- Chimera-users - RBVI Mailing Lists

Access to "Match Align" programmatically
by Miguel Ortiz Lombardía 26 Oct '15

26 Oct '15

Hi, Is it possible to call "Match Align" from a script or a 'com' file without using the GUI? I would use that possibility, if it does exist, to check pair-wise rmsd's of previously superimposed structures. I guess people may have asked this question before, but I couldn't find an answer in the usual places... Cheers, Miguel

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Query on Cryo-EM map
by Aditya Padhi 25 Oct '15

25 Oct '15

Dear Chimera Users, I have a cryo-em map file and I would like to convert it into a PDB file. How can I do that? I tried saving the .pdb file but it throws an error saying “No model chosen to save”. Another question, If I open a .map file of a protein complex in Chimera, how can I select a subregion (a particular chain) and colour the surface of that part differently? I am not able to select the chain when I upload the .map file. Thank you, Aditya

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How to make a microtubule model
by Tom Goddard 22 Oct '15

22 Oct '15

The following page shows a “bent microtubule” model made with a Chimera Python script https://www.cgl.ucsf.edu/chimera/data/microtubule_aug2013/bent_mt.html <https://www.cgl.ucsf.edu/chimera/data/microtubule_aug2013/bent_mt.html> The bend makes it more complicated than a straight microtubule. Here is an explanation of how the Chimera “sym” command can make a straight microtubule model. These commands in Chimera (menu Favorites / Command-line to enter commands) make a straight microtubule from a PDB model as shown in the attached image. open 1jff sym #0 group h,9.8,27.7,13*shift,8,80.0 surf true axis x center 0,115,0 res 5 The sym command took the tubulin dimer (shown in red and blue in the image) and made copies in a helical pattern to look like a microtuble. The trick is to find the right helical parameters. I just did a few minutes trial and error to find the above. The “group” option says make a helix where each subunit is shifted 9.8 Angstroms from the previous one and by 27.7 degrees around the axis from the previous one, and make 13 copies (for a 13 protofilament microtubule). This makes a single turn of the microtubule. A microtubule does not have helical symmetry, the one turn achieves a shift of 1.5 subunits creating a seam where alpha and beta tubulin are touching in two adjacent protofilaments. So I just make one turn. Then the above command says shift that one turn by 80 Angstroms along the axis for each of 8 copies. The “surf true” option says show the copies as surfaces. Without that it will copy the atomic model and use a ton of memory. The helix axis is x (just judged by eye after opening tubulin dimer 1jff. The 1jff dimer seems to be centered not far from 0,0,0 so I shifted the helix axis 115 Angstroms along y to make the diameter about 23 nm. Here are the docs for the sym command: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/sym.html <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/sym.html> Here’s a web page where I did something more sensible to get better symmetry parameters — I fit the tubulin dimer to an EM map of a microtubule. http://www.cgl.ucsf.edu/chimera/data/cellcomplexity06/tcell-demo.html <http://www.cgl.ucsf.edu/chimera/data/cellcomplexity06/tcell-demo.html> Tom

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center of mass
by erik.laurini＠di3.units.it 21 Oct '15

21 Oct '15

Dear Chimera users, I would to plot the distance between the centers of mass of a ligand and a specific portion of its biologic target during the corresponding MD trajectory. I tried with the "MD plot" but it seems that it works only with atom selection. Do you have any advice? Thanks in advance! -erik- Dr. Erik Laurini Department of Engineering and Architecture University of Trieste, Via Valerio 10, 34127, Trieste (Italy) Tel. + 39 0405583440

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Calculating the total areaSAS from a series of PDB files
by ros 21 Oct '15

21 Oct '15

Hello! I would like to measure the SAS from a series of PDB files to see how the surface value changes over time (the PDB files are from an MD simulation). I know that If I open a PDB file and calculate the surface, I get the areaSAS value, but I do not want to do this 5000 times. I am making progress on a python script to automate the process, which is: -------------------------------------------- import os from chimera import runCommand as rc from chimera import replyobj os.chdir("/home/tmp/pdb") file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")] for fn in file_names: replyobj.status("Processing " + fn) rc("open " + fn) rc("surf") rc("sel :1-6") from chimera.selection import currentResidues residues = currentResidues() outf = open("/home/tmp/sas.dat", "w") for r in residues: print>>outf, r, r.areaSAS rc("stop now") -------------------------------------------- The PDB's consist of only 6 residues (DNA residues). With this script, I get the output: #1 DA 1 320.8377808 #2 DC 3 277.614161432 #2 DG 4 323.883637217 #1 DC 3 284.934065707 #2 DT 6 221.04715555 #0 DA 1 321.883850728 #1 DC 5 345.231659889 #0 DC 2 179.379177183 #2 DC 5 350.455405176 #0 DC 3 285.785918236 #1 DT 6 245.048330456 #0 DG 4 303.501165912 #1 DG 4 314.409510799 #0 DC 5 352.639633257 #1 DC 2 193.509086639 #0 DT 6 214.883334659 #2 DC 2 183.766654447 #2 DA 1 344.369126737 using 3 test pdb's. Is there a way to get the total value of areaSAS of each model and not for each residue? I am interested in having a file just like (using for example 3 pdb's): Model # total areaSAS value #0 123123.123122 #1 123123.12312 #3 123123.12312 ... etc. I have tried deleting the residues loop, but I do not know how the total areaSAS attribute is stored or how to assign it to a variable. Thank you for your help! Rodrigo. PS. The main goal is to be able to do this without the PDB files and just reading an AMBER topology/trajectory...

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Change chain id of blank chain
by Tom Goddard 20 Oct '15

20 Oct '15

Hi Joshua, Eric looked at the code and said the changechains command can’t change the blank chain id because it won’t accept a quoted space character as the chain letter. It could be done with Python code, or as you mention you can do it with the change chain ids gui. Tom > On Oct 20, 2015, at 2:07 PM, Broyde, Joshua E. <wrote: > > Dear Tom, > Hope you are well. I am having an issue with redefining the chains in a pdb open in Chimera. If a model has two chains (A and B) then it is easy to reassign the chain ids using: > changechains A,B B,A > > However, if one of the chains does not have a chain id already, (what Chimera calls, the "principle chain"), how do I assign a chain id? This is easy to do in the GUI, but I cannot find a command for doing so. > > Sincerely, > Joshua Broyde

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Color blobs automatically
by Petr.Brazda＠seznam.cz 19 Oct '15

19 Oct '15

Hello, I have both periodically distributed blobs and blobs, which are randomly distributed in my volume data. I know the translational vectors of the periodic net of blobs and I would like to automatically color them to distinguish them from the rest of the blobs. Is there a way to tell Chimera to color the blobs, which contain voxel with particular x, y, z coordinates? Or is there some other way to do this job? Best regards, Petr

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mouse selection not working
by Joel Meyerson 19 Oct '15

19 Oct '15

Hi, I'm unable to click-and-drag to select objects in the latest version of Chimera. Specifically, when I hold 'ctrl' and drag over an object, no selection is made. This is something that worked just fine in previous versions of the program. Any suggestions on how to fix the issue? I'm using Chimera production version 1.10.2 (build 40686) and running Mac OS X 10.10.4. Thanks, Joel

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on movie command
by Smith Liu 18 Oct '15

18 Oct '15

Dear All, Suppose there is a 100-residue protein opened in chimera, and it was scaled to a windows which can hold 10 residues, for example residue 10-20. Is any good way we first center on residue 15, then smoothly center on residue 16 (window hold residue 11-21), then smoothly center on residue 17 (window hold residue 12-22), then smoothly center on residue 18 (window hold residue 13-23), ......., until we center on residue 100? Here I emphasize "smoothly" so that the residue "move" was not too sudden to the eye. Best regards. Smith

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label residues
by Albert 17 Oct '15

17 Oct '15

Hello: I got a question on label residues in Chimera. Is it possible to use a simple command line to label all protein residue name and number displayed in the workspace? Thanks you very much Albert

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can you provide more opition for webGL?
by Albert 16 Oct '15

16 Oct '15

Hello everybody: I am just fascinated by the webGL function in Chimera and I am googling it today. Here I found something is even more interesting: http://istar.cse.cuhk.edu.hk/iview/ As far as we can see, it provide much more options in the above link. I am just wondering, could the Chimera developer also consider provide more options for the exported webGL file? That's definitely would be very attractive for the users. Thanks a lot Albert

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uneditable format
by Oliver Clarke 16 Oct '15

16 Oct '15

Hi Eric, I had no idea you could do this, it works great and could be very handy!! The colors and lighting (and positions) don’t seem to be preserved though and differ between firefox and safari - see the attached screenshots and test webgl of 1BL* with EDS maps (WebGL link: https://www.dropbox.com/s/jlwt8ynrz59w5qx/test_webgl.html?dl=0 <https://www.dropbox.com/s/jlwt8ynrz59w5qx/test_webgl.html?dl=0>). Oli. > Hi Albert, > Look at the File->Export Scene menu. That allows you to export to various file formats that your recipient may be able to view without any easy ability to save the result as a PDB file. In particular the “WebGL” export can be viewed as a web page in most modern browsers, with the ability to manipulate the structure interactively. > > —Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > > > On Oct 16, 2015, at 6:41 AM, Albert <mailmd2011 at gmail.com <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>> wrote: > > > > Hello: > > > > I've made a Chimera section which I would like to share with somebody else. However, I don't want the PDB within Chimera section to be exported by others. Is it possible for us to export some special file format so that other users can only visualize my file, but they cannot edit or export file into PDB coordinate? > > > > Thanks a lot > > > > Albert > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users at cgl.ucsf.edu <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>

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uneditable format
by Albert 16 Oct '15

16 Oct '15

Hello: I've made a Chimera section which I would like to share with somebody else. However, I don't want the PDB within Chimera section to be exported by others. Is it possible for us to export some special file format so that other users can only visualize my file, but they cannot edit or export file into PDB coordinate? Thanks a lot Albert

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Failure to reproduce complete Consurf output
by George Tzotzos 16 Oct '15

16 Oct '15

Hi everybody, I’m attaching a snapshot of the output of a Consurf job (snapshot1). Trying to save the file in EPS format produces only A PART of the right-hand-side pane of the output. No histogram is produced (see output.eps). I’d appreciate any suggestions as to how to produce a complete output. Thank you in advance George

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Re: [Chimera-users] uneditable format
by Oliver Clarke 16 Oct '15

16 Oct '15

Hi Albert, I'm pretty sure this doesn't exist at present, and I guess it would require substantial changes to make it work - You'd need to make sure that chimera couldn't write out anything after reading that session, and given that Chimera is open source and has many different ways of writing data out that might be tricky. However, that said, I think having a read-only packaged session format would be a very valuable addition (particularly if it incorporated support for maps), because it would solve a long standing issue in peer review of structural biology results - how to provide raw data for inspection to reviewers without providing maps and models with no strings attached, which many PIs are disinclined to do. Cheers, Oliver. >Hello: > >I've made a Chimera section which I would like to share with somebody >else. However, I don't want the PDB within Chimera section to be >exported by others. Is it possible for us to export some special file >format so that other users can only visualize my file, but they cannot >edit or export file into PDB coordinate? > >Thanks a lot > >Albert

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on mrz file
by Smith Liu 16 Oct '15

16 Oct '15

Dear All, Suppose I have 2 mrc files which are similar on the same protein, we call one map A one map B, and suppose onece we open them by chimera, A was in the centre of the window and B was not. By mouse dragging we moved map B almost overlap with chain B, then we fit map B to map A by the chimera "Fit in map" function. Is any way we can save map B, so that when we open map A and the saved map B by chimera, both A and B were in the centre of the Windows and A and B fitted as just before we saved map B? Best regards. Smith

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on scale command
by Smith Liu 15 Oct '15

15 Oct '15

Dear All, If I have used "scale 1.04" to scale up, will you please tell me the factor x in "scale x" by which I can return to the original size before I used "scale 1.04" ? Best regards. Smith

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Suggestion - autofilter history by typed substring?
by Oliver Clarke 14 Oct '15

14 Oct '15

Hi all, Just a suggestion (I guess for chimera 2) - would it be possible to autofilter the command history based on the typed substring? That is if I have typed “sel” and hit the up arrow, to only cycle through those commands in the history that start with “sel”. This would be particularly handy for scrolling quickly through recent “sel” and “color” commands - a similar mechanism is implemented in several shells and it works well. Cheers, Oliver.

