- Chimera-users - RBVI Mailing Lists

Export Scene, Mesh Surface, wrl
by Cynthia Turner 02 Feb '16

02 Feb '16

Dear Chimera, I would like to export a scene of 1PRH (PDB of Cyclooxygenase) with a surface mesh, in wrl format for import into Cinema4D. (Screen shot attached) I am able to import scenes with ball and stick, sphere, solid surface, ribbons etc, in this way without problem. However, the mesh doesn’t seem to be in the wrl file once imported. The ribbon is there, but the mesh is not, or the mesh is not imaging for some reason. Am I missing something, or missing a step? Thank you so much for your assistance in advance, Kind regards, Cynthia Turner

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Running out of memory when recording movies
by Oliver Clarke 01 Feb '16

01 Feb '16

Hello, I am consistently running out of memory when recording long-ish movies (using the Animation tool) on a Macbook pro with 16GB RAM. Admittedly there are a lot of atoms in the model I am using (~120,000), but most are not displayed (only ribbons). Chimera is consistently crashing at about the 300 frame mark and looking at the activity monitor during the recording I can see memory pressure gradually increasing until Chimera freezes (which is generally not recoverable). Is there any way to reduce the amount of memory required for movie recording? Will deleting all undisplayed atoms help? Is there some way to perform these operations on disk rather than in memory (most likely a silly question)? Cheers, Oli.

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Morph groups of maps?
by Oliver Clarke 01 Feb '16

01 Feb '16

Hello, In a situation where I have maps for two conformations, and I've extracted out domain specific maps in both cases, is it possible to run morph maps on both groups of maps simultaneously? Or is there any way to apply color zone to the trajectory generated by morph maps? I would like to generate a morph map movie where the map is colored by domain throughout the morph, and can't figure out how to do so. Cheers, Oli

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Joining models question
by Kyle J. Lauersen 29 Jan '16

29 Jan '16

Hello, I am trying to join the two models attached to this sequence. I have used the sequence selection code in atom specifier: #1:559.a@C #0:2.a@N Where model #0 is YFP and #1 is PcPs. When I go to join models, the Apply button is not accessible. Can you indicate if I am doing something incorrect in the selection of the C and N atoms? Thank you for your time. Kyle Dr. Kyle J. Lauersen Algae Biotechnology & Bioenergy Center for Biotechnology Bielefeld University p: +49 (0) 521 106 12289 e: kyle.lauersen(a)uni-bielefeld.de <mailto:kyle.lauersen@uni-bielefeld.de>

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Question from PhD student
by T-I 28 Jan '16

28 Jan '16

Dear Chimera, I would like to know exactly how to enclose my EM density map within a cube of specified size (where x, y and z have equal dimensions, i.e x,y,z = 150 pixels). It seems that when I place a marker (from volume tracer) on my map and then specify the padding number a rectangular cube is produced instead. I there a simple command to do this or can it be done from the GUI? Many thanks T.I PhD student, London

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Tool:Structure Editing:Model:Refine loops
by Jingchuan Sun 26 Jan '16

26 Jan '16

Hello, When I tried MODEL plugin to model loop, the changes in result model is not just the selected loop to be modelled. It renumbered residues. There are several missing residues outside the selected loop in my old model. They become connected (in not accepting way) in returned models. Could I disable this "over-reach"? I only need to model the selected loop, no change to other places or renumbering. Best, Jingchuan

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rendering of custom annotation
by Helge 26 Jan '16

26 Jan '16

Dear Chimera users, I have some data, which contains numbers of hits for each given residue of a chain (in my case the 25S rRNA). The data consists of a table with two columns: residues and corresponding hits. I would now like to color each residue in Chimera, relative to the amount of hits, with the highest number always getting a defined color. Is this possible? best regards, Helge

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Add Charges failure (libquadmath)
by Lluis Blancafort 25 Jan '16

25 Jan '16

Hi, I’m running Chimera alpha version 1.11 on Mac OSX El Capitan 10.11.2 The Add Charges tool does not work for non-standard residues with AM1-BCC. The Reply Log reports a problem with libquadmath and later with sqm utility (see below). I don’t have libquadmath.0.dylib installed. Can anybody help? Thanks! Lluís Blancafort Institut de Química Computacional i Catàlisi Universitat de Girona 17071 Girona Spain (1) Charge model: AMBER ff14SB Assigning partial charges to residue SGA (net charge -1) with am1-bcc method Running ANTECHAMBER command: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/antechamber -ek qm_theory='AM1', -i /var/folders/6j/nf071g8n2b5csd0rdcm8n5sc0000gn/T/tmpKi57P0/ante.in.mol2 -fi mol2 -o /var/folders/6j/nf071g8n2b5csd0rdcm8n5sc0000gn/T/tmpKi57P0/ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 (SGA) (SGA) dyld: Library not loaded: /usr/local/lib/libquadmath.0.dylib (SGA) Referenced from: /Applications/Chimera.app/Contents/Resources/lib/libgfortran.3.dylib (SGA) Reason: image not found SGA) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac (SGA) (SGA) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (SGA) Total number of electrons: 136; net charge: -1 (SGA) (SGA) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out (SGA) Error: cannot run "/Applications/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit

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my question
by Yanli Li 25 Jan '16

25 Jan '16

Dear sirs/madams, I am a PhD student in Universitat Autònoma de Barcelona. I am working on the Porcine Reproductive and Respiratory Syndrome Virus (PRRSV). I have got differences of cytokine profiles and phenotype regulation of antigen presenting cells by different isolates through the lab work. Now I intend to predict the structure of the whole or some parts of the viral particle with UCSF CHIMERA. However, there are only three relevant structures(nucleocapsid, nsp1, nsp4) that have been published. Is it possible to realize it? If yes, can you tell me the method in brief? Thanks a lot! Waiting for your reply. Best wishes, Yanli LI

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the fastest way to convert a pdb to density map
by 李智海 22 Jan '16

22 Jan '16

Hi, Here I want to calculate a model-to-map FSC curve. If I am not wrong, firstly I am supposed to convert the pdb file to a density map. So I was just wondering in Chimera, how to use command molmap to generated a map with the same pixel size and dimensions as the corresponding map? Any help will be high appreciated. Best, Zhihai Li

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Select residues with missing atoms?
by Oliver Clarke 19 Jan '16

19 Jan '16

Hello, Is there any way to select/color all protein residues with incomplete sidechains? This would be very helpful when looking at a structure and deciding whether it is necessary to run dock prep to fill them in prior to performing other calculations (e.g. sometimes I am only concerned with what is going on around a ligand binding site). Cheers, Oliver.

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question
by A G Szabo 15 Jan '16

15 Jan '16

I have to admit that my understanding of the various commands to use for very specific functions in Chimera is difficult for me to find the correct command. I know how to color a specific residue using the sequence table and the color chart. So how do I color a specific atom in a residue. For example I am interested in coloring the nitrogen of the Asn amide side chain say color red. How can I do this? When I highlight a residue and visualize it as a ball and stick, then color it different from the color of the helix, the color of that part of the helix changes to the color of the ball and stick, different from the color of the rest of the helix. How can I reset the color of the helix location of that residue, leaving the ball and stick as another color. Thank you Arthur Szabo Professor Emeritus Chemistry and Biochemistry Wilfrid Laurier University Waterloo Canada.

