- Chimera-users - RBVI Mailing Lists

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 13 Oct '15

13 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 13 Oct '15

13 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 09 Oct '15

09 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

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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

2 1

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.

2 1

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

2 1

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 23 Sep '15

23 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 21 Sep '15

21 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 15 Sep '15

15 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 10 Sep '15

10 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

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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.

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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

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Align and average intensity images in Chimera
by 許紹君 07 Sep '15

07 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

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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

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Re: [Chimera-users] [chimera-dev] distance measurements
by Elaine Meng 19 Aug '15

19 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

2 1

~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.

2 2

odd chimera benchmark performance
by Dan Lin 13 Aug '15

13 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

3 4

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.

3 3

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.

1 0

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.

2 1

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

2 1

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

2 1

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.

3 6

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.

2 1

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:

1 0

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…

2 1

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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Placing markers in specific points of an EM map using command line
by Ana Lucia Alvarez Cabrera 07 Aug '15

07 Aug '15

Dear colleagues, I would like to know how can I place markers in specific points within an EM map, using commands (and not the Volume Tracer option in the graphic interface). I am doing a movie and I need to place markers in different regions of a map. By placing the markers first manually with the mouse (using the Volume Tracer option in the graphic interface) into the map and saving the respective marker set I can know the specific coordinates for each marker by reading the output marker file "suffix.cmm" (for example: <marker id="1" x="22.28" y="24.608" z="17.976" r="1" g="0.49804" b="0" radius="2"/> ), but I still don't know how to use this information when writing the command for placing the marker in that position. Thanks in advance, Ana-Lucia

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Re: [Chimera-users] Help Generating Spheres
by Repic Matej 07 Aug '15

07 Aug '15

Dear Daniel, The error you are getting only says that the sphgen program is not in your $PATH and therefore the shell cannot find the executable to run. Make sure you have installed DOCK6, which is not bundled with Chimera. You need to apply for the DOCK6 license (free for academia) and the "sphgen" program will be bundled with it. Apply here: http://dock.compbio.ucsf.edu/Online_Licensing/dock_license_application.html After you have made sure DOCK6 is properly installed by following the instructions below, you can follow all the tutorials available online. http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Installation Best, Matej ------------------------------------------------------ Dr. Matej Repic Ecole Polytechnique Fédérale de Lausanne Laboratory of Computational Chemistry and Biochemistry SB - ISIC – LCBC BCH 4108 CH - 1015 Lausanne ------------------------------------------------------ From: <chimera-users-bounces(a)cgl.ucsf.edu<mailto:chimera-users-bounces@cgl.ucsf.edu>> on behalf of "Flaherty, Daniel P" <dflaher(a)purdue.edu<mailto:dflaher@purdue.edu>> Date: Friday, August 7, 2015 at 04:38 To: "chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>" <chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Subject: [Chimera-users] Help Generating Spheres Hello, I’m teaching myself to perform molecular modeling and docking using your tutorials. I am trying to prepare a protein for a vHTS and I have run into a snag during the sphere generation tutorial (http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_…) In the section where it says,"To generate the spheres, simply use the command "sphgen" in the same folder that contains the INSPH and the rec.ms files. The output will be two files: rec.sph<http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/rec.sph>, which contains the spheres in clusters, and OUTSPH<http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/OUTSPH>, which contains general information about the calculation.” I am getting an error that says Unrecognized command: “sphgen”. I downloaded the INSPH text file but I have no idea what to do with it. I don’t know what “folder” the tutorial refers to when it says,”use the command ‘sphgen’ in the same folder that contains the INSPH and rec.ms files." Any help would be greatly appreciated! Thanks, Dan

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Help Generating Spheres
by Flaherty, Daniel P 06 Aug '15

06 Aug '15

Hello, I’m teaching myself to perform molecular modeling and docking using your tutorials. I am trying to prepare a protein for a vHTS and I have run into a snag during the sphere generation tutorial (http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_…) In the section where it says,"To generate the spheres, simply use the command "sphgen" in the same folder that contains the INSPH and the rec.ms files. The output will be two files: rec.sph<http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/rec.sph>, which contains the spheres in clusters, and OUTSPH<http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/OUTSPH>, which contains general information about the calculation.” I am getting an error that says Unrecognized command: “sphgen”. I downloaded the INSPH text file but I have no idea what to do with it. I don’t know what “folder” the tutorial refers to when it says,”use the command ‘sphgen’ in the same folder that contains the INSPH and rec.ms files." Any help would be greatly appreciated! Thanks, Dan

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Morphing with pipes and planks
by Tom Goddard 06 Aug '15

06 Aug '15

Hi Corey, Pipes and planks depictions don’t update when the molecule changes shape. It is also slow to compute so it wouldn’t work interactively. But if you want to make a movie it can be done with some trickery. The tricky part is that there is no command to make the pipes and planks depiction. But a few lines of Python (file updatepp.py attached) can update the pipes and planks. So after creating the morph and the initial pipes and planks I can record a movie with the following command sequence: movie record super 3 ; coordset #2 0,100 ; perframe "open /Users/goddard/ucsf/chimera/libs/PipesAndPlanks/updatepp.py" frames 100 ; wait 100 ; movie encode ~/Desktop/planks.mp4 Tom > On Aug 6, 2015, at 2:35 PM, Corey Dambacher wrote: > > Hi Tom, > > Gabe lander suggested I email you regarding morph maps between two models: > > Is there a way to do a morph using pipes and planks? I have a couple of models I would like to morph, and this works very well when in ribbon, but it doesn't seem to work when I have the pipes and planks depiction... > > Thanks for your time and consideration, > > Corey

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vop cover for maps from EDS server?
by Oliver Clarke 05 Aug '15

05 Aug '15

Hi all, I would like to use the command ‘vop cover’ (https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover) with option fbox so that I can easily extend 2fo-fc maps downloaded from the EDS using ‘Fetch by ID’ to cover multiple unit cells. At the moment, this command does not seem to respect the lattice symmetry of the input map (see attached) - is there any way to make it do so? I have tried explicitly specifying the option ‘useSymmetry true’, but it shows the same behaviour. The example PDB ID I used for the attached screenshot was 3CH3. Cheers, Oliver.

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How to find a specific motif from a protein structure?
by Jing Tang 05 Aug '15

05 Aug '15

Hi, I would like to know how to identify a given motif such as DFG in a protein kinase structure. I have thought to use "select: asp,phe,gly" but it found all the residues rather than the motif. A related question would be then how to identify the activation loop or other more specific domains such as p-loop p+1 loop etc. from a structure. Thanks, Jing

2 1

How to record the movie in the main window as well as in the sideview window?
by zhongjun hu 05 Aug '15

05 Aug '15

Hello, Everyone: I want to record the movie of main window as well as the side view window. Until now, I haven't find any simple way. Are there any suggestions or ideas? Thank you so much! Best, Zhongjun Hu 08/05

2 1

opening *cif format
by Dmitry 05 Aug '15

05 Aug '15

Dear Colleagues, I'm trying to open 4fe1-sf.cif file with chimera 1.10.2. But nothing is happening. Although the program saying : "Done opening ....." Could you please explain how to open *cif files ? Sincerely, Dmitry

2 1

FoxS in Chimera for SAXS curve fitting
by Eugene Valkov 05 Aug '15

05 Aug '15

I was wondering what version of FoxS the current release of Chimera employs for goodness-of-fit calculations to small-angle X-ray scattering curves using crystal structure models? Also, if any specific parameters are used other than what is default? I obtain quite different values using standalone FoxS binary or using the online server versus what is output by Chimera. Thanks, Eugene

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multiple (redundant) distances in command line >file.txt
by Olexandr Dybkov 04 Aug '15

04 Aug '15

Dear UCSF Chimera team, I am trying to measure and draw multiple distances by pasting into the command line respective commands. As outcome I would like to have: 1. the dashed lines between each pair of atoms that I am checking 2. the distances shown above/on the lines 3. a log or a file with all the distances checked (one line per each distance command I executed) For example, dist :540@ca/pdbSegment=A :573@ca/pdbSegment=A dist :453@ca/pdbSegment=B :479@ca/pdbSegment=B dist :695@ca/pdbSegment=B :395@ca/pdbSegment=A dist :2059@ca/pdbSegment=B :1421@ca/pdbSegment=B dist :426@ca/pdbSegment=B :944@ca/pdbSegment=B dist :2059@ca/pdbSegment=B :1514@ca/pdbSegment=D dist :2059@ca/pdbSegment=B :1417@ca/pdbSegment=B dist :1421@ca/pdbSegment=B :2059@ca/pdbSegment=B dist :421@ca/pdbSegment=C :439@ca/pdbSegment=C dist :453@ca/pdbSegment=B :487@ca/pdbSegment=B and so on Resulting in Distance between #50 LYS 540 CA and #50 LYS 573 CA: 13.0 Distance between #35 LYS 453.B CA and #35 LYS 479.B CA: 22.7 Distance between #35 LYS 695.B CA and #50 LYS 395 CA: 8.8 Distance between #35 LYS 2059.B CA and #35 LYS 1421.B CA: 20.5 Distance between #35 LYS 426.B CA and #35 LYS 944.B CA: 25.7 Distance between #35 LYS 2059.B CA and #53 LYS 1514.T CA: 115.7 Distance between #35 LYS 2059.B CA and #35 LYS 1417.B CA: 15.2 Distance monitor already exists That is, 8 out of 10 distances were checked. Since the 8th line was a swap of atom1 and atom2 of 4th, the Chimera Error window popped up and execution of further commands was stopped Similarly, the execution is interrupted if: - one or both atoms are missing - one or both atoms are present in multiple copies - if such distance was checked already Is there a way to ignore/skip this kind of check points and just report such cases in the log? I used to do this in pymol and the python script reported all distances (even redundant) and errors (atom 1 or/and atom 2 are missing) without stopping. At the end I had a txt file with exactly one line for each command. It would be nice to have the same functionality in UCSF Chimera as well. Thank you very much for your help! Kind regards, Olexandr -- ----------------------------------------------------------------- Dr. Olexandr Dybkov Max-Planck-Institute for Biophysical Chemistry Department of Cellular Biochemistry Am Fassberg 11 37077 Göttingen Germany Tel. ++49-551-201 1979 Fax ++49-551-201 1197 email: odybkov(a)gwdg.de ----------------------------------------------------------------

