July 2021 - ChimeraX-users - RBVI Mailing Lists

Custom colour for atoms with bfactor==0
by Lorena Zuzic 27 Jul '21

27 Jul '21

Hi, I wanted to know if there is a way of colouring my structure by bfactor, but with an additional condition where all bfactor==0 atoms are coloured in grey. Currently, I am using a white to red gradient for my B-factors: color bfactor range -2.2, 2.2 In this case, bfactor==0 values are coloured white. However, I would like them to be grey and outside the gradient (as they represent an unmapped portion of the protein). Thanks! Lorena

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create mask from "shapes"
by Roberto Marabini 27 Jul '21

27 Jul '21

Hi, It is possible to create a mask from a shape?. For example from the result of "*shape icosahedron".* If the command does not exist I guess I may create it as follows * the input would be the 3D map to be masked and the shape to be used as mask * request all the (varray, tarray) from the shape. * from varray,tarray build the triangles that define the surface of the shape * for each triangle create the normal vector * multiply each normal vector by the position of each voxel (dot product) * keep those voxels that have negative dot products for all the triangles. thanks for the help

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Automated Fitting of models into maps and saving fits with a correlation score > X
by Vorländer,Matthias Kopano 26 Jul '21

26 Jul '21

Dear all, I have a set of 100 “artificial” tomograms, each containing approx 100 copies of a simulated density map of my protein of interest. I would like to fit each tomogram with the PDB of my POI, and save copies for all fits with a correlation score > 90%. Using the fitmap command in Chimera and then manually selecting the fits that meet the criterium works, but takes quiet a long time for a larger amount of data. I wonder if this could be automated, and if somehow would be able me to put together a script (is it possible to execute such tasks in a non-gui way, by submitting it to a cluster so that it could be parallelized?). Thanks a lot in advance, Best, Matthias

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unexpected behavior of build start
by Alexis Rohou 26 Jul '21

26 Jul '21

Hi ChimeraX team, I'm running into unexpected behavior when using the build tool. Here's what I'm doing: - open map --> model #1 - open PDB --> model #2 - fit #2 in #1 (the PDB moves by ~20 Å at this step) - cofr centerOfView showPivot true - move the view around so that the pivot axes intersect where I want to place a new atom - build start atom #2 expected result: a new H atom is created exactly at the center of view (where the pivot axes intersect) actual result: the new H atom is created some distance away; I think the vector from where the new H atom is built to the cofr is the same vector as the PDB model was displaced by the fitting into the map (my second step, above), but I haven't checked that carefully. Is this what is expected? It confused me :) Is there a command I can use to move the atom to the correct location after it's been created? Interestingly, if I add a H atom into a new model, then it appears where I expect it, at the cofr: - build start atom "custom built" This is with 1.2.5 (2021-05-24) Cheers, Alexis

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question
by 王镐锋 26 Jul '21

26 Jul '21

Dear guys, Sorry to disturb you guys. When I use the UCSF ChimeraX, I try to define the second structure for part of model. I type the command like "dssp (#1 & sel) energy cutoff 0.5 minheliexlen 3", it works for the whole model instead of what I choose specially. Could you please help me? Thanks so much! Best, Haofeng Wang Ph.D student Tianjin University, China

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measure volume in ChimeraX
by Andrew Blyth 24 Jul '21

24 Jul '21

Hi, I am having trouble getting the ‘measure volume’ and ‘measure area’ command to work in chimera. I have been trying the command: measure volume #3/A:457 for the structure that I have been using, however, nothing happens when I execute this command. Could you please provide me with an example command that will work for measuring the volume or area of a residue? Thanks, Andrew Blyth PhD Candidate Medical Biochemistry - Flinders University Room 6E109 Flinders Medical Centre | South Australia 5001, Australia Phone: +61 8 8204 5098 | E: andrew.blyth(a)flinders.edu.au<mailto:andrew.blyth@flinders.edu.au>

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Model missing residues in Chimera X
by He, Amy 23 Jul '21

23 Jul '21

Dear Chimera X community, I’m a new user of Chimera X and I have a question about the built-in Modeller function in Chimera X Previously in Chimera 2, we use the “Model/Refine Loop” function to model missing residues in the experimental structure, before any further calculation or simulations. The “Model/Refine Loop” function uses Modeller and the function provides modeled, complete structures in which the non-missing residues do not move. In Chimera X, a similar function is “Modeller Comparative” but it works differently. The “Modeller Comparative” performs a modeling for the full structure with the given sequence. Is possible in Chimera X to model the missing residues, without moving the existent residues? Thank you for your kind advice in advance! Thanks, Amy -- Amy He Chemistry Graduate Teaching Assistant Hadad Research Group Ohio State University he.1768(a)osu.edu<mailto:he.1768@osu.edu>

