November 2024 - ChimeraX-users - RBVI Mailing Lists

Re: IMOD Segmentation to ChimeraX (.mod to .cmm Conversion)
by Tom Goddard 27 Nov '24

27 Nov '24

Glad you got it to work. Tom > On Nov 27, 2024, at 3:30 PM, LENKA MILOJEVIC <lenka11(a)g.ucla.edu> wrote: > > Dear Dr. Goddard, > > Thank you so much! That worked! I thought I’d have to produce a .cmm file or mask the map using the volume tool and the .mod file as a surface. > > I really appreciate your swift responses! This was incredibly helpful. > > Have a great rest of your day! > > Sincerely, > Lenka > > On Wed, 27 Nov 2024 at 15:26, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> Hi Lenka, >> >> Seems like you got what you wanted "I was wondering if there's any way that I could convert the .mod file into a .cmm file because my goal is to segment a map in ChimeraX using the Color Zone tool, according to the contours from IMOD." Your image shows the traced curves as connected markers (fake atoms connected by bonds). To color the nearby density you would then use the Color Zone tool, menu Tools / Volume Data / Color Zone and it has a Split Map button that would let you make a new map that includes just the colored part near your curves. The equivalent ChimeraX command is "color zone" >> >> https://www.cgl.ucsf.edu/chimerax/docs/user/commands/color.html#zone >> >> If the command syntax is confusing just use the graphical Color Zone tool and it will log the equivalent command to the Log panel and you will have a better idea of how to type a command if you want to use some of the fancier options (like bondPointSpacing) that the graphical tool does not offer. >> >> Tom >> >> >>> On Nov 27, 2024, at 2:46 PM, LENKA MILOJEVIC via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> In the event that I want to mask map #3 using the .mod file in #1 , which command exactly do I run? I'm attaching a screenshot showing my current session. >>> <image.png> >>> >>> >>> On Wed, Nov 27, 2024 at 2:42 PM LENKA MILOJEVIC <lenka11(a)g.ucla.edu <mailto:lenka11@g.ucla.edu>> wrote: >>>> Hi Elaine, >>>> >>>> If I don't input contours true, nothing shows up on my screen. It just states it read it. >>>> open <> C:/Users/lenkamilojevic/Box/HSV-1/Front/HSV1_9_overcoils.mod >>>> Read IMOD model C:/Users/lenkamilojevic/Box/HSV-1/Front/HSV1_9_overcoils.mod, pixel size 0.568 >>>> >>>> Sorry for the trouble. I really appreciate your help. >>>> >>>> Best, >>>> Lenka >>>> >>>> On Wed, Nov 27, 2024 at 2:09 PM Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: >>>>> Hi Lenka, >>>>> Contours true is to make it into markers and links (fake atoms and bonds) instead of a surface. You do not need markers and links for masking, you only need a surface model (meshes true contours false). >>>>> >>>>> Just open the file directly without any options and by default it should make a surface model that you can use in "volume mask" - I thought "meshes true" would still make the surface but maybe it only does that when contours is false. >>>>> >>>>> I'm sorry I mentioned the contours option since it was confusing... I only did so because at first I thought you wanted markers. >>>>> >>>>> I hope this helps, >>>>> Elaine >>>>> ----- >>>>> Elaine C. Meng, Ph.D. >>>>> UCSF Chimera(X) team >>>>> Resource for Biocomputing, Visualization, and Informatics >>>>> Department of Pharmaceutical Chemistry >>>>> University of California, San Francisco >>>>> >>>>> > On Nov 27, 2024, at 1:34 PM, LENKA MILOJEVIC via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>>> > >>>>> > Dear Dr. Meng, >>>>> > >>>>> > Thank you! I've now managed to open the segmentation with open C:Path format imod meshes true contours true. But If I run volume mask it just outputs: >>>>> > volume mask #3 surfaces #1 fullMap true >>>>> > No surfaces specified >>>>> > volume mask #3 #1 extend 3 >>>>> > Missing required "surfaces" argument >>>>> > volume mask #3 surfaces #1 >>>>> > No surfaces specified >>>>> > >>>>> > Any advice? Is the contour not actually a surface yet? Or am I writing the command wrong. >>>>> > >>>>> > Thank you so so much! >>>>> > >>>>> > Best, >>>>> > Lenka >>>>> > >>>>> > On Wed, Nov 27, 2024 at 1:45 PM Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: >>>>> > Hi Lenka, >>>>> > The link that you sent is to the Chimera documentation (not ChimeraX): >>>>> > <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#object> >>>>> > >>>>> > Since they are different programs, there are differences... but not in this case! ChimeraX can also open these IMOD segmentations: >>>>> > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#segmentation> >>>>> > <https://rbvi.ucsf.edu/chimerax/docs/user/formats/imod.html> >>>>> > >>>>> > These segmentation models are surfaces, not the atoms or pseudoatoms (markers) that you would need to define a zone with Color Zone. Although the second link above explains that you can make the IMOD surface mesh into markers/links by opening the file with the "open" command option "contours false," that is unlikely to make them suitable for defining zones. Mainly it is used to improve display. >>>>> > >>>>> > Instead you can use "volume mask" to mask parts of your map with the IMOD segmentation surfaces. >>>>> > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#mask> >>>>> > >>>>> > I hope this helps, >>>>> > Elaine >>>>> > ----- >>>>> > Elaine C. Meng, Ph.D. >>>>> > UCSF Chimera(X) team >>>>> > Resource for Biocomputing, Visualization, and Informatics >>>>> > Department of Pharmaceutical Chemistry >>>>> > University of California, San Francisco >>>>> > >>>>> > > On Nov 27, 2024, at 11:56 AM, LENKA MILOJEVIC via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>>> > > >>>>> > > Dear Sir or Madam, >>>>> > > >>>>> > > While the 'Input File Types' page lists .mod and .imod files under 3D objects ChimeraX can open, when I try to open a .mod file (e.g., run command open C:/*PathToFile* or through the GUI), the file doesn't show up even though the log output states 'Read IMOD model C:/*PathToFile*, pixel size X'. >>>>> > > >>>>> > > I was wondering if there's any way that I could convert the .mod file into a .cmm file because my goal is to segment a map in ChimeraX using the Color Zone tool, according to the contours from IMOD. >>>>> > > >>>>> > > I appreciate your time and assistance! >>>>> > > >>>>> > > Sincerely, >>>>> > > Lenka >>>>> > >>>>> > _______________________________________________ >>>>> > ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> >>>>> > To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> >>>>> > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >>>>> >>> _______________________________________________ >>> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> >>> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> >>> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >>