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Geometric Center
by tobias.eilert＠uni-ulm.de 15 Jan '16

15 Jan '16

Hello, I want to translocate a protein such that its geometric center is the origin. Finally I want to save this new configuration in a pdb-file, so it is conserved like this. Do you have any suggestions? With kind regards Tobias Eilert

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save command
by Dougherty, Matthew T 11 Jan '16

11 Jan '16

The FILE pull down menu allows for "save" and "save as". The command "save" allows for two options: with or without a session_name. Without a session_name, a dialog box is presented and effectively I am doing the "save as" in the FILE menu at that point. With a session_name, it functions as a 'save as' without the dialog box. How do I create the same effect as FILE pull down menu "save", using the save command? Looking for a generic approach for any session, not knowing the file/session name apriori, & having to type the session name everytime. I suppose there is a python method to get the session filename & path, then build the command string. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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header intact
by maozhouhe 08 Jan '16

08 Jan '16

confirm 4cb1de59074527102f482c8970f4d33506347705

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Re: [Chimera-users] [chimera-dev] Volume Eraser: Recentering the eraser
by Tom Goddard 07 Jan '16

07 Jan '16

Hi Mohan, Here are a few more details about how to erase the density inside the capsid of a virus density map. The trick as you’ve seen is getting the sphere centered at the center of the virus and having the correct radius. Here’s how I do this. First I adjust the volume eraser sphere radius so it visually looks about the same radius as the outside of the virus map. Then I move the sphere with the mouse to try to center it on the virus. I rotate to look at it from different view angles and center with the mouse at each view direction. It helps if the radius of the sphere is set so that just a little bit of the density pokes through so you can visually see whether the same amount of density is poking through on all sides. Now I have the right centering and I try to get the radius I want. For this it helps to clip the map and sphere using menu Favorites / Side View and move the left vertical yellow line to the right to clip the models. I move the clip plane to cut through near the center of the virus, then adjust the sphere radius. In this view you can see the sphere size relative to the concentric layers of density. It helps here to make the sphere not transparent by clicking the color square in the Volume Eraser dialog and setting the A (opacity) channel to 1. I’ve attached a pickture. To do this in a more precise way I create a sphere and mask using it with commands shape sphere radius 240 center 0,0,0 coordinateSystem #0 color blue mask #0 #2 invert true This requires that the origin of the map is set to the center of the virus capsid. You can choose this center grid point using Volume Viewer menu Features / Coordinates setting the Origin Index. Tom > On Jan 7, 2016, at 9:38 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Hello Mohan, > If you read the Help for Volume Eraser (press the Help button on the dialog to see it), it explains how to move and resize the eraser sphere. Or, you can see this information on our website: > > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/voleras…> > > Basically you can set which mouse button will be used to move the sphere, and then use the mouse to move it to where you want, including with Shift to move in Z (toward or away from you). There isn’t a feature to automatically put it at the center of the capsid. > > For user questions, the better address is chimera-users(a)cgl.ucsf.edu (not this address chimera-dev, which is more for programming questions). > > 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 Jan 6, 2016, at 9:01 AM, Mohan Sudabattula <mk.sudabattula(a)gmail.com> wrote: >> >> Hello, >> >> My name is Mohan Sudabattula, I am fairly new at using Chimera so please excuse my lack of understanding the program. >> >> I am currently utilizing the Volume Eraser tool and am trying to employ it erase the internal structure of a viral capsid. Upon opening the Volume Eraser it always seems to orient itself to the "frontmost face of the current display region". This is problematic because it is now only partially erasing what I am needing to be erased. >> >> Instead I am looking to have it oriented so that it is in the center of my virus. Is there any way to reorient the eraser so that this may be the case? >> >> Thank you! >> Mohan Sudabattula >> > > > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev >

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Drawing shapes given coordinates
by Oliver Clarke 07 Jan '16

07 Jan '16

Dear Rebecca, I have used Elaine's suggestion before, and it works well, as in the following alias: alias ^pbond dist sel; setattr p label "" sel; setattr p drawMode 1 sel; setattr p radius 0.03 sel which places a thin black cylinder between two selected atoms. To make invisible dummy atoms at arbitrary coordinates, I would use the "mc" accelerator ("ac mc" on the command line), which places and selects a dummy atom at the center of rotation. So something like: cofr x1,y1,z1; ac mc; namesel atom1; cofr x2,y2,z2; ac mc; namesel atom2; sel atom1|atom2; pbond; vdwdefine 0.01 sel; transparency 100,a sel should work. Cheers, Oli. ------------------------------ Thank you! Theoretically if I was to create dummy atoms with coordinates at the locations where I want the cylinders to end, I could connect them with pseudobonds. I can easily shape my data that way, and if it doesn't work the BILD files will probably be fine. Thanks for the help! Cheers, Rebecca On 1/4/16, 5:20 PM, "Elaine Meng" <meng at cgl.ucsf.edu <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>> wrote: >*Hi Rebecca, *>*There are two approaches for adding cylinders independent of atomsŠ but I *>*don¹t know if either will be satisfactory: *>>*(1) ³shape cylinder² is command-line and doesn¹t require using atoms as *>*endpoints, but it doesn¹t allow specifying endpoint coordinates directly. *>* A cylinder is specified by only its center, height, radius, and a *>*rotation angle. I don¹t think it is easy to figure out what angle gives *>*the desired endpoint coordinates. (We¹ve discussed the need to improve *>*this, but it may be deferred to our next-generation software in *>*development.) *>*<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi> *>*mera_docs_UsersGuide_midas_shape.html-23cylinder&d=CwIFaQ&c=TzEZu9LIcihmW3 *>*7vx9Ah6w&r=Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH6akd *>*4eXf6HdP_BL9dt0gv_zz3oMdq8&s=9vZCIh2K2i-8UrGF7HkSZwZwT7CRFcS9RUZsHUsson4&e *>*= > *>>*(2) BILD-format input allows specifying endpoint coordinates of a *>*cylinder, but it is not a command. You generate a BILD text file *>*describing the objects and read it in to Chimera. BILD format is very *>*simple, however: *>*<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi> *>*mera_docs_UsersGuide_bild.html&d=CwIFaQ&c=TzEZu9LIcihmW37vx9Ah6w&r=Z2BqCMu *>*wlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH6akd4eXf6HdP_BL9dt0gv_ *>*zz3oMdq8&s=2A5wPT06BJ7QN1TDyA4kS36ILONzhA703a7xRpdnJKY&e= > *>>*The objects created with ³shape² are surface models, so you can change *>*their colors afterward. The BILD objects are not surface models and *>*cannot be recolored and do not work well with transparency. *>>*There are two approaches that depend on atoms: *>>*(1) pseudobonds can be created with the ³distance² command (or atom pairs *>*can be read in from a file with Pseudobond Reader), but pseudobonds *>*require atoms as endpoints. *>*<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi> *>*mera_docs_UsersGuide_midas_distance.html&d=CwIFaQ&c=TzEZu9LIcihmW37vx9Ah6w *>*&r=Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH6akd4eXf6HdP *>*_BL9dt0gv_zz3oMdq8&s=tUGhl0z5yTsTqr2tyEgexdraCTB8o2JtwjuJZTgMwvo&e= > *>*<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi> *>*mera_docs_ContributedSoftware_pbreader_pbreader.html&d=CwIFaQ&c=TzEZu9LIci *>*hmW37vx9Ah6w&r=Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH *>*6akd4eXf6HdP_BL9dt0gv_zz3oMdq8&s=nRvWQ2FPg5n33Obqd9Bee1ovSNmgCCdbaT1EH6Uc1 *>*I8&e= > *>>*(2) the ³define² command (or Axes/Planes/Centroids) tool will show *>*cylindrical axes that are best fits to specified sets of atoms. However, *>*there is currently little control over lengthŠ it is automatically *>*determined from the atomic coordinates. *>*<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi> *>*mera_docs_UsersGuide_midas_define.html&d=CwIFaQ&c=TzEZu9LIcihmW37vx9Ah6w&r *>*=Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH6akd4eXf6HdP_B *>*L9dt0gv_zz3oMdq8&s=t9I-WC_-VvEvmTfphtU3ey2GT0sMRiFtO62hFkRj7Rk&e= > *>>*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 Jan 4, 2016, at 12:09 PM, Rebecca Swett <Rebecca_Swett at vrtx.com <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>> *>>*wrote: *>>>>* Hi all, *>>* I'm trying to add some 3d shapes to a visualization. I was wondering if *>>*it would be possible to draw either a cylinder or tube given starting *>>*and ending coordinates rather than atom names/numbers or centroid? For *>>*example, if I had this coordinate pair: *>>* 6.17 1.10 -15.33 20.82 -0.70 -8.39 *>>>>* What would be the best way to go about drawing a line of some sort *>>*between those two points? I have dozens of pairs of coordinates so *>>*something command line would be ideal. *>>* Cheers, *>>* Rebecca *> This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you.