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Coloring an specific area along a morphing serie among several maps
by Ana Lucia Alvarez Cabrera 04 Aug '15

04 Aug '15

Dear Srs, I made a chimera movie where six different conformations of the same complex are morphed in a sequence, changing on to the next one (the aim is showing a conformational change occurring in a number of steps, in this case the six electron microscopy maps). My complex has an specially flexible domain and I need to highlight this area along the morphing sequence of the six maps. I suppose that this can be done using the markers and color zone options, but I don't know how to implement this orders in the .cmd script of my movie. Thanks in advance for your help. Sincerely, Ana-Lucia ________________________________ Ana Lucia Alvarez Cabrera Unidad de Bioinformática. Lab. B-13 Dept. Estructura de Macromoléculas Centro Nacional de Biotecnología (CSIC) C/ Darwin 3, Campus de Cantoblanco 28049, Madrid, España Tel: (34) 915854510

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Re: [Chimera-users] Mirror image proteins
by Elaine Meng 04 Aug '15

04 Aug '15

Dear Dikran, You would need to open the structure before running the script, otherwise the script has nothing to work on. Elaine > On Aug 4, 2015, at 12:22 PM, Sarko, Dikran <dikran.sarko(a)yahoo.com> wrote: > > Dear Elaine, > > Thank you very much for your reply. > I am not familiar with programing, however, I did exactly as described in the page you had refered to. > > import chimera > m = chimera.openModels.list()[0] > for a in m.atoms: > crd = a.coord() > crd.x = 0 - crd.x > a.setCoord(crd) > > then I opened the 4LLZ pdb file as a test, however when I saved the structure and tried to combare it with the original one. Chimera opened only one structure (not tow as I expected). > > Is there anything wrong, ore any additional advice. > > PS: I suggest to incorporate an additional function in the next release of Cheimera that consider the generation of mirror image protein of pdb file as a function within the tools, or other appropriate function. Such function will attract a lot of attention, and Cheimera will be (to my knowledge), the 1st modeling program that offer such a function. > > Thank you very much > Dikran > > Von: Elaine Meng <meng(a)cgl.ucsf.edu> > An: "Sarko, Dikran" <dikran.sarko(a)yahoo.com> > CC: Mailing List <chimera-users(a)cgl.ucsf.edu> > Gesendet: 19:54 Montag, 3.August 2015 > Betreff: Re: [Chimera-users] Mirror image proteins > > Hello Dikran, > Only with a little scripting, but somebody asked the same thing a few years ago and a simple python script was posted to the list. Please see: > > <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-January/005882.html> > <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-January/005883.html> > > Remember that in python the indentation is important. > 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 2, 2015, at 1:11 PM, Sarko, Dikran <dikran.sarko(a)yahoo.com> wrote: > > > > Hello, > > is there any way to generate mirror image proteins (All AA in D-form) from an already exsist pdb file. > > Thank you in advance > > Dikran > >

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segment map & mesh view
by Dmitry 04 Aug '15

04 Aug '15

Dear Colleagues, Does anybody know how to: 1. Delete selected segment from segment map and save the result. 2. Change the mesh view properties - because for the volume the mesh size is different then for the segment map. Sincerely, Dmitry

2 1

Feature suggestion - turn about pre-defined axis.
by Oliver Clarke 03 Aug '15

03 Aug '15

Hi all, Just have a minor feature suggestion that I think would make the command “turn” more useful in certain circumstances. Currently, one can use “turn” to rotate about the x,y or z axes; an arbitrary vector; or about a bond or pair of selected atoms (http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/turn.html) Would it be possible for chimera to treat a predefined axis (e.g a helix axis, or the symmetry axis of an ion channel) as an atom-spec for the purposes of turn? As an example, “turn a1 45” would rotate 45 degrees about axis a1, with the default center of rotation corresponding to the midpoint of the axis. This would be very helpful for adjusting the relative orientations of symmetric oligomers, amongst other use cases. Cheers, Oliver.

3 3

Mirror image proteins
by Sarko, Dikran 03 Aug '15

03 Aug '15

Hello, is there any way to generate mirror image proteins (All AA in D-form) from an already exsist pdb file. Thank you in advanceDikran

2 1

Average structure
by George Tzotzos 03 Aug '15

03 Aug '15

Hi everybody, I’m analysing the Principal Components of an Amber trajectory. I have generated a number of representative pdb files which are concatenated for each PC. Question: Is there a way to generate an average structure in Chimera from the concatenated PDB files? I know this can be done using MD movie but this solution requires that I generate a new topology file for my complex (the original topology file contains ligands and water molecules). Thank you in advance for any suggestions Regards George

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Re: [Chimera-users] Chimera-users Digest, Vol 148, Issue 6
by feisun＠ibp.ac.cn 03 Aug '15

03 Aug '15

From: feisun(a)ibp.ac.cn Subject: I am in a vacation. I am now taking a vacation from Aug. 1st to Aug. 9th. I will reply to you after Aug. 10th. Sorry for the delay. Fei

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Re: [Chimera-users] Chimera-users Digest, Vol 148, Issue 5
by feisun＠ibp.ac.cn 03 Aug '15

03 Aug '15

From: feisun(a)ibp.ac.cn Subject: I am in a vacation. I am now taking a vacation from Aug. 1st to Aug. 9th. I will reply to you after Aug. 10th. Sorry for the delay. Fei

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Morphing a residue through MD trajectories
by George Tzotzos 02 Aug '15

02 Aug '15

Hi, I have an MD trajectory which I can load successfully on Chimera. My objective is to monitor changes in conformations of one particular residue in the receptor (:123) throughout the trajectory and generate a movie. If I could do this in tandem with a bound ligand so much the better. I’ve tried to follow the instructions but obviously, I get it wrong. I opened the Morph Conformations tool, I selected the trajectory and clicked on Add. This generated a 2nd MD Movie panel of just one frame. Any help would be most welcome Regards George

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Re: [Chimera-users] Chimera-users Digest, Vol 148, Issue 4
by feisun＠ibp.ac.cn 02 Aug '15

02 Aug '15

From: feisun(a)ibp.ac.cn Subject: I am in a vacation. I am now taking a vacation from Aug. 1st to Aug. 9th. I will reply to you after Aug. 10th. Sorry for the delay. Fei

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Re: [Chimera-users] Chimera-users Digest, Vol 148, Issue 3
by feisun＠ibp.ac.cn 01 Aug '15

01 Aug '15

From: feisun(a)ibp.ac.cn Subject: I am in a vacation. I am now taking a vacation from Aug. 1st to Aug. 9th. I will reply to you after Aug. 10th. Sorry for the delay. Fei

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Re: [Chimera-users] Chimera-users Digest, Vol 148, Issue 2
by feisun＠ibp.ac.cn 01 Aug '15

01 Aug '15

From: feisun(a)ibp.ac.cn Subject: I am in a vacation. I am now taking a vacation from Aug. 1st to Aug. 9th. I will reply to you after Aug. 10th. Sorry for the delay. Fei

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Re: [Chimera-users] Chimera-users Digest, Vol 148, Issue 1
by feisun＠ibp.ac.cn 01 Aug '15

01 Aug '15

From: feisun(a)ibp.ac.cn Subject: I am in a vacation. I am now taking a vacation from Aug. 1st to Aug. 9th. I will reply to you after Aug. 10th. Sorry for the delay. Fei

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Open model from pdb with designated model id?
by Oliver Clarke 31 Jul '15

31 Jul '15

Hi all, I would like to write an alias to load a pdb and the associated 2fo-fc and fo-fc maps with a single command (and adjust the contours and appearance of the maps and model). To do this, I need to be able to open the models with specific output ids, so I can issue commands to alter their appearance later in the alias. Looking at the documentation (http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/open.html <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/open.html>), it seems like this should be possible, but when I give an output model id it seems that chimera is ignoring it and still choosing the lowest available id. I have tried the following commands, “open 1bl8 100”, “open 1bl8 #100”, “open 1bl8 model-id:100” but they all either fail or load 1bl8 with model id 1. Am I missing something about the syntax here? Or is there another flag for the output model id? Cheers, Oliver.

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Option to not record duplicates in the command history?
by Oliver Clarke 31 Jul '15

31 Jul '15

Hi all, I like the command history in chimera a lot - it makes it very quick to repeat previous commands. One minor alteration that might make it a little bit better would be to have an option (maybe in the Command Line section of the preferences?) to not record sequential duplicate commands in the history (like the “ignoredups” option for the bash history). I will often repeat the same command a bunch of times (for example “turn x 5” or one of the various aliases I use for navigation and recentering), and so not having all these duplicates recorded in the history would make it a lot faster to find recently used commands. Cheers, Oliver.

