- Chimera-users - RBVI Mailing Lists

creating virus capsid
by Elaine Meng 27 May '10

27 May '10

On May 25, 2010, at 10:39 PM, 江一波 wrote: > hello meng! > how can i construct a virus by chimera? > i have get a nucleocapsid protein about a virus from > http://www.rcsb.org/pdb/results/results.do?outformat=&qrid=9B6E87D9&tabtosh… > such as ,i get ID :2I9F structure...one of a nucleocapsid for a virus ...this is symmetrical structure! > i want construct a virus ...how can i do? is there somethings paper about how to construct ? > thank you!!! Sometimes the PDB file will include matrix information needed to build the capsid. If it does, you can use the Chimera tool "Multiscale Models" to show the whole thing. However, the authors of this structure (2I9F) did not include the necessary information in the PDB file. Next I tried to see if that structure is in VIPERdb, which would also allow showing the whole thing in Chimera. However, when I tried "File... Fetch by ID" and entered 2i9f for the VIPERdb database, it was not found. Sorry, I don't have any ideas about how to make a whole capsid from this structure. A different structure that does include the information is 1POV. If you open that one, then start Multiscale Models (under Tools... Higher-Order Structure) and click the "Make models" button near the bottom, it will show the whole capsid. Please send Chimera questions to the chimera-users(a)cgl.ucsf.edu address. 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

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translation of proteins with added pseudobonds
by Joern Lenz 26 May '10

26 May '10

Dear all, here is my problem: I have a protein and added pseudobonds that make up a triangle in order to highlight a pharmacophore. However, as soon as I loaded in the pseudobonds and translate my protein afterwards, the triangle made of pseudobonds does not do the same translation but kept being at its original position. Is this a bug or am I doing something wrong ? Any answer is much appreaciated. Cheers, Joern

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problems reading .rec file
by Shawkey,Matthew D 25 May '10

25 May '10

Hi, I have a .rec density map 2000x2000x1000 (xyz) but when i open it in Chimera it only shows the first image of the series (i.e. the dimensions are 2000x2000x1). do i need to convert it to a different format? thanks Matt ***************************** Matthew D. Shawkey, Ph.D. Assistant Professor Department of Biology Integrated Bioscience Program University of Akron Akron, OH 44325-3908 (office) +1 330-972-8192 (lab) +1 330-526-3225 http://gozips.uakron.edu/~shawkey

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measure rotation rod
by le monk 25 May '10

25 May '10

Hi all, I have used measure rotation to draw a rod down an axis of symmetry. Does anyone know a way of altering the diameter, length and color of the rod? Many thanks _________________________________________________________________ http://clk.atdmt.com/UKM/go/197222280/direct/01/ We want to hear all your funny, exciting and crazy Hotmail stories. Tell us now

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prmtop
by richardbonnet 24 May '10

24 May '10

Dear, Is there a way to use writeprmtop with the command line? Is it a way to use chimera to write prmtop amd inpcrd files for a ligand (gaff type + am1-bcc charge) + the corresponding protein (Gasteiger charges + ff99sb) with the command line? I have lot of problems with input format for antechmaber. It can intersting to use chimera with the command line to solve this type of stuff. Thank a lot per avance, Richard Bonnet

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Amino acid substitution with Chimera
by Hayeon Kwak 19 May '10

19 May '10

Hi, I am currently working on a homology-modelled protein. How do I mutate a certain amino acid with Chimera? For example, if I wanted to mutate 55N into 55K to look at how the structure changes, what would I do? Any help would be appreciated. Thank you.

