I could try a workaround by creating the protein and re-saving it before solvation, and then solvating it while avoiding any mouse movement,or using ambertool cooman line, but maybe there is another solution, or perhaps an "untransformed" button could be implemented in the prmtop tool? Sincerely, Vis

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Chimera running on a remote computer over ssh >>>> use virtualgl to avoid graphics problems
by Dieter Blaas 19 Sep '12

19 Sep '12

Those who encountered lots of problems with the graphics when running chimera remotely for example you receive error messages like this one: X Error of failed request: GLXBadContextTag Major opcode of failed request: 153 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1352 Current serial number in output stream: 1352 might be interested in the following solution: 1) install VirtualGL (http://www.virtualgl.org/) on both PCs 2) outcomment the indicated lines in the 'chimera' startup script 3) connect to the server by using 'vglconnect' 4) start chimera on the server with 'vglrun chimera' that's it! if [ -z "$nogui" ] then case "`uname -s`" in Linux) # preload our C++ runtime to avoid # ATI graphics driver bug # LD_PRELOAD=libotf.so <<<<<<<<< # export LD_PRELOAD <<<<<<<<< if test -e "$CHIMERA/bin/python2.7" then python="$CHIMERA/bin/python2.7" else in those cases where chimera works without this trick you might still see a substancial improvement in transmission speed! Best, Dieter -- ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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Re: [Chimera-users] chimera utility help
by Elaine Meng 17 Sep '12

17 Sep '12

Dear Sotirios, You would use Join Models option "C-N peptide bond" as described in these instructions: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.ht…> "C-N peptide bond - specialized case of joining two peptides. The N-terminal N of one peptide and the C-terminal (carbonyl or carboxyl) C of the other should be selected. Each selected atom must be bonded to only one carbon; however, it may also be bonded to hydrogen and/or OXT, and if so, these atoms will be replaced as appropriate by the new peptide bond." If you do not see that option, maybe you have an older version of Chimera and should upgrade to a newer version. If you do see that option and you have followed the instructions as above but are still not able to apply, please save a session file and use menu "Help... Report a Bug" and attach the session file to the bugreport. I just tried it on two example proteins and seemed OK, but maybe there is something different about your structure. Thanks! 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 Sep 17, 2012, at 9:10 AM, Sotirios Katsamakas wrote: > Dear Elaine C. Meng, > I followed your suggestion and I created a separate side chain of the 25 amino acids with specified phi and psi values for its residues. But I am still not able to Join Models, through the homonymous section. I am selecting the C terminus of the constructed side chain (#0:25@C) and the N terminus of the protein (#1:26@N) respectively, but when I go to the panel the apply button stays inactive. I am sure it must be something obvious but it eludes me. Thank you in advance and I am looking forward in hearing from you. > > Best Regards, > Sotirios Katsamakas.

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Difference between atoms' coordinates on screen and in a PDB file
by Mateusz Dobrychłop 14 Sep '12

14 Sep '12

Hello, I load 3 protein models into Chimera and enter several "move" commands. The structures change their positions. Then, I save them as a PDB file, and immediately open the PDB file. The structures are not overlapping (screenshot: http://i.imgur.com/gtGBN.png ). Why does it work like this and what can I do to obtain accurate coordinates on my screen without re-opening the model (after I finish my sequence of translations)? Mateusz

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Denaturing a protein
by vamsee 14 Sep '12

14 Sep '12

Hi Elaine, Thanks for the answer for the previous question. I am back with one more :) Is there a way to completely denature a protein in Chimera? The idea is to completely unfold a particular protein (for ex: chemical denaturation GdHCl/Urea or thermal denaturation) to its primary structure. Also can this be modeled in such a way that we can extract thermodynamic parameters from the modeling? I do understand this sounds a lot like a Molecular Dynamics simulation but maybe there is a way in Chimera? Thanks again Vamsee