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Re: [Chimera-users] Interactive Protein Structure and Sequence Alignment?
by Elaine Meng 14 Oct '15

14 Oct '15

On Oct 13, 2015, at 6:44 PM, Abba Leffler <aleffler(a)alumni.princeton.edu> wrote: > Dear Professor Meng, > I'm a frequent user of Chimera, mostly for visualization of homology models of large complexes. There's one feature I've search for in Chimera and not found. I wonder if you can help me. > > I would like to do two things, which are related. > > First, I would like to be able to visualize where inserts, deletions, and mutations are on the template structure relative to the target sequence. Is there any way to do that? I haven't found one. > > In a related question, I'd like to be able to interactively edit the sequence alignment (i.e. move indels that are in secondary structure elements) and then recompute the homology model to see if the DOPE score gets better or worse. Is that a possibility? > > I've found that many people have told me that alignments have to be "manually corrected", but there don't seem to be many tools out there for doing that in a sane way. If there are any you could recommend, I would sincerely appreciate it. > > All best, > -Abba Dear Abba, (1) Any time you have a structure open in Chimera and associated with some sequence in MultAlign Viewer (Chimera’s sequence viewer), you can easily map between the sequence and structure. It can be an individual sequence or one within a multiple sequence alignment. You can just highlight an area of interest on the sequence with the mouse and it will be highlighted on the structure. See the Sequences and Structures tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/super.html> … and/or the Multalign Viewer documentation, especially the part about sequence-structure association: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/f…> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> If you used the Modeller interface in Chimera, you already have the target-template sequence alignment open in Chimera. Then you could just use the mouse to highlight where in the sequence there is a mutation or insertion to have it highlighted on the structure(s). Actually this does selection. Then you can use the Actions menu to do something (e.g. coloring) to the current structure selection. While you can’t highlight something in the sequence that isn’t there (a deletion), you could certainly highlight the positions around it. (2) Multalign Viewer does allow for some small amount of manual editing, but it is not optimized for this purpose and other programs should be more suitable for any serious amount of editing. However, I don’t do this myself so I cannot advise... maybe JalView? Here are the instructions for manual editing in Multalign Viewer: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/m…> I hope this helps. I’ve CC’d this reply to chimera-users, which is the address we recommend for asking Chimera questions. 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

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Announcing the 2015/2016 EMDataBank Model Challenge
by Cathy Lawson 14 Oct '15

14 Oct '15

Dear Chimera User List Members, EMDataBank is pleased to announce the 2015/2016 Model Challenge. All members of the Scientific Community--at all levels of experience--are invited to participate as Challengers, and/or as Assessors. Benchmark targets of varying size and complexity have been selected from recently deposited 3DEM structures based on current state-of-the-art detectors and processing methods, in the resolution range 2.2-4.5 Å. Challengers are sought to create and validate models from challenge target maps in four different categories (1. optimize current cryoEM model, 2. fit known related cryoEM, crystallographic, or comparative models, 3. ab initio model building, 4. any other method of map interpretation), and upload their results with associated details. Assessors are sought to participate in evaluating submitted models. Registration is now open for all interested participants. Challengers may submit their models between November and April. Before submissions open, all are encouraged to provide feedback on submission requirements. An open assessment period will commence in late 2016. To learn more about this challenge and to register, please visit http://challenges.emdatabank.org and click on "MODEL CHALLENGE" in the menu bar. This is the second of two community-wide challenges being sponsored by EMDataBank this year to critically evaluate 3DEM methods that are coming into use, with the ultimate goal of developing validation criteria associated with every 3DEM map and map-derived model. The first challenge is focused on creating reconstructions from raw 2D image data and is currently in progress (click on "MAP CHALLENGE" in the menu bar). Sincerely, Cathy Lawson on behalf of the EMDataBank Team and the Model Challenge Committee emdatabank.org www.facebook.com/emdatabank3dem

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Show symmetry axis?
by Oliver Clarke 14 Oct '15

14 Oct '15

Hi all, Is there any way to easily generate an axis (of the type created by define axis, not a BILD file) corresponding to the z-axis of a map? Or of the symmetry axis of a map as identified by measure symmetry (which should be the same thing I guess)? I would like to be able to align Cn symmetric maps, which in general have the Cn symmetry axis coincident with z, while strictly obeying the Cn symmetry of the map. There is no built-in way to do this in chimera that I know of, but if I could create an axis corresponding to z for both maps, I could measure correlation between the two maps about that axis, after first aligning the symmetry axes of the two maps and approximately matching their translations along that axis (incidentally, for the same purpose it would be handy to have an additional option for "measure correlation rotationaxis", to measure correlation in a distance range corresponding to +/- x Å from the current position along the specified axis - angleRange is currently present, “distanceRange” seems like it could be a useful extension). The closest I have come so far is the following alias: alias ^screen_axis cofr view; savepos tmp; ac mc; namesel z1; clip hither -50;clip yon -50;cofr view; ac mc; namesel z2; sel z1 | z2; define axis sel; ~disp sel; reset tmp This will generate an axis perpendicular to and in the center of the screen, but this seems like a bit of a hack… also when I use measure correlation with this axis ("measure correlation #2 #0 rotationAxis a1”, where #2 and #0 are the two maps and the axis is a1), I get the attached error - is this a bug or did I make a stupid mistake somewhere? Cheers, Oliver.

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Show symmetry axis?
by Oliver Clarke 14 Oct '15

14 Oct '15

Actually never mind… just realized I have requested similar previously and there is already a ticket open (http://plato.cgl.ucsf.edu/trac/chimera/ticket/13829 <http://plato.cgl.ucsf.edu/trac/chimera/ticket/13829>). Nevertheless, consider this another vote for constraining fitmap to the symmetry of the input maps (or models) - would be very very helpful when dealing with ion channels. Cheers, Oliver. > > Message: 1 > Date: Tue, 13 Oct 2015 20:13:37 -0400 > From: Oliver Clarke <olibclarke(a)gmail.com> > To: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > Subject: [Chimera-users] Show symmetry axis? > Message-ID: <5DBFD175-0F48-4731-9E7E-C3F635BC571D(a)gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi all, > > Is there any way to easily generate an axis (of the type created by define axis, not a BILD file) corresponding to the z-axis of a map? Or of the symmetry axis of a map as identified by measure symmetry (which should be the same thing I guess)? > > I would like to be able to align Cn symmetric maps, which in general have the Cn symmetry axis coincident with z, while strictly obeying the Cn symmetry of the map. > > There is no built-in way to do this in chimera that I know of, but if I could create an axis corresponding to z for both maps, I could measure correlation between the two maps about that axis, after first aligning the symmetry axes of the two maps and approximately matching their translations along that axis (incidentally, for the same purpose it would be handy to have an additional option for "measure correlation rotationaxis", to measure correlation in a distance range corresponding to +/- x ? from the current position along the specified axis - angleRange is currently present, ?distanceRange? seems like it could be a useful extension). > > The closest I have come so far is the following alias: > > alias ^screen_axis cofr view; savepos tmp; ac mc; namesel z1; clip hither -50;clip yon -50;cofr view; ac mc; namesel z2; sel z1 | z2; define axis sel; ~disp sel; reset tmp > > This will generate an axis perpendicular to and in the center of the screen, but this seems like a bit of a hack? also when I use measure correlation with this axis ("measure correlation #2 #0 rotationAxis a1?, where #2 and #0 are the two maps and the axis is a1), I get the attached error - is this a bug or did I make a stupid mistake somewhere? > > Cheers, > Oliver. > > > > >

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drawing single stranded dna
by Sanders, Melanie - ARS 13 Oct '15

13 Oct '15

Dear, Is it possible to draw a single stranded dna. I always get a double stranded one if I enter the nucleic acids. Best regards, Melanie Sanders, PhD. Mycotoxin Prevention and Applied Microbiology USDA-ARS 1815 North University Street Peoria, Illinois 61604-3999 Phone: 309-681-6208 e-mail: melanie.sanders(a)ars.usda.gov<mailto:melanie.sanders@ars.usda.gov>

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output hdf5
by gijs 13 Oct '15

13 Oct '15

Dear Sir/Madam. First of all I want to complement the chimera team for writing a fantastic package for view macromolecular complexes. I am a researcher from the coherent X-ray diffraction community and we are also producing 3D models using our software [1]. However, we write data in a hdf5 format. Would you be interested to incorporate our file system into your package, or, and I think this is for now the better solution, could you provide a way I can write my hdf5 file to a chimera readable format and visa versa? For instance, I am trying to open a .map file from the EM databank, but do not know to exactly how to convert it. Are there tools? What file tree in hdf5 do I need? With kind regards, Gijs van der Schot [1] http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.114.098102

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on 2d label related movie command
by Smith Liu 13 Oct '15

13 Oct '15

Dear All, By chimera is any method we label a residue in a protein after scaling-up around that residue in a movie? Best regards. Smith

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rmsd overlay
by Francesco Pietra 12 Oct '15

12 Oct '15

Hello; Ho to superimpose a fake atom (pdb file available) to a coordiated metal in a protein? I could change the name of the fake atom to that of the metal, but then I need an rmsd overlay. hope it is clear. thanks francesco pietra

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python/model panel
by Dougherty, Matthew T 10 Oct '15