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Re: [Chimera-users] weighted distance
by Greg Couch 19 May '10

19 May '10

On 05/19/2010 02:07 PM, Eric Pettersen wrote: > Hi Bala, > > On May 18, 2010, at 2:04 AM, Bala subramanian wrote: > >> 1) When i type help(object) in chimera's python shell, it shows the >> help message, is there any to way to make the help information to be >> displayed in a separate window. I tried in config setting but i >> couldnt make it. > > I don't know of any way to make help() output go elsewhere. > Here's a technique to bring up the help() documention in your web brower: (1) start the IDLE tool in chimera (2) type into the IDLE dialog: import pydoc pydoc.gui() At that point, pydoc brings up a dialog where it says it started up a web server on your computer and you can "open browser" to browse all of the builtin chimera and Python documentation. There are a couple downsides: (1) chimera becomes unresponsive until you press the "quit serving" button and then chimera exits -- so browse the documentation with one chimera and program in another, (2) pydoc fails for some chimera modules, e.g., the important chimera module -- that's a pydoc bug unfortunately. - Greg

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weighted distance
by Bala subramanian 19 May '10

19 May '10

Dear Friends, Is there any way to display weighted distance in chimera. For example, in the attached data file, we have distance in column 1 and its corresponding importance in column 2. What i would like to do is to load the structure, display the distance between two group of residues and adjust the width of the line (created by distance monitor) according to the importance of the distance in the data file. Thank you, Baa

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Re: [Chimera-users] Grouping models
by Thomas Goddard 19 May '10

19 May '10

Hi Thomas, I don't understand well enough what you are doing. You can move several models at once with commands like turn y 30 models #15-25 coord #1 which will rotate models 15 through 25 about the y axis of model 1 by 30 degrees. I'm not sure if a Chimea command can save multiple PDB models in a single file. It looks like the "write" command can't do that. I'm not sure why it would be limited since the Chimera Save PDB... dialog can save multiple models. Probably Elaine or Eric can explain that. You could use the "combine" command to make one molecule from several molecules using multiple chains, but PDB format is limited to 62 chains (single letter upper/lowercase/number chain identifier). The combined molecule could then be saved with the "write" command. Tom > Hi Tom, > > we are working at the interphase of EM and atomic structures and would > like to do some interactive docking/prediction/validations etc . So our > wish would be if we can use chimera in an automatic fashion to load > atomic coordinates and simulate the structures by positioning them at > various positions within a volumetric box (such as applying a rotation, > turn around x, etc). The problem that we have is that we have to load > many structures (>60 !) at the same time as we are working with a highly > oligomeric complex. It would be great, if we can use a chimera > command-line based option to do the modifications of coordinates on a > sub-group of the loaded structures (Q: can we group several models > easily ?) and save the new coos in a single file. For now, we would need > to do it by hand, as we couldn't find a command line based saving > options into a single pdb-file .... but this can be quite tedious, if > one would like to test hundreds of possibilities. Do you have a > procedure that you would recommend for generating such simulations (for > now, we treat the structures as rigid bodies) ? > > Best, > -Thomas > >

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Saving BRIX volume file, missing data
by Thomas Goddard 18 May '10

18 May '10

Hi Miguel, I just tested saving volume data in BRIX file format on Chimera 1.4 and also with the current daily build and both worked correctly, nothing left out. Could you send me an MRC map that when I open it and save it as BRIX does not work correctly? Also please give me the exact Chimera version and operating system (Help / About Chimera...). BRIX format saves only 8-bit values. So if you have a large range of values -- say most map values are 0-10 and then one is 10000, then all the 0-10 values will be reduced to the same value (0) when it is forced into the 8-bit BRIX value range by a linear scaling. Thanks, Tom > Hi Tom, > > Thank you! This way I can extend the number of total torsions at least ten times, though I'm not sure I'm gaining much with that. I will see better once I start filling VdW volumens. > > Just a remark: I have noticed something wrong with brix format maps: they are not saved properly, a part of them is left out. I haven't found out whether this is a problem with a certain count threshold, or a number of grid points, the fact is that a good part of the map is lost. This happens whether I save it from the script as you say or from the GUI using the File menu of the Volume Viewer. So I am using MRC format for the time being, which works fine in all cases. > > Best regards, > > > Miguel > > Le 17 mai 2010 à 19:40, Thomas Goddard a écrit : > >> Hi Miguel, >> >> The Python call to save your volume data model v in a file is >> >> v.write_file('/tmp/myfile.brix', format = 'dsn6') >> >> If you do not want to create the volume model you can instead directly write out the grid object. >> >> from VolumeData import save_grid_data >> save_grid_data(grid, path, format) >> >> I figured this out by looking at the write_file() Python code in >> >> chimera/share/VolumeViewer/volume.py >> >> The allowed formats are listed in the file_writers variable in >> >> chimera/share/VolumeData/fileformats.py >> >> Tom >>