3 2

sphgen format
by Brian Fochtman 13 Sep '12

13 Sep '12

Hello, I read in the release notes for version 1.6 that Chimera is now able to input files in the dock .sph format. Thank you for this feature, it will be very helpful. Unfortunately I am having some trouble using it. (File -> Open -> file.sph) declares a syntax error for the following file (I've only included the beginning of the file because the output says the synax error is on line 2). Is there another method to read in these files? Thank you, Brian Fochtman cluster 1 number of spheres in cluster 72 1 20.51900 -17.55400 15.86300 0.700 1 2 21.04300 -18.55700 16.07400 0.700 2 3 22.17700 -17.60500 16.24100 0.700 3 4 22.17500 -17.84200 15.30900 0.700 4 5 21.41300 -20.08800 15.15700 0.700 5 6 20.64000 -20.83100 16.58800 0.700 6 7 21.63200 -18.65500 14.15300 0.700 7 8 23.13800 -16.98900 16.54500 0.700 8 9 21.18800 -21.21200 14.71200 0.700 9 10 17.88800 -26.45300 19.89900 0.700 10 11 21.83900 -17.33000 12.81300 0.700 11 12 21.28600 -20.42100 13.28900 0.700 12 13 23.77100 -15.65400 16.91100 0.700 13 14 21.15100 -21.76500 13.92000 0.700 14 15 21.38500 -19.46300 12.20200 0.700 15 16 20.39500 -21.75600 13.41100 0.700 16

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Gromac .xtc format
by Eric Pettersen 13 Sep '12

13 Sep '12

Hi, For you Chimera/Gromacs users out there, the current daily build allows you to use .xtc format coordinates now as an alternative to .trr . --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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chimera utility help
by Sotirios Katsamakas 13 Sep '12

13 Sep '12

Dear sir or madam, I am a recent user of the chimera software on Linux-Ubuntu (11.10) operating system and I confronted a dead end on the following issue. I reconstructed a missing side chain of 25 amino acids in a PDB file but I cant seem to find how to set the secondary structure and so on for these 25 residues. So they are stuck in a linear formation externaly from my protein. For your consideration I am attaching also the PDB file. Thank you in advance and looking forward in hearing from you regarding my problem. Best Regards, Sotirios Katsamakas

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Re: [Chimera-users] Match->Align command line option?
by Eric Pettersen 12 Sep '12

12 Sep '12

On Sep 12, 2012, at 11:16 AM, Chetanya Pandya wrote: > Hello, > > I want to superimpose multiple structure sets and get the corresponding multiple sequence alignments using Chimera. I've been using the Match->Align option from the Tools menu. Now, I want to automate the process using the Python interface. > > Unfortunately, I'm unable to find a command line option which does this. Can you help me out with this? Hi Chetanya, It's a little ambiguous if you are asking about a command version of Match->Align, or how to call it from Python. The issue is moot though since there currently is no command version of Match->Align, so you have to call it from Python! I don't know how familiar you are with Python or programming with Python, but the Chimera Programmer's Guide has some info to help. http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html If you don't know Python at all, follow the link in the Guide to the Python Tutorial and work through that, or at least the first few sections of that. Then for some Chimera-specific info, look at some of the Examples and the "basic primer" linked on the page. Assuming you've written a script that has gotten to the stage where the structures are already open and superimposed, here's the info you'll need to use the Match->Align API: 1) Getting the list of open molecules: from chimera import openModels, Molecule mols = openModels.list(modelTypes=[Molecule]) 2) Getting the list of chains to use. This example code assumes they're chain A: chains = [m.sequence('A') for m in mols] 3) Call Match->Align to create the alignment. from StructSeqAlign import makeAlignment mav = makeAlignment(chains) Note that the makeAlignment call will only return the Multalign Viewer instance starting with tomorrow's daily build (i.e. I made that change today!). Also, the makeAlignment call has a lot of optional arguments to change the parameters used in computing the alignment (e.g. cutoff, iteration, reference chain). Look at <your Chimera>/share/StructSeqAlign/__init__.py to see what the options are if you need to change the default behavior. (On a Mac, "<your Chimera>" is Chimera.app/Contents/Resources). 4) Save the alignment to a FASTA format file (named "x.fa") and Quit the MAV instance: f = open("x.fa", "w") from MultAlignViewer.formatters.saveFASTA import save save(f, mav, mav.seqs, mav.fileMarkups) f.close() mav.Quit() I hope this helps. Since this is pretty Python-intensive, I set followups to go to the chimera-dev mailing list rather than chimera-users. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Visualization of protein aqueous solution
by Nikolay Igorovich Rodionov 10 Sep '12

10 Sep '12

Hi all, Could anyone tell me how I could solvate my protein in a solution of a specific molarity solution with both water molecules and Na+ Cl- ions. I have no trouble adding the water molecules, but I am not sure how to go about adding the ions into the visualization. I've tried using add-ion but I haven't had good results. Are there any other options? This is for purely visual purposes, I'm creating a conceptual image, so I don't need the system to be 100% accurate or capable of conducting calculations. Much Thanks! Nikolay Rodionov

