August 2020 - ChimeraX-users - RBVI Mailing Lists

Surface dust command in the .cxc script
by 李泽 24 Feb '25

24 Feb '25

Hi all: I'm trying to use the .cxc script to run the software, I found that the "surface dust" command has never been executed in it. Have anyone met the same problem? Any suggestions. Thank you all. Best, Ze

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Get color code of a custom color
by Ahmad Khalifa 11 Feb '25

11 Feb '25

I created a custom color that I want to use in a different session. is there a way to do that besides trying to match colors by eye? Regards.

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Double and Triple Bond Stick Style
by Smith, Chase 05 Feb '25

05 Feb '25

Dear ChimeraX, I was just wondering why there is no way to represent a double or triple bond in either the ligands or the protein amino acids when viewing as a Stick or Ball-and-Stick representation? I sometimes use Chimera or ChimeraX to make visuals for my lectures, and the students often have difficulty in understanding due to the absence of the multiple bonds. I would love to have the ability to represent the double or triple bonds with multiple lines between the atoms. Thank you, Chase Smith ... ChaseSmith, PhD Chair, Department of Pharmaceutical Sciences & Associate Professor of Medicinal Chemistry School of Pharmacy MCPHS University 19 Foster Street | WorcesterMA01608 T 508.373.5717F 508.890.5618C 978.855.7203 chase.smith(a)mcphs.edu www.mcphs.edu MCPHS University Confidentiality Note: This e-mail, and any attachment to it, is intended to be confidential and might be legally privileged. It is intended solely for the use of the addressee. If you are not the intended recipient, you are hereby notified that reading, copying, disseminating or distributing this email is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.

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Re: [chimerax-users] [Chimera-users] color by zone in chimeraX
by Elaine Meng 20 Nov '20

20 Nov '20

Hi Pranav, I’m Cc'ing the chimerax-users(a)cgl.ucsf.edu list (recommended for ChimeraX questions). I believe the problem is that when coloring the chains you are using “target c” which means to color only cartoons, whereas coloring by zone uses the atom colors. Since you only colored the cartoons, the atoms probably still had heteroatom color-coding. If you use “target ac” instead (even if the atoms aren’t shown), then as long as the color zone distance is big enough, I think you will get the color zones you expect. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 20, 2019, at 10:54 AM, Pranav Shah <p.shah.lab(a)gmail.com> wrote: > > Hi Elaine and Co., > > I am trying to color a virus map with the relevant pdb file, the > series of commands I am running are as follows, > open virus.mrc > open virus.pdb > color /A plum target c > color /B lightgreen target c > color /C dodger blue target c > color zone #1 near #2 dist 3 > However, the resultant surface is rendered in splotches of red and > blue, which leads me to think the it is coloring the surface using > atom type. Could you tell me how I can get Chimera X to color the > surface using the colors of the chains only? FYI, color by zone works > flawlessly in chimera. > > Cheers, > Pranav

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Center of cube in mrc
by Luis José Castillo Valverde 24 Sep '20

24 Sep '20

Hello, I want to move a mrc near another mrc from terminal controlled, the problem is that I don't know how ChimeraX defines the center point of movement when loading a mrc file. So I wanted to know if you can explain to me that ChimeraX defines the X, Y, Z coordinates in which it will load the center of the cube? Best regards, Luis -- Luis José Castillo Valverde Ingeniero en Computación, TEC Costa Rica Estudiante de maestría (MSc) académica en Computación, TEC Costa Rica Telegram: @LCastillo98 LinkedIn: luisjosecastillo98

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Re: [chimerax-users] [Chimera-users] User-defined graphics in chimera: NMR tensor plotting
by Tom Goddard 31 Aug '20