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Re: [Chimera-users] Save session for movie
by Eric Pettersen 18 May '10

18 May '10

Hi Francesco, On Apr 19, 2010, at 12:29 AM, Francesco Pietra wrote: > If at all, I did not understand if a continuous trace of the centroid > (instead of a series of balls) can be obtained in the context of the > protein. That would improve the presentation further. Otherwise, the > series of balls for the centroid, with appropriate choice of radius > and step size, shows the pathway of the ligand through the protein > adequately. Nothing simple comes to mind. One way that's a bit of work would be to save the centroid information to a file (the 'Save' button on the Axes/Planes/Centroids interface) and the use a text editor to create a BILD file (BILD format) showing lines/cylinders connecting the centroid centers. > As a minor point, I was unable to render helices transparent. > Transparency would help to to see the centroid trajectory in between > helices. Should be possible unless there's something wrong with your graphics cards. Try this: Select->Structure->secondary structure->helix Actions->Color->from editor This will bring up a color editor. Try making a transparent red. For me, the editor looks like this when I do that: (note the "Opacity" box is checked) and the structure looks like this: --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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accessing atom information
by Bala subramanian 17 May '10

17 May '10

Friends, I have just begun to explore the chimera-python linkage. I loaded a pdb file using chimera.openModels function. Then i tried to loop through the residues and display atom information based on a condition. >>>for r in mymodel.residues: *#this works for me* if r.type=='ARG': print r.atoms >>>for r in mymodel.residues: *#this dose not work. I know there is a ARG residue with id 151.* if r.id=='151': print r.atoms I dnt understand how atom attributes are packaged within a residue. Kindly write me few examples of accessing atom information from a residue. Thanks, Bala

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clip planes in vrml
by Daniel Gurnon 17 May '10

17 May '10

Hi all, I'm thinking of the 3D printing of physical models, and how informative clipping planes can be....would it be feasible to add capped-clip planes to vrml output? I also ran into a problem when I exported a surface to vrml and tried to view it with Adobe 3D reviewer. The color information didn't transfer. This isn't a problem when saving ribbons or bonds as vrml. Dan -- ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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Re: [Chimera-users] Creating movies
by Tom Goddard 15 May '10

15 May '10

Hi Matthew, The movie images including the command-line is very weird -- never heard of that happening before. It is almost certainly a graphics driver problem. You can try a Chimera daily build which uses a different image capture method. Also you can report the bug with the version you are using Chimera menu entry Help / Report a Bug.... That will give us information about your graphics card and driver that may help us advise you further. Tom > Tom, > > Thanks for the note -- regarding "all my commands show during the > movie" -- > > When I use the command line interface, the entire chimera window gets > recorded, not the viewing window with the protein. When I play back > the movie, I see the tool bar complete with the command line. I > even get to watch the text appear in the command line as it was > entered. I am using the linux version and will take the opportunity > to try the daily build. > Thanks for the help. I'll keep you updated. > > Cheers, > Matthew > > > > > Tom Goddard wrote: >> Hi Matt, >> >> Not sure what you mean by "all my commands show during the movie". >> Your second problem sounds like part of the image is corrupted and >> that is most likely a graphics driver problem causing the saved >> images to be wrong. You might want to try a Chimera daily build >> instead of the Chimera 1.4.1 production release because the daily >> builds use a different image capture method that may work better on >> your machine. >> >> You might also look at the 2009 movie course material which is more >> up-to-date than the 2008 material. >> >> http://www.cgl.ucsf.edu/chimera/tutorials/movies09/moviemaking.html >> >> Both 2008 and 2009 materials primarily use command scripts and that >> is the recommended approach. >> >> Tom >> >> >>> Hello, >>> >>> I am fairly new to using chimera and created my first movie using >>> command line syntax. I am mostly pleased with the results, except >>> for two things: >>> (1) I used the 'movie record' option and all my commands show during >>> the movie. >>> (2) the right hand side of the image looks like 'snow'. >>> >>> I followed similar instructions to the tutorial for ligand flying >>> into unbound conformation from: >>> http://www.cgl.ucsf.edu/chimera/tutorials/movies08/moviemaking.html >>> >>> Should I be using a script instead? Is there a better way to do this? >>> >>> Thanks for any help. >>> Matt Skeels >>

