- Chimera-users - RBVI Mailing Lists

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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