- ChimeraX-users - RBVI Mailing Lists

Making a movie from a group in PDB file
by Aleksandar Donev 21 Feb '23

21 Feb '23

Hi, I am trying to create a simple animation of a demo molecular dynamics program https://github.com/stochasticHydroTools/DemoMD using either chimerax or chimera. The code creates a .pdb file that has multiple time frames in it, which show up in chimerax as a "group". How do I make chimera show the frames one by one and then make a movie out of that or save each frame as an image? I used to be able to do that in chimera but either the interface has changed or I have forgotten. I found lots of instructions about how to make movies by manipulating one data set (say rotating a molecule) but could not find anything about animation in time. Thanks, Aleks -- Aleksandar Donev, Professor of Mathematics Courant Institute of Mathematical Sciences Office: 1016 Warren Weaver Hall, New York University E-mail: donev(a)courant.nyu.edu Phone: (212) 992-7315; Fax: (212) 995-4121 Mailing address: 251 Mercer St, New York, NY 10012 Web: http://cims.nyu.edu/~donev

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Distance maps and all atom distances
by André Graça 17 Feb '23

17 Feb '23

Hi everyone! Does ChimeraX have a tool to calculate distance maps in the same fashion as Chimera does with RRDistMaps? I believe Chimera's RRDistMaps only calculates intermodal distances between C-alpha atoms. Does anyone know a tool or have a script that could calculate all atom distances from two sequence identical models? Cheers, André

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Image saving/exporting options
by Matthew Graneri 16 Feb '23

16 Feb '23

Hi there, I was wondering if there was an option to set the resolution of an image you want to export? In the older Chimera application, there were many more options open to you when you wanted to save an image (I’ve attached a screenshot of the old and new image saving screens for comparison). If not, is there any chance of implementing a resolution specification option sometime in the future? I was also wondering if it was possible to save images from ChimeraX as PDF files? I find that they usually maintain a high resolution without being particularly big, in terms of memory. Apart from that, really enjoying ChimeraX! Regards, Matthew

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Loading MTZ data - volume is restricted to a small sphere within the protein model
by Lewis James martin 15 Feb '23

15 Feb '23

Hi folks, I recently installed Clipper, and on loading some example PDB and MTZ data, I'm seeing just a sphere of density data that does not cover the full protein model. This behaviour is not restricted to a single example. Is it expected? The example files I used are in 6DIL <https://www.rcsb.org/structure/6DIL>. I downloaded "PDB Format" and "Map Coefficients (MTZ Format)" from the drop-down menu. Loading the PDB by drag-and-drop into ChimeraX works as expected (coordinates do show). On loading the MTZ by drag-and-drop, and selecting the PDB model to import data into, I see the below representation. The density does not cover the full set of protein coordinates - it's limited to a sphere within the protein. Curiously, I saw this on coot too - so maybe I'm just getting the options incorrect? I did try shifting the cutoffs in the "Volume Viewer" Tool, and the mesh does change but it's still limited to this sphere. Changing from a mesh surface to "Maximum" shows that the available data is limited to a cube that does not cover the protein. Is there a way to view the full density? Out of interest, I also tried generating the mesh myself, but only got halfway. This at least shows that the data does cover the whole protein: import gemmi import numpy as np import meshplot as mp from skimage.measure import marching_cubes #run 'gemmi mtz2cif 6dil_phases.mtz 6dil_phases.cif' first doc = gemmi.cif.read('/Users/ljmartin/Desktop/6dil_phases.cif') rblocks = gemmi.as_refln_blocks(doc) rblock = rblocks[0] size = rblock.get_size_for_hkl(sample_rate=2.6) full = rblock.get_f_phi_on_grid('pdbx_FWT', 'pdbx_PHWT', size) array = np.array(full, copy=False) complex_map = np.fft.ifftn(array.conj()) scale_factor = complex_map.size / full.unit_cell.volume real_map = np.real(complex_map) * scale_factor v,f,n,_ = marching_cubes(real_map, 0.05) mp.plot(v, f)

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move models relative to each other
by Raik Grunberg 14 Feb '23

14 Feb '23

Dear ChimeraX developers and users, I would like to move to different proteins that I have opened separately into a particular position relative to each other. In the old Chimera, this is possible by going to the Model panel, then selecting one of the two models as "Active" and the other one not and then making the normal rotation and translation moves which will now only happen on the "active" model. However, this "Active" column is missing in the ChimeraX Model panel and I cannot find any alternative way of doing this. Any suggestions? Thanks a lot in advance Raik -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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Re: [chimerax-users] Transparency with soft lighting
by Tom Goddard 10 Feb '23