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Addh function and fake N, C-terminii
by gaelle garet 31 Jul '15

31 Jul '15

Hi, I want to use Addh function to add hydrogens and protonate N, C-terminii but I don't understand very well how you detect if a terminus is fake or not. For example, for the structure 3L4F, I obtain the following log : Chain-initial residues that are actual N terminii: MET 586.A, MET 586.B, MET 586.C Chain-initial residues that are not actual N terminii: GLY 652.D Chain-final residues that are actual C terminii: LEU 646.A, LEU 646.B Chain-final residues that are not actual C terminii: ASP 638.C, ARG 758.D I don't understand why GLY 652.D, ASP638.C and ARG 758.D are not terminii, can you explain me why and how the algorithm detect that ? Thank you in advance for your answer. -- Gaëlle

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How to explore two protein structures on the same screen?
by Jing Tang 31 Jul '15

31 Jul '15

Hi, I opened two protein structures, say 2JIT and 4WA9 and they were partially overlapped on the screen. How to move one protein so that they can be separated more? I can only move the two proteins as a whole but not individually. Further, I would like to highlight one residue for a particular protein and I could not find a way to first select a protein and then a residue. Thanks, Jing

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Recent problems with linux x64 version
by Peter L. 30 Jul '15

30 Jul '15

Hello, Recently I used Chimera for a internship/volunteer work with my older brother, and it did not start up due to some seemingly graphics drivers problems. I'm running Ubuntu 15.04 on a AMD radion 5450M on this machine and NVidea gtx 760 on another. Both would not start up due to having libGL error: unable to load driver: nouveau_dri.so etc etc, as so documented here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015February/010734.html (Error from the NvIdia machine) and would not load r600. However both had the same fix, that seemigly works by removing the file /Chimera64-1.10.2/lib/libstdc++.so.6, I renamed it to libstdc++.so.6.bak in case I might need it, but it works on both machines now. It seems as some older libs are colliding with mesa drivers, and casung them to break, and removing this fixes the problem. Its been documented before with other programs here, where the fix is simular. http://askubuntu.com/questions/614422/problem-with-installing-steam-on-ubun… I also found that in the chimera mail I found, it was recommend to update some drivers, or Nvidia drivers, however, nvidia drivers for linux tend to break the system a lot or cause other problems. Hope this helps!, Peter

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Volume level rms option
by Oliver Clarke 30 Jul '15

30 Jul '15

Hi all, Just a minor usability suggestion - I was wondering if it would be possible to add a flag to the ‘volume level’ command that allows the user to directly set the map threshold to x*RMS or x*SD? E.g. volume level rms 5 to set to 5xRMS of the map, using the values reported by measure mapstats? At present it is possible to normalize the map to rms, which is very handy, but it would be also convenient (for the purposes of reporting absolute threshold levels in figure legends etc) to be able to set the level as 5*rms but still check the absolute e-/Å^3 contour that this corresponds to. Also on a completely different matter, is there any way to access the “Zone” feature of Volume viewer from the command line? I would like to write an alias that places a dummy atom at the CoFR and displays a spherical zone of the selected map (without generating a new map using vop zone), but I can’t find the corresponding command line function. Cheers, Oliver.

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Useful aliases
by Oliver Clarke 30 Jul '15

30 Jul '15

Attached are a bunch of aliases that I find very useful in Chimera. Usage and intended purpose of the alias is described in the #comments immediately preceding the alias. Some of these will only work in the latest nightly build because they take advantage of command options that were only added recently. Hopefully someone else finds these useful too! If any other chimera users have aliases or shortcuts they find particularly handy maybe we could exchange ideas/code snippets in this thread? Oliver.

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Center of rotation cross-hair
by Tom Goddard 28 Jul '15

28 Jul '15

Hi Oliver, I added display of a cross hair (plus sign) at the center of rotation in the graphics window. You turn it on with command set showCofR and turn it off with ~set showCofR The crosshair is white on black (and dark) backgrounds and black on white (or light) backgrounds. This will be in tonight’s daily build. Tom

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"newmap" command? (Or other way to resample on arbitrary grid?)
by Oliver Clarke 28 Jul '15

28 Jul '15

Hi all, Is there any way to use vop to resample on an arbitrary grid, that is, not the grid of an existing map? This would be useful, for example, when one wants to interpolate to finer grid spacing than is present in the input map (but otherwise keeping the original dimensions and origin). I note in the old chimera documentation that there used to be a command called “newmap” (http://www.cgl.ucsf.edu/chimera/experimental/resample_map/resamplemap.html) which allowed for the generation of an arbitrary map which one could use for exactly this purpose, but this command does not seem to be recognized by modern Chimera builds. Does this command still exist somewhere under a different name? Or is there another way to accomplish this? Cheers, Oliver.

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Hydrogen Bond Criteria
by jjeon＠caltech.edu 28 Jul '15

28 Jul '15

Hello, I would like to learn more about the distance/angle settings that Chimera uses for hydrogen bonds. I have read that the criteria are outlined in the paper Three-dimensional hydrogen-bond geometry and probability information from a crystal survey. I have been waiting to be granted access to the full version since I can only seem to find the abstract on other sites. Is there a website that offers access to the full paper for free? Thank you, Janice

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hbonds
by leila karami 27 Jul '15

27 Jul '15

Dear chimera users I have 2 models in my system (#0 for protein and #1 for ligand). I want to use hbonds command for showing the hydrogen bonds between #0 and #1 models? (I know how to do this using FindHBond, but I want to know related command). What is the best options for hbonds command to get above state? Best, Leila

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DNA ladder different color than backbone
by Belle Lin 25 Jul '15

25 Jul '15

Dear Chimera users/developers, Is there a way to make the DNA ladders a different color than the backbone? I am able to do so when the side (sugar/base) is shown in the "tube/slab" mode, but when I change it to the "ladder" mode I am unable to change the color of the rungs. I have included photos below which hopefully make my question more clear. Thank you in advance for your help!! Thanks, Belle Lin _____________________________________________________________ Able to create: [image: Inline image 3] [image: Inline image 2] Trying to create: [image: Inline image 1]

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Announcing the 2015 EMDataBank Map Challenge
by Cathy Lawson 23 Jul '15

23 Jul '15

Dear Chimera User List Members, EMDataBank/Unified Data Resource for 3DEM is pleased to announce the 2015 Map Challenge. All members of the Scientific Community--at all levels of experience--are invited to participate as Challengers, and/or as Assessors. Seven benchmark raw image datasets have been selected for the challenge. Six are selected from recently described single 3D electron microscopy single particle structure determinations with image data collected as multi-frame movies; one is based on simulated (in silico) images. Challengers are sought to create single particle reconstructions from the targets, and then to upload their results with associated details. Assessors are sought to participate in evaluating submitted reconstructions. Registration is now open for all interested participants. Challengers may submit maps between August and December. Before submissions open, all are encouraged to provide feedback on submission requirements. An open assessment period will commence in early 2016. To learn more about this challenge and to register, please visit http://challenges.emdatabank.org and click on "MAP CHALLENGE" in the menu bar. The map challenge is the first 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 second challenge, focused on creating coordinate models from 3DEM maps, will be announced later this year. Sincerely, Cathy Lawson on behalf of the EMDataBank Team and the Map Challenge Committee emdatabank.org www.facebook.com/emdatabank3dem

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Mac-Book Pro
by Bobby Barnett 22 Jul '15

22 Jul '15

I have some students who have mac's, so I tried to download and install chimera on my Mac-Book Pro 17" . I get the following message. I downloaded chimera-1.10.1-mac64.dmg from your site. I am the only user on my computer. Any suggestions? Should I try and downloading it again? Bobby Barnett “Chimera” can’t be opened because the identity of the developer cannot be confirmed.

2 1

PB lines visualization
by Sana Saeed 22 Jul '15

22 Jul '15

is it possible to visualize periodic boundary lines (solvated box) in chimera.

2 1

On the fly map sharpening?
by Oliver Clarke 21 Jul '15

21 Jul '15

Hi, just a request for a future chimera version (probably Chimera 2 I guess) - would it be possible to integrate on the fly map sharpening into chimera, perhaps as an option for vop? It would be great to be able to play with different negative B-factors within chimera and thereby get instant feedback on map contrast and detail in different regions. Alternatively, would it be possible to call an external program that does the same thing from within chimera, perhaps bfactor from the Grigorieff lab or similar? Cheers, Oliver,

2 2

Electrostatic Potential based on Poisson-Boltzmann using APBS
by leila karami 18 Jul '15

18 Jul '15

Dear chimera users, I am using chimera 1.10.1. I did following steps to obtain Electrostatic Potential based on Poisson-Boltzmann using APBS: open... pr.pdb action... surface... show to obtain *.dx file, I typed APBS in command line, after minutes, *.dx file was created and surface color window was opened, I pressed color tab. Please see the figure in following link: https://www.dropbox.com/s/99gjecypqu910hu/apbs.png?dl=0 Why are the colors black and white in the surface, instead of blue and red? Any help will highly appreciated.

2 16

RMSD
by Valerio Chiarini 17 Jul '15

17 Jul '15

Hi everyone, I am dealing with an NMR structure and I noticed in literature that among the parameters required for presentation is included "RMSD from the ideal geometry". Does anyone know if is possible to calculate such value from chimera and how? Currently I just know how to calculate RMSD to the mean coordinate... thank you all in advance Val

2 2

question
by leila karami 16 Jul '15

16 Jul '15

Dear chimera users, 1) I want to have electrostatic surface of my protein in chimera. To this, I used *Tools... Surface/Binding Analysis... Coulombic surface coloring* A new window is opened, but apply bottom is inactive. 2) There are ray command in pymol to obtain better image of molecular structures. Is there a similar command or utility in chimera? Any help will highly appreciated. Best wishes, Leila

2 1

adjusting threshold values on volume rendering
by Dougherty, Matthew T 15 Jul '15

15 Jul '15

Hi, I can access threshold values from solid/volume rendering. eg: from VolumeViewer import active_volume v = active_volume() if v==None: return levels = getattr(v, "solid_levels") t,a=levels[0] How can I change a threshold value? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

2 1

Error opening file
by Sneha Poondru 10 Jul '15

10 Jul '15

Hello! I’m trying to prepare a receptor for dock6, so I downloaded a file (1tvb_.all.sph) from our cluster onto my desktop. However, when I click to open it, I keep getting this error message from Chimera: non-standard sph header Error while processing /Users/SnehaPoondru/Desktop/Project/1tvb_.all.sph: cannot open file "/Users/SnehaPoondru/Desktop/Project/1tvb_.all.sph": syntax error, line 1832 Any help is appreciated! Thanks! ~Sneha

2 1

Structureviz Cytoscope plugin problem
by Ahmed Ezat 10 Jul '15

10 Jul '15

Dear Sir, I am trying to use structureviz Cytoscope plugin to launch Chimera, but it does not work. I installed Chimera and Cytoscope properly and set the path to Chimera in structureviz settings but it is not working. What can I do? I am using windows 7. I have also a problem to install chimera on Linux. if possible,c Can you send me detailed procedure for the installation process. Best Ahmed A Ezat

3 2

swapaa: choosing rotamers
by roz orchidea 09 Jul '15

09 Jul '15

Dear all, I would like to use swapaa and choose which rotamer I want. Foe example I want from library dynameomics the second rotamer that appears in the pop-up menu of Arg. is it possible? Thank you for your time, Alex