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Suggested Improvement of Command Line
by Eric Berg 06 Jan '16

06 Jan '16

Hello, I have noticed that when giving the command line a list of residue indexes using the "select" function, the inclusion of white space will cause an error (see attachment). This is technically a pretty small quibble, but it may be beneficial in these instances to include something to filter out white space prior to parsing. Eric

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volume eraser and imod isosurface
by Wouter Van Putte 06 Jan '16

06 Jan '16

Dear, I would like to use chimera for removing some densities manually of an isosurface generated with imod. I've loaded the map/model (.mod) and already used the function 'hide dust' to remove most of the noise. I now would like to use 'volume eraser' to remove the other noise manually. This however doesn't work, probably due to the file format (.mod). I thought saving in another file format would help, but it gave me errors when opening the file. How should I proceed? best wishes, Wouter

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Chimera and imod isosurface (*.mod files) and 'volume eraser'
by Wouter Van Putte 06 Jan '16

06 Jan '16

Dear, I would like to use chimera for removing some densities manually of an isosurface generated with imod. I've loaded the map/model (.mod) and already used the function 'hide dust' to remove most of the noise. I now would like to use 'volume eraser' to remove the other noise manually. This however doesn't work, probably due to the file format (.mod). I thought saving in another file format would help, but it gave me errors when opening the file. How should I proceed? best wishes, Wouter

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Drawing shapes given coordinates
by Rebecca Swett 05 Jan '16

05 Jan '16

Hi all, I'm trying to add some 3d shapes to a visualization. I was wondering if it would be possible to draw either a cylinder or tube given starting and ending coordinates rather than atom names/numbers or centroid? For example, if I had this coordinate pair: 6.17 1.10 -15.33 20.82 -0.70 -8.39 What would be the best way to go about drawing a line of some sort between those two points? I have dozens of pairs of coordinates so something command line would be ideal. Cheers, Rebecca This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you.

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Identify hinges and rigid groups using Morph Conformations?
by Oliver Clarke 04 Jan '16

04 Jan '16

Hi, I gather from reading the documentation for “Morph Conformations” (https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html) that Chimera identifies hinge regions and rigid groups as part of the procedure (as per http://nar.oxfordjournals.org/content/28/8/1665.long) Would it be possible to expose these to the user (or maybe this is already possible?), such that one can color/label the hinges and rigid entities as desired? This would be helpful for visual simplification of complex conformational changes. Cheers, Oliver.

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Include "perframe" command as action in Animation panel?
by Oliver Clarke 30 Dec '15

30 Dec '15

Hi, I really like the animation panel of chimera because it makes it incredibly easy to create a nice looking movie, but transitions are still a bit limited compared to what one can do in a script - e.g. smoothly transitioning from one contour level to another, moving along a chain and highlighting specific residues, etc. On the command line, it is easy to do this and a bunch of other iterative processes using the “perframe” command. Perhaps it might be worth considering inclusion (in ChimeraX presumably) of an equivalent of the “perframe" command as an action in the animation GUI (One could call it “Custom” or “Script” to avoid confusion), to enable mixing in code snippets into the animation GUI? It would only need to have a couple of parameters - the frame range, variable range, interval, and command to execute (with a checker to catch invalid syntax prior to execution). Alternatively/additionally, it would be nice to have the option to export the current animation setup as an editable script, to provide a starting point for a more complex movie, although I am not sure whether this is feasible given the way the animation tool incorporates scenes. Cheers, Oliver.

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HLS color adjustments?
by Oliver Clarke 30 Dec '15

30 Dec '15

Hi all, Suggestion for ChimeraX: Allow tweaking (not replacing) color of selection, to adjust hue, lightness or saturation of selection (which could contain multiple colors). This would be handy when creating duotone images, where one selection is one color and another selection is a lighter (or darker) version of the same color; Or for creating Goodsell-style images where carbons are one color and heavier elements are a darker version of the same color. In general this would also be useful in cases where you want to edit a color that is close to but not quite the desired one - currently, launching the color editor defaults the selection to black, and it can sometimes be difficult to locate the exact color one had previously, so a way to edit colors in place would be useful for this purpose. Another suggestion to consider - would it be possible to allow exporting to a format (perhaps SVG?) where both vector and bitmap information can be edited separately? Specifically, I’m envisioning a three-layer file, with a bitmap + text and lineart, where lineart would include pseudobonds and potentially silhouettes. This would allow easy adjustment of the thickness, style etc of silhouettes and pseudo bonds post-Chimera, and editing/reformatting of text labels. I am not sure how practical this is, but if it is feasible to implement eventually it would certainly be useful. Cheers, Oliver.