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color by RMSD
by Daniel Gurnon 10 Sep '12

10 Sep '12

Hi everyone, To color a trajectory by RMSD, comparing each frame to the final frame. My approach was to save the last frame of the trajectory as a pdb, load it as a separate model, and then run something like this script: mm #0 #1 show true rangecolor mavRMSD min white mid pink max red This works, but of course my screen quickly fills with multialign-viewer windows. Without "show true" in the script, coloring doesn't work past the first frame. Is there a way to do this without displaying the MAV window? thanks Dan -- ____________________________ Daniel Gurnon, Ph. D. Associate Professor of Chemistry and Biochemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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Ribbon gradient coloring
by vamsee 10 Sep '12

10 Sep '12

Hi All, Is there a way to color the ribbon with a gradient? In my case, it has to be an increasing and then decreasing gradient. Ex: Let's say I have data that shows that a certain region of a protein is highly dynamic. This region consists of approx 11 residues and the most dynamic region in these 11 are the residues 5,6 and 7. Now, I need to color the ribbon in such a way that residues 1 and 11 are the same color (green), 2 and 10 (yellow), 3 and 9 (light orange) 4 and 8 (orange) 5,6 and 7 (red). I could do this by coding it but it becomes a step gradient and it doesn't look so good plus if I need to do this for residues in a bunch of proteins/peptides, the task quickly becomes tedious. I would rather write 2 lines of code for the complete protein than write 1 line/residue/protein. Any ideas? Thanks in advance Vamsee

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selection of multiple atoms in a session with multiple pdb structures
by Anindito Sen 09 Sep '12

09 Sep '12

Dear All, I have a Chimera session where 4 different atomic structures (pdb files) are docked in the computed density map of a macromolecular complex. I need to select multiple amino acids positioned at different places of the different docked atomic structures. To explain the situation- Say the 4 docked Atomic structures are A, B, C & D I need to select 276aa of A, 15aa of B, 246aa of C and so on... How can I do that ? Thanks Dr. Anindito Sen (Ph.D) >Department of Cell Biology & Anatomy >Graduate School of Medicine >University of Tokyo >Tel & fax: +81-3-5841-3339

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Distance between two benzene rings
by George Tzotzos 06 Sep '12

06 Sep '12

Hi everybody, I'm trying to work out stacking interactions between two benzene rings. Is there a way to measure the distance from the center of the benzene rings of a Tyr to the center of the benzene ring of a Phe residue? Your help suggestions / help much appreciated as always Regards George

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Fwd: [Chimera] #11323: Chimera using local GLUT installation (was: Chimera bug report submission)
by George Tzotzos 05 Sep '12

05 Sep '12

Apologies for sending this to the List but I haven't received any information regarding the bug report below. Maybe I missed the mail. I have reinstalled Chimera but I get the same error message. Any suggestions how to solve this problem? Many thanks George Begin forwarded message: > From: Chimera <chimera-bugs-admin(a)cgl.ucsf.edu> > Subject: Re: [Chimera] #11323: Chimera using local GLUT installation (was: Chimera bug report submission) > Date: August 27, 2012 7:12:02 PM GMT+02:00 > To: Undisclosed recipients: ; > Reply-To: chimera-bugs(a)cgl.ucsf.edu > > #11323: Chimera using local GLUT installation > ---------------------------------+------------------------------------- > Reporter: gtzotzos@… | Owner: gregc > Type: defect | Status: assigned > Priority: normal | Milestone: Release 1.7 > Component: Platform | Version: 1.6.2 (b36855) > Severity: normal | Resolution: > Keywords: | Blocked By: > Blocking: | Notify when closed: > Platform: Mac OS X (Cocoa 64) | Project: chimera > ---------------------------------+------------------------------------- > Changes (by pett): > > * status: new => assigned > * component: Unassigned => Platform > * project: => chimera > * platform: => Mac OS X (Cocoa 64) > * version: => 1.6.2 (b36855) > * milestone: => Release 1.7 > * owner: pett => gregc > > > -- > Ticket URL: <http://plato.cgl.ucsf.edu/trac/chimera/ticket/11323#comment:1> > Chimera <http://plato.cgl.ucsf.edu/trac/chimera> > Chimera Issue Tracker

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H-bond analysis in case of TIP4P water model ?
by Marek Maly 04 Sep '12

04 Sep '12

Hello, it seem to me that Chimera is not able to do H-bond analysis between water molecules when TIP4P water model is used. Am I right or I overlooked something ? Thank you very much for the answer in advance ! Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/