4 6

How to display two EM map and a PBD simultaneously
by 师扬 08 Jul '15

08 Jul '15

Dear all, Recently, I have a task to display two EM density map ('A' and 'B') and one PDB ('C') at the same time. B and C fit in map to A. So, I need to make A and B transparent to observe them simultaneously. However, one strange thing happened when I made A and B transparent. I can only see the density which A is lager than B or B is larger than A, and I could not see the buried density. In another words, when I make both A and B transparent, the map can be changed in to the 'A+B' map, and I could not see any 'A-B' or 'B-A' information. Have anyone met this problem? Do change something in setting can solve this problem? Best regards Yang

2 1

on the movie command “turn y 3 120”
by Smith Liu 07 Jul '15

07 Jul '15

Dear All, For movie command "turn y 3 120", the molecule will turn counter-clockwise. Will you lease tell me the movie command which makes the molecule turn clockwise？ Best regards. Smith

2 1

Measure translation of two domains?
by Oliver Clarke 07 Jul '15

07 Jul '15

Hi all, I’m puzzling how to measure the translation of two domains in Chimera, in a situation where there is small but non-zero translation. I expected I could do this by first using match to superimpose the two selections, then using measure rotation to obtain the rotation (if any) and translation. This has worked fine for me in measuring rotation of domains. However, on a purely translational test case, this gives confusing results. I have attached two structures of 1bl8, one of which has been displaced from the other manually by 20 Å. If I match one to the other, it successfully superimposes the two structures. If I then use measure rotation to try to recover the translation, I get a message telling me that the rotation angle is near zero (which is not surprising), but when I check the reply log, the listed translation along the axis is only 1.7Å (see screenshot attached), rather than the 20Å I expect. What am I doing wrong here? Is there another command I ought to be using? Or am I misinterpreting the output? Cheers, Oliver.

2 1

question
by A G Szabo 07 Jul '15

07 Jul '15

I am pleased to inform you that I have been using aspects of Chimera that permit me to prepare images of proteins deposited in the pdb. It was a pleasant surprise to find that the learning curve was not as steep as I thought it might be. Mind you, there are many aspects of Chimera that I have not yet attempted to use. Now I wish to do something that may not be possible to do with Chimera. And I am not sure where to look in the tutorials. I have a ribbon diagram of a protein-RNA complex, PDB 4p3e, two proteins, SRP 19 and SRP68, bound to a segment of 7SL RNA. I can also obtain the structure of another protein SRP54 which also bind to this complex. However, the structure of pdb 4p3e with SRP54 is not available. I know where SRP54 should bind to the RNA, and I know which domain of SRP54 binds to the RNA. How can I somehow combine the two files, one for SRP54 and the other 4p3e and locate SRP54 onto the 4p3e structure? (not sure it is possible) Of course crystallographers know how to achieve this structural combination. I don't have a clue. I checked the tutorial list and the closest I seemed to come was the Merge command. However, the tutorial did not seem to deal with what I wanted to do. Thank you in advance for your assistance. Arthur G. Szabo Ph.D. Professor Emeritus, Chemistry Wilfrid Laurier University Waterloo, Canada.

2 4

Question
by Damjanovic Marko 07 Jul '15

07 Jul '15

To whom it may concern, I am trying to solve a problem that is more of mathematical nature, and I would be very grateful if I could get any advice or pointers on how it may be possible to do this (in Chimera or some other program I am not aware of). I have a molecule that is more or less of cylindrical shape (quite simple shape). I would need a way to surround this molecule with a certain number of layers of solvent molecules that fit around the surface of a cylinder (preferably 1 layer and then going up gradually). The solvent molecules should be packed around the central molecule efficiently (closest packing). An alternative way to approach this would be to take a sphere made out of solvent molecules, put in the centre of the sphere the one cylindrical molecule what is of interest, and let the big sphere accommodate the new molecule. Also, for the sake of simplicity, the solvent molecules can be approximated as small spheres as well (their exact shape is not that relevant). When this is done, all I would need is to get this file in a format like cif, mol or gjf. I underline here that I am looking for a relatively crude model. Could anyone please advise me on how to do something like this? Thanks in advance and best wishes, Damjanovic Marko

3 3

chimera extensions & dialog location
by Dougherty, Matthew T 06 Jul '15

06 Jul '15

1) How can I reload an extension when chimera is running? At the present, after I modify python code I restart chimera for the s/w changes to take effect. Is there a way through idle, etc, that I can cause user code modifications to load without restarting chimera? 2) How can I position the location of IDLE using python? I have IDLE on autostart. In a user extension I have a button, when pressed it organizes the various dialogs, placing them in specific locations. When I try to do something with IDLE, running dialogs.activeDialogs() does not show IDLE in the list. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

2 1

change B factor
by McCafferty, Caitlyn (NIH/NEI) [F] 06 Jul '15

06 Jul '15

Hi, Is there a feature in Chimera that allows you to change the B-factor of the Amino Acids. I have a txt file with the values that I would like to replace the current B-factors with. Thank you, Caitie

2 1

Undisplay pseudo bonds (missing segments) in pipes-and-planks representation?
by Oliver Clarke 03 Jul '15

03 Jul '15

Hi all, just wondering if there is an option I am missing to undisplay pseudobonds when using pipes-and-planks? At present chimera seems to represent missing segments in pipes-and-planks as a continuation of the chain rather than a break, which is a little confusing, e.g. check the following pair of snapshots (chain break in green section corresponds to missing 10aa loop): https://www.dropbox.com/s/cbwar1i197kt3ep/Screenshot%202015-07-03%2010.09.5… <https://www.dropbox.com/s/cbwar1i197kt3ep/Screenshot%202015-07-03%2010.09.5…> https://www.dropbox.com/s/we058qjv3ibwjmn/Screenshot%202015-07-03%2010.10.0… <https://www.dropbox.com/s/we058qjv3ibwjmn/Screenshot%202015-07-03%2010.10.0…> Also in general it would be nice if cylindrical representations of helices were more integrated into chimera, perhaps with their own style adjustments (e.g. allowing for curved cylinders), as for large structures they provide much less visual clutter, but I guess that is probably something for Chimera 2. Cheers, Oliver.

2 2

Cross eyed stereo pair generated by default
by Oliver Clarke 02 Jul '15

02 Jul '15

Hi all, I’ve noticed that when I save a stereo pair (using File/Save Image/Image Type/stereo pair), the resultant stereo pair is suitable for cross-eyed viewing. This is great for me, as I can’t do wall eyed stereo, but the default for many journals is to provide a wall-eyed stereo pair. Of course it is easy enough to convert by swapping the two halves of the pair, but for the sake of convenience, would it be possible to list stereo pair (cross eye) and stereo pair (wall eye) as two separate options in this dialogue? Cheers, Oliver.

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Re: [Chimera-users] Chimera-users Digest, Vol 147, Issue 4
by Oliver Clarke 02 Jul '15

02 Jul '15

Thanks Greg! To clarify, I wasn't actually intending these for use with a viewer of any sort - just to provide in a paper for use as a stereo pair, viewed by either diverging or crossing one's eyes to superimpose the two halves of the pair. Some people can easily view wall-eyed pairs, while others (myself included) can only view cross-eyed pairs, so it would be nice to have the option of generating either. Cheers, Oliver. On Thu, Jul 2, 2015 at 3:00 PM, <chimera-users-request(a)cgl.ucsf.edu> wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: on beta strand assignmet by chimera (Elaine Meng) > 2. Cross eyed stereo pair generated by default (Oliver Clarke) > 3. Re: Cross eyed stereo pair generated by default (Greg Couch) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 2 Jul 2015 09:55:55 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > To: Smith Liu <smith_liu123(a)163.com> > Cc: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] on beta strand assignmet by chimera > Message-ID: <E1E1B5D3-B0A5-4849-88D2-237944AFFA48(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=utf-8 > > Dear Smith, > If the PDB files came from the Protein Data Bank repository, generally the > proteins already have secondary structure assigned in HELIX and SHEET > records. If so, Chimera just uses those assignments. > < > http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#se… > > > > If the PDB file of a peptide/protein doesn?t have HELIX and SHEET records > in it, then it runs a method ?ksdssp? described here: > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html> > > If you don?t like the results for some reason, you could try re-running > the ?ksdssp? command (or the ?compute SS? function in the Model Panel) with > different (nondefault) parameters, or just manually assign residues as > helix or strand however you like with the ?setattr? command, as shown in > the lower part of this previous post: > < > http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-January/009574.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 Jul 2, 2015, at 6:09 AM, Smith Liu <smith_liu123(a)163.com> wrote: > > > > Dear All, > > > > I have a protein, which contains fragment aa 239-251. The protein has > been fitted its map with 2 different (minor difference) resolution, and > thus I have 2 PDB. For PDB 1 (the first resolution), the H-bonds inside aa > 239-251 include: > > #2 Gly 245.A N-Asn 242.A O 2.708A > > #2 Asn 242.A N-Tyr 246.A O 3.120 A > > #2 Val 248.A N-Val 240.A O 3.120 A > > #2 GLN 251.A N-Ser 238.A 0 3.033 A > > > > For PDB 2 (the second resolution), the H-bonds inside aa 239-251 include: > > #0 Gly 245.A N-Asn 242.A O 2.715A > > #0 Asn 242.A N-Tyr 246.A O 3.1206 A > > #o Val 248.A N-Val 240.A O 2.858 A > > #0 GLN 251.A N-Ser 238.A 0 3.074 A > > > > Naked eye check found the H-bonds in PDB 1 were almost the same H-bonds > in PDB 2. > > > > However for PDB 2, aa23-242 and aa 247-251 form 2 strands, but for PDB > 1, it was a un-disconnected loop for aa 239-251. > > > > Will you please explain how chimer assign beta strand? > > > > Best regards. > > > > Smith > > > > > > ------------------------------ > > Message: 2 > Date: Thu, 2 Jul 2015 14:20:01 -0400 > From: Oliver Clarke <olibclarke(a)gmail.com> > To: Mailing List <chimera-users(a)cgl.ucsf.edu> > Subject: [Chimera-users] Cross eyed stereo pair generated by default > Message-ID: <B5D941AF-2692-4E71-8D5A-2A9C8D1610E2(a)gmail.com> > Content-Type: text/plain; charset=utf-8 > > Hi all, > > I?ve noticed that when I save a stereo pair (using File/Save Image/Image > Type/stereo pair), the resultant stereo pair is suitable for cross-eyed > viewing. > > This is great for me, as I can?t do wall eyed stereo, but the default for > many journals is to provide a wall-eyed stereo pair. > > Of course it is easy enough to convert by swapping the two halves of the > pair, but for the sake of convenience, would it be possible to list stereo > pair (cross eye) and stereo pair (wall eye) as two separate options in this > dialogue? > > Cheers, > Oliver. > > > ------------------------------ > > Message: 3 > Date: Thu, 02 Jul 2015 11:39:26 -0700 > From: Greg Couch <gregc(a)cgl.ucsf.edu> > To: chimera-users(a)cgl.ucsf.edu > Subject: Re: [Chimera-users] Cross eyed stereo pair generated by > default > Message-ID: <5595855E.4020903(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > I'll look into it. > > FYI, cross-eyed stereo is the standard for stereo PNG and stereo JPEG > files. There is a buglet in stereo image saving -- the .png files > should be renamed to have a .pns suffix, and the stereo JPEG images > should have a .jps suffix. However there aren't many viewers other than > the one that comes with NVIDIA's 3D Vision setup. > > -- Greg > > On 07/02/2015 11:20 AM, Oliver Clarke wrote: > > Hi all, > > > > I?ve noticed that when I save a stereo pair (using File/Save Image/Image > Type/stereo pair), the resultant stereo pair is suitable for cross-eyed > viewing. > > > > This is great for me, as I can?t do wall eyed stereo, but the default > for many journals is to provide a wall-eyed stereo pair. > > > > Of course it is easy enough to convert by swapping the two halves of the > pair, but for the sake of convenience, would it be possible to list stereo > pair (cross eye) and stereo pair (wall eye) as two separate options in this > dialogue? > > > > Cheers, > > Oliver. > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 147, Issue 4 > ********************************************* >