31 Aug '20

Hi Albert, Not sure if you are talking about using a modified version that spherical Python code in Chimera or using it in ChimeraX. I'll assume ChimeraX. http://plato.cgl.ucsf.edu/trac/chimera/wiki/SphericalHarmonics <http://plato.cgl.ucsf.edu/trac/chimera/wiki/SphericalHarmonics> It is much easier to shift and rotate the vertices than your approach. Python numpy arrays make this very convenient. After the line of code that makes the numpy array of vertices va = array(vertices, float32) you could shift it to a new origin with just va += (32.5, 13, -24.1) Rotation is also easy. from chimerax.geometry import rotation r = rotation(axis = (0,1,0), angle = 45) va = r * va na = r * na Here I rotate the vertices and the normal vectors about 0,0,0. Then I could apply the translation after that. You might want to do a rotation given by a 3 by 3 rotation matrix and the translation in one step, like this from chimerax.geometry import Place t = Place(matrix = ((0,1,0, 32.5), (-1,0,0, 13), (0,0,1, -24.1))) t.transform_points(va, in_place = True) t.transform_vectors(na, in_place = True) Here I used a 3 by 4 matrix where the first 3 columns were the rotation and the 4th column is the translation. I'll update the example code to show this. These geometric transforms are described in the ChimeraX Python programming documentation: https://www.cgl.ucsf.edu/chimerax/docs/devel/bundles/geometry/src/geometry.… As for what went wrong with you np.array([x0,y0,z0]).T approach -- that transpose operation put the vertices in a non-standard memory order -- you created a 3 by N array and then did a transpose to get an N by 3 array but numpy is smart and does not allocate a new array and instead just adjusts the strides and uses the original array. My guess is the calculate_surface_normals() code has a bug in that it does not handle non-standard orders for the vertex array. So the normals were completely wrong and that effects the lighting. In the ChimeraX Python shell (menu Tools / General / Shell) the variable "session" is the ChimeraX session. Tom > On Aug 31, 2020, at 2:43 PM, Albert Smith-Penzel <Albert.Smith-Penzel(a)medizin.uni-leipzig.de> wrote: > > Dear all, > > Thanks for such quick replies and helpful answers. I had two follow-up questions on the approach that Tom suggested in ChimeraX. > > The first is maybe a glitch, or more likely something I don’t fully understand in python/chimera. > > In the code Tom links to (http://plato.cgl.ucsf.edu/trac/chimera/wiki/SphericalHarmonics <http://plato.cgl.ucsf.edu/trac/chimera/wiki/SphericalHarmonics>), a list of vertices (x,y,z tuples) is created. Suppose I want to shift the center of the spherical harmonic and/or rotate it. One way to do this is to extract x,y,z from the vertices list and modify them, then put them back in the list. My first step is to switch the tuple to a list in the code (switch xyz = (r*sp*ct, r*sp*st, r*cp) to xyz = [r*sp*ct, r*sp*st, r*cp] ). Then I extract the elements, do some editing, and then put them back into a list of vertices. > > x0,y0,z0=np.array(vertices).T > #Some editing of x0,y0,z0 - although editing is not required to produce the strange effects. > vertices=np.array([[x,y,z] for x,y,z in zip(x0,y0,z0)]) > #vertices=np.array([x0,y0,z0]).T > > Finally, I need to reconstruct the vertices list. The first approach (currently uncommented) works just fine. The second approach (commented) doesn’t create any errors, but the lighting is very strange, in that there are alternating dark and light areas on the surface of the harmonic. I would have claimed that the two approaches should produce practically identical numpy arrays, but clearly that’s not the case. > > Anyway, it’s not particularly important for me, since I can work around it, but it does take some time to figure out, because one would think the latter approach should also work. > > The second question is: is it possible to get the “session” object into an interactive python session? Usually, I work interactively with python, and have a number of functions that create various scripts and input files for chimera, and then launch chimera from a shell, calling some script on startup. While this works, it would be really nice if one could manipulate an existing chimera session (maybe a bit off of the original topic now). > > In any case, the new graphics with the tensors come out very nicely- thanks so much for your help. > > Cheers, > Albert > > > >> On 28. Aug 2020, at 20:58, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> WARNUNG: Diese E-Mail kam von außerhalb der Organisation. Klicken Sie nicht auf Links oder öffnen Sie keine Anhänge, es sei denn, Sie kennen den Absender und wissen, dass der Inhalt sicher ist. >> >> Hi Albert, >> >> You need finer phi and theta steps to get a smoother appearance. I found that 10 degree steps gives chunky appearance, while 3 degree steps givs smooth appearance. Chimera does not have code to make an arbitrary surface smoother. >> >> Maybe you are interested in making these surfaces all in Python instead of using BILD. Here is how it is done in our newer ChimeraX program. >> >> http://plato.cgl.ucsf.edu/trac/chimera/wiki/SphericalHarmonics <http://plato.cgl.ucsf.edu/trac/chimera/wiki/SphericalHarmonics> >> >> Tom >> >> <harmonics.png> >> >>> On Aug 28, 2020, at 1:54 AM, Albert Smith-Penzel <Albert.Smith-Penzel(a)medizin.uni-leipzig.de <mailto:Albert.Smith-Penzel@medizin.uni-leipzig.de>> wrote: >>> >>> Hello, >>> >>> I have a question about improving user defined graphics in Chimera. >>> >>> For background (maybe not necessary for answering): >>> I’m working with nuclear magnetic resonance and MD simulation, and so I want to plot dynamically averaged spin-spin (H–C) dipole tensors, obtained from MD, on top of the corresponding H–C bonds. I’ve been relatively successful, but while one has a very high-resolution picture of the molecule itself, the tensors themselves are visibly triangulated. >>> >>> How I get this plot: >>> Each tensor is expressed first in spherical coordinate (theta, phi, r). In python, I run Delauney from scipy.spatial on theta and phi to get a list of vertices that can be used for triangulation of the tensor. Then, for each tensor, I convert theta, phi, and r into cartesian coordinates, shift the center so that the tensor sits on top of the correct bond. Finally, I create a .bild file where I write out each triangle using the coordinates and vertices. Tensors have negative and positive values (red and blue in the plot), and so I only take triangles for which r for all vertices is positive, and then in a second step, take only triangles where all vertices are negative. This all gets written to the .bild file, and then opened in chimera on top of the molecule (see picture). >>> >>> The question: >>> The result is certainly acceptable, however, there is clearly a quality difference in the molecule rendering vs. the tensor rendering (obviously, because the tensors are just made of triangles that I’ve created in python). Is there a better way to bring the surface data describing the tensors into chimera that would then allow usage of some sort of smoothing within chimera for a nicer image? (And possibly with a relatively simple data format….) >>> >>> Thanks for your help! >>> >>> Cheers, >>> Albert Smith >>> >>> <example_triangulation.png> >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users> >> > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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Fit in Map - Overlap
by Luis José Castillo Valverde 28 Aug '20