10 Oct '15

I would like to print out the model ID, name and input files as they are listed in the model panel. Can you point me in the direction of how to loop over the model panel ? Such as elevant variables, and what would be a block of code in chimera that I should study. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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Re: [Chimera-users] pipes & planks
by Tom Goddard 09 Oct '15

09 Oct '15

Hi Gabe, I've added a "pipes" command to tonight's Chimera daily build, for example, pipes #0 helixColor pink strandColor salmon and to delete the pipes and planks ~pipes #0 Other command options with default values are: helixColor = None, helixEdgeColor = None, helixArrow = True, helixFixedRadius = True, helixRadius = 1.25, helixSplit = False, helixSplitRatio = 2.5, strandColor = None, strandEdgeColor = None, strandArrow = True, strandFixedWidth = True, strandWidth = 2.5, strandFixedThickness = True, strandThickness = 1.0, strandSplit = False, strandSplitRatio = 2.5, displayCoils = True, displayTurns = True, turnColor = None, turnEdgeColor = None, turnResolution = 10, turnWidth = 0.25, turnThickness = 0.25 Colors by default match the ribbon color, or molecule color. Tom > On Oct 9, 2015, at 1:12 AM, Gabriel Lander wrote: > > Hi Tom, > 2 quick questions: > > 1) is there a way to turn generate a pipes & planks model from the command line? > 2) Can the coils in the pipes & planks be depicted as rounded instead of edged? > > Thanks as always, > -gabe > >

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bootstrap wanted boxsize
by Marlovits,Thomas 09 Oct '15

09 Oct '15

Hi Chimera-developers, I am wondering, whether there is a command to generate a new (empty) volume box from scratch? This would be a great help. Many thanks, -Thomas

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Chimera crashes when I try to open a .gro file
by Raag Saluja 09 Oct '15

09 Oct '15

Hi! Chimera crashes when I try to open a .gro file (created through GROMACS). I wanted to open the .gro file and then superimpose it on a .pdb file. Can you please guide? Thank you! Regards, Raag

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display a coordinate system in view
by Byrd, Robert A. (NIH/NCI) [E] 09 Oct '15

09 Oct '15

I would like to represent a xyz coordinate system by the unit vectors on the display with a molecule. Ideally, for a two domain protein, I would like to have two coordinate systems, one for each domain. In an ensemble of structures where one domain changes orientation with respect to the other, one coordinate system would move to the new position. It would be nice to then morph from one position to the next. This is straightforward with a set of structures and the morph utility in CHIMERA. The ability to add the two coordinate systems to the display, and have them ‘move’ or morph from one position to the other, would highlight the geometrical averaging that takes place. Is this possible in CHIMERA? Thanks Andy Byrd

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on command scripts related to movie by chimera
by Smith Liu 09 Oct '15

09 Oct '15

Dear All, I want to learn several commands on chimera movie preparation. Only read the on-line material I find I still meet some difficulty. Suppose I have 2 scripts， each for 1 movie. Will you please tell me by which command in the script I can link the 2 scripts so that the 2 movie will change into 1 movie? Suppose in Chimera I have opened 2 PDB files. Will you please show me the commands to view the structure in the first PDB, then change to view the structure of the second PDB （different from the purpose of morph）? And how about if then we see the 2 structures together, all in a single movie? Best regards. Smith

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3D-visualization of protein chain and mutation
by Elaine Meng 09 Oct '15

09 Oct '15

> From: "Coci, Emanuele" <Emanuele.Coci(a)akh-celle.de<mailto:Emanuele.Coci@akh-celle.de>> > Date: Friday, October 2, 2015 at 8:54 AM > Subject: 3D-visualization of protein chain > > Deat Chimera team, > my name is Emanuele Coci, MD PhD. > > I would kindly ask you for help about Chimera software in solving the following technical issue. I want to visualize the 3D-structure of a mutated protein chain. > > Which of the chimera tools is more indicated to visualize the 3D structure? > Is the toll open source? > Which software do I need to download the tool on my PC : JAVA, …? > > Best regards and many thanks in advance? > Emanuele Coci Dear Emanuele Coci, Chimera is a free download for any noncommercial use (research, education, …) and is available for Windows, Mac, and Linux. You should not have to download any other software to use it. All you need is a reasonably modern computer. See Chimera homepage and download links: <http://www.rbvi.ucsf.edu/chimera/index.html> <http://www.rbvi.ucsf.edu/chimera/download.html> I’ve CC’d chimera-users(a)cgl.ucsf.edu — that is the proper address for user questions. There are many possible styles of displaying a protein, and you have to use your own judgement and artistic taste to decide which style is best for what you want to see for yourself or show to others. There are several step-by-step tutorials for learning how to use Chimera, including “getting started” for beginners and some example image tutorials: <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html> For showing a mutation, the first thing you could do is just show the location of that amino acid on the structure (without mutating it), for example coloring it differently than the rest of the structure. It may be helpful to show the sequence of the protein so that you can identify the correct position (Chimera menu: Favorites… Sequence). You can choose a residue with the mouse in the sequence window, which will automatically select-highlight it in the structure. Secondly, you could try “mutating” that residue computationally. This could be done with the Rotamers tool (in menu under Tools… Structure Editing) or the “swapaa” command. There is an example of using the Rotamers tool in the “Structure Analysis and Comparison” tutorial: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/rotamer…> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html> However, Chimera will not predict any larger-scale changes in the structure from the mutation or calculate changes in stability or affinity. It will only change the sidechain and not move anything else. You can use Rotamers to analyze the H-bonds and clashes (bad contacts) of different conformations of the sidechain, which may allow you to hypothesize whether the mutation would be disruptive to the stability or interactions of the protein. 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

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Newlines in labelopt string
by Repic Matej 07 Oct '15

07 Oct '15

Hi everyone, I have pretty long atom labels and it would be nice if I could split them with newlines. I set labels with labelopt info %(name)s %(ee).2f %(ea).2f %(er).2f # what I have C3 0.41 0.22 0.14 # what I want C3 0.41 0.22 0.14 The obvious \n does not work. Any ideas? Thank you, ------------------------------------------------------ Dr. Matej Repic Ecole Polytechnique Fédérale de Lausanne Laboratory of Computational Chemistry and Biochemistry SB - ISIC LCBC BCH 4108 CH - 1015 Lausanne ------------------------------------------------------

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Joining Models + Avoiding Steric Clashes
by Carlos Gonzalez Oliver, Mr 06 Oct '15

06 Oct '15

Dear Chimera, I have been trying to use Join Models to make a C-N bond between the globular domain of a protein and a region of it (a C-terminal tail) whose structure I simulated using MD. However, when I do the joining with Join Models C-N bond option, I get some serious steric clashes. I have tried to resolve them by hand by adjusting the bond's torsion and angles but it is too complicated. Other than trying to use other software to minimize clashes, I think I might have to use a brute force method and try a bunch of the structures my MD generated until one of them works. So what I am trying to do now is write a script to do the model joining automatically with many different structures that I generated, and return the one with the least number of clashes. But I haven't been able to find a command line equivalent of the Join Models window.. I was wondering if you know if such a command exists, if not what combination of commands would work? (for repositioning the models and forming the bond) Thanks! -- Carlos G. Oliver M.Sc. Student Vogel Lab Department of Biology McGill University Montréal, QC, Canada

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Problem on Nucleic Acid Ribbon
by Francesco Papi 06 Oct '15

06 Oct '15

Good morning, I'm working on a DNA X-ray structure. The problem I have observed is that the terminal nucleotide of the DNA sequence is excluded from the backbone ribbon, in other terms the backbone ribbon is shown and it is ok, but it is made of all the residues except the terminal one, which is linked to the ribbon by a long phosphodiester bond (see the attached image). Moreover, if I put the representation "Show side (sugar/base)", from the option "Nucleotides", to be "fill/slab", the terminal residue still features an "Atom & Bonds" style. The PDB file seems to be ok, as confirmed by a colleague. Do you how to solve this problem? Best regards Francesco Papi

2 1

solid rendering color voxel by voxel?
by Oliver Clarke 06 Oct '15

06 Oct '15

Hi all, I don’t think this is possible right now, but i just wanted to check and maybe put in a request for addition to Chimera 2 at some point if you think it would be a useful feature. I like generating looping maximum intensity projection movies like the following (using EMDB 2807 as an example): https://www.dropbox.com/s/elt2f5so6azvvhk/emdb2807_example1.mp4?dl=0 <https://www.dropbox.com/s/elt2f5so6azvvhk/emdb2807_example1.mp4?dl=0> https://www.dropbox.com/s/julh586sc9yxl7g/emdb2807_example2.mp4?dl=0 <https://www.dropbox.com/s/julh586sc9yxl7g/emdb2807_example2.mp4?dl=0> Command used to generate representation: #Makes a pseudoprojection style view of the given volume #Usage: volume_project #map_id alias ^volume_project background solid black; volume $1 step 1 sdlevel 0,0 color white sdlevel 20,1 color white style solid projectionMode 3d maximumIntensityProjection true btCorrection true linearInterpolation true; unset depthCue I feel like even at small sizes, this gives a good idea of the overall quality of the electron density, in both mobile and well-ordered regions, due to the non-thresholded nature of the representation. It seems to me that this would be a natural fit for Resmap coloring to color a map by local resolution, as one of the issues I have with the application of Resmap in surface representation is that if you contour the map at a sufficiently low threshold to see the less well ordered parts of the structure, you can’t see the voxels that have the best local resolution (necessitating slabbing of the map). This would also be handy for using Color Zone to color different regions of the map based on the model. Would it be possible to add per-voxel coloring in solid representation at some point, similar to scolor for surface representation, to make this kind of thing possible? Cheers, Oliver.

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Exporting coarse-grained models of proteins
by Hamish Todd 06 Oct '15

06 Oct '15

Hello all, So sorry to bother you all but I've tried googling a lot of things and not found out how to create a coarse grained protein surface like this one <http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/stmvrna/capsid.png>. Creating a *surface* is easy of course, but where does that nice, intuitive, bulbous STMV protein come from? And when I get it, can I export the vertex and polygon data? Hamish -- Hamish Todd 07722 400 806 Personal Website <http://www.musicofthespheresgame.com/?page_id=21>

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Saving images of all scenes in session?
by Oliver Clarke 02 Oct '15

02 Oct '15

Hi all, Apologies for yet another post and thank you for your patience! :-) Feature suggestion (or maybe this exists already?): I would like a way to iterate over all scenes in a session and save an image at each scene, with the same display settings (e.g keep background or make transparent, image format, wall-eye/cross-eye stereo, etc). This would be really very helpful when making, remaking and updating figures. Most of the time, I will have a session, say “Fig1.py”, within which I will have a bunch of scenes corresponding to each panel. It would be really advantageous to be able to take images of each scene all at once, saving each as (for example) Fig1_scene_name.jpg, Fig1_scene_name2.jpg etc. This could work in the same way as saving series of maps or models does now - just have a checkbox in the Save Image dialog for “save images for all scenes in session”, or something similar. It can take quite a while to save each image when on a slow computer, or when using graphics intensive settings such as silhouettes and shadows, so being able to save matched sets of images (e.g. low and hi-res versions, stereo versions, etc) with a couple of clicks would save a lot of time, particularly for example if you realize that the versions you saved the first time were all too low res and you want to go back and save a higher res version of every panel. I realize you guys might not have time to implement this for Chimera 1, as development of Chimera 2 is top priority, so maybe I can write a script to do this in the meantime? Is there any way to return a list of scene names using one of the built in python functions? I guess something in Animate.Scenes ought to do this, but not being much of a python programmer I can’t quite figure it out - any tips much appreciated. Cheers, Oli.