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Can Chimera specifically superimpose renamed atoms of a ligand ?
by Yogendra Ramtirtha 29 Dec '15

29 Dec '15

I have to detect the presence of a ligand in many PDB files. So I have renamed all the Carbon atoms of the "HETATM" entries in these PDB files and I have also renamed the Carbon atoms of the file with known ligand. Can I use Chimera to specifically superimpose these renamed atoms ? If yes, can you tell me how can I do this ? In general, can Chimera superimpose ligands in 2 PDB files ? Thank you

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SaveScene Error
by Alvaro Rossan De Brandão Prieto Da Silva 28 Dec '15

28 Dec '15

I can't save UCSF Chimera sessions with saved scenes. What should I do in order to circumscribe this error? My ReplyLog Error in after-models callback: KeyError: (-1, 0) File "C:\Program Files\Chimera 1.10.2\share\Animate\SceneState.py", line 1252, in modelsLookup mList = [ m for m in SimpleSession.modelMap[ref] See reply log for Python traceback. -- Dr. Álvaro Prieto, D.Sci PqC-IV *Biologia Molecular de Toxinas Animais* Laboratório de Genética Tel +55 11 26279721 Mob. +55 11 982227144 email alvaro.prieto(a)butantan.gov.br

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Fwd: Fit to segments
by Elaine Meng 24 Dec '15

24 Dec '15

Begin forwarded message: > From: Greg Pintilie <gregdp(a)gmail.com> > Subject: Re: [Chimera-users] Fit to segments > Date: December 24, 2015 at 9:38:59 AM PST > > […] that’s a good question… some comments below. > >> Begin forwarded message: >> >> From: Luca Pellegrini <lp212(a)cam.ac.uk> >> Subject: [Chimera-users] Fit to segments >> Date: December 18, 2015 at 4:07:08 AM PST >> To: chimera-users(a)cgl.ucsf.edu >> >> Hi, >> I am using ‘Fit to Segments’ to fit a crystal structure into the appropriate segment of an 18A EM map of a larger protein complex. The structure is one subunit of the complex. >> >> After initial manual alignment of the structure, fitting to the selected segment works well and produces what I believe is the correct orientation of the structure in the map. However, the fitting stats (Corr/At. Incl.) for the wrong hits are almost as good (within a few percent points), even though for some of them the structure is clearly misplaced in the segment. >> > > This can happen quite often especially at lower resolutions, so I’m not too surprised. Try looking at the Z-score as well. For more details see the “Docking Scores” section at http://ncmi.bcm.edu/ncmi/software/segger/docs. It like won’t be too high either in this case though. In such cases it’s often useful to argue that this is the correct fit using other experimental evidence. >> Can anyone please comment/advise on this? It looks like fitting and relative statistics are calculated relative to the entire map rather than the selected segment. I am using Chimera 1.10.1, build 40415. >> > > Yes, it is true the scores are calculated using the whole map. One way to use only the selected segment is to extract the densities for that segment first and then do the fitting procedure using that segment only.

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2dlab problem
by jrb53 24 Dec '15

24 Dec '15

Hello all, I am making a movie in Chimera and labelling the various proteins as they appear. For some reason I am having trouble with 2dlab If I write 2dlab create kvlab4 text “Voltage-gated potassium channel” size 48 style bold color blue xpos .04 ypos .9 I get the error Keyword 'potassium' doesn't match any known keywords Its like it doesn’t get that the quotes are even there and it sees the label as multiple command line arguments. I get the same error with single quotes. If I use one word labels, it works fine. Any idea? Or am I missing something simple? John

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Chimera User's guide for command ine usage
by Yogendra Ramtirtha 22 Dec '15

22 Dec '15

I would be prefer me a PDF version of the user's guide to run commands through the command line Is the Chimera home page down ? Thank you, Yogendra

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Re: [Chimera-users] multi GPU rendering
by Tom Goddard 18 Dec '15

