October 2021 - ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] labelling hbond atoms
by Rangarajan, Amith 14 Oct '21

14 Oct '21

Dear Group, I have a possibly rookie level question. When i use name flag with hbonds command to define two groups of hbonds like this hbonds (#1.1 & protein) restrict (#1.2.* ) distslop .2 reveal t rad .2 color gold name HBONDS-1 hbonds(#1.1 & ~protein) restrict(#1.2.*) distslop .2 reveal t rad .2 color magenta name HBONDS-2 then when i try to label the hbond atoms , la hbondatoms residues font "Rockwell Extra Bold" height .6 bg 20,20,20 I am not getting the labels. I am not getting any errors so i figured that it got to do with hbonds being given a name , however i am not able to fix this. welcome to hear your suggestions. thanks again., amith

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ProblemI am attempting he installation of ChmimeraX Installing ChimeraX on Debian mv-10
by Stephen P. Molnar 14 Oct '21

14 Oct '21

I am attempting the installation of ChimeraC-1.2.5(chimerax-1.2.5-rc-2021.05.24) on my up to date Debian v-1064 bit platform. I open the tar.gz package without any difficulties, but when I attempt to execute ChmieraX i get the following: comp@AbNormal:~/Apps/chimerax-1.2.5-rc-2021.05.24/bin$ ./ChimeraX qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found. This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, xcb. Fatal Python error: Aborted Current thread 0x00007fcb3dafd740 (most recent call first): File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/chimerax/ui/gui.py", line 157 in __init__ File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/ChimeraX_main.py", line 577 in init File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/ChimeraX_main.py", line 1015 in <module> File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/runpy.py", line 87 in _run_code File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/runpy.py", line 194 in _run_module_as_main Aborted comp@AbNormal:~/Apps/chimerax-1.2.5-rc-2021.05.24/bin$ xcb is installed, but the Debian v-10 default version of python is 3.7. Is this the problem? Is there a solution? Reinstalling did not fix the problem. Thanks in advance. -- Stephen P. Molnar, Ph.D. www.molecular-modeling.net 614.312.7528 (c) Skype: smolnar1

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Question about pruned set in rmsd
by Chang Jang 14 Oct '21

14 Oct '21

Hi Chimera Users, I want to understand a result from "match" command. There are two results for 1) pruned set and 2) across all. What exactly is the pruned set in this calculation? Thanks, Chang Woon Jang

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Use values printed from Log inside a script (e.g. RMSD)
by Steven Truong 12 Oct '21

12 Oct '21

Dear ChimeraX Admins, I was hoping to use the “rmsd” command in ChimeraX to measure distances between models within a .py script. Is there a way to use the output of “rmsd” (or generally any other output in Log) within the script? For example, if rmsd > 2 Angstroms, then do X. Ultimately, I am attempting to align chains between models. Because my protein is asymmetric, chain A on Model #1 might actually be chain B on Model #2. I was hoping to use “rmsd” to map one chain to the other. Is it a better idea to do this in another program and re-write chain IDs in the .PDB file? If so, what other program would be better at making RMSD calculations between .PDB chains? Thank you, Steven Truong Cambridge University

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Electrostatic color key problem
by Luca Pellegrini 12 Oct '21

12 Oct '21

Hi, Coloring a surface with ‘electrostatic’ in the ‘Molecule display’ works fine. However, when I try to modify the red-blue boundary values from the default -10, 10 in the color key box, the surface color doesn’t seem to change. Can you please advise? Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK

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fold
by Ruggero Gabbrielli 11 Oct '21

11 Oct '21

Maybe it’s a little too early for that, but can’t you just add a button for folding a sequence?

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"fly" interrupting "turn"
by Anderson, Jacob 11 Oct '21

11 Oct '21

Dear ChimeraX Users, Making a movie with a CXC script/command file, I find that the "fly" command interrupts the "turn" command. For example if I run these two lines: turn y 0.25 1440 fly Frame_01 400 Frame_02 400 Frame_03 400 Frame_04 400 Frame_05 Before the turn completes, the view goes to Frame_01. Is this the expected behavior? If not, would love any tips on how to complete a turn of the molecular model before flying to Frame_01 (or p1 in the ChimeraX fly user help documentation). Jacob

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Re: [chimerax-users] Measuring Colocalisation using ChimeraX
by Tom Goddard 08 Oct '21