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Problems detecting h-bonds
by Felipe Vasquez 02 Oct '15

02 Oct '15

Hi, I have recently obtained some docking results (I have a complex) and I am trying to detect any protein-ligand h-bonds. Soon, I faced a first problem when I obtain this error message: "More than 2 coplanar positions specified!", and I think I solved it once my ligand was selected and I enter into the command line: "setattr a idatmType sel". However, I obtained later an entire panel (with a big list in it) asking me to indicate the expetd geometries and number of substituents for a large list of atoms, from both ligand and protein. How could I overcome this issue knowing that there is several expected h-bonds to be detected in my complex? Thanks in advance for your help. Best regards, *Andrés Felipe Vásquez J., BSc, MSc.* Profesional - Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN Bogotá, D.C., Colombia

2 1

Morphs
by Dr Kereiche 02 Oct '15

02 Oct '15

Dear Chimera team, lately I am facing some problems for creating a movie in which I would like to combine 2 morphs with each other. To make it clearer, I hope, I have 2 Em maps representing 2 states of my structure (vol #1 & vol #2) I did a morph maps (volume/ Morph map) after having recenter and align the 2 maps. it works perfectly. I did similar procedure with 2 pdb files (1.pdb & 2.pdb), corresponding to the fitted molecular structures of the 2 states (vol#1 & vol #2) , using the tool/Structures comparison/ morph conformation. The pbds are aligned with the EM map using VOP command. Now I would like to combine the 2 morphs together to have a final morph of the EM maps with the molecular structure, but I could not find a way to combine them. Thus I would like to know if it is possible to do it ? and if yes how to do it. Moreover is it possible to play the morph of the pdbs in way of the morph of the EM maps back and forth? Thank you in advance, Sincerely Sami

2 2

Angle between pseudobond and principal axis
by Yasser Almeida Hernández 01 Oct '15

01 Oct '15

Hi all, I want to measure the angle between a pseudobond and the X, Y, Z axis. How can I do so? Best Yasser

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Re: [Chimera-users] metal coordination to display off
by Eric Pettersen 30 Sep '15

30 Sep '15

On 9/28/15 6:13 PM, "Luigi Di Costanzo" <dicostanzo(a)rcsb.rutgers.edu <mailto:dicostanzo@rcsb.rutgers.edu>> wrote: > > We have fetched 2MHR with Chimera and noticed that the middle nitrogen > of azide is bonded through a dashed line as following: > > FE2 FEO A 119 N2 AZI A 120 > > From the "structure analysis" tool and "metal geometry" window we are > unable to display off that dashed lines that is incorrect. > > The coordination table does not show that particular link and we can not > deselect it. > > Could you please look into it and provide some suggestions? > > Thanks. Hi Luigi, The spurious dashed line is due to a corresponding CONECT record in the PDB file. So one option is to locate that CONECT record and delete it. The other is to use the Metal Coordination tool to clean up the coordination of that iron. First, it is highly unlikely that the histidine nitrogens coordinating the iron are protonated, so you should select those hydrogens and “del sel” to get rid of them. Then if you bring up the metal coordination tool for the iron it will properly show the nitrogens as coordinating. If you already had the tool up when you deleted the hydrogens then you will have to force the tool to consider the newly deprotonated nitrogens by selecting them and clicking the “Add atoms selected in the graphics window" button. You can now remove the spurious coordination you noted above by first clicking the last atom in the coordination table (HIS 25.A NE2) and then clicking the “Create/Update metal-complex pseudobonds” button. I hope this helps. Let me know if you have any questions. —Eric Eric Pettersen UCSF Computer Graphics Lab

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Chimera
by Scapin, Giovanna 30 Sep '15

30 Sep '15

Good afternoon I am interested in downloading and installing CHIMERA. Could you let me know if there is any licensing cost involved and if so whom I should contact? Thank you very much Giovanna Scapin Giovanna Scapin Principal Scientist Structural Chemistry Merck & Co., Inc. 2000 Galloping Hill Rd K15-1800 Room B133C Kenilworth NJ 07033 Phone +1 908 740 3632 Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth, New Jersey, USA 07033), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.

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Proportional representation of missing segments?
by Oliver Clarke 28 Sep '15

28 Sep '15

Hi all, I think it would be handy, in a future version of chimera, to have an option to represent missing segments in a manner that is proportional to the volume of protein missing - this would be very useful for getting a sense of which chain breaks correspond to very large missing regions (e.g. whole domains), and which correspond to short linkers or loops that are missing. For example, in the structure of the ryanodine receptor, there are missing segments ranging in length from ~5-250 residues in length - it would be very handy to be able to get a quick sense, upon first opening a structure, about what fraction of the crystallized or reconstructed protein is actually present in the model. I can think of a couple of ways of doing this. One way would be to associate an attribute with each missing segment, corresponding to the number of missing residues, and allow the user to scale the radius, color or opacity of the missing segments in proportion to this value (maybe this attribute already exists somewhere internally?). Another way might be to create a completely different missing segment representation - perhaps an ellipsoid, with the ends of the ellipsoid at the N and C-terminal breakpoints, and the volume of the ellipsoid scaled to the volume of a random polymer of the known number of missing residues. I would try to do this myself by creating an extension, but I don’t really know where to start to get the information that would be required - I don’t know how to iterate over all missing segments, calculate the number of residues in each, and create a new representation. I guess there is probably a list somewhere in Chimera corresponding to the missing segments and their properties, but I have no idea how to find it. Cheers, Oliver.

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Forcefields and Molecular Radii
by Cale Martin 25 Sep '15

25 Sep '15

Dear Chimera users, Over the last few days I have been using Chimera 1.9 to model the Poisson-Boltzmann surface potential of a protein. I have been using the APBS software and the two main forcefields I have been using are the TYL06 and AMBER. When I model the chemokine using the AMBER forcefield the result seems to be normal and as expected, but when using the TYL06 forcefield, the final molecule surface seems to have larger molecule radii almost making it look a little more "bubbly" for lack of a better term. Is this a function of the forcefield in any way? Should this be expected from these two different forcefields? Another issue that I have had along the same line involves the APBS program. The settings allow for the selection of a "Smoothed Molecular Surface" and one that is just "Molecular Surface" but when I run the program with every thing the same except these settings, the results look exactly the same. Should this setting affect the visualization of my molecule surface in any way? Thank you, Cale Martin

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FW: How can I find H-bond between ligand and protein residues within selected angstrom?
by Williams, Joanne 25 Sep '15

25 Sep '15

On 9/19/15 1:29 AM, "高木友理子" <kagaribi-firefly(a)bs.s.u-tokyo.ac.jp> wrote: > Dear Chimera creator, > > I use Chimera to analyse protein-ligand interaction. > Especially, I would like to find H-bond between these. > I clicked HBonds and tried to search H-bond within selected distance. > However,I could not. > I guess the reason is that I was not able to understand "Relax > constraints" in H-Bond parameter window. > I ,of course, checked chimera's help. > What is relax constraints? > What does 0.4 angstroms indicate? Is this the Max distance between ligand > and protein residue? > I would like to find H-bond between them within selected angstrom. > What should I do to know that? > Please teach me how to do. > Thank you for being patient with my English. > > Best regards, > > Yuriko Takagi > Tokyo university student

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Way to extract path to file from model ID
by Oliver Clarke 24 Sep '15

24 Sep '15

Hi all, I’m wondering, is there any way (presumably via a python function) to get the path to the original file from the model ID? I’ve written a little python jiffy (below) so I can lowpass filter maps to a specified resolution on the fly inside chimera using EMAN, but is quite slow because I need to first write a copy of the map out (so I know where it is) and then modify it. If anyone knows of an easier way to do such things I would be most grateful. Cheers, Oli. Script: def cmd_lowpass(lowpass,args): from Midas.midas_text import doExtensionFunc def lowpass(model,resol): import os from chimera import runCommand import subprocess import sys #You may need to change the below to .bash_profile if on mac. #You must have EMAN2 in your bash path for this to work correctly. #If running multiple times, you need to close the first instance of lowpass.mrc before creating a second. bashrc_path=os.path.expanduser("~/.bashrc") freq=1.0/resol command="cd ~; system mkdir chimera_tmp; cd chimera_tmp; volume "+model+" save ./tmp1.mrc" runCommand(command) pathvar=os.path.expanduser("~/chimera_tmp") os.chdir(pathvar) e2string="--process=filter.lowpass.gauss:cutoff_freq="+str(freq) print(e2string) mrc_in=pathvar+"/tmp1.mrc" mrc_out=pathvar+"/lowpass.mrc" e2command="source "+bashrc_path+"; bash -c \"e2proc3d.py"+" "+mrc_in+" "+mrc_out+" "+e2string+"\"" print(e2command) proc=subprocess.Popen(e2command,stdout=subprocess.PIPE, stderr=subprocess.PIPE,shell=True) out, err = proc.communicate() print 'stdout:', out print 'stderr:', err runCommand("open lowpass.mrc") doExtensionFunc(lowpass,args) from Midas.midas_text import addCommand addCommand("lowpass", cmd_lowpass, help=False)

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Rendering protein molecule to a geometry format by Chimera
by Hsin-Yi Yeh 24 Sep '15

24 Sep '15

Hi, I try to render a protein molecule to a geometry format (from .pdb format to .obj format) by Chimera. I use 'Multiscale models' tool in 'Higher-Order Structure' choice and then make the model by resurfacing at some appropriate resolution. It turns out that the whole protein molecule can be modeled pretty nicely. However, I now have a similar problem; instead of rendering the whole protein molecule, I would like to render the whole structure separately. I want to render the exposed residues (those residues on the surface) and non-exposed/buried residues separately, so I will have two obj files (one for the exposed residues and the others for the non-exposed residues). I haven't been able to figure this problem out yet. Thus, I am wondering could you please give me some direction? Any advice will be greatly appreciated! Thank you, Hsin-Yi (Cindy) Yeh -- Hsin-Yi (Cindy) Yeh PhD Student Parasol Lab, Department of Computer Science and Engineering Texas A&M University Email: hyeh(a)cse.tamu.edu https://parasol.tamu.edu/people/hyeh/