18 Dec '15

Hi Ben, One more bit of useful info regarding rendering large maps with solid style. The “perpendicular to view” projection mode is not the same as the mode “x, y, or z planes”. The perpendicular mode uses an OpenGL graphics 3d texture and slices the map perpendicular to the viewing direction and uses trilinear interpolation on the graphics card. The x,y,z planes mode uses OpenGL 2d textures perpendicular to one of the x, y, or z axes. While the perpendicular mode seems better the trouble is that 3d textures are generally not used in video games, so this is a very obscure graphics feature that may not be well optimized in the graphics driver, it may be slow (e.g. be done with no hardware acceleration), it may have limits to the size of the volume. On the other hand 2d textures are used in every video game and are optimized to the hilt — they are what is used to put color patterns on any surface. With some graphics cards and drivers the 3d textures will work as well as 2d textures, particularly the high-end cards, but you will only find this out by trial and error. The default “auto” projection mode never uses perpendicular to view because it is a bad choice on many low-end graphics cards. Tom > On Dec 18, 2015, at 1:38 AM, Benoît Zuber <benoit.zuber(a)ana.unibe.ch> wrote: > > Hi Tom > > Thanks for the additional info. I didn't know about the projection mode option. I was wondering before why under some conditions z planes were super thin when viewed perpendicular to z axis and why sometimes the gaps were filled. This was a bit problematic for some data sets where we actually mainly look in this orientation. Now using projection mode "perpendicular to view" instead of auto forces the planes to be rendered thick. great. > > watching nvidia-smi outputs confirms that only one GPU is used for rendering. Watching is also very useful to know how much the volume must be cropped before switching to the next step size without saturating the GPU memory. > Now I got it, if we want to watch bigger volumes, we just need to get a top geforce with 12 Gb instead of 3 Gb (Santa if you can hear me) > > Cheers > Ben > On 18.12.2015 01:02, Tom Goddard wrote: >> Hi Ben, >> >> From what I read both Nvidia SLI and AMD CrossFire for using multiple graphics cards both require hardware jumpers between the cards. >> >> The Chimera solid benchmark makes a cube shaped volume and times rendering it. A 1024 cubed volume takes 2 Gbytes on the graphics card because each grid point takes two bytes, one for the gray level and one for the transparency. An important thing to know about the solid rendering with really big volumes is that by default when you rotate it will make up to 3 full copies of the data — so up to 6 Gbytes in the benchmark example. It makes a copy when you rotate to viewing a different face of the cube. It then treats it as slices parallel to that face. So for a cube shaped map you will see a freeze when you rotate beyond 45 degrees. For non-cube maps I think the rule is it uses the face of the box that is showing the most area. For big volumes if you don’t care so much about looking at it along x and y directions then you might change projection mode the Features / Solid Rendering Options from “auto” to “z planes”. You probably want to know what auto does — it uses z planes if the volume is a thin slab, but "x, y, or z planes” if it is not a thin slab. Thin means x or y at least 4 times larger than z (I pressed Help on Volume Viewer dialog to learn that bit, even though I wrote the code). Once “projection mode” is “z plane” then you won’t get any of the extra copies. >> >> For really big volumes I could probably the transparency and use one byte per grid point. I could just scale transparency with intensity (which is what volume viewer does anyways). That makes the data of the graphics card half as big so it would be possible to show larger maps. I’ll try that in our next generation ChimeraX software — would be a nice improvement. >> >> Back to using multiple graphics cards — I don’t think the driver can possibly split the volume solid rendering data (2d OpenGL textures) — it will try to put all of it on both graphics cards — so you won’t get more memory by using more cards. >> >> Tom >> >> >>> On Dec 17, 2015, at 2:39 PM, < <mailto:benoit.zuber@ana.unibe.ch>benoit.zuber(a)ana.unibe.ch <mailto:benoit.zuber@ana.unibe.ch>> <benoit.zuber(a)ana.unibe.ch <mailto:benoit.zuber@ana.unibe.ch>> wrote: >>> >>> Hi Tom >>> >>> Thanks for your thorough reply. I am not in front of the workstation but I’ll use the gpu activity monitor to guess if chimera is using the three GPUs. I have some doubts that the OS / openGL driver is distributing rendering work on each gpu in our configuration. I think that for the SLI to work you need to wire both cards together, which is not the case in our workstation. But anyway, I’ll check activity. >>> >>> The rendering case I was referring to consists of solid rendering. I never try to render the full dataset at full resolution as we are talking about datasets of around 50 Gb. I use a very high step to select a sub region, then I gradually decrease step size and fine tune the contrast transfer function. When I am happy I render at step 2 or step 1, depending on the sub region size. Clearly there is time needed to read data from disk; when reading is done the program still computes stuff for a few seconds. Then I can rotate, zoom, …, the volume. If the sub region is not too large then it is super smooth. But if I select a too large sub volume, then I can rotate some degrees, then it freezes for a while, then it is smooth again, etc. So I guess it corresponds to your description of the problem. >>> >>> I took a look at the benchmark. That’s very useful! Obviously I am not going to get better performance with a quadro (at least one in the benchmark: All quadro except K4000 get worse scores for solid rendering than the GTX 780 Ti. K4000 actually got the same score as the 780 Ti. Only with a GTX Titan would I get a nearly 2x improvement, which makes sense since this card has 2x the memory of the 780 Ti (6Gb vs 3Gb). The GTX Titan X is not in the benchmark yet but it should be even better as it has 12 Gb Ram. Possibly the quadro k6000, which is not in the benchmark either, could have similar or better performance as this one (it also has 12 Gb RAM) but … it costs about 4 times more than a Titan X. Sad that only the quadro work for stereo under linux (but for that we bought a once state of the art quadro on eBay for 150$ and installed it on another PC :-) >>> >>> Cheers >>> Ben >>> >>> De : Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> >>> Date : jeudi, 17 décembre 2015 19:22 >>> À : Benoit Zuber <benoit.zuber(a)ana.unibe.ch <mailto:benoit.zuber@ana.unibe.ch>> >>> Cc : chimera users list <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> >>> Objet : Re: [Chimera-users] multi GPU rendering >>> >>>> Hi Ben, >>>> >>>> I haven’t tried Chimera with 2 or more graphics cards working together. I don’t know if it is likely to improve rendering speed. I don’t think applications need any special support to use multiple cards — the system graphics driver distributes the work across 2 or more cards. With Nvidia cards this technology is called SLI and with AMD cards it is called CrossFire. From what I understand they do thing like have each of 2 cards render every other frame — since the graphics are pipelined the current frame and next frame could be rendered simultaneously possibly doubling the speed. I have my doubts that this will improve Chimera rendering speed for large density maps. I think slow rendering of maps in solid (grayscale) style typically happens in Chimera when the map data doesn’t fit on the graphics card, so every frame it has to transfer all the data to the card — the performance plummets once you get a map that big. If the data does fit on the graphics card, it usually renders at full frame rate (60 frames per second), although that isn’t true of all graphics cards. This all relates to the speed rotating the model. When you first load a big map it can take a long time because disk drive speed is slow — a solid state drive helps speed this up. If you explain exactly the case where you see slow rendering I can perhaps advise. >>>> >>>> In general I think the Geforce cards perform better (fewer bugs, faster speed) than the Quadro cards, and would only recommend Quadro if you use stereoscopic display with shutter glasses. Here are Chimera benchmarks for a range of graphics cards: >>>> >>>> <http://plato.cgl.ucsf.edu/trac/chimera/wiki/benchmarks>http://plato.cgl.ucsf.edu/trac/chimera/wiki/benchmarks <http://plato.cgl.ucsf.edu/trac/chimera/wiki/benchmarks> >>>> >>>> Tom >>>> >>>> >>>> >>>>> On Dec 17, 2015, at 5:28 AM, wrote: >>>>> >>>>> Hi >>>>> >>>>> Can chimera make use of more than one GPU for 3D rendering? We have 3 Geforce GTX 780 Ti (mainly used for number crunching) on a particular workstation and would be interested to make full use of them for rendering tomograms or serial block face imaging data. >>>>> >>>>> Another question: has anyone done benchmark comparison for 3D rendering in Chimera between a top of the line Geforce GTX card and a top Quadro card? Is there a strong improvement with the Quadro, which might justify the price gap? >>>>> >>>>> Thanks >>>>> Ben >>>>> -- >>>>> Prof. Benoît Zuber >>>>> Institute of Anatomy >>>>> University of Bern >>>>> Baltzerstrasse 2 >>>>> Postfach 922 >>>>> 3000 Bern 9 >>>>> Switzerland >>>>> <mailto:benoit.zuber@ana.unibe.ch>benoit.zuber(a)ana.unibe.ch <mailto:benoit.zuber@ana.unibe.ch> >>>>> +41 31 631 84 40 >>>>> <http://www.ana.unibe.ch/research/experimental_morphology/index_eng.html>http://www.ana.unibe.ch/research/experimental_morphology/index_eng.html <http://www.ana.unibe.ch/research/experimental_morphology/index_eng.html>_______________________________________________ >>>>> 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> >>>> >> >

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[MGMS-DS]: Molecular Modelling Workshop April 4-6, 2016 in Erlangen, Germany
by Harald Lanig 18 Dec '15

18 Dec '15

Dear list subscribers, I am very happy to announce that the 30th Molecular Modelling Workshop in Erlangen takes place on April, Monday 4th to Wednesday 6th, 2016. Starting on Monday after lunch should allow to avoid travelling on weekend and keeping the expenses at a minimum. This time, the scientific program of the meeting is conducted by Prof. Tim Clark, Technical Director of the Computer-Chemistry-Center in Erlangen, Germany. As usual, the workshop is organised by the German Section of the Molecular Graphics and Modelling Society. ####### Plenary Speakers ####### Over the last few decades computational chemistry, molecular modelling, and chemoinformatics became more and more an integral part of research in various areas of the chemical industry and at universities. A lot of new tools and new approaches together with a huge increase in computer power facilitate this development. We are very pleased to announce Prof. Brian Shoichet University of California, San Francisco, USA and Dr. Marcus A. Neumann Avant-Garde Materials Simulation Deutschland GmbH giving plenary presentations as leading experts their respective fields. ####### Poster and Lecture Awards ####### As in the past years, there will be two poster awards of EUR 100 each and three lecture awards for the best oral presentations: 1st Winner: Travel bursary to attend the Young Modeller's Forum in London, UK, plus a speaker slot option at YMF 2016 (travel expenses are reimbursed up to EUR 500) 2nd Winner: EUR 200 travel expenses reimbursement 3rd Winner: EUR 100 travel expenses reimbursement Only undergraduate and graduate research students qualify for the poster and lecture awards. ####### Registration ####### As every year, an interesting and successful workshop depends on your contributions! Therefore let me invite you to submit talks and/or poster titles via the registration form accessible on the workshop website http://mmws2016.mgms-ds.de/index.php?m=register This website will provide all necessary information about the meeting! The deadline for all submissions is February 26th, 2016. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Please note that the week before the 30th Molecular Modelling Workshop, on Wednesday March 30th to Friday April 1st 2016, a Symposium Commemorating the Life and Work of Paul von Ragué Schleyer will take place at the same venue. If you are interested in this meeting, please follow the link http://schleyersymposium.mgms-ds.de for further information. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ We are looking forward to meeting you in Erlangen soon! -Harald Lanig Chairman of the MGMS-DS e.V. http://www.mgms-ds.de -- ------------------------------------------------------------------------ PD Dr. Harald Lanig Universitaet Erlangen/Nuernberg Zentralinstitut fuer Scientific Computing (ZISC) Geschaeftsfuehrer Martensstrasse 5a, 91058 Erlangen Fon +49 9131-85 20781 harald.lanig(a)fau.de Fax +49 9131-85 20785 http://www.zisc.uni-erlangen.de ------------------------------------------------------------------------