08 Oct '21

Hi Dominic, Ok, here is a way to do what you described that does not need any Python. First you place a marker at the enter of the green blob using ChimeraX Markers toolbar using the Center mode (mark center of connected surface). Once you select that mouse mode, right click on the green blob to place the marker. Then make a sphere centered at that marker with the shape command, e.g. "shape sphere center #3 radius 100". Then mask the red map to get just the part inside that sphere, e.g. "volume mask #1 surface #4". Then measure the volume enclosed in that masked map surface, e.g. "measure volume #5". You might also be interested in exactly how much red blob is inside the green blob and you could mask the red using the surface of the green to do that. Tom > On Oct 8, 2021, at 2:33 AM, BINGHAM Dominic <dominic.BINGHAM(a)univ-amu.fr> wrote: > > The custom python code sounds more applicable to what I am doing. I will give that a try but also would greatly appreciate some tips > > > To give context, I have several maps like shown above, with 2-channels showing the staining of one protein each. Each map is a synapse, and these are taken from 3D-STORM images contains several synapses. I have 3 different conditions, and I would like to compare what I measure and how it changes between these conditions. So for instance, ideally, what I would like to do is to measure from the centre of the large green structure which is colocalised to the large red structure (Circle on image above). I would then like a value to represent the relative amount of the ‘red’ protein within a set volume around the ‘green’ structure. I would then compare this value between each condition. > > So any tips on the code for python would be great here! > > Thanks so much for the help! > > Dominic > >> Le 6 oct. 2021 à 20:08, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> a écrit : >> >> Hi Dominic, >> >> The ChimeraX Distances tools measures distances between atoms in an atomic structure. You have image data, not an atomic structure so that is why it will not report any distances. >> >> One way to proceed would be to place a marker on every connected surface piece in each of the two images, then measure distances between these centroid markers. There is code to place the markers using ChimeraX here >> >> https://rbvi.github.io/chimerax-recipes/mark_blobs/mark_blobs.html <https://rbvi.github.io/chimerax-recipes/mark_blobs/mark_blobs.html> >> >> Markers are treated just like atoms in ChimeraX so the Distance tool would work. But you want all nearby distances so you might try the Contacts tool >> >> https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html> >> >> That may not give you what you want. Very likely you would need to write some custom Python code to get exactly what you want. Probably you also want the volume enclosed in each blob. If you need tips on how to write that Python code I can advise if you give specifics of what you want. >> >> Tom >> >> >> >> >> >> >>> On Oct 6, 2021, at 4:11 AM, BINGHAM Dominic via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Hello, >>> >>> I have a problem with which I’m trying to use chimeraX to solve. I have some images of synapses with which I have super-resolved two proteins in 3D (so two images/channels). I want to quantify the colocalisation of a structure of one protein to the blobs of the other protein within a certain distance. Shown below is the non-segmented map of the 2 images of proteins. So for example I would want to quantify the colocalisation of the red blobs within a certain distance of specific larger green blobs. I want to then compare these between different conditions. >>> <Capture d’écran 2021-10-06 à 12.58.42.png> >>> >>> I have segmented the images already using "segmentat map ». I have been trying to start with the « distance » tool to measure how far one blob of protein is from the structure (Image shown below of two selected structures in just the map of one protein to practice). >>> >>> <Capture d’écran 2021-10-06 à 12.57.28.png> >>> >>> However, this doesn’t seem to work functionally as no distance is shown when I try to perform the function. Also, this function may possibly be too basic for what Im trying to do. That said, any help on how to use this function would still be greatly appreciated. >>> >>> >>> Ultimately, I think the best thing for what I would like is to be able to select a specific structure and have a measurement of all the blobs of the other protein within a defined 3D radius of this structure, and then compare this value between different conditions. I have been looking through the user manual and I can’t seem to find anything that will do something like this… I (and my PhD) would be monumentally grateful if you could possibly help me with this problem? Either by pointing me to the correct function, or even a thread that has discussed a similar problem that I may have missed? >>> >>> >>> Thanks and have a wonderful day, >>> >>> Dominic Bingham >>> PhD student at Aix-Marseille University >>> >>> _______________________________________________ >>> 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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hbonds display problem
by Maciej Basczok 08 Oct '21

08 Oct '21

Dear Expert, at the beginning would like to thank you for developing such a wonderful tool as ChimeraX is! I have one problem, namely, when hbonds calculation is run on an RNA molecule with an option to display as pseudobonds, there are many hbonds detected, but displayed are only two of them. Do I keep doing something wrong? I would be very grateful for your help. Kind regards, Maciek

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polishing video
by Ruchika Bajaj 07 Oct '21

07 Oct '21

Hi Elaine Hope you're doing well !! I need to polish my videos. I am mainly using the following commands. I am just wondering if you have any more suggestions to improve the quality of the movie. Please let me know. I would appreciate your help in this regard. Thanks !! Regards Ruchika set bgColor white; lighting simple; graphics silhouettes true; lighting soft movie record supersample 3; movie encode quality higher

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ChimeraX-users October 2021