28 Aug '20

Hi, As I understand it, the overlay resulting from the "Fit in Map" command corresponds to the sum over the fit map grid points of the product of the fit map value and the reference map value at that point, determined by trilinear interpolation. I want to calculate the percentage of overlap of two maps, it would be as simple as calculating the formula "min ((sum of the grid points of map 1), (sum of the grid points of map 2)) / (overlap obtained from the fit ) "the problem I have that I do not know how to obtain those values (" sum of the grid points of map 1 "," sum of the grid points of map 2 "); I tried to do "Fit in Map" of map 1 with map 1 and use the overlap that returns as the sum of the points of map 1 but it didn't work. So I wanted to know if you can tell me how to get the sum of the grid points of a given map. Regards, Luis -- Luis José Castillo Valverde Ingeniero en Computación, TEC Costa Rica Estudiante de maestría (MSc) académica en Computación, TEC Costa Rica Telegram: @LCastillo98 LinkedIn: luisjosecastillo98

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MD trajectories in ChimeraX
by David Slochower 24 Aug '20

24 Aug '20

Hi, are there any plans to implement a "metafile" interface (e.g., http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#…) for loading trajectories with ChimeraX? In particular, it would be great to be able to load `prmtop` and `nc` trajectories, even if it were available only through the command line and without a GUI. (This can be considered a follow up to this message: http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-December/000773.html) I'm aware of the Molecular Dynamics Viewer in the Toolshed, but that appears to be geared for multi-PDB trajectories. Thanks.

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Stack sidebar tools as tabs
by Sean Connell 22 Aug '20

22 Aug '20

Hello, I was wondering if there is a command to automatically stack the tools (i.e. log, volume viewer) in the sidebar as TABs? For example to put in the preferences so it starts this way or to make an alias so it can be done quickly. Thanks in advance for any tips you have. Sean

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ChimeraX depthCue
by Gokhan Tolun 18 Aug '20

18 Aug '20

Hi, Based on here: https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html I am trying to adjust the depth cue using the depthCue true | false depthCueColor color-spec depthCueStart start depthCueEnd end commands, but I get the error Unknown command: Any suggestions? Thanks, Gökhan PS: ChimeraX 1.0

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