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Ligand parametrization
by Miro Moman 04 Sep '12

04 Sep '12

Hello, When energy minimising protein-ligand complexes, I have observed that Chimera seldom, if ever, complains about missing parameters. However, when I try to generate a Pmrtop file for the same complexes, quite often sLeap is unable to complete the request due to its inability to recognise certain atom types.. Provided that the minimization engine (MMTK) is using the Amber force filed, I was wondering: Are parameters computed in the same way? If not, what are the differences? Maybe a different forcefield version? In addition, is there a way to inspect the parameters that have been generated for minimising a given ligand or non-standard residue? Kind regards, Miro

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saving spheres
by MARY VARUGHESE 04 Sep '12

04 Sep '12

Hi, I saved the combined sph(two clusters) file. But the file contains two clusters with single ID, so i cant create the box including both clusters, since in the box.in file of dock i can give only one cluster number. How can i assign both clusters into single cluster. or any other suggestion. Thanking You.

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Fwd: Installation problems
by prashant kurkute 04 Sep '12

04 Sep '12

Respected sir, Sorry for making you disturb. I am novice to linux. I am trying to install chimera in ubuntu 12.04 LTS. I follow following instruction. sudo chmod +x chimera-1.6.2-linux_x86_64.bin ./chimera-1.6.2-linux_x86_64.bin (I also triied with root sudo ./chimera-1.6.2-linux_x86_64.bin) I got following reply bash: ./chimera-1.6.2-linux_x86_64.bin: cannot execute binary file Sir please help me to solve problem. I will be greatly thankful to your help. With Best wishes and regards.

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volume of an ensemble
by R. Andrew Byrd 31 Aug '12

31 Aug '12

Dear Chimera Team, Is it possible to get the total volume that encompasses an ensemble of structures? For example, if a docking or structure calculation produces an ensemble of structures, can one calculate the volume that encompasses all the members of the ensemble? A docking calculation may have one component superimposable and the second component represent an ensemble, and it is that ensemble that I would I like a measure of the total volume. Thanks! Andy

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adjust resolution of alignment .eps in Multalign viewer
by Gesa Volkers 30 Aug '12

30 Aug '12

Hi all, I would like to extract a high resolution publication quality image from my alignment from the Multalign viewer. Only option I see is to save it a as .eps, but when I open that file the resolution is not sufficient. Is it possible to get a higher resolution image? Thanks, Gesa

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reasonable minimization times
by David Belnap 30 Aug '12

30 Aug '12

I am trying to link the crystal structure of an Fc domain with two Fab structures. I am using the command "minimize spec sel fragment true" on the command line. When various options come up, I've selected "if alternate locations, keep only highest occupancy", "add hydrogens", "add charges", "consider each model in isolation from all others", "also consider H-bonds", and AMBER ff12SB and ANTECHAMBER to assign charges. I've had jobs run overnight that didn't finish. What is a reasonable time for about 8-10 residues to be minimized? Can you suggest any ways to speed this up? Thanks, David

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problem with loading color scheme in Multalign viewer
by Gesa Volkers 29 Aug '12

29 Aug '12

Hi all, I encountered a problem when I tried to open a color scheme (tried it with custom.par from the Chimera website) in the Multalign viewer. I get the following error: "File "C:\Program Files\Chimera 1.6.2\share\MultAlignViewer\PrefDialog.py", line 69, in addColorScheme self._resColorOpt.set(colorFile) See reply log for Python traceback." I reported a bug. Though has anyone found a way to solve this problem and is able to open a .par file again? Thanks, Gesa

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making a movie problem
by Boskovic.Jasminka 29 Aug '12

29 Aug '12

Hi, I am trying to make a movie with chimera but instead of filming just a molecule's movement the program is making the frames of all the chimera window showing the "File, Select, Actions etc" bottoms and the command line? How can I remove this option and film just the molecule window? Thank you in advance! Best regards, Jasminka Boskovic, PhD Centro Nacional de Investigaciones Oncologicas-CNIO (Spanish National Cancer Research Centre-CNIO) Melchor Fernandez Almagro 3 28029 Madrid Spain Tel.: + (34) 917 328 000 (ext 3031) Fax: + (34) 912 246 980 e-mail: jboskovic(a)cnio.es **NOTA DE CONFIDENCIALIDAD** Este correo electr�nico, y en su caso los ficheros adjuntos, pueden contener informaci�n protegida para el uso exclusivo de su destinatario. Se proh�be la distribuci�n, reproducci�n o cualquier otro tipo de transmisi�n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.