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on beta strand assignmet by chimera
by Smith Liu 02 Jul '15

02 Jul '15

Dear All, I have a protein, which contains fragment aa 239-251. The protein has been fitted its map with 2 different (minor difference) resolution, and thus I have 2 PDB. For PDB 1 (the first resolution), the H-bonds inside aa 239-251 include: #2 Gly 245.A N-Asn 242.A O 2.708A #2 Asn 242.A N-Tyr 246.A O 3.120 A #2 Val 248.A N-Val 240.A O 3.120 A #2 GLN 251.A N-Ser 238.A 0 3.033 A For PDB 2 (the second resolution), the H-bonds inside aa 239-251 include: #0 Gly 245.A N-Asn 242.A O 2.715A #0 Asn 242.A N-Tyr 246.A O 3.1206 A #o Val 248.A N-Val 240.A O 2.858 A #0 GLN 251.A N-Ser 238.A 0 3.074 A Naked eye check found the H-bonds in PDB 1 were almost the same H-bonds in PDB 2. However for PDB 2, aa23-242 and aa 247-251 form 2 strands, but for PDB 1, it was a un-disconnected loop for aa 239-251. Will you please explain how chimer assign beta strand? Best regards. Smith

2 1

gzip error while starting REST server on Windows
by Mungo Carstairs (Staff) 02 Jul '15

02 Jul '15

I'm testing Jalview starting Chimera (1.10.1) with RESTServer on a Windows 7 machine without gzip installed. On starting the Chimera process: new ProcessBuilder().start("chimera.exe", "--start", "RESTServer") I get two lines of response: Cannot execute 'gzip': no automatic decompression of .Z files REST server on host 127.0.0.1 port nnnnn which is ok - I can get the REST port number I need and carry on. Am I safe to ignore the other message? I can't see what file (I assume part of the Chimera installation) it is arising from. Thanks, Mungo Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology College of Life Sciences University of Dundee, Dundee, Scotland, UK. www.jalview.org<http://www.jalview.org/> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk/> The University of Dundee is a registered Scottish Charity, No: SC015096

2 1

Worm representation / command line
by Xavier ROBERT 01 Jul '15

01 Jul '15

Dear all, I am wondering if there is a way to call "Render by Attribute" at the command line in order to render a worm representation? If not, is this feature planned for the near future and is there any workaround for this? Thank you very much in advance. Kind regards, Xavier R.

2 1

generating symmetry mates of a surface model created with shape command
by Carmen San Martin 01 Jul '15

01 Jul '15

Dear all, is it possible to generate symmetry-related copies of a surface model created by the shape command? I am interested in masking out certain map regions related by symmetry. I got the right shape at the right place but now cannot figure out how to create the shape symmetry mates. The sym command followed by the model number of my shape complaints that no molecules are specified. Thanks, Carmen ------------------------------------------------------------- Carmen San Martín, Ph. D. Centro Nacional de Biotecnología (CNB-CSIC) Darwin, 3 28049-Madrid (SPAIN) Email: carmen(a)cnb.csic.es Phone: 34-91-5855450 Fax: 34-91-5854506 http://www.cnb.csic.es/ http://tinyurl.com/carmensanmartinlab http://orcid.org/0000-0001-9799-175X ------------------------------------------------------------

2 3

Using Chimera to read Maestro files
by CG Deer 30 Jun '15

30 Jun '15

Hello Chimera Developers and Users, My name is Christopher Deer, and I am trying to use Chimera as part of a workflow for getting a maestro file (.mae) ready for presentation in a CAVE environment. The .mae file contains color references and specifics defined by a researcher. However, these details are not appearing when I open the file in Chimera. So is there any way to open this file type without having to redefine all the specific features the researcher originally made? Here is a screenshot of what I am seeing in Chimera, and I have attached what the researcher originally wanted it to look like (minus white background).[image: Inline image 1] Thank you for your help, --Chris Deer University of Arizona Research Computing, Data Visualization Specialist

2 1

animation error
by Hartzell Jr., Criss 30 Jun '15

30 Jun '15

I am at a meeting making an animation for a talk using my MacAir. When I play it back from the animation panel, about half way through the animation, I receive this error and the animation crashes. Can you help debug? Thanks. File "/Volumes/ChimeraInstaller 1/Chimera.app/Contents/Resources/share/Animate/SceneState.py", line 1031, in _msmsSameColors return false NameError: global name 'false' is not defined Criss Hartzell Professor Department of Cell Biology Emory University School of Medicine Atlanta, GA 30322 404-242-5719 (cell) For Fedex, UPS, other courier: Criss Hartzell 615 Michael St. 535 Whitehead Building Emory University Atlanta, GA 30322 ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

3 2

morph volumes after alignment
by Haselbach, David 30 Jun '15

30 Jun '15

Dear all, I have a few volumetric cryo EM Maps of the same protein in different conformations. And I would like to morph between those conformations. However, the volumes are not perfectly aligned in first place. So I align all of them on one of the maps using the "fit in map" functionality. This works great and when I look through the different structures with the volume viewer, they are perfectly aligned. However, if I morph through the maps using the following command: vop morph #0-19 playstep 0.003 constantVolume true frames 1000 the maps are morphed in their original position so the morph is quite jumpy. Is there a way to morph through them in the aligned coordinate system directly? Kind regards David ----------------------------------------------------------------------------------- Dr. David Haselbach Max-Planck-Institut für biophysikalische Chemie AG Stark Am Fassberg 11 D-37077 Goettingen dhaselb(a)gwdg.de<mailto:dhaselb@gwdg.de> +49-551-2011302

2 1

Linux and stereo in the vizvault
by Greg Couch 29 Jun '15

29 Jun '15

So it works with some caveats -- iff the projector is the primary and only display and you use reverse sequential stereo. Getting there was difficult, you have to disable the LCD monitor with the system display settings instead of the amdcccle interface that appears to do the same thing. But you need to use the amdcccle interface to turn on quad-buffered stereo. Once quad-buffered stereo is setup (after several reboots), you can turn on and off the LCD monitor, but the stereo-sync signal is only generated only if the LCD monitor is turned off. The driver also got confused occasionally and wouldn't display a stereo image -- that was fixed by reenabling the LCD monitor and disabling it again. -- Greg

1 1

on chimera saved PDB file
by Smith Liu 29 Jun '15

29 Jun '15

Dear All, By chimera I have saved a PDB file, but at the end of the saved PDB there are following sentences which I do not understand: CONECT 3 2 4 17 CONECT14560145591456114574 CONECT29117291162911829131 Will you please explain it to me the meaning of "CONECT 3 2 4 17" and the other 2 sentences? And why there is no space in "CONECT14560145591456114574"? Smith

2 1

Morph volumes after alignment
by Haselbach, David 28 Jun '15

28 Jun '15

Dear all, I have a few volumetric cryo EM Maps of the same protein in different conformations. And I would like to morph between those conformations. However, the volumes are not perfectly aligned in first place. So I align all of them on one of the maps using the "fit in map" functionality. This works great and when I look through the different structures with the volume viewer, they are perfectly aligned. However, if I morph through the maps using the following command: vop morph #0-19 playstep 0.003 constantVolume true frames 1000 the maps are morphed in their original position so the morph is quite jumpy. Is there a way to morph through them in the aligned coordinate system directly? Kind regards David ----------------------------------------------------------------------------------- Dr. David Haselbach Max-Planck-Institut für biophysikalische Chemie AG Stark Am Fassberg 11 D-37077 Goettingen dhaselb(a)gwdg.de<mailto:dhaselb@gwdg.de> +49-551-2011302

1 0

ViewDock
by leila karami 27 Jun '15

27 Jun '15

Dear all Now, I want to save 1 pdb file containing target + one of poses of ligand for example, number 3. For this aim, what to do? I did following steps, but I did not succeed: file ---> save pdb ... In save models section, I selected both of target.pdb (#0) and (#1.3) In file name section, I wrote complex.pdb and then save. I encountered with error (see the below link): https://www.dropbox.com/s/bdkq1x1db96amhi/chimera%20error.png?dl=0 I tested other names such as $target.pdb and $1.3.pdb. Unfortunately, I encountered with the same error. Best regards,