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IMOD Segmentation to ChimeraX (.mod to .cmm Conversion)
by LENKA MILOJEVIC 27 Nov '24

27 Nov '24

Dear Sir or Madam, While the 'Input File Types' page <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html> lists .mod and .imod files under 3D objects ChimeraX can open, when I try to open a .mod file (e.g., run command open C:/*PathToFile* or through the GUI), the file doesn't show up even though the log output states 'Read IMOD model C:/*PathToFile*, pixel size X'. I was wondering if there's any way that I could convert the .mod file into a .cmm file because my goal is to segment a map in ChimeraX using the Color Zone tool, according to the contours from IMOD. I appreciate your time and assistance! Sincerely, Lenka Lenka Milojević Biophysics PhD Candidate Z. Hong Zhou Lab University of California, Los Angeles

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Closest distance list between residues/atoms; And selecting first/last residue in a chain
by pm676＠cam.ac.uk 27 Nov '24

27 Nov '24

Hi Is there a way by command line to generate a list of residue to residue (or atom to atom) distances ranked by closest to furthest, for say, all residues within 4A of each other at an interface between two protein chains? Can it also state the type of interaction, e.g. salt bridge, H-bond, vdW? Also, completely separately, is there a way by command line to select the first and last residue in a chain (without having to find their number)? No worries if not. Thanks so much! Cheers, Paul

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Visualization of methyls rotations
by Enrico Martinez 27 Nov '24

27 Nov '24

Dear ChimeraX users! In visualizing the MD trajectory, I noticed a small issue with the depiction of the rapid rotations of the ligand's methyl groups. Specifically, the hydrogens appear to periodically collapse into a singularity before returning to their expected positions. Could this be addressed through additional post-processing of the trajectory data? Many thanks in advance Enrico

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Question about using AF3-competitor outputs
by David S. Fay 26 Nov '24

26 Nov '24

Hi, Apologies if this already came up and I missed it. I just ran a few dimer models on the Chai Discovery website (https://lab.chaidiscovery.com/dashboard) and it seems to work quite well. However, when I tried to upload the relevant json file using the Structure Prediction - AlphaFold Error Plot pulldown menu, ChimeraX failed to recognize the file. I tried a few other files and something similar happened. Do you know of a workaround or is this something that is likely to get patched soon? I should mention that Chai may be putting the relevant PAE information into a “npy" file, (e.g., pae.model_idx_0.rank_1.npy) based on the size of that file, and I haven’t yet tried to convert npy to a json or know if that’s even possible. I also wonder if Boltz-1, another AF3 competitor, will have different outputs as well. They don’t seem to have a GUI yet and perhaps they won’t, so I haven’t been able tyo test this yet. I assume this has all been topic of discussions at ChimeraX though… Thanks in advance for your help! David David S. Fay Ph.D. Professor, Department of Molecular Biology Associate Director, National Institutes of Health Wyoming INBRE University of Wyoming email: davidfay(a)uwyo.edu

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How to remove specific H bonds
by Sen, Anindito 26 Nov '24

26 Nov '24

Dear ChimeraX group, How do I remove certain 'H' bonds from an atomic model, leaving the important 'H' bonds Regards Stay safe & Regards Anindito Sen. Ph.D

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Some questions about electrostatic potiential surface
by Quek 26 Nov '24

26 Nov '24

Dear Administrator, May I ask why the electrostatic potential surface I generated in Chimera X is entirely red without any blue? Is it because the electrostatic range is not set correctly? Could you tell me in which module I can set the range for the electrostatic potential? Additionally, how can I display the color scale for the electrostatic potential? Looking forward to your reply. Quek 1171543499(a)qq.com  

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RMSD between nonidentical atomic models
by Roden Deng Luo 26 Nov '24

26 Nov '24

Hi, If two atomic models do not have the exact same atoms, rmsd command does not run. One workaround would be to use matchmaker beforehand, and there is indeed a reported RMSD between "pruned atom pairs." However, this applies the matching