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Trivial question
by George Tzotzos 28 Aug '12

28 Aug '12

It seems that a standard feature of Chimera is upon loading a pdb file of a complex, a number of nearby residues also show up. My question is whether there's a rule, let's say a cutoff distance, or other. Thanks in advance for any advice on this Regards George

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Batch energy minimisation
by Miro Moman 24 Aug '12

24 Aug '12

Hello, Searching through the archives, I have found that performing DockPrep in batch mode is quite straightforward: http://mailman.docking.org/pipermail/dock-fans/2007-May/001043.html I have also noticed that, when working from the GUI, energy minimisation involves a previous DockPrep step. I would like to perform the energy minimisation of several protein-ligand complexes, can this be easily done in batch mode? Furthermore, I would also be interested of computing the binding energy both prior and after minimisation (possibly including APBS-computed electrostatic terms...). However, this is of secondary importance as it can be easily achieved with other tools. Best regards, Miro Moman

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graphics problems after update from UCSF-Chimera64-1.5.3 to UCSF-Chimera64-1.6.2
by Dieter Blaas 21 Aug '12

21 Aug '12

Hi, I replaced the previous version of Chimera, UCSF-Chimera64-1.5.3 with the new one UCSF-Chimera64-1.6.2 on our cluster running Linux l22 2.6.32-131.17.1.el6.x86_64 #1 SMP Wed Oct 5 17:19:54 CDT 2011 x86_64 x86_64 x86_64 GNU/Linux whereas everything was perfect so far I now get the error message: X Error of failed request: GLXBadContextTag Major opcode of failed request: 153 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1352 Current serial number in output stream: 1352 followed by a crash. This is annoying since I need the new version for compatibility with some sessions saved with the new version on another machine. Thanks a lot for hints, Dieter -- ------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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a problem with silhouettes
by Alja Oblak 20 Aug '12

20 Aug '12

Dear Chimera users, I am trying to create an image for a publication using Chimera 1.6.1. Whenever I turn on "silhouette" dark spots appear on the screen and on the saved image. They seem totally random but they move along with the structure when rotated. When I zoom on them they look like small "umbrella-shaped" discs. The "show shadows" option is turned off. Does anybody know what are those spots and how to get rid of them? Thank you very much for any help. Regards, Alja Oblak

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how to use antechamber?
by 何永辉 16 Aug '12

16 Aug '12

Hello, Can you show me how to use the ambertool antechamber in Chimera? Thanks! Yonghui Dr. Yonghui He Central South University 932 Lushan South Road Changsha, China.

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em fit refinement
by Bala subramanian 15 Aug '12

15 Aug '12

Friends, I used "fit" command to fit a structure onto a EM map and obtained a list of fits. Now i want to choose the best fit and refine it further. I would like to know if there is any way to refine a fit produced by fit command in Chimera. Or can i use any other software for the same, which can take chimera's fit as input and refine it further. Thanks, Bala -- C. Balasubramanian

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Mountain Lion
by John (Jack) Johnson 13 Aug '12

13 Aug '12

Are there any issues with the current Mac version of Chimera (1.6.2) and Mac OS 10.8 (Mountain Lion)? Also, for a MacBook Pro (latest version) should one be using 32 or 64 bit version of Chimera. Thanks, Jack John E. Johnson Elden R. Strahm Professor of Structural Virology PHONE 858-784-9705 Department of Molecular Biology, MB31 FAX 858-784 -8660 The Scripps Research Institute EMAIL jackj(a)scripps.edu<mailto:jackj@scripps.edu> 10550 N. Torrey Pines Rd. La Jolla, CA 92037 http://johnsonlab.scripps.edu/ Virus Partcle ExploreR (VIPER) http://viperdb.scripps.edu/ ******************************************************************************** Olive Ireland PHONE 858-784-2947 Administrative Assistant EMAIL ireland(a)scripps.edu<mailto:ireland@scripps.edu>

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Elongating TMV capsid
by Jeremiah Gassensmith 13 Aug '12

13 Aug '12

Hello, I've downloaded the tobacco mosaic virus structure from the PDB and used Multiscale Models to build the biological unit. Unfortunately, only about 45 or so of the 2200 protein monomers show up. Is there a way I can multiply the biological unit to elongate the TMV structure? I don't need all 2200 monomers, but something a bit longer would be helpful. Thanks! Jeremiah Dr. Jeremiah J. Gassensmith Stoddart Mechanostereochemistry Group Northwestern University 2145 Sheridan Road Evanston, IL 60208-3113 Phone (W) +1(847)467-5936 Fax +1(847)491-1009