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Creating movies
by Matthew Skeels 15 May '10

15 May '10

Hello, I am fairly new to using chimera and created my first movie using command line syntax. I am mostly pleased with the results, except for two things: (1) I used the 'movie record' option and all my commands show during the movie. (2) the right hand side of the image looks like 'snow'. I followed similar instructions to the tutorial for ligand flying into unbound conformation from: http://www.cgl.ucsf.edu/chimera/tutorials/movies08/moviemaking.html Should I be using a script instead? Is there a better way to do this? Thanks for any help. Matt Skeels

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Energy Minimization
by Eric Pettersen 13 May '10

13 May '10

Dear All, Using Minimize command, I can minimize the the energy of the protein. But is there a way by which I can check the energy the protein before I perform the minimization and after minimization or least after minimization. Thanks and Regards Monisha (originally sent to chimera-bugs)

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Solvate RNA-protein Complex
by Andrew Tran 12 May '10

12 May '10

Hi Chimera support, I am trying to analyze a protein-RNA complex and would like to neutralize the phosphate backbone with ions and solvate the complex. When I try to do this using Chimera (through AMBERtools?), the complex dissociates. Is there a way to add ions and solvate without dissociation of the complex? Andrew Tran Brown University Biochemistry and Molecular Biology

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error
by zxd 11 May '10

11 May '10

Hi, I'm helping Chinese Academy of Sciences test 3D Stereo display with your Chimera-1.4.1. We are using the Samsung Syncmaster 2233 monitor, Nvidia 3D Vision kit (transmitter plus glasses). I'm able to open the software. When I select, tools->camera->sequential stereo, the application will enounter an error and exit. Attached are the snapshots of the error message and details of our computer. Xiaodong Zhao 2010-05-11 zxd

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Chimera failed abnormally
by emirate14 10 May '10

10 May '10

Hi, I've downloaded the chimera-1.4.1-win32.I am succeeded to run it for several times. However, the program had a error named as "Chimera failed abnormally; the exit code was: 1. use the --debug command line option for the full error message." and I can not start it anymore (same as Johan Börjesson, http://www.cgl.ucsf.edu/pipermail/chimera-users/2005-November/000578.html) I notice there is a note in debug box "Type=screen distance must be positive", does it cause the problem? I am looking forward to your reply. Thank you very much. Best regards . Qian Wang Zhejiang University, Hangzhou, China

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ksdssp assignments
by Tom Duncan 10 May '10

10 May '10

I noticed that the secondary structure assignments for a specific protein by ksdssp (default parameters) show a few significant differences versus the DSSP assignments shown at the PDB (file = 1aqt). Any idea why? Thanks, Tom

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output data from findclash
by Kim, Sunghoon 10 May '10

10 May '10

I'm trying to see clashes of a specific sidechain with its rotating chi angles using 'findclash' command in python script. At this point, because I 'm just looking for a set of rotamers that doesn't have any contacts or clashes, I just want to see the number of contacts from a set of specific rotameric states, rather than a detailed information. But I don't know how to print 'the number of contacts' together with its corresponding chi angles. Is there any way to write a output file from findclash calculation? Or can I modify reply log as I want ? Thanks, Sunghoon

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Re: [Chimera-users] presets, python and printing
by Greg Couch 10 May '10