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Fit to segments
by Luca Pellegrini 18 Dec '15

18 Dec '15

Hi, I am using ‘Fit to Segments’ to fit a crystal structure into the appropriate segment of an 18A EM map of a larger protein complex. The structure is one subunit of the complex. After initial manual alignment of the structure, fitting to the selected segment works well and produces what I believe is the correct orientation of the structure in the map. However, the fitting stats (Corr/At. Incl.) for the wrong hits are almost as good (within a few percent points), even though for some of them the structure is clearly misplaced in the segment. Can anyone please comment/advise on this? It looks like fitting and relative statistics are calculated relative to the entire map rather than the selected segment. I am using Chimera 1.10.1, build 40415. Best wishes, Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA UK Email: lp212(a)cam.ac.uk Phone: 0044-1223-760469

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multi GPU rendering
by benoit.zuber＠ana.unibe.ch 17 Dec '15

17 Dec '15

Hi Can chimera make use of more than one GPU for 3D rendering? We have 3 Geforce GTX 780 Ti (mainly used for number crunching) on a particular workstation and would be interested to make full use of them for rendering tomograms or serial block face imaging data. Another question: has anyone done benchmark comparison for 3D rendering in Chimera between a top of the line Geforce GTX card and a top Quadro card? Is there a strong improvement with the Quadro, which might justify the price gap? Thanks Ben -- Prof. Benoît Zuber Institute of Anatomy University of Bern Baltzerstrasse 2 Postfach 922 3000 Bern 9 Switzerland benoit.zuber(a)ana.unibe.ch +41 31 631 84 40 http://www.ana.unibe.ch/research/experimental_morphology/index_eng.html

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dashed distance line
by A G Szabo 16 Dec '15

16 Dec '15

I recently used the distance feature to determine the distance between two alpha carbons in a protein. The view on the image showed a dashed line and the distance in Angstroms. I had managed to change the color of the line and numbers to a dark green, and thicker line. So I then snipped the image and put it in power point. Figure below: As you can see the line and numbers are there. Now look at the Jpeg file that is attached. The dashed line does not show up. No big deal but perhaps there is a setting that I missed when I saved the image. Thank you. Arthur G. Szabo Professor Emeritus Chemistry and Biochemistry Wilfrid Laurier University Waterloo Canada

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solid threshold in a python script
by benoit.zuber＠ana.unibe.ch 14 Dec '15

14 Dec '15

Hello I would like to add several threshold markers for volume solid rendering. I would like to do it in a script. I guess the only way is to do it through a python script. I tried modifying the solid_levels and solid_colors attributes of the active volume but I could not find how I can then get the depending volume attributes, such as transfer_function and the gui (both rendered volume and the volume viewer dialog) to be correctly updated. Could anyone please give me a few pointers? Thanks in advance Ben -- Prof. Benoît Zuber Institute of Anatomy University of Bern Baltzerstrasse 2<x-apple-data-detectors://1> Postfach 922<x-apple-data-detectors://2/0> 3000 Bern<x-apple-data-detectors://2/0> 9 Switzerland benoit.zuber(a)ana.unibe.ch<mailto:benoit.zuber@ana.unibe.ch> +41 31 631 84 40<tel:+41%2031%20631%2084%2040> http://www.ana.unibe.ch/research/experimental_morphology/index_eng.html

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on preset interactive 1 color
by Smith Liu 12 Dec '15

12 Dec '15

Dear All, If by chimera we select preset interactive 1 for a protein complex, each chain will take a different color. As for when we describe the corresponding colors in a paper we need to know the names of each color by the chimera preset interactive 1 function, and the colors by this function are usualy very close to each other, will you please introduce to me the color names colored by the function preset interactive 1? Smith

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Movie Making in Chimera
by Florian Drechsler 10 Dec '15

10 Dec '15

Dear Chimera Support Team, I have a question regarding movie making in Chimera: I would like to be able to record a movie, based on a chimera script, and have exact frame-wise control over what is recorded. Chimera seems to make a funny distinction between "internal trajectory frames" and "movie frames" which I don't get. I would like a one-to-one correspondence between these, no interpolation or anything like that. More precisely, I would like to be able to do the following, in strict sequential order: - Load some models, - rotate one of the models, - move one of the models, - capture a movie frame of the resulting configuration, and again - rotate one of the models, - move one of the models, - capture a movie frame of the resulting configuration, etc. I have tried using "perframe" commands, where each perframe operation comprises a "move" and a "turn" command, and has the option "frames 1". Still, I don't get exactly what I want: the resulting movie doesn't consist of the number of frames I'd expect - movie encoding seems to start before all commands have actually been executed. I can see a message saying that the movie has been finished, while things are still moving. I've provided a code snippet below. Moreover, rather than using "perframe", surely there must be a more elegant and natural way of enforcing sequential execution of commands, as one would expect from any normal programming language. Thank you very much in advance for your help, Best regards, Florian Drechsler -------------------------- Florian Drechsler Universität Ulm Institut für Biophysik Albert-Einstein-Allee 11 D-89081 Ulm ------------------------ ============================================================== # This is a command file to be opened from UCSF Chimera. # It loads several molecules from PDB files, and arranges them in docked conformations. # These conformations are the result of a Bayesian inference carried out by FastNPS. # Upon execution of this file, Chimera will generate a movie clip showing a set of docked # conformations, in the manner of a flip-book. # This file can be edited if any particular colour or lighting options etc. are desired. # --- load PDBs --- open ./2waq.pdb open ./1D3U_movedtoCentrePol_noTFB.pdb ################################################################################## ##### E d i t a b l e s e c t i o n for custom viewing preferences ##### ##### (colour, lighting, background, etc.) ##### ################################################################################## set bg_color white color dark slate gray #0:.A-Q 2dlabel create title text "Samples of configurations of docking scenario, 2WAQ vs. 1D3U" xpos 0.04 ypos 0.92 color black 2dlabel create sub text "Motion does not represent dynamics" size 12 xpos 0.04 ypos 0.88 color black ################################################################################## ##### E n d o f e d i t a b l e s e c t i o n ##### ################################################################################## move x 14.5577 model #1 move y 10.7525 model #1 move z 13.1320 model #1 windowsize 800 600 scale 0.8 movie record supersample 3 move 0.9432,3.3367,-3.9733 model #1 wait move -3.1264,-2.5812,5.6072 model #1 wait move -2.9523,2.8959,-3.9907 model #1 wait move -14.0968,0.5720,-12.9560 model #1 perframe "move -14.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframeperframe "move -14.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move -14.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move -14.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move -14.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe wait move 8.4475,0.1,0.1 model #1 perframe "move 2.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move 2.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move 2.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move 2.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move 2.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move 2.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move 2.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move 2.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe perframe "move 2.0968,0.5720,-12.9560 model #1; turn y 1 model #0;" frames 1 ~perframe wait move 8.4475,4.5142,16.4771 model #1 turn z 2 wait move -12.9187,-0.7126,-7.8443 model #1 turn z 2 wait move 9.5982,-3.2342,8.4843 model #1 turn z 2 wait move 3.2604,3.3466,-4.2558 model #1 turn z 2 wait move 0.5383,-1.8787,5.0346 model #1 turn z 2 wait move -0.6887,1.1472,-2.6070 model #1 turn z 2 wait move -0.0759,-1.7268,1.1365 model #1 turn z 2 wait move -3.1444,0.7922,-1.0015 model #1 turn z 2 wait move 5.2841,0.0361,0.6118 model #1 turn z 2 wait movie encode docking.mp4 bitrate 10000 framerate 60