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Chimera inquiry: .py to .u3d conversion
by Will Jones 13 Aug '12

13 Aug '12

Hello, My name is Will. I'm a researcher at the University of Iowa. Our group has been using your Chimera software to visualize a model of our protein of interest. It's been very helpful but I've run into a small issue that I'd like to ask your advice on. I'm trying to convert the 3d image of the saved .py file into a universal 3D file (.u3d). I have tried several types of conversion software including polytrans/nugraph, 3DVIA Composer, and CS5 Adobe Photoshop with no success. Could you please tell me if conversion of .py to .u3d is possible, and if so how I might go about it. Thank you, I appreciate your time. Sincerely, Will -- Department of Biochemistry University of Illinois Urbana-Champaign Class of 2012

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Saving Images
by Hobbs, Merlin Eric 09 Aug '12

09 Aug '12

We are having trouble saving images to look a certain way. More specifically we are trying to make an image with the distance from a residue to a metal ion shown. The problem arises when we save the image the 'thickness' of the distance line doesn't change on the actual saved image. So no matter what the thickness is on chimera the image will always show the distance line as being less thick. Thanks Eric -- Merlin Eric Hobbs | Graduate Student, Biochemistry and Biophysics | Raushel Lab | Rm 2510 | Texas A&M University | College Station, TX 77842 | 979-845-9163 | eric0zero(a)tamu.edu

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Re: [Chimera-users] Rapid Access - a different question/request
by Eric Pettersen 08 Aug '12

08 Aug '12

On Aug 8, 2012, at 2:25 PM, Boaz Shaanan wrote: > OK Eric, thanks. I'll wait for the scroll bar since my window is already stretched to the limit. Okay, there will be a scrollbar in tonight's daily build. Worked fine in my tests. Speak up if it turns out I botched something! --Eric

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Rapid Access - a different question/request
by Boaz Shaanan 08 Aug '12

08 Aug '12

Hi Eric, I actually find the Rapid Access very convenient, however I wonder: is the list limited to the n most recent sessions/pdb ? I actually am missing the option of paging further down the list to jobs that are not in the list but which are quite recent. Is there already an option to do this? The browse button does other things (at list in my hands). 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 Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: chimera-users-bounces(a)cgl.ucsf.edu [chimera-users-bounces(a)cgl.ucsf.edu] on behalf of chimera-users-request(a)cgl.ucsf.edu [chimera-users-request(a)cgl.ucsf.edu] Sent: Monday, August 06, 2012 10:00 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 112, Issue 6 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. Modelling of missing regions ussing Chimera (Gleb Novicov) 2. (no subject) (Merced Malabanan) 3. Re: Rapid Access file list (Eric Pettersen) ---------------------------------------------------------------------- Message: 1 Date: Sat, 4 Aug 2012 15:44:12 +0400 From: Gleb Novicov <gnovikov87(a)gmail.com> To: chimera-users(a)cgl.ucsf.edu Subject: [Chimera-users] Modelling of missing regions ussing Chimera Message-ID: <CAN=J6WkT9_GH8YYT8U=Nbt-3hhor_YvNHrndwXK6L4ix75uHvA(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Dear Chimera's users! I need to model some missing segments ( In particular case I need to build missing N and C termi ) of my protein ussing Modeller's options. Could you tell me about possible solution of that issue ? On my win7 I have installed Chimera as well as Modeller v 9.10 suite. I've defined Modeller pathways in the Chimera's Model pool options but when I've selected option Prune seection to define region of interest I didnt obtain anythinf from both of Chimera or Modeller. On other hand the option Structure -> Modeller tools also not available for me. Does it means that I've installed modeller incorrectly ? Also I've used runmod.dat script with defined variables from which I obtained the below C:\Users\own\Desktop\worktemp>runmod.bat usage: mod9.10 script [...] Doest this means that all work fine ? By the way after executing of that script I could not launch modeller by means of mod9.10.exe from modeller folder. The error from modeller was C:\Program Files\Modeller\bin>mod9.10.exe FATAL ERROR: MODINSTALL9v10 environment variable not set: incomplete MODELLER in stallation Could you explain me whats I've done wrong and how I could fix this problem? Thanks for help Gleb

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