2 1

drawing shapes
by Bala subramanian 25 Jun '15

25 Jun '15

Friends, I have used HOLE program ( http://www.sciencedirect.com/science/article/pii/S026378559700009X) to find the pore radius of a channel as a function of z-axis. As output, the program gives the location of capsules (that were filled inside the channel), capsule length and radius etc, as a function of z-axis. Capsule graph option***** Data: cenxyz.cvec eff.rad area CAP.LEN cap.rad angle.X-axi cen.line.di integ.s/(ar point sourc *-14.00000* *2.23465* 15.68804 *1.72142* 1.39301 73.21487 0.00000 0.03187 (sampled) -14.50000 2.40709 18.20262 1.96609 1.46141 58.41143 -0.54015 0.05934 (sampled) -15.00000 2.51292 19.83844 1.37866 1.78410 73.19154 -1.11224 0.08454 (sampled) -15.50000 2.69525 22.82171 1.34834 1.97026 87.40431 -1.71545 0.10645 (sampled) I was wondering if i can use the shape command to draw the capsules in Chimera. I thought to create 'tube' with 'shape' command but i was not lucky. For instance, the following command didnt work (i opened channel as model #0) shape tube #0 radius *2.23* bandLength *1.72* center 0, 0, *-14.00 * Pls help to know some way to do this. Thanks, Bala -- C. Balasubramanian

2 2

Windows 8.1 and nVidia Quadro drivers.. grrr
by Kenward Vaughan 24 Jun '15

24 Jun '15

Hello! I have Chimera working wonderfully with sequential stereo under Linux with our Quadro card (a K4200), but am getting terribly frustrated with trying to have it work at all under Win 8.1. The latest non-beta driver is installed. It took me a while to find where the nVidia control panel is located after finding that Chimera didn't recognize any stereo-capable hardware (including some references to togl and pixels). Blah. I started up the "wizard" of 3D, which gave me a nice slide show, but Chimera didn't see anything. Interestingly, rebooting directly into Linux gave the same problem, which had me fuming and frothing all over the place. A shutdown followed by fresh start into Linux reset the card. So the Windows driver touches something inside the card which has to be reset hard. There are multiple things installed when this driver is put on the system. Is it possible that there are things I don't want, which are slyly strengthening my thoughts about Windoze? Some searching of the archives was inconclusive for this system. I have played with the settings in the control panel but have found no combination that gets sequential stereo working. Does anyone know what settings should be changed from the defaults to get this working? Many thanks for any help! Kenward -- In a completely rational society, the best of us would aspire to be _teachers_ and the rest of us would have to settle for something less, because passing civilization along from one generation to the next ought to be the highest honor and the highest responsibility anyone could have. - Lee Iacocca

2 5

savepos
by Dougherty, Matthew T 24 Jun '15

24 Jun '15

in defining the text string view_name, spaces are disallowed, eg "rotate 30". Although the position will be created, the reset command will not properly access the position key. What are the allowable characters? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

3 3

ViewDock
by leila karami 24 Jun '15

24 Jun '15

Dear Elaine, Thanks for your guidance. It was very good. Now, I want to know there is this possibility to have these separate 252 pdb files as 1 pdb file? Thanks for your time and consideration. Best

3 2

How to crop a map
by Tom Goddard 24 Jun '15

24 Jun '15

You can crop a map using volume dialog menu Features / Region Bounds, then save it with volume dialog File / Save Map As…. Other Chimera map capabilities are described in the Guide to Volume Data Display in Chimera: http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html <http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html> Tom > On Jun 23, 2015, at 7:52 PM, 李智海 wrote: > > Adding to the previous one. > the map I want to convert has a same pixel size with the data set. So maybe the question could be that how can I cutting the boundaries of the map to fit the size of reconstruction images. > > Thanks! > > Zhihai Li > > >> On Jun 24, 2015, at 10:44 AM, 李智海 wrote: >> >> Hi, Tom >> An another question, >> I want to make a reference map for reconstruction, here I have a map but with different map size from my raw image, how can I scale the map dimensions into a specific value without changing the centre coordinates. >> Thanks! >> >> Zhihai Li >> >> >>> On Jun 24, 2015, at 2:00 AM, Tom Goddard wrote: >>> >>> If you used the Chimera Segment Map dialog (volume dialog menu Tools / Segment Map) then you select a segment (ctrl click on it) and use Segment Map menu entry Regions / Mean and SD. If you segmented the map by some other means and have the pieces as separate maps use volume dialog menu Tools / Measure Mean, SD, RMS. >>> >>> Tom >>> >>> >>>> On Jun 23, 2015, at 6:42 AM, 李智海 wrote: >>>> >>>> Hi, >>>> Here I want to evaluate the flexibility of variable domains of a density map. How can I quantify the mean intensity of segmented parts by Chimera? Thanks! >>>> >>>> Best wishes! >>>> >>>> Zhihai Li >>>> >>>> Ph.D student in State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics. >>>> School of Life Sciences, Xiamen University. >>>> Xiang'an Road(South), Xiang'an District, Xiamen City, >>>> Fujian Province, China. >>>> >>>> _______________________________________________ >>>> Chimera-users mailing list >>>> Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >>> >> >

1 0

PDB not opening
by YAikhombA Mutum 24 Jun '15

24 Jun '15

Hi 1. I'm not able to fetch pdb's from Chimera by the command 'open 121p'. It just says 'opened 121p' in the reply log while it display a blank black screen. There are no active models displayed too (in the active models panel, there are no active tabs for models (0,1,2...)) despite the status in the reply log. The internet connections are ok (my browser is working fine). On checking the preferences (Favorites ---> preferences), everything seems fine (for instance in Category: Fetch (save fetched flie: True and use local files:True/False (I've tried both cases))). Even the category of web access seems ok. A day before I'd been able to fetch pdb's by just the command (open 1zik (say)). Now, the only way to retrieve it is to go to the rcsb website, download the pdb from a browser and then run it in chimera. Moreover, even if it (the pdb file) is already downloaded it doesn't run by entering the command (again the preferences are fine). How can I sort out this? 2. Is there a way to color the capped surface (the flat surface when you cut a protein virtually) based on sequence conservation color range. I tried the same way B factor surface capping is done as in the tutorials but the one for conservation doesn't work. It instead colors the 'whole' surface something else (Automatically uses default 'color by heteroatom' (red, tan and blue) not the colors I used for the sequence conservation). The same when I try to cap a surface based on hydrophobicity. Thanks in advance! Yaikhomba

3 2

Issue with cytoscape plugin
by Juan Eiros Zamora 23 Jun '15

23 Jun '15

Hi Chimera users, I'm using cytoscape and structureviz to visualize interaction networks of my MD simulations. I've been using it for quite awhile now on the normal structure of my protein. Now I am simulating it with two adjacent phosphorylated serines (all is done with AMBER), and I think there are some issues with this because: 1) If I select a region of the protein that does not contain this "special" aminoacids, the RIN visualization works just fine 2) When I select the region that contains these two phosphorylated Serines (about +-10 aminoacids from them), when the RIN is set up on cytoscape I get the following error: RINLayout Fetching coordinates from Chimera... null Which is pretty generic. What is more confusing is that if I select all the system (which is not interesting for me, but I've done it anyway to try) it seems to work as well. My cytoscape version is 3.2.0 and all the apps in it are up to date: structureViz2 1.0.1 RINalyzer 2.0.0 I think the RIN is being calculated just fine, but it's having problems recognising the 3D shape in Chimera. Also, it fails to synchronize the colours, I don't know if this is related to what I'm reporting here, but I suspect it is. Does anyone know how can I proceed? It would be very useful for me to compare the RINS of the non-phosphorylated version of my system to the phosphorylated version. Thanks for any help, Juan Eiros

2 1

ViewDock
by leila karami 23 Jun '15

23 Jun '15

Dear chimera users I have docking outputs from Swissdock (there is 252 binding modes for my ligand relative to the target protein). I used following to view my outputs: 1) File > Open , then load target.pdb 2) Tools > Surface/Binding Analysis > ViewDock, choose clusters.dock4.pdb (Dock 4, 5 or 6 format) Now, I want to have several pdb files in which there is target protein and each of binding modes, that is 252 pdb files. How to do this? Any help will highly appreciated.

2 1

measure a mean intensity of a segmented map
by 李智海 23 Jun '15

23 Jun '15

Hi, Here I want to evaluate the flexibility of variable domains of a density map. How can I quantify the mean intensity of segmented parts by Chimera? Thanks! Best wishes! Zhihai Li Ph.D student in State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics. School of Life Sciences, Xiamen University. Xiang'an Road(South), Xiang'an District, Xiamen City, Fujian Province, China.

2 1

Attribute Error: 'AtomType' object has no attribute 'amber_atom_type'
by Karl Sebby 22 Jun '15

22 Jun '15

Hi I am modifying several ligand/protein complexes; usually with the “Build Structures” tool. I modify ligands by changing and deleting atoms, or by using “Join Models” after building or importing a structure with “Start structure”. Sometimes, minimizing the ligand works fine, but other times I get the error: “Attribute Error: ‘AtomType’ object has no attribute ‘amber_atom_type’”. I cannot figure out what is causing this error or how to fix it. It seems to happen when I begin working from a saved session or a pdb that was written with the ‘write’ command and not when I go through a whole series of steps in one shot. Any ideas on what is going on? Thanks, All the best, Karl -- Dr Karl Sebby Left Side Research LLC 1661 K M Ranch Road Whitefish Montana 59937 Office: 406 623 4773

2 2

Using the findHbond via Python Midas Module
by Ahir Pushpanath 22 Jun '15

22 Jun '15

Dear All, I am confused about what input I need to provide to the findHbond command in the FindHBond midas module. This is the help() on the command. findHBonds(models, intermodel=True, intramodel=True, donors=None, acceptors=None, distSlop=0.0, angleSlop=0.0, interSubmodel=False, cacheDA=False). For example if I want to find all H bonds between a pre-selected group of residues in loop, saved as: loop = chimera.selection.currentAtoms() and the rest of the protein molecule, what command would I have to run? I am assuming the output(such as the one given in the findHbonds runcommand) would be saved into a variable if I provide one? Ahir -- Dr. Ahir Pushpanath* PhD.* Senior Biologist, Johnson Matthey.