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multi protein complexes
by A G Szabo 09 Dec '15

09 Dec '15

I am working with a protein PDB 4KHZ. It is a recent PDB deposition of the maltose transporter system. It is a multisubunit protein complex. There are five separate chains that come together. I know how to select and visualize each of them or in pairs or whatever. Two of the subunits have a maltose substrate bound within their interior. I know how to visualize the maltose molecules using the Select menu. When I go to the Select menu, open Residues - click on GLC (Glucose) all of the maltose molecules become visible in both proteins. Is it possible somehow to visualize only one of the maltose molecules in one of the proteins in this case the maltose in chain E. - and not have the maltose in G or F visualized. Thank you Arthur G. Szabo Professor Emeritus Chemistry and Biochemistry. Wilfrid Laurier University.

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Re: [Chimera-users] Save the map after hide dust
by Tom Goddard 08 Dec '15

08 Dec '15

Hi Gary, Good to hear from you. The hide dust feature does not change the density map, it only hides the small connected surface pieces. You could set the map grid points to zero inside the dust blobs with the mask command. But first you need to be able to show only the dust and there is no command to do that. I've attached a Python script that does that. You select the map surface (ctrl-click) that you have done hide dust on, then open the surfinvert.py script to show only the dust. Then use the mask command mask #0 sel invert true to mask the density map (#0) to the selected surface (dust blobs only shown) and invert, since you want to keep everything outside the dust blobs, not everything inside the dust blobs. I tried it, works. But if you lower the threshold on the new map then of course you see more dust. Tom The surfinvert.py script is also on the Chimera Python scripts page http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts> > On Dec 8, 2015, at 5:05 PM, Gang (Gary) Ren wrote: > > Hi Tom, > > I like the density map after hide density map, is there any way to save the > density map after dust hide? Every time I save the density map, it saved the > original map instead of density map after hidden dust. > > Thanks a lot > Gary > > > >

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subregion selection of a map
by Anindito Sen 08 Dec '15

08 Dec '15

Dear All, Is there a simple way that I can select a portion of a map using 'subregion selection' option where I can change the orientation of box (used for selection). Thanks Andy

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Sequential stereo problems in Chimera in Mac after updating to OSX EL Capitan
by Engelhardt, Peter 08 Dec '15

08 Dec '15

Hi, No sequential stereo is working in Chimera after updating of our Macs to OS X El Capitan - 10.11.1 in the CRTs linked to MacPros Error remarks: - unable to turn on stereo viewing - "Unable to find hardware stereo support ... " (see attachment). This problem has not appeared in with earlier OSX updates! We hope this problem will be fixed soon. Cheers Peter Peter Engelhardt, PhD, docent Adjunct Professor in Molecular Genetics Unit of Molecular Electron Tomography Nanomicroscopy Center (NMC), Department of Applied Physics Aalto University, School of Science and Technology, Puumiehenkuja 2, FI02150 Espoo Finland Department of Pathology Haartman Institute P.O.Box 21 (Haartmaninkatu 3) FIN-00014 University of Helsinki, Finland Email: Peter.Engelhardt(a)Helsinki.Fi Email: Peter.Engelhardt(a)Aalto.Fi URL: http://www.lce.hut.fi/~engelhar/ Mobil: +358-400193342 Home address: Lindstedstvägen 1 B 7 FIN-02700 Grankulla, Finland Home Tel: +358-505113192 ________________________________________ From: chimera-users-bounces(a)cgl.ucsf.edu <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of chimera-users-request(a)cgl.ucsf.edu <chimera-users-request(a)cgl.ucsf.edu> Sent: Monday, November 30, 2015 10:00 PM To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 151, Issue 35 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. inserting missing residue (Francesco Pietra) ---------------------------------------------------------------------- Message: 1 Date: Mon, 30 Nov 2015 19:40:50 +0100 From: Francesco Pietra <chiendarret(a)gmail.com> To: chimera <chimera-users(a)cgl.ucsf.edu> Subject: [Chimera-users] inserting missing residue Message-ID: <CAEv0nmtYfsQJBkbzkypX+uzqbYU7EMLhFZrybVhzj5W1hdM_OQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi: II would like to insert a single non-terminal missing amino acid in a big peptide. By using MODELLER with CHIMERA, I don't find any option for NOT modeling loops. Just inserting the missing residue without moving the adjacent residues. In the sequence that appears by invoking modeling, the missing residue is not marked in any way, the sequence just continues as if no non-terminal residue were missing. thanks francesco pietra

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Copy the Rotation matrix and translation to the third image
by Morris, Kyle 08 Dec '15

08 Dec '15

Peggy, Tom graciously answers enough of my requests, so I can take some of the slack from him here, I asked this recently (Re: [Chimera-users] Volume transformation based on Phenix symmetry operators). You can use the ‘matrixset command. Save your 4x3 matrix to a text file with a header ‘Model 2.0’ then in chimera use the following: setmatrix /path/to/matrix/text/file This will translate and rotate model #2 according to the matrix in the file you saved from the reply log. This function is documented here http://www.rbvi.ucsf.edu/home/meng/docs/UsersGuide/midas/matrixset.html. Have fun! Best, Kyle Date: Tue, 8 Dec 2015 16:48:56 +0800 From: ??? <peggyschsu(a)gate.sinica.edu.tw<mailto:peggyschsu@gate.sinica.edu.tw>> To: <chimera-users(a)cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Subject: [Chimera-users] Copy the Rotation matrix and translation to the third image Message-ID: <009701d13195$45ce4850$d16ad8f0$(a)gate.sinica.edu.tw<mailto:009701d13195$45ce4850$d16ad8f0$@gate.sinica.edu.tw>> Content-Type: text/plain; charset="big5" Dear All, Here I had fitted two images with the function ?Fit in Map? and gotten the rotation matrix and translation value from the reply log. Could anyone help me to apply the same matrix and rotation to the third image? Thank you for your help! Sincerely, Peggy -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20151208/7d37…> -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: application/octet-stream Size: 41241 bytes Desc: not available URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20151208/7d37…> ------------------------------

