- Chimera-users - RBVI Mailing Lists

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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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