10 Feb '23

Hi Scott, I made a ChimeraX recipe web page to show this transparency and shadows trick. https://rbvi.github.io/chimerax-recipes/shadows/shadows.html That's amazing Esther refound it in that long fitting video. Tom > On Feb 10, 2023, at 12:23 PM, Scott Stagg <sstagg(a)fsu.edu> wrote: > > Thanks, Tom. That’s exactly what I was looking for! Esther Bullit found the video. It’s this one > https://www.youtube.com/watch?v=v3jI43YJQMg > Fitting an atomic model in an electron microscopy map with ChimeraX > youtube.com > Scott > > >> On Feb 10, 2023, at 3:09 PM, Tom Goddard <goddard(a)sonic.net> wrote: >> >> Hi Scott, >> >> I'm not sure what video that is in. But there is some obscure ChimeraX magic involved. If you use the "soft" lighting (shadows cast from all directions) with a transparent surface it looks horrible because transparent surfaces by default don't cast shadows in ChimeraX. The reason for that default is often you are showing a molecule inside a transparent surface and then the molecule is dark (black actually) and hard to see. Because the transparent surface doesn't cast shadows it does not shadow itself so you don't get any of the darkened cavities that help 3D appearance. To make transparent surface cast shadows use ChimeraX command >> >> material transparentCastShadows true >> >> If you have an atomic structure (#2) inside the surface it will look black (shadowed), but you can tell it not to accept shadows >> >> lighting model #2 multishadow false >> >> The model inside can look pretty horrible and flat with soft lighting and you might try full lighting that adds a spot light, and also use silhouette edges. >> >> Here is an example of all these tricks. >> >> open 1080 from emdb >> light soft >> volume level 0.6 >> open 1grl >> preset cylinders >> fitmap #2 in #1 >> transparency #1 80 >> material transparentCastShadows true >> lighting model #2 multishadow false >> graphics silhouettes true >> set bgColor white >> light full >> >> Thanks for asking! >> >> Tom >> >> Opaque map, and transparent map, and transparent map with shadows with soft lighting. >> >> <image1.png><image2.png><image3.png> >> Atomic model is dark inside transparent map casting shadows. Can make atomic model not accept shadows. "Full" lighting instead of soft can make the atomic look less flat. >> >> <image4.png><image5.png><image6.png> >> >> >>> On Feb 10, 2023, at 6:48 AM, Scott Stagg via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>> >>> Hi everybody, >>> >>> I’m writing because I saw in a YouTube video that you used “soft” lighting with transparency for an EM density map. It looked great. I can’t find the video again or the right documentation on how to do it. There was some command with the lighting that you typed in the command line. Do you know what I’m talking about? >>> >>> Thanks, >>> Scott >>> >>> Scott Stagg >>> Professor >>> >>> Institute of Molecular Biophysics >>> Department of Biological Sciences >>> Florida State University >>> Tallahassee, FL 32306-4380 >>> w: 850-645-7872 >>> f: 850-644-7244 >>> sstagg(a)fsu.edu >>> https://www.stagglab.com <https://urldefense.com/v3/__https://www.stagglab.com__;!!PhOWcWs!3QUvw8SGqe…> >>> >>> >>> >>> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu >>> Manage subscription: >>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/mailman/listinfo/chim…> >> >

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Transparency with soft lighting
by Scott Stagg 10 Feb '23

10 Feb '23

Hi everybody, I’m writing because I saw in a YouTube video that you used “soft” lighting with transparency for an EM density map. It looked great. I can’t find the video again or the right documentation on how to do it. There was some command with the lighting that you typed in the command line. Do you know what I’m talking about? Thanks, Scott Scott Stagg Professor Institute of Molecular Biophysics Department of Biological Sciences Florida State University Tallahassee, FL 32306-4380 w: 850-645-7872 f: 850-644-7244 sstagg(a)fsu.edu https://www.stagglab.com

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About plotting independent component analysis vectors
by Tianming Qu 09 Feb '23

09 Feb '23

Dear all, Is there any way I can display the eigenvectors I got from the independent component analysis on ChimeraX, which is calculated from the protein MD trajectory. Best, Tianming

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Show palette range scale
by Gomez Barillas, Andrea 08 Feb '23

08 Feb '23

Dear ChimeraX developers, I've mapped sequence conservation into my protein structure by defining a specific attribute and I colored it using a specific palette. I was wondering how I can show in my model the scale of colors for the range I've stablished in my map. Maybe there is a command I can use to show the range I used for mapping and what the colors represent. Thank you for your help, Andrea

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Re: [chimerax-users] Help getting rmsd value per residue of 2 similar structures.
by Elaine Meng 08 Feb '23

08 Feb '23

Hi Binh, This is almost the same question as asked yesterday on chimerax-users(a)cgl.ucsf.edu, so I have the same answer: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2023-February/004923.html> That answer assumes you are using Matchmaker to superimpose these structures first, which has an option to display the pairwise sequence alignment with RMSD values per column, which can then be written out, used for coloring, etc, as detailed in that answer. Note that this RMSD is only using CA atoms so for two structures, it is simply the distance between the 2 CA atoms. You can use the Sequence Viewer settings to make it use the 4 backbone atoms per residue instead (N,CA,C,O): <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2023-February/004923.html> Secondarily, remember that Chimera and ChimeraX are two different programs and if you are viewing help/answers for Chimera they may not pertain to ChimeraX. Finally, for the best chance of getting a good answer to ChimeraX questions in the future, please use chimerax-users(a)cgl.ucsf.edu unless you are including private data. Thanks! Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 8, 2023, at 12:39 PM, Binh Nguyen <AnBinh.Nguyen(a)UTSouthwestern.edu> wrote: > > Dear Elaine, > > Is there a way to generate the rmsd per residue of 2 similar structures using chimeraX? I have searched through but I can only manage to get the overall RMSD. > > I have found this too but I have no idea how to get such information. > https://www.rbvi.ucsf.edu/pipermail/chimera-users/2019-February/015415.html > > Please help, thank you. > > B

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