10 May '10

On 05/09/2010 07:51 AM, Daniel Gurnon wrote: > Hello everyone, > My colleague and I are planning to incorporate 3D physical models into > the introductory biochemistry course at our university, and I want > students to use Chimera in the design of models. I've seen the > technotes on 3D models made by the uPrint printer > (http://www.cgl.ucsf.edu/Outreach/technotes/uprint.html) We'll > hopefully be collaborating with the folks at MSOE on this, using their > Z-corporation printer. They use RasMol to design models, but the file > read by the printer is in .stl format. > > Here are my questions: > 1) Has anyone used Chimera to create models to be printed on a Z-corp > printer? (if yes, I'll have many more questions for you...) If you are using a Z-corp printer, you should look into sending it chimera's VRML output. That is because chimera's STL output works well when you limit it to surfaces and ribbons, but the triangles generated for bonds and atoms (interpenetrating cylinders and spheres) confuse some printer's software. The Z-corp printers come with their ZPrint software that accepts VRML and should do the proper triangulation for their printers (I say "should" because we've never tested it, but from everything I've read, I expect it to work). - Greg

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Volume covered by a group of atoms
by Miguel Ortiz Lombardia 10 May '10

10 May '10

Dear all, I would like to represent as a volume the space that would be covered by a set of atoms that are bound by "torsionable" bonds when one systematically modifies those torsion angles. An example would be the side-chain of an amino acid; imagine I would like to have a glimpse of what part of the space could be occupied by that side-chain. As a first approximation I wouldn't care about clashes. I would appreciate if someone can point me to an existing way of obtaining such representation or to an algorithm that could be implemented within chimera (which I would be happy to share with other interested people; if I manage to code it, that's it!) Cheers, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II 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 e-mail: miguel.ortiz-lombardia(a)afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2

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Ensemble Cluster via command line
by Jan H. Löhr 10 May '10

10 May '10

Dear Chimera users, I have been using the Ensemble Cluster tool to cluster a set of PDB-files. Now I would like to do this via command line or python script without GUI in order to run it multiple times. However, it seems the Ensemble Cluster tool cannot be used via command line. The only thing I have been able to is to load it up with 'start Ensemble Cluster'. Is there a way to access the tool via command line? Or is there a way to record my mouse actions and translate them to commandline-style? Here are the steps I am trying to do: Load PDB-file (multiple models in it) Start Ensemble Cluster Parts to Match: :xxx-yyy (optional) OK Write List of modelnames/cluster End This can be done by mouse, but apparently not by commandline, can it? Thank You Jan Univ. Hamburg, Germany

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presets, python and printing
by Daniel Gurnon 10 May '10

10 May '10

Hello everyone, My colleague and I are planning to incorporate 3D physical models into the introductory biochemistry course at our university, and I want students to use Chimera in the design of models. I've seen the technotes on 3D models made by the uPrint printer ( http://www.cgl.ucsf.edu/Outreach/technotes/uprint.html) We'll hopefully be collaborating with the folks at MSOE on this, using their Z-corporation printer. They use RasMol to design models, but the file read by the printer is in .stl format. Here are my questions: 1) Has anyone used Chimera to create models to be printed on a Z-corp printer? (if yes, I'll have many more questions for you...) 2) Is it possible to define a user preset in Chimera with Python? I know this isn't currently possible with chimera commands, and I am *just* getting into Python now. Because students have difficulty jumping in to a project like this if they first have to learn to enter commands at a prompt, I want to make some presets that apply settings compatible with a 3D model; bond thickness, colors, etc. 3)If one knew Python, would it be possible to design a simplified user interface for Chimera? Even as simple as a pop-up window that contained the key features I want students to have access to right away? 4) Probably the biggest drawback to using Chimera with undergrads is the lack of an "Undo" button. I'm guessing this is extremely difficult to implement because of all 3rd party extensions incorporated into Chimera? What about an option to autosave every five or ten minutes? Thanks Dan -- ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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