2 1

applying charges calculated by DFT to ligands in protein models
by Anne-Frances Miller 22 Sep '15

22 Sep '15

Dear Sir or Madam, Our protein has a bound FMN and the various tools accessible via Chimera are not able to apply charges to the atoms in FMN. However I have NBO charges for all the atoms from DFT calculations. Is there a way I can provide these to the FMN in my pdb file or in my Chimera session in order to then display a Coulomb electrostatic potential for the protein + FMN? My charges are not simply +1 or -1, but fractional charges for each atom. Can Chimera accommodate this ? If not, no problem, I will still benefit greatly even if all I can do is add -1 to the one atom at which most of the excess electron density is concentrated. Many Thanks, Anne-Frances Anne-Frances Miller Professor of Chemistry Director, Magnetic Resonance Centre University of Kentucky Dept. Chemistry, 505 Rose Street Lexington KY 40506-0055 “You never change things by fighting the existing reality. To change something, build a new model that makes the existing model obsolete.” Buckminster Fuller

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Fetch by ID EMDB + fit PDBs enhancement suggestion
by Ingvar Lagerstedt 21 Sep '15

21 Sep '15

Dear Chimera, Attempting to Fetch by ID an EMDB entry with a fitted model, where the model does exist in PDB format, causes an error: No such ID. The map is retrieved but not opened in Chimera. The two main reasons that the model is not available: A. The model is only available in mmCIF format. Since a wwPDB remediation at the end of last year, entries that are larger than what the PDB format can handle are no longer distributed as split entries. They are only distributed as mmCIF (and PDBx) files. This is common for say ribosomes. EMD-6315 with fitted model 3j9z is an example. Changing the command so that it attempts to retrieve mmCIF files rather than PDB files would fix this issue. B. The model has not been released, EMDB and PDB releases for maps and models are not always synchronised. An example would be EMD-6413, where the model 3jb9 is currently waiting for author approval. In this case it would be nice if the map was loaded. Many Thanks, Ingvar

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Re: [Chimera-users] large file size exporting scene with spheres
by Elaine Meng 17 Sep '15

17 Sep '15

On Sep 17, 2015, at 10:48 AM, Tom Goddard <goddard(a)sonic.net> wrote: Hi Elaine, Bill, Chimera export first writes x3d and then converts that to STL or VRML or whatever you requested. For atom spheres it writes the center and radius of the sphere in x3d. It does not write the number of triangles or the amount subdivision. The Chimera program x3d2stl controls how many triangles a sphere is turned into. It uses 100 triangles per square Angstrom. There is no option to change that. But it is possible to run x3d2stl by hand and specify the resolution option “-r 1” to request 1 triangle per square Angstrom, resulting in a file that is 100 times smaller and the spheres still look fine (using about 40 triangles per atom). ~/Desktop/Chimera\ 1.10.2.app/Contents/Resources/bin/.x3d2stl -o 1a0m_r1.stl -r 1 < 1a0m.x3d Note that .x3d2stl has a period as the first character. Eric Bell reported this problem about a year and a half ago but the ridiculous defaul STL sphere subdivision has unfortunately not been changed. http://plato.cgl.ucsf.edu/trac/chimera/ticket/13183 Tom > On Sep 17, 2015, at 9:51 AM, Eliason, William <william.eliason(a)yale.edu> wrote: > > Elaine, > > Thanks again for your suggestions. I had already seen that previous post you listed and found that the stl file size for spheres was unchanged with changes to the zoom. The subdivision box in the effects tool changes the spheres on on the chimera display but has no effect on the stl file size when exporting a scene. > > I will keep looking for a solution. If you have any other suggestions please email me. > > Thanks Again, > > Bill > ________________________________________ > From: Elaine Meng [meng(a)cgl.ucsf.edu] > Sent: Tuesday, September 15, 2015 3:42 PM > To: Eliason, William > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] large file size exporting scene with spheres > > Hi Bill, > You can decrease the “subdivision” setting in the Effects dialog (menu Tools… Viewing Controls… Effects) and also zoom out the view before exporting. > > These are discussed in more detail in this previous post: > <https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_pipe… > > > 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 Sep 15, 2015, at 11:52 AM, Eliason, William <william.eliason(a)yale.edu> wrote: >> >> Chimera-users, >> >> I am very new to chimera. I would like to export a scene with spheres for 3d printing but the ( .stl) file size is enormous. They contain way to many triangles. I tested a smallish molecule in MeshLab and I could decrease the number of faces from 699732 (34MB) to 34986 faces (1.7MB) with minor flattening of the sphere. Is there a way to have chimera generate spheres with fewer faces? >> >> Thank you, >> >> Bill Eliason > >

1 0

Saving sessions including maps?
by Oliver Clarke 17 Sep '15

17 Sep '15

Hi all, Is there any possibility of altering the chimera session format (or adding a separate option) such that all maps (including those created during the session) are also saved? This would greatly facilitate sharing data with collaborators, and would also allow one to provide chimera sessions with saved scenes as supplementary data when publishing. It would also make saving sessions more practical when many different volumes are created during the session - for example, when using a molmap low resolution representation for each domain. This would not necessarily require creating a new format - just creating a tarball or folder with all the maps and relative paths specified in the python file would work fine I think? Cheers, Oli.

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Re: [Chimera-users] FW: eps image in publication quality
by Mahendra B Thapa 16 Sep '15

16 Sep '15

Dear Eric & Greg Thank you for the suggestions. The only available option to save the *sequence alignment image* is EPS format, actually I am looking a way to save the image in tif or png format. In the pop-up window of sequence alignment image , there are following options available under 'File' heading: Save as, save EPS, save Association info, Hide & quit. As Greg pointed out, I didn't find "Save Image dialog". Eric, when I copied the so generated EPS image in MS-Powerpoint for further editing, the quality of the image was not good. I have attached one of the EPS image ( in which I have aligned two structures: pdb id 4ICB & 3BCI.) Thank you for help, Mahendra Thapa University of Cincinnati,OH On Tue, Sep 15, 2015 at 8:42 PM, Thapa, Mahendra (thapamb) < thapamb(a)mail.uc.edu> wrote: > > ------------------------------ > *From:* gregc(a)cgl.ucsf.edu > *Sent:* Tuesday, September 15, 2015 6:42:06 PM (UTC-06:00) Central America > *To:* Eric Pettersen; Thapa, Mahendra (thapamb) > *Cc:* chimera-users(a)cgl.ucsf.edu > *Subject:* Re: [Chimera-users] eps image in publication quality > > Actually, chimera's EPS files are at a fixed resolution. To get a higher > resolution, save the image with a higher resolution. An easy way to get a > reasonable resolution is to switch to print units in the Save Image dialog, > and choose a size in inches or cm. The default "Print resolution" of > 100dpi is generally more than adequate since printers need many dots to > represent a single pixel and most computer monitors are roughly 100dpi. > > Also, note that EPS files are huge compared to PNG or TIFF files. Most, > if not all, journals now accept TIFF or PNG images, so there is no need to > generate an EPS file. > > -- Greg > > September 15 2015 5:18 PM, "Eric Pettersen" <pett(a)cgl.ucsf.edu > <%22Eric%20Pettersen%22%20%3Cpett(a)cgl.ucsf.edu%3E>> wrote: > > EPS (Encapsulated PostScript) is resolution independent — it essentially > has infinite resolution. If it doesn’t look good in a viewer it’s because > the viewer is doing a poor job of rendering it. What are you using to look > at the EPS file? > —Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > > > On Sep 15, 2015, at 9:04 AM, Mahendra B Thapa <thapamb(a)mail.uc.edu> wrote: > > Dear Chimera Users, > Using the following procedures in chimera window, I saved a sequence > allignment image in eps format ( which looked like the first image of " > file:///opt/UCSF/Chimera64-1.6.1/share/chimera/helpdir/ContributedSoftware/multalignviewer/framemav.html"). > The image in the pop of window is nice but the saved image in the eps > format is not so clear. Let me suggest how to save the image in the > publication quality. > (i) structure ---> matchmaker > (ii) Tools ---> sequence ---> match ---> align > (iii) file ---> save as ---> eps > Thank you, > Mahendra Thapa > University of Cincinnati, OH > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

2 1

large file size exporting scene with spheres
by Eliason, William 16 Sep '15

16 Sep '15

Chimera-users, I am very new to chimera. I would like to export a scene with spheres for 3d printing but the ( .stl) file size is enormous. They contain way to many triangles. I tested a smallish molecule in MeshLab and I could decrease the number of faces from 699732 (34MB) to 34986 faces (1.7MB) with minor flattening of the sphere. Is there a way to have chimera generate spheres with fewer faces? Thank you, Bill Eliason

2 2

eps image in publication quality
by Mahendra B Thapa 16 Sep '15

16 Sep '15

Dear Chimera Users, Using the following procedures in chimera window, I saved a sequence allignment image in eps format ( which looked like the first image of "file:///opt/UCSF/Chimera64-1.6.1/share/chimera/helpdir/ContributedSoftware/multalignviewer/framemav.html"). The image in the pop of window is nice but the saved image in the eps format is not so clear. Let me suggest how to save the image in the publication quality. (i) structure ---> matchmaker (ii) Tools ---> sequence ---> match ---> align (iii) file ---> save as ---> eps Thank you, Mahendra Thapa University of Cincinnati, OH

3 2

how to move subunits of a pentamer receptor in a controlled way
by Zhang, Yinghui 14 Sep '15

14 Sep '15

Dear Sir, This is Yinghui Zhang from Massachusetts General Hospital. I am a frequent user of Chimera to understand the structure of a neuronal pentamer receptor which is ion channel. Now we want to do some modification of the receptor by manipulating the coordinates of the atoms of the receptor pdb files. The aim is to move each subunit radially away from the receptor’s central symmetry axis(which should be the central channel axis ) or tilt each subunit outward. The symmetry of the receptor cannot be disrupted and we want to do it in a quantitative manner(move by a specific ‎Å or tilt by a specific degree value). Could you please give us some clues if we can realize these aims in Chimera? Many thanks and regards! Yinghui Zhang The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

2 1

setting solvent density threshold at 2.5 times of the bulk solvent density
by Mohan Pradhan 11 Sep '15

11 Sep '15

Dear Chimera users, I am using the Volume Viewer application in Chimera to visualize the solvent density around protein at a threshold value of 2.5 times of the bulk solvent density. My understanding is that the iso value corresponding to the bulk solvent density is marked by the peak in the plot of the volume viewer. I am then multiplying the iso value of the peak by 2.5Is this the right way of identifying regions in protein that have a solvent density of 2.5 times of the bulk solvent density? Kindly suggest. Thanks,Mohan

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Question regarding 3D surface coordinates
by Guirguis, Christopher Amin 10 Sep '15

10 Sep '15

Hello, A quick question: is there any output file type where coordinates of the surfaces are typed rather than just the center of the individual atoms? I want to insert my molecules into a modeling software like Maya to create an .obj file for viewing on mobile devices. Thank you for your time. Best, Chris Guirguis

3 4

question
by A G Szabo 09 Sep '15

09 Sep '15

I go to tools and open the sequence of the protein that I am interested in. The minimum number of amino acids in a row that I can select is 2. I am interested in visualizing a selected number of amino acids that are not in linked to one another. Eg. A specific Lys residue in a helical sequence. I have found a work around. I highlight two adjacent residues, and visualize the two of them as sticks. I then select the amino acid I do not wish to highlight together with the amino acid on the other side of the one that I am interested in. I can that way eventually deselect and not highlight the amino acid I am not interested in. There has to be a simpler way. Thanks for your assistance. Arthur G. Szabo Professor Emeritus Chemistry Wilfrid Laurier University.