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How to access ChimeraX remotely from macbook (OS mojave)?
by Rayees Mattoo 22 Jul '21

22 Jul '21

Hi, I am trying to access ChimeraX remotley using my mac book pro. The ChimeraX is installed on linux machine. Upon launching, the chimeraX GUI appears and suddenly disappears with the following error message: "ChimeraX requires OpenGL graphics version 3.3. Your computer graphics driver provided version 1.4, Try updating your graphics driver". My mac currently has macOS mojave version 10.14.6 and it seems it does not have OpenGL graphics version 3.3 required to display chimeraX remotely. Is there any way out to fix the problem? Not sure if updating my macbook to Catalina or BigSur is going to help! Best Rayees

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Re: [chimerax-users] How to access ChimeraX remotely from macbook (OS mojave)?
by Tom Goddard 22 Jul '21

22 Jul '21

Hi Rayees, Mac Air graphics is pretty slow for running ISOLDE. But Tristan Croll who develops ISOLDE added a nice option "Sim Fidelity" to the ISOLDE panel in the middle -- by default it is set to "High" and setting it to "Quick" will make the simulations run much faster. Here is what Tristan told me about what it does: "The latest ISOLDE release has new “sim fidelity” radio buttons on the “Sim settings” tab. The “quick” mode (no implicit solvent, nonbonded cutoff tightened to 9 Å) runs about 4x faster on my MacBook Air and still gives reasonable results in good density. Still not *fast*, but I think definitely usable." This is in ISOLDE 1.2.2. If you need to update ISOLDE use ChimeraX menu Tools / More Tools.... If this is still too slow, I'm afraid it is a limitation. You have to use faster hardware. The realtime dynamics simulations used by ISOLDE need fast graphics - the molecular dynamics is done with OpenMM using OpenCL or CUDA GPU accelerated computation. CUDA is fastest and needs Nvidia graphics and the CUDA driver installed -- Macs don't support Nvidia gpus. The macOS OpenCL implementation is very slow, almost as slow as just running on the CPU. Tristan has ISOLDE benchmarks on different hardware here https://isolde.cimr.cam.ac.uk/performance-benchmarks/ Tom > On Jul 22, 2021, at 6:03 PM, Rayees Mattoo <rmattoo(a)stanford.edu> wrote: > > Hi Tom, > Thanks for responding. Actually, I wanted to run ISOLDE from chimeraX and already tried it running on Mac with my 500KDa protein complex. It was very slow, wanted to try on linux machine and ran into the OpenGL problem. Do you have any suggestions how to run ISOLDE faster on mac? > > Best > Rayees > From: Tom Goddard <goddard(a)sonic.net> > Sent: Thursday, July 22, 2021 5:32 PM > To: Rayees Mattoo <rmattoo(a)stanford.edu> > Cc: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu>; chimerax-bugs(a)cgl.ucsf.edu <chimerax-bugs(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] How to access ChimeraX remotely from macbook (OS mojave)? > > Hi Rayees, > > I guess you have X Windows (XQuartz) running on your Mac and are hoping that X remote display from Linux to the Mac will work with ChimeraX. Unfortunately X Windows remote display of 3D OpenGL graphics has not worked reliably since the days Silicon Graphics computers in the 1990s. It is possible to get it to work between two Linux machines with identical OpenGL drivers. But it would be a near miracle if the XQuartz implementation of X Windows on Mac could handle the OpenGL from a Linux machine. > > The sensible approach is to run ChimeraX directly on your MacBook Pro. We don't recommend remote display even when it works because rendering speed is likely to be poor. > > Tom > > >> On Jul 22, 2021, at 1:31 PM, Rayees Mattoo via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> Hi, >> I am trying to access ChimeraX remotley using my mac book pro. The ChimeraX is installed on linux machine. Upon launching, the chimeraX GUI appears and suddenly disappears with the following error message: "ChimeraX requires OpenGL graphics version 3.3. Your computer graphics driver provided version 1.4, Try updating your graphics driver". >> My mac currently has macOS mojave version 10.14.6 and it seems it does not have OpenGL graphics version 3.3 required to display chimeraX remotely. Is there any way out to fix the problem? Not sure if updating my macbook to Catalina or BigSur is going to help! >> >> Best >> Rayees >> >> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>

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Re: [chimerax-users] python loop with ChimeraX
by Rangarajan, Amith 21 Jul '21

21 Jul '21

Hi, I am new to chimeraX , i want to loop through a set of biological assemblies measuring SASA of selecting residues and write them to a file. I need some help with starting on this .How to include this into the .cxc script? is there a example somewhere? please share your tips and suggestions, thanks everyone ! warm regards, Amith

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ChimeraX-users July 2021