2 1

help please
by Sezer Akgöl 22 Jun '15

22 Jun '15

how can I associate 2 protein with each other from their C and N terminals respectively

2 1

Feature request - lock center of rotation to center of view ("pseudo-Coot mode")
by Oliver Clarke 22 Jun '15

22 Jun '15

Hi, I have a request for a future version of Chimera - would it be possible to add a command or menu item that (reversibly) locks the center of rotation to the center of view, such that when the view is translated, the cofr is updated automatically also? This is the way structure navigation works in Coot, and I find it is a much more intuitive and precise way to travel when examining the finer details of a structure (as one would expect given that the main purpose of Coot is model building while Chimera is exceptionally good for structural analysis and visualization). This would make navigation of large structures much easier, particularly when one is just browsing around the structure. In addition, it would be nice to have a dynamically updated pseudoatom to indicate the current center of rotation - this is implemented in Coot as the “pink pointer”, and I find it very helpful for getting my bearings. Cheers, Oliver.

2 1

Chimera in Virtual machine
by Milo Westler 18 Jun '15

18 Jun '15

Well I thought I had this figured out, but then my VM broke and I can't get chimera to run in my VM again. I am running Vritualbox with a guest system of ubuntu-mate 15.04. I want to be able to use chimera in the VM for a workshop that we are presenting. I have installed the 64 bit version for linux. I get: ~> chimera pci id for fd 4: 80ee:beef, driver (null) libGL error: core dri or dri2 extension not found libGL error: failed to load driver: vboxvideo libGL error: unable to load driver: swrast_dri.so libGL error: failed to load driver: swrast X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 154 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Value in failed request: 0x0 Serial number of failed request: 751 Current serial number in output stream: 752 ~> And when I run: /opt/UCSF/Chimera64-1.10.1/share> python __main__.py Chimera is misconfigured. Please reinstall chimera. Thanks, -- -- Milo =================================================== National Magnetic Resonance Facility at Madison An NIH-Supported Resource Center W. Milo Westler, Ph.D. NMRFAM Director Senior Scientist and Adjunct Professor Department of Biochemistry University of Wisconsin-Madison DeLuca Biochemistry Laboratories 433 Babcock Drive Rm B160D Madison, WI USA 53706-1544 EMAIL: milo(a)nmrfam.wisc.edu PHONE: (608)-263-9599 FAX: (608)-263-1722 ======================================================================= ========

2 1

Query on GPI-anchor proteins
by Aditya Padhi 17 Jun '15

17 Jun '15

Dear Chimera Users, I am working on a protein, which is known to cleave few GPI-anchor proteins (Glycosylphosphatidylinisotol). Also, I know that there are several other candidate GPI-anchor proteins which may or may not be cleaved by my protein of interest. I was wondering, if there is any tool/method in Chimera using which I can atleast get some preliminary information on which of the proteins that could be probably cleaved by my protein of interest. The 3D structure of my protein of interest and most of the GPI-anchor proteins is not available. I was therefore wondering if there is any such tools/methods available that I am missing using which I can find out which of the GPI-anchor proteins are being cleaved. Any suggestion/guidance would be highly appreciated. Thank you so much, Aditya

2 1

What happened to my model?
by Sara Cuellar 17 Jun '15

17 Jun '15

So, in my line of work we are focusing on the protein Dihydrofolate Reductase. Using Jmol, I was able to remove all chains except for chain A, and also increased the diameter of the backbone so that it may be printed. When I opened it in Chimera to export it from VRML file to an STL file, it still looked fine. However, when it was opened in my 3d printing program, parts of the protein were missing. All I see is floating fragments. Is there any way I can fix this using chimera? I have included images of the protein.

2 2

Scripted registration of a perframe python script
by Kersey Black 17 Jun '15

17 Jun '15

Hi, I have been 'opening' a python script file from within Chimera to start a session and in that script I open the MovieDialog manager (mdm) and read in a pdb with a series of models to be viewed as a trajectory. That part is working thanks to help from other responses in chimera-users. To modify the molecule (color, etc) it seems like the mdm.ensemble.molecule is giving me the access, though that may not be the right approach for my needs, because it seems to act on all frames. What I would like to do, from within this same initial python script, is to apply/register a perframe (also in python) script to control things like color on a frame by frame basis. I would like to do this as a way of keeping all of the setup in a single script file such that then I just need to record the movie manually, or perhaps there is a way to do this also from the script. Thanks much for any help and/or direction to documentation on the python api to the MovieDialog that allows control of these functions. Kersey

3 2

ImportError: no module named chimera
by 陈雷 16 Jun '15

16 Jun '15

Hello, I got a problem when calling chimera in a python script. ImportError: no module named chimera Here is the line in my script: from chimera import runCommand. Python version is 2.6.6 and chimera is 1.8 in Linux. Would you please help me out with this? Thanks. Best regards, Ryan

2 1

ImportError: no module named chimera
by ryanch＠mail.ecust.edu.cn 15 Jun '15

15 Jun '15

Hello, I got a problem when calling chimera in a python script. ImportError: no module named chimera Here is the line in my script: from chimera import runCommand. Python version is 2.6.6 and chimera is 1.8 in Linux. Would you please help me out with this? Thanks. Best regards, Ryan

1 0

restoring sessions with python & triggers
by Dougherty, Matthew T 15 Jun '15

15 Jun '15

Normally a save session by a python extension is invoked by a trigger SAVE_SESSION. For restoring a session, several related chimera APIs are available that are typically not used. 1) post model restore: SimpleSession.registerAfterModelsCB(afterModelsRestoredCB, arg) 2) BEGIN_RESTORE_SESSION and END_RESTORE_SESSION triggers. I need to reset extension gui values based on midas positions. I presume a normal restore in the session file does not guarantee that these midas positions will be loaded at that time, so I need to delay the gui updates until the restore process has ended or possibly when the models are loaded loaded. What is the distinction between END_RESTORE_SESSION and registerAfterModelsCB? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

2 1

setting viewing pref using python
by Dougherty, Matthew T 15 Jun '15

15 Jun '15

the viewing dialog sets the Camera:Stereo parameters:units to inches, and Side View:Side to right. using python how can I reset them to mm & top? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

2 1

Re: [Chimera-users] Request for axes measurements
by Elaine Meng 14 Jun '15

14 Jun '15

Hi, You’re welcome, but I don’t have any further details than what is already given in the manual: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/str…> It’s recommended you send Chimera questions to chimera-users(a)cgl.ucsf.edu instead of me directly, in case others may be able to provide better answers! Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Mar 31, 2015, at 6:26 PM, Jayaraman T <jram(a)pusan.ac.kr> wrote: > > Hi Elaine Meng, > Yes i could figure now the axes as well as angle measurements between them and thanks for your timely help. > > I would be happy if you could tell me the principle on which these axes are calculated. I have noticed that it's from Eigen vector values that are calculated for the coordinates of the set of atoms. > > I'm really interested on the backend for this calculation particularly, might help a bit progressing more for my research. > > Thanks again.

2 6

on MD movie and morph conformation by chimera
by Smith Liu 12 Jun '15

12 Jun '15

Dear All, Will you please introduce to me on how to combine chimera MD movie function and morph conformation function to make conformation change movie files to insert into PPT files? Smith

2 1

mol2 for NH3
by MPI 11 Jun '15

11 Jun '15

Dear Users, I try to prepare a mol2 from pdb for ammonia (NH3) and ammonium (NH4+), respectively. I used two commands: addh and addcharge with am1 method. eg, addh addcharge all method am1 It turns out that Chimera gave two similar mol2 files for NH4+ but NOT for NH3. I wonder what command and parameters are needed to produce a correct mol2 for NH3. Here are the input pdb files for NH3 and NH4, respectively. # NH3 HETATM 2860 N NH3 A 402 53.512 -12.964 -36.364 0.88 45.66 N # NH4 HETATM 2858 N NH4 A 404 56.362 -12.467 -27.097 1.00 30.80 N Thanks, Dewey

2 5

Problems detecting a left-handed helix
by Felipe Vasquez 11 Jun '15

11 Jun '15

Hi, I am trying to visualize several of the secondary structure details on a protein of interest, and I recently had notice (by several research papers) about the existence of a left-handed helix on it. However, I could not detect the helix using UCSF Chimera (it is simply considered as a loop). Why could this happen and how could be resolved? I have tried to modify the ksdssp cut-off parameter, but it was unsuccessful, so I think now that maybe the specific nature of the helix (left-handed polyproline-like type II) could be a bit tricky for the program. What would you suggest? Thanks in advance for your help an patience. Best regards, *Andrés Felipe Vásquez J., BSc, MSc.* 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 +57 (1) 2207700 ext. 1419 Bogotá, D.C., Colombia

2 3

Determination of angles formed by distances and ring axes
by Felipe Vasquez 10 Jun '15

10 Jun '15

Hi, I have problems trying to calculate the angle between two lines: one is really built as the distance between a residue atom from a protein and the centroid of a benzene ring (from a ligand), and the other is the line corresponding to the axis of the benzene ring. How could I accomplish this objective? I have read similar issues by chimera-users on the web, but I could not find enough information to complete the calculation (I could only estimate the first distance). In case of problems to clearly comprehend this particular task, please refer to the page 3, Fig 1, panel C in the attached research paper (phi angle). PD: Is it normal that the centroid of a benzene ring is above the ring itself? Because in the process of build the first distance, I don't know whether I have to calculate the distance between the centroid and the residue atom (which I found to be shorter), or instead calculate the distance between the center itself of the plane and the residue atom (which would be a bit longer). Thanks in advance for your time and assistance in this matter. Best regards, *Andrés Felipe Vásquez J., BSc, MSc.* 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 +57 (1) 2207700 ext. 1419 Bogotá, D.C., Colombia

2 1

file size of a trajectory
by MPI 10 Jun '15

10 Jun '15

Dear Users, I use the lastest version of Chimera to read trajectory (.xtc) files output from Gromacs ver 4.6.5. When a .xtc file size larger than 2GB in most cases and 1GB in some cases, Chimera gets choked and crashed. When a .xtc file size < 1GB, Chimera works very well. I wonder if this is a limitation for reading Gromacs trajectory files. Is there a solution ? Thank you. Dewey

3 4

tetrahedral symmetry
by Morris, Kyle 10 Jun '15

10 Jun '15

Dear Chimera Developers, I have a volume reconstructed from Relion 1.3 imposing tetrahedral symmetry. Curiously, I am not able to find the symmetry group using: $ measure symmetry #0 Chimera returns C3, even with adjusting the parameters it uses to identify the symmetry group. The model is aligned as following the Xmipp convention for T symmetry (http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Symmetry#T) which is the same as what Chimera calls T,z3? Any advice on getting the measure command to work in this convention would be greatly appreciated. Thanks! Best wishes, Kyle Morris University of Warwick, UK