2 3

on mrc map
by Smith Liu 09 Sep '15

09 Sep '15

Dear All, Suppose I have a mcr map for a protein of 4 subunits. Will you please introduce to me how to split the whole map to 4 different maps, with each map corresponding to the part of each subunit in the whole map, without loosing any data in the spitted map in comparison to that specific subunit part of the whole map? Best regards. Smith

2 1

Help needed urgently
by Clare Nattress 08 Sep '15

08 Sep '15

Hello there, I have just sent this file to a 3D printers and sadly it has disintegrated when post printed and the model has been bathed and washed. Attached is the link to the STL. file https://www.dropbox.com/sh/2nytyw6989h0v2l/AADiXrhb8mUfi53J95co-Bvja?dl=0 I was wondering how I could perhaps make the structure 3D print safe. Would you be able to help me join the bonds and also make them a lot thicker? Any help would be most appreciated as this is meant to be in an exhibition come Friday. Best Wishes, Clare Nattress Artist/Writer www.clare-nattress.com LinkedIn - Clare Nattress @ClareNattress

3 3

Align and average intensity images in Chimera
by 許紹君 08 Sep '15

08 Sep '15

To whom it may concern, I am willing to use Chimera for aligning several images from the structure illumination microscope (SIM). Here is the surface maps generated by Chimera from two images. cid:image005.jpg@01D0E986.2CF5F370 After alignment by the tool “Fit in Map”, they are aligned very well. cid:image006.jpg@01D0E986.2CF5F370 My next step is to average the intensity from two aligned images and generate a new map which will be used to fit other images. Can anyone tell me how to do it in Chimera? By the way, please also tell me what the values mean in the reply log. cid:image007.jpg@01D0E986.2CF5F370 It helps me to use another software to complete the mission, if I can get the rotation, voxel shift, or even scaling values from the alignment. Thank you! All Best, Peggy Hsu, PhD Institute of Cellular and Organismic Biology, Academia Sinica 128 Academia Rd Sec 2, Nankang, Taipei 11529, Taiwan Tel: 886-2-2787-1531 (O) email: peggyschsu(a)gate.sinica.edu.tw

2 1

Distance in pi-interactions
by George Tzotzos 03 Sep '15

03 Sep '15

I’m trying to work out the distance between two arene rings involved in pi-interactions. Is there a way of measuring the distance centre-to-centre of each arene ring? Or any other sensible way? I’m attaching a snapshot for easy reference. Thanks in advance for any suggestions. Regards George

2 5

make a movie showing the process from an ASU model to the complete model of virus
by 李智海 02 Sep '15

02 Sep '15

Hi, I just obtained an atomic model of the asymmetric unit of an icosahedral T=7 virus capsid , and I want to make a movie to play the whole process from the ASU model to the full capsid model by imposing its icosahedral symmetry. Please show me some examples of the command lines to generate such kind of movies. Thanks! Best regards! Zhihai Li

2 1

chimera visualization
by Valerio Chiarini 02 Sep '15

02 Sep '15

Dear Elaine, I would like to produce images from chimera showing an NMR bundle structure (backbone only) with stick-represented residues each one belonging to different single structures. I know it´s possible to do it with pymol but unfortunately the structures superimposition is not as good as in chimera. Would it be possible? Thank you in advance, Valerio

2 3

Rapid residue identification near ligands
by Korbin West 01 Sep '15

01 Sep '15

Greetings all, We need to be able to easily assign ligands to a chain (or chains) and to rapidly ID the residues in contact with it. I believe Chimera processes the structures and immediately displays ligands and maybe contacts, so it "knows" this information somehow. Does anyone know of a way to identify these easily and quickly so we can analyze large numbers of files? Also, if the output could be in the form of a text file or such that would be beneficial as well. Thank you all for your help. Best, Korbin West Wabash College

2 1

make a movie showing the process from an ASU model to the complete model of virus
by 李智海 01 Sep '15

01 Sep '15

Hi, I just obtained an atomic model of the asymmetric unit of an icosahedral T=7 virus capsid , and I want to make a movie to play the whole process from the ASU model to the full capsid model by imposing its icosahedral symmetry. Please show me some examples of the command lines to generate such kind of movies. Thanks! Best regards! Zhihai

1 0

Hydrogen bonding calculation issues with PDB2PQR/AMBER/CHIMERA
by Fenton Heirtzler 31 Aug '15

31 Aug '15

Hello- I’m trying to use CHIMERA to model the hexameric hydrogen bonding of isophthalic acid. I’m just an organic chemist, not a computational chemist. The PDB2PQR subroutine is returning the reply “Error encountered: No heavy atoms found!”. Here is sequentially what I have done: 1. A pdb file of isophthalic acid hexamer was imported. 2. The covalent bond lengths and angles were set to realistic ones. 3. The names of the concerned atoms were defined in the Build Structure/Modify Structure/Change Modified Residue’s name box, as described in the User Guide (i.e., Cac, O2, O3 and H) 4. The default limits of 3.4 Å and 30° were used 5. The AMBER force field was chosen. Thanks very much Fenton (PS – I’m a private person, not associated with either academia nor industry) -- Dr. Fenton Heirtzler Phone: +1-301-312-5145 On LinkedIn <http://www.linkedin.com/in/fentonhorgchem/> Skype: fentonheirtzler Supporter of the International Day of Climate Action <http://www.350.org/> *********

2 4

Query related to chimera
by Akhilesh Verma 31 Aug '15

31 Aug '15

Dear Manager, Is it possible to do Protein protein docking using chimera program? Your response will be highly appreciated. Thanking you. -- Sincerely yours, *Akalesh Kumar Verma* *Morehouse School of Medicine* *Microbiology, Biochemistry & Immunology* Atlanta, Georgia, USA Pin / Zip: 30329 *Mobile: +1 (678) 497-6404* *http://www.msm.edu/ <http://www.msm.edu/>* _______________________ ______________ *Personal Disclaimer:--* *Any information contained in this e-mail and/or any attachments is confidential and only intended for reception and use by the specified person. If you are not the intended recipient, please return the email to the sender and delete it afterwards. In this case any copying, forwarding, printing, disclosure and use are strictly prohibited.* *_________________* *__________*

2 1

How can I can calculate or know Gibbs free energy from UCSF Chimera
by Awah.Chidiebere.U＠mh-hannover.de 28 Aug '15

28 Aug '15

Dear Colleagues, Thanks for developing such wonderful tools as Chimera for molecular dynamics analysis of structure. Please I have two questions: 1. Is it possible to calculate Gibbs free energy from complexes on UCSF Chimera, for examples when complexes are solvated? 2. On building structures , is it possible to simulate how a given complex could bind DNA oligos , for example when one makes changes in single nucleotides and ask a given DNA binding TF structure to bind it on Chimera? I would look forward to your response to these questions. I would also be very happy if I could speak by phone with the administrators. Thanks. Best wishes, Chidiebere U Awah MD Msc PhD student , Molecular Medicine Hannover Medical School , Germany.

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Re: [Chimera-users] a question relate to Chimera
by Elaine Meng 27 Aug '15

27 Aug '15

On Aug 26, 2015, at 6:27 PM, Smith Liu <smith_liu123(a)163.com> wrote: > Dear Elaine, > Thanks for the reply. > > Here let us consider the first question on "a particle has a diameter of 100 pixels ", which I think may be done by Chimera with your help. From http://www.imagescience.de/fsc/index.htm, we can download a software which can be used to calculate the resolution of the map by FSC. When we use that software for calculation, we need to input "Filling degree" D/L, where the value of object size D in voxels, and the L, the linear ssize of the 3D volume (x, y,z). A typical value of "Filling degree" D/L would be 0.66, indicating that 2/3 of the linear width of the 3D volume is filled by the object. > > Thus will you please show me by Chimera how can we know "the value of object size D in voxels"? > > I am looking forward to getting your reply. > > Best regards. > Smith Dear Smith, Please send Chimera questions to chimera-users(a)cgl.ucsf.edu (instead of to me directly). Others may be able to answer your questions better than I can, for example in this case where I don’t know the answer. For linear size of the whole volume (the map), we already discussed that you can see the number of grid units (voxels) in X,Y,Z to the right of the dataset name in the Volume Viewer dialog, and see angstroms per grid unit in the Features: Coordinates section of Volume Viewer. You could multiply the values to get the size of the map in angstroms. <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-August/011437.html> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-August/011433.html> However, I don’t know how you could measure the voxel size of the object in Chimera. As far as I know you could only estimate it by eye, or by measuring angstrom dimensions, converting to grid units, and then multiplying them to roughly estimate the area of the object in voxels. It would only be an estimate, assuming your object is not a perfect circle or square. See previous posts on measuring angstrom dimensions in a map: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010609.html> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-January/009503.html> My guess is that people would normally get this information from the software used in the original data collection, not by doing measurements in Chimera. 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

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Re: [Chimera-users] Icosahedral net from PDB
by Tom Goddard 27 Aug '15

27 Aug '15

Hi James, There are a few Chimera commands that let you show a icosahedral cage around a virus PDB model. Basically you use the sym command to make the virus capsid from the PDB asymmetric unit, then use the shape command to make the cage, then optionally use the meshmol command to show the cage with cylinders instead of lines. For example, open 2bbv sym #0 surf true shape icos radius 200 lattice 1,1 meshmol #2 3 color gold #3 There’s also a video showing how to make the cage for an electron microscopy map http://www.cgl.ucsf.edu/chimera/videodoc/cage/index.html <http://www.cgl.ucsf.edu/chimera/videodoc/cage/index.html> Here is the command documentation for more info about sym, shape, meshmol commands: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/framecommand.html <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/framecommand.html> Tom > On Aug 27, 2015, at 5:11 AM, Geraets, James A > Hi Tom, > > A colleague of mine has told me that you have previously made available a script for displaying icosahedrally-symmetric pdb files on an icosahedron net. Would you happen to still have it? I can’t find any sign of it online… > > Cheers (and thanks for your continued work on Chimera) > > James > > ---------- > > James Geraets > EU Marie Curie Actions Fellow > AIROPico Project > > Institute of Biotechnology > PL 56 > FI-00014 University of Helsinki > Finland