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Cubic vop zone boxes
by Morris, Kyle 08 Dec '15

08 Dec '15

Hi Chimera team and users, I am cutting out multiple sub-volumes from a much larger volume (#0) with fitted PDB co-ordinates (#1-n) using a script, but having trouble making the final sub-volumes cubic. At present I am using cutting out sub-volumes using '$ vop zone #0 #1 10 minimalBounds true’ to make the sub-volume more manageable. I am aware of the previous questions posted at http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-April/010942.html for reducing a volume size and the trick at http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-April/006208.html for expanding a volume. Is there however a way to make the volume cubic at the vop zone stage or a one liner command to expand a box after cutting with minimalBounds so that this can be efficiently scripted? Thanks for your help! Kyle

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Copy the Rotation matrix and translation to the third image
by 許紹君 08 Dec '15

08 Dec '15

Dear All, Here I had fitted two images with the function “Fit in Map” and gotten the rotation matrix and translation value from the reply log. Could anyone help me to apply the same matrix and rotation to the third image? Thank you for your help! Sincerely, Peggy

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Edge lengths of virus particles
by vamsee 07 Dec '15

07 Dec '15

Hello Elaine, I am trying to find the edge lengths of virus particles using Chimera. The method I came up with is to 1. Create an icosahedron with the diameter of the virus. 2. Create two atoms that sit on adjacent vertices of the icosahedron 3. Measure the distance between the two atoms But this method gives me the edge length of the icosahedron and not the virus itself. Is it possible to get the edge lengths of the actual virus without having to go through this process? Thank you Vamsee

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Surface-display option
by Puthiyaveetil, Sujith 07 Dec '15

07 Dec '15

Hi Chimera developer, I encounter a problem with surface calculation/display when using the biological assembly (dimer) of 1Q90. The monomer on its own, as in pdb file 1Q90, displays the surface with no problem. I have tried the "split" command without success on the biological assembly. Also tried changing parameters to no effect. Would you please help. Regards, Sujith Sujith Puthiyaveetil Postdoctoral research associate Institute of Biological Chemistry Washington State University Pullman, WA 99164. Phone: +1 509-715-7435

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Re: [Chimera-users] helices
by Elaine Meng 07 Dec '15

07 Dec '15

Hi Arthur, There isn’t anything in the menu to do that, but it can be done with commands or in the Selection Inspector. I’ll describe one way. When you show ball-and-stick, the balls are at some fraction of the VDW radii. When you show spheres, it is the full VDW radii. You could change the VDW radii, but probably a better method is to show ball-and-stick but change what fraction they are of the VDW radii. The default is 0.25. To change it you could use a command something like: setattr m ballScale 0.5 That would make ball-and-stick balls half the radius of the spheres. Of course, you could try other values and just see what you like. The “m” is because this setting is for the whole molecule model; you can’t have different values for different atoms in the same model. You can show the command line from the Favorites menu. You can also make sticks fatter and thinner in a similar way, with stickScale (default 1.0). 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 Nov 18, 2015, at 2:25 PM, A G Szabo <agszabo(a)bell.net> wrote: > Elaine > > But now I have another question that is related to the one I managed to > figure out. > > When I highlight an amino acid residue on a structure I know how to > visualize the amino acid as a ball and stick structure. I also know how to > have the residue shown as spheres. Except the Spheres are way too large. > > Is there a way in which I can reduce the size of the spheres? > > I couldn't find anything obvious in the Tools menu. > > Thank you > > Arthur G. Szabo

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(hopefully) simple rendering question
by Lybrand, Terry P. 03 Dec '15

03 Dec '15

Hello, I am looking for suggestions from the CHIMERA developers and users’ community to address a rendering problem I have. I have computed electric field data for protein ligand binding sites (wt and related mutants) and would like to render this field data as a collection of vectors, superimposed over a nice rendering of the binding site structures. The field results are from a series of QM/MM calculations we have performed, and are in a simple ASCII format: cartesian coordinates for N grid points, followed by cartesian coordinates of the N field vectors that originate from the corresponding grid points. I’ve debated whether I might be able to subvert the PseudoBond reader to somehow process these data, but still don’t have an easy option to display each field vector as a short arrow. Note that I don’t want to render the electric field data as a set of continuous color-coded field lines. That is easy in any number of molecular graphics programs. I know that rendering fields as a collection of vectors (arrows) is “old-fashioned”, but in this case we are convinced the old-fashioned render is a more effective way to communicate our results. Thanks in advance for any suggestions. Terry L. P.S. Greetings to all my former colleagues at UCSF. ++++++++++++++++++++++++++++++++++++++++++++ Terry P. Lybrand Prof. of Chemistry - College of Arts & Science Professor of Pharmacology - School of Medicine Vanderbilt University Center for Structural Biology 5-154C BioSciences/MRB III Nashville, TN 37232-8725 Telephone: 615-343-1247 Fax: 615-936-2211 e-mail: terry.p.lybrand(a)vanderbilt.edu<mailto:terry.p.lybrand@vanderbilt.edu> WWW: http://structbio.vanderbilt.edu/lybrand

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color actions on toolbar
by Julian von der Ecken 02 Dec '15

02 Dec '15

Hi, I use Chimera extensively and really appreciate its functionality! I work with "Color Actions” all the time and it would be so great to have it on the toolbar and not only the “Color Editor”. If you could incorporate it to the next release or let me know how to set it (I do not see it in "Favorites-Add to Favorites/Toolbar”)? Thanks in advanced Julian ————————————————————————————————— Julian von der Ecken Max-Planck-Institute of Molecular Physiology Department of Structural Biochemistry Otto-Hahn-Str. 11 44227 Dortmund, Germany room: B2.27 tel: (+49) (0)231 133-2307 e-mail: julian.von-der-ecken(a)mpi-dortmund.mpg.de lab: http://www.raunser-lab.de institute: http://www.mpi-dortmund.mpg.de

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Write a PDB with Python API
by Jaime Rodríguez-Guerra Pedregal 02 Dec '15

02 Dec '15

Hi again! So in my quest to use OpenMM from Chimera, my first proof-of-concept attempts consist of using a PDB file as intermediate to convert chimera.Molecule objects to OpenMM Topologies (using openmm.app.PDBFile loader). While not ideal yet, it'd be convenient to use StringIO() as a memory file, and I have been more or less successful. This is my strategy: memfile = StringIO() m = chimera.openModels.list() chimera.pdbWrite(m, m[0].openState.xform, memfile) memfile.seek(0) # pass memfile to openmm.app.PDBFile and do OpenMM stuff memfile.close() It works, but some residues are not properly recognised... I dumped the converted PDB to an actual file and saw that the problematic residue (an ARG) is totally messed up! I've attached the results: original file is the mol2, the converted one is the pdb, and also a Chimera session with both superimposed. What's the recommended method to convert a chimera.Molecule to a PDB file (if possible, in-memory) with Chimera Python API? Thanks a lot!

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