2 1

Save Cluster Figure as Phython Object
by Beuerle, Matthias 09 Jun '15

09 Jun '15

Dear all, I have been using the Clustering tool in the MD Movie/Analysis/Cluster to examine my trajectories and I found it very useful. Now I would somehow like to save the box-chart matplotlib object in order to adjust the figure, so that I can use it for a publication, since the dialog buttons do not allow a lot of modifications. Is this possible somehow? Alternatively I would be very happy as well if one could use the output obtained from the 'Save' button to recreate a similar figure (in which I have failed so far). Help is very much appreciated. Kind regards, Matthias

2 1

joining two proteins
by López de Heredia Alonso, Miguel 08 Jun '15

08 Jun '15

Hi, I am new to Chimera, so perhaps someone could give me a hand. I have used Robetta for predicting the structure of a protein I am interested in and it gave back models for different parts of the protein. I would like to join them, so I am trying to join two models by a C-N peptide bond. I have selected the corresponding atoms in the last amino acid in one of the proteins and in the first amino acid of the other protein I want to join. With both atoms selected I took the "Join Models" option in "Build Structure" with the "C-N peptide bond" selected. And the "Apply" button does not activate. (See the screen shot attached) I have gone through the manual and I do not see what I am missing or what I am doing wrong. Any help is welcome. Thank you very much in advance. Kind regards, Miguel

2 1

APBS electrostatic potential
by Felipe Vasquez 06 Jun '15

06 Jun '15

Hi, I am interested on calculating the electrostatic potential of a molecular surface on a protein (specifically visualizing that potential on a previously cavity determined by CASTp). However, althought I did get reasonable results using Coulombic potential, I could not obtain similar results using APBS potential (I obtained a surface too electrostatic, charged negatively and the values have a huge range, not only from -10 to 10 as in the case of Coulombic potential). Should I modify some default values out of the calculation parameters in order to get a similar result to that obtain by Coulombic potential? And it is absolutely indispensable add hydrogens in an APBS estimation? Thanks in advance for your help. Best regards, *Andrés Felipe Vásquez J., BSc, MSc.* 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 +57 (1) 2207700 ext. 1419 Bogotá, D.C., Colombia

2 2

surfaces and
by A G Szabo 03 Jun '15

03 Jun '15

I have been working with a very large structure of many subunits, the E.Coli Ribosome particle with the Signal Recognition Particle attached (PDB 2J28) I was able to create an image of the SRP part of the complex. I selected that subunit. And was able to hide all the other subunits. So with the subunit selected I tried to visualize only that image as a surface. Wouldn't let me, getting an error message that it was too large and I should somehow split it. Don't know how to do that. I know the whole dataset is very large, but the SRP portion is only 400 amino acids. A work around would be if I could somehow select the SRP subunit and have it as a dataset to reload as that subunit alone. Then not so big. Don't know how to do that either. Your suggestions. I couldn't find anything in the tutorials that might help. I was able to show the surface of another PDB file that was much smaller. Arthur G. Szabo Professor Emeritus Chemistry Wilfrid Laurier University Waterloo Ontario Canada.

2 1

Re: [Chimera-users] FW: Python code problem
by Mahendra B Thapa 03 Jun '15

03 Jun '15

Dear Eric I had not realized that not every amino acid consisted of CB atom. Thank you for the code which worked; just want to add a very minor addition ( """ ) to the left of the code, i.e. *sel = OSLSelection("""#0.1:%d.B@CB""" %i)* instead of *sel = OSLSelection(#0.1:%d.B@CB""" %i)* I tried another code as import string rc("open " + 'test.pdb') # 60 models, each model has chains A,B,C for i in [2196,2197]: for j in range(3429,3450): for *k* in ['A','B','C']: sel = OSLSelection("""#0.3:%d.%s@CA""" %(j,k)) sol = OSLSelection("""#0.2:%d.B@CA""" %i) if ((len(sel.residues()) != 1) or (len(sel.residues()) != 1)): continue if ((len(sol.residues()) != 1) and (len(sol.residues()) != 1)): continue rc("""distance #0.2:%d.B@CA #0.3:%d.%s@CA""" %(i,j,k)) I got the output as (without any error message) Distance between #0.2:2196.B@CA and #0.3:3450*.C*@CA: 104.315 The 'for' loop did not work for *k* (above) and only gave results for C only but not for A and B. Thank you for help, Mahendra Thapa University of Cincinnati,OH On Fri, May 29, 2015 at 1:55 PM, Thapa, Mahendra (thapamb) < thapamb(a)mail.uc.edu> wrote: > > ------------------------------ > *From:* Eric Pettersen > *Sent:* Friday, May 29, 2015 11:55:18 AM (UTC-06:00) Central America > *To:* Thapa, Mahendra (thapamb) > *Cc:* chimera-users(a)cgl.ucsf.edu > *Subject:* Re: [Chimera-users] Python code problem > > Hi Mahendra, > In the first case, as you saw, it tries exactly two distances; the first > involving :2011.B and the second involving :2420.B. In the second case it > will try every distance from :2011.B through :2419.B (note that the range > command does not include the ending number in the range). This means if > the structure is missing *any* of those residues then the distance > command will fail with the error you got, since the atom spec will only > select one atom. > So you either need to explicitly use just the residue numbers that exist, > or you need to test if the residue you are about to try to use exists. So > code to do that might be: > > from chimera.selection import OSLSelection > sel = OSLSelection(#0.1:%d.B@CB""" %i) > if len(sel.residues()) != 1: > continue > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > On May 29, 2015, at 6:37 AM, Mahendra B Thapa <thapamb(a)mail.uc.edu> > wrote: > > Dear Chimera users, > > The command I used was > chimera --nogui test.py > I tried two codes (following previous posts and tutorials in chimera) in > 'test.py' as follows > > (i) > import os > from chimera import runCommand as rc > from chimera import replyobj > rc("open " + 'test.pdb') > for i in [2011,2420]: > rc("""distance #0.2:2010.B@CB #0.1:%d.B@CB""" %i) > > *This code gave the result as expected*: > Executing test.py... > Opening test.pdb... > 60 models opened > Distance between #0.2:2010.B@CB and #0.1:2011.B@CB: 72.346 > Distance between #0.2:2010.B@CB and #0.1:2420.B@CB: 92.979 > Executed test.py > > (ii) > import os > from chimera import runCommand as rc > from chimera import replyobj > rc("open " + 'test.pdb') > for i in range(2011,2420): > rc("""distance #0.2:2010.B@CB #0.1:%d.B@CB""" %i) > > * This code gave the result as* > ' You selected %d.' % numSelected) > MidasError: Exactly two atoms/axes/planes must be selected. You selected > 1. > Error while processing test.py: > MidasError: Exactly two atoms/axes/planes must be selected. You selected > 1. > > File "/opt/UCSF/Chimera64-1.5.3/share/Midas/__init__.py", line 1266, in > distance > ' You selected %d.' % numSelected) > > What could be the error this code? Only difference between two codes is: > "for > * i in [2011,2420]:" & "for i in range(2011,2420):" * > That is, I am interested to use range operator in 2nd case instead of two > values as in the 1st case. > > Thank you for help, > 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 > > > > >

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savepos
by Dougherty, Matthew T 03 Jun '15

03 Jun '15

Hi, I have been automating the creation of positions using python scripts. Something relatively simple like p001, p002, etc. When I examine the positions using the python commands from Midas import positions pnames = positions.keys() at first things appear as I would expect, but later the sequence changes relative to the index, why is that? for example, using this to print the positions pnames = positions.keys() i=0 for pname in pnames: print i,pnames[i] i=i+1 I get these results: savepos p000 savepos p001 0 p000 1 p001 (as expected) savepos p002 0 p000 1 p001 2 p002 (as expected) savepos p003 0 p000 1 p001 2 p002 3 p003 (as expected) savepos p004 0 p004 1 p000 2 p001 3 p002 4 p003 (not as expected) savepos p005 0 p004 1 p005 2 p000 3 p001 4 p002 5 p003 (not as expected) I would expect pnames[0] to correspond to the first position created, pnames[1] to the second posiiton created, etc., assuming no ~savepos used. Want to create a situation where the default names would be pxxx, but could later be altered to more meaningful names but maintain the order of creation, or getting a session file from someone I would use their position names and tack on my default names to the end of the position list. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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to color EM map
by Smith Liu 03 Jun '15

03 Jun '15

Dear All, Suppose I have an EM map for a protein complex of 4 subunits. I have fitted them in chimera. Will you please tell me how to give each part of the map a different color based on the subunits? For example, for subunit A, B,C, D part of the EM map, how to color the map accordingly in blue, red, yellow and purple? Smith

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volume viewer/Data menu
by Dougherty, Matthew T 02 Jun '15

02 Jun '15

Hi, What is the pattern for the sequence of the Data list? Is there a way to sequence it the same as the Model Panel? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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Unable to Change Lighting of Side Chains / Atoms
by David Nelson Bunck 02 Jun '15

02 Jun '15

Hello, Recently, for some reason, the settings changed on Chimera such that the atoms and side chains do not change color when I try to change the lighting settings. Thus when I get the protein (in ribbon format) to look appealing and shiny, the metal atoms in the protein remain black. Changing colors or lighting do not make any difference. The same is true for the side chains as well. This also occurs on several different sequences, so it is not just the one file. Sorry for the seemingly trivial question, but I have poked around for a while at the different settings and can't seem to find how to undo this change. Thanks for your help! david -- david bunck bunck(a)caltech.edu (626) 395-8919 Postdoctoral Scholar Heath Research Group Division of Chemistry and Chemical Engineering California Institute of Technology

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Cage maker
by Anindito Sen 02 Jun '15

02 Jun '15

Dear All, Is it possible to generate a synthetic 3d density map of hexagons and/ pentagons using the Cage building option with file extension like mrc or spi or pif ( the usuals). If so, how to save it in such a format ? Thanks Andy Sent from my iPad

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