1 0

addgrp command
by UCSF-xiaobowan 26 Aug '15

26 Aug '15

Hi all, I am Xiaobo Wan, a postdoc at UCSF. I would like to learn how to add chemical groups (such as methyl) or change chemical atoms (Fluorine to Nitrogen) using the command in Chimera because I have thousands of compounds to do the same modification. I know the Build Structure in the Graphic interface can do this. I am not sure whether the addgrp command was supported by chimera now. Best, Xiaobo

3 2

color suggestion
by Dougherty, Matthew T 26 Aug '15

26 Aug '15

1) button on the model panel to bring up the color editor that will edit the model selected. 2) very short pulldown menu on the color editor of the primary & secondary colors, along with black, white and gray50. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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Re: [Chimera-users] a question relate to Chimera
by Elaine Meng 26 Aug '15

26 Aug '15

On Aug 25, 2015, at 6:16 PM, Smith Liu <smith_liu123(a)163.com> wrote: > Dear Elaine, > Here there is a sentence "a particle has a diameter of 100 pixels and the width of the reconstruction box is 256 pixels". Will you please tell me by Chimera how can I know the diameter of the particle and the width of the reconstruction box, as described in the cited sentence? > > I am looking forward to getting a reply from you. > Best regards. > Smith Dear Smith, It is recommended to send Chimera questions to chimera-users(a)cgl.ucsf.edu (CC’d here) instead of to me directly. I don’t know where that sentence came from, so I’m not even sure it is a Chimera question. By “pixels” maybe the authors mean grid units. They probably just knew this about their own data without trying to get it from Chimera, but at least for the width of the box, you can see the grid dimensions just to the right of the dataset name in the Volume Viewer dialog. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/fram…> 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

1 0

on point-group symmetry used for the 3-D calculation
by Smith Liu 25 Aug '15

25 Aug '15

Dear All, By chimera, can we know the point-group symmetry used for the 3-D calculation? Best regards. Smith

2 1

on voxel size measured in angstroms
by Smith Liu 25 Aug '15

25 Aug '15

Dear All, Will you please tell me by Chimera how can we know the voxel size measured in angstroms? Smith

2 1

is the connection present?
by Dmitry 25 Aug '15

25 Aug '15

Dear Colleagues, I have 3d tetramer volume density where I fitted known x-ray structure of monomer (to each unit of tetramer). I want to check the inter-monomeric space, whether there is connections between 2 monomers. Is there a command or script that checks the presence of contacts between bounds of 2 structures? Thank you Sincerely, Dmitry

2 1

Electrostatic Potential Visualization
by Chun, Minju 25 Aug '15

25 Aug '15

Hello, I am an intern working with Chimera, and I was wondering if I was missing a plug-in that calculated electrostatic potential. I attempted to load a dx and cube file to emulate electrostatic potential, but there seemed to be a problem finding/reading the files(perhaps I'm doing this wrong too). I thought that if I calculated electrostatic potential directly with Chimera, I could see electrostatic potential. It says on your website that Chimera can calculate the electrostatic potential with APBS: "electrostatic potential calculated with Adaptive Poisson-Boltzmann Solver<http://www.poissonboltzmann.org/apbs/> (APBS); the APBS<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html> tool in Chimera runs this program via web service provided by the NBCR<http://nbcr.ucsd.edu/>" Do you have a tutorial that goes in more detail in how to calculate potential with APBS? Thank you, Minju Chun

2 5

Flattening of coloured icosahedron
by R.I.Koning＠lumc.nl 24 Aug '15

24 Aug '15

Is it possible to flatten a coloured icosahedron surface? I have an electron density of a virus, and using shape icosahedron and colour icosahedron surface and surface colour I can colour it according to this density. I would really like to generate a flattened icosahedron (compared to the flatten icosahedron command) from the coloured icosahedron surface. In order to get a 2D map of the colours. Is this possible somehow in Chimera? Is it otherwise possible to export the icosahedron with the coloured surfaces and try in another program (like Maya of Cinema4D?). Best regards, Roman Koning

3 2

layering problem
by Joseph Atherton 20 Aug '15

20 Aug '15

Hi! I'm trying to make videos at the moment but I have a problem with layering, as in the model seems to be 'hiding' behind the density even when the density is transparent. This occurs when I set transparency also in the model, even at low transparency (e.g command #19:transparency 5,a,r #0:259-271). See the example attached- the left hand most part of the model, and the ADP is hidden when their transparency is non-zero. Can I prevent this? Cheers, Joe

3 7

Re: [Chimera-users] [chimera-dev] distance measurements
by Elaine Meng 20 Aug '15

20 Aug '15

Hi Feixia! Yes, you could use Chimera to measure all lysine CA-CA distances in many structures, but it would require some scripting to loop through the structures, find the lysines, and do the measurements. There is some information on looping through structures and running Chimera commands here: <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> Now, for each structure, you might imagine the script should first find all the lysines and then use the “distance" command on each pairwise combination, substituting in the proper residue numbers. However, there is an easier way with the “findclash” command. You can use it for multiple distance measurement in a single command. For example: open 2gbp findclash :lys@ca test self overlap -1000 log true … will measure all distances among lysine CA atoms in structure 2gbp and list results in the Reply Log (open from Favorites menu). The -1000 in the command says to measure the distance even if the atoms are “overlapping” by -1000 (more than 1000 angstroms apart). The last column in the results is the atom-atom distance, and they are given in order of increasing distance, in this case: 464 contacts atom1 atom2 overlap distance LYS 191.A CA LYS 189.A CA -1.802 5.562 LYS 227.A CA LYS 223.A CA -2.137 5.897 LYS 300.A CA LYS 246.A CA -2.800 6.560 LYS 169.A CA LYS 164.A CA -4.676 8.436 LYS 270.A CA LYS 276.A CA -4.677 8.437 [… several lines removed …] LYS 276.A CA LYS 203.A CA -53.705 57.465 LYS 276.A CA LYS 137.A CA -56.756 60.516 LYS 61.A CA LYS 137.A CA -56.829 60.589 LYS 58.A CA LYS 137.A CA -59.598 63.358 464 contacts The log contents can be saved to a text file, for example see <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003184.html> However, your log would have a huge amount of results for all structures and it might be hard to tell which results go with which structures, so another possibility would be to save a separate file of results for each structure, and in that case your script would need to substitute in an output filename, e.g. findclash :lys@ca test self overlap -1000 saveFile ~/Desktop/2gbp.log See findclash documentation for all the options. Then you can embed the command in the python looping script as described in the first link above. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.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 Aug 18, 2015, at 8:36 AM, Feixia <feixia.chu(a)unh.edu> wrote: > Hi there, > I am interested in retrieving distance information from large dataset in an automatic fashion. For instance, can we use Chimera to get the distances between lysine alpha-carbons of current PDB entries. Presumably, we can download all PDB structures on our local desktop, and just call functions one structure at a time. I wonder if we can do that with Chimera. Your advice will be highly appreciated. > Best, > Feixia

3 3

measure the vertical distance between aromatic planes
by Wang, Bing 19 Aug '15

19 Aug '15

Hi Chimera, Is there a way to measure the vertical distance of two planes in the structure? I do know how to measure the angle between two planes or one line and one plane by the Axes/Planes/Centroids in Chimera. I don't need the distance of two centroid of two planes. I do need the vertical distance of two planes. Could you please show me in detail? Thanks a lot! Bing Wang

3 2

How to select a plane from the command line
by JUAN PABLO REYES VALVERDE 17 Aug '15

17 Aug '15

Dear UCSF Chimera Team: Please, I would much appreciate your advice on the following: First issue: Given a number of planes - calculated/created through the 'define' command - I would like to select one of them, with some command entered at the command line .... How can I do it? The reason why I want to select it through the command line, and not by directly by clicking at it at the axes/planes/centroids table, is because later I would like to use the command inside a runCommand statement, in a Python/IDLE script (with *.py extension) ... Second issue: By the way, do you think this piece of code could work? Assume that the desired plane is already selected .... I want to internally handle the plane as 'p1' in my Python code: p1= chimera.Plane() from chimera import selection p1= selection or perhaps this single instruction ..... p1= chimera.selection Let me try to explain: Within my Python code, I want to have a way to make reference to a plane created by the 'define' command ( should I call it a ' handle'? ... not sure whether it is the correct term ...). Well, I hope that I managed to make it sufficiently clear ... Thanks in advance for your kind attention. Cheers, Juan Dr. Juan Pablo Reyes Valverde Laboratorio de Neurobiología Molecular y Celular (D15) Instituto de Neurobiología UNAM Campus UNAM Juriquilla Boulevard Juriquilla 3001 Querétaro, QRO CP 76230 MÉXICO Tel +52 (442) 2381064

2 1

Charges for PTR+DT
by Amali Guruge 17 Aug '15

17 Aug '15

Dear all, I have to prepare the pdb structure 1K4T to my study. When I do the dock prep process, it gives net charges as, PTR+DT -2 TGP +0 I added charges for standard resides by AMBER ff12SB. For other residues, I added charges by Gasteiger method. My problem is why PTR+DT gives -2 charge? I am not familiar with this one. <http://www.google.lk/intl/en/options/> Can anyone help me? Thank you.

2 2

Modification of ribbon scaling to intersect guide atoms at termini and chain breaks?
by Oliver Clarke 14 Aug '15

14 Aug '15

Suggestion - would it be possible at some point in the future to add a new ribbon scaling option (I guess in Chimera 2.0 or later) so that all internal residues behave like the current “Bspline” scaling, but residues at termini or chain breaks behave like “cardinal” - where the ribbon path exactly intersects the guide atoms? The attached image illustrates the kind of situation this would address - where one wants to show secondary structure in cartoon, but pick out a loop or structural feature of interest in backbone or CA+sidechains, with no ugly discontinuities between the all-atom and ribbon representations. This would allow seamless mixing of nice looking cartoon representation and nice looking backbone or C-alpha+sidechains representation, which I don’t believe is possible at the moment. Cheers, Oliver. Also, in case anyone finds it useful, the following alias applied to a selection or model will generate the CA+sidechains representation depicted below: #Show CA trace with sidechains #Usage: ca_and_sidechains #model_id (or selection/atom-spec) alias ^ca_and_sidechains sel $1; namesel tmp; ~ribbon tmp; ~disp tmp; sel tmp&@CA&protein; repr stick sel; disp sel; setattr m stickScale 1.00 tmp; sel side chain/base.without CA/C1'&tmp; repr stick sel; disp sel; setattr b radius 0.1 sel; color orange tmp; color byhet tmp; sel @CAA |@CB; namesel tmp2; sel tmp&tmp2; repr stick sel; setattr b radius 0.1 sel; sel @CD,N&:pro&tmp; disp sel; repr stick sel; setattr b radius 0.. 1 sel; ~sel

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~select doesn't work on axes?
by Oliver Clarke 14 Aug '15

14 Aug '15

The command "~sel” does not unselect selected axes/planes/centroids - is this intended, and/or is there another way to unselect these objects from the command line? Also, is there a command to undisplay selected axes/planes/centroids? I can only figure out how to do so from the GUI but I would like to do this from the command line, as when you have many axes defined and only want to hide a few it would be easier to have an equivalent of “~disp sel” rather than hunting for the specific axes in the Axes/Planes/Centroids list. Cheers, Oliver.

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odd chimera benchmark performance
by Dan Lin 14 Aug '15

14 Aug '15

Hello: I was wondering if anyone had any experience tracking down performance problems in chimera. I've noticed that I am getting really sluggish performance when managing a lot of atoms, even when everything is shown as backbone traces only. To take a look at the performance, I ran the benchmark and got the following numbers: Volume benchmark scores surface mesh contour solid recolor 981 1291 280 589 393 Null Wire Stick BStick Ribbon Sphere Ops 6249.5 158.7 1.5 0.9 27.4 0.4 89.3 compared to a benchmark posted on the website of the same graphics card: 2125 2026 302 512 491 213 492 452 3259 169 128 Apparently I'm getting awful benchmarks for most of the molecule benchmarks, while the volume performance is pretty comparable. I re-ran the molecule benchmarks to make sure they were reproducible and got pretty much the same numbers. Would anybody have any suggestions for figuring out what's going on? For reference, I'm running ubuntu 12.04 with up to date nvidia drivers for a GTX 560 Ti. Thanks, Dan

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axis-axis distance definition
by Oliver Clarke 13 Aug '15

13 Aug '15

Quick question - how is the distance between two axes (as reported by Axes/Planes/Centroids) calculated? Is it the minimum distance between two axes (I guess yes, because it does not seem to match the center to center distance)? And does it assume the axes are of infinite length, and calculate the displacement required for them to intersect, or does it measure the minimum distance between the axes with the length and end positions as displayed? Cheers, Oliver.

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place label at arbitrary position in 3D
by Oliver Clarke 13 Aug '15

13 Aug '15

In case it is useful to anyone else - I was trying to figure out a way to place a label at an arbitrary position in 3D, so that I can for example generate a chimera session of a protein with all helices labeled and annotated appropriately. I couldn’t figure out a way to easily do this with the built in tools (rlabel, labelopt etc all seem to require you to set an offset from an atom in the structure), so I made the following alias, which gets around this by placing an invisible marker atom at the center of rotation (which I mostly keep locked to the center of view), and attaching a label to that. Hope it is useful to somebody else too. #Place label here (at center of rotation). #Usage: label_here "label_text" (replace spaces in desired label text with _; they will be replaced by spaces in label) alias ^label_here ~sel; ac mc; color black sel; repr bs sel; vdwdefine 0.01 sel; setattr a label $1 sel; transparency 100,a sel; ~sel Cheers, Oliver.

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curved helices - cylinder representation?
by Oliver Clarke 12 Aug '15

12 Aug '15

Hi all, I’d like to have an extended version of the “Pipes and planks” representation, where helices are represented as cylinders, except as a regular, easily modifiable ribbon representation, and allowing for helix curvature rather than breaking up curved helices. I realize this is not currently implemented and is unlikely to be addressed until Chimera 2.0 due to the many other more important things on the drawing board, so I’m trying to figure out a way to hack something together that will generate acceptable results in the meantime. I figure that one way to do this might be to use a create a pdb file with guide atoms located on the helix axis, which one can approximate by placing a guide atom (P or CA) at the center of mass of a six residue sliding window of C-alpha atoms, and then use these guide atoms to create a thick, smoothed (with B-spline) licorice tube. This works quite well for an individual helix, as you can see in the attached pics, but I am a little at a loss as to how to automate this procedure across all the helices in a structure, or even for a given (selected) helix (and it’s only really the helices I care about - strands are fine as is, but having a curved cylinder representation for helices would be very handy). I guess I can do so using a python script of some sort, but if anyone has any pointers as to how to get started, they would be most appreciated. So I guess I need to loop through all the residues in a selection, calculating the center of mass in a sliding window and placing atoms as appropriate, then write out a pdb file with appropriate atom names. This shouldn’t be too hard, but if anyone can point me towards code that I can adapt for this purpose it would be most helpful. Cheers, Oliver.

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question
by A G Szabo 11 Aug '15

11 Aug '15

Today I was trying to Fetch a series of files from the PDB. Their accession codes are 3J7O, 3J7Q, 3J7R, and 3J7P. These are structures of the ribosome complexed with a trimeric translocon, Sec61. Each time Chimera responded with an error message indicating that there was no such file. The files come from a paper by R M Voorhees, (2014) Cell 157:1632. I went to the PDB website and was able to access each of the files. So they do exist. However, when I tried to visualize them using Protein Workshop the structure that appeared was a mixture of surfaces and ribbon structures. I was not able to do anything with any of the structures using Protein Workshop. I could not delete any of the several components, nor change them to ribbon structures. I have been able to fetch, using Chimera, other PDB files that have the entire ribosome complexed with proteins of interest. I sent a message to PDB relating what I have encountered and am waiting for a response. My question to Chimera is to determine if there is a work around to get at any of these files. Thank you Arthur G. Szabo Professor Emeritus Chemistry Wilfrid Laurier University

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is Chimera able to do spin albeling in silico
by Shu-Hao Liou 10 Aug '15

10 Aug '15

Hi, Thank you for reading this email. I'd like to have a rough protein structure with certain spin label on one of the cysteine. Is chimera be able to provide the reasonable structure for that? Sincerely, Shu-hao Liou UC Davis

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Attribute "distance" generated by shortcut "ac sd" not saved between sessions?
by Oliver Clarke 10 Aug '15

10 Aug '15

Hi all, I use the command “ac sd” to color dotted surfaces such as the attached by pore radius (I generate a molmap surface corresponding to the channel axis and then use "ac sd" to generate an attribute “distance", which in this case corresponds to the pore radius, which I can then use to color the dotted surface pdb using Render by Attribute). The dotted surface is generated using the program HOLE (http://www.smartsci.uk/hole/) along with the attached script to make it readable by chimera. This all works fine, however I have noted that the attribute generated by "ac sd” is not present when I reload the saved session, whereas other attributes (e.g. those created explicitly with defattr) are. I can just regenerate it of course, but it would be convenient if it were saved with the session, as it can take a while (~10 minutes) to calculate for large dotted surfaces. Cheers, Oliver.

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A video of 'view dock'
by Amali Guruge 10 Aug '15

10 Aug '15

Dear All, Can we save the movie play in 'view dock' option? Can anyone help me? Thank you.

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Re: [Chimera-users] PDB: 3NZ4 (Chimera vs Pmol Visualization)
by Elaine Meng 07 Aug '15

07 Aug '15

Hi Kevin, What you are seeing is weird-looking bonds between the ribbon and the residues named MDO. It is an artifact caused by the default smoothing of the ribbon path, the amino acid derivation of MDO, and the default hiding of “backbone” atoms in Chimera when the ribbon is displayed. More on that here, if anybody wants details... <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbo…> As you found, you could just show atoms without ribbons to solve the problem. However, if you really wanted to show ribbons at the same time, here are some choices as to what you could do in Chimera to make it look less deformed: (1) enable display of all atoms of the MDO at the same time as the ribbon, for example with command: ribbackbone .. however, side effects you may not like are that this will also show backbone atoms of the other residues that are displayed, and MDO and these other residues may be obviously detached (as if “floating” away) from the smoothed ribbon. You could try hiding the backbone atoms of the other residues with: ~disp @n,c,o & ~:mdo … or you could go back to the original behavior of disabling simultaneous backbone-atom and ribbon display with: ~ribbackbone (2) use a non-smoothed ribbon path that is forced to go through the CA atoms, for example with command: ribspline cardinal … however, this is still ugly because the ribbon makes a sharp turn near this derived residue, and the methyl group comes off of the ribbon at a strange angle. You can go back to the default ribbon path with: ribspline b Sorry, neither makes a beautiful picture. But I hope this helps to explain what is going on. 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 Pictures before and after using “ribbackbone” command:

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PDB: 3NZ4 (Chimera vs Pmol Visualization)
by Kevin D. Walker 07 Aug '15

07 Aug '15

A specialized prosthesis within the PDB 3NZ4 structure looks proper in Pmol but looks skewed in Chimera (my choice), and I wonder why the prosthesis is rendered as such in Chimera? Kevin ---------------------------------- Kevin D Walker Associate Professor Michigan State University Department of Chemistry and Department of Biochemistry & Molecular Biology 578 S Shaw Lane; Room 208 East Lansing, MI 48824 Phone: 517 355 9715 x 257 Fax: 517 353 1793 websites: 1) http://bmb.natsci.msu.edu/about/directory/faculty/kevin-d-walker/current-re…

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clipping and capping
by George Tzotzos 07 Aug '15

07 Aug '15

I’m a real novice in this kind of operation so I shall try in some detail what I’m trying to achieve. I’m dealing with a long serendipitous ligand that spans through a homodimer (2erb) (see screenshot1). I would like to generate something like the B-factor colouring feature (http://www.cgl.ucsf.edu/chimera/features.html <http://www.cgl.ucsf.edu/chimera/features.html>). I’ve opened the Depiction tool and tried surface clipping and capping to no avail. Reading the manual, I figured out that first I have to generate a volume and then use the sop clip command. If this is the routine, I’m seeking advice on how to generate the volume data and then pass it to the sop clip command. As always grateful for your kind help Regards George

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Changing license agreement email
by Flaherty, Daniel P 07 Aug '15

07 Aug '15

Hello, I am using the academic license agreement for Chimera from my previous position at the University of Kansas. However, I have now moved to Purdue and am starting my own laboratory. I would like to utilize Chimera in my lab. I sent an email earlier regarding generating spheres when preparing a protein for docking from my Purdue email and it told me I was not a registered user. I subsequently re-sent the email from my KU email since that is what I was licensed under. Long story short. How to I switch the license agreement to recognize my Purdue email as the registered user? Do I need to un-install Chimera and go through the steps to accept the academic licensing again using my new Purdue email account? Sorry for the confusing email. Thanks! Dan Daniel P. Flaherty, Ph.D. Assistant Professor Department of Medicinal Chemistry and Molecular Pharmacology Purdue University dflaher(a)purdue.edu Office - (765) 494-4761 [cid:8F36A2D2-6664-4FA0-B72D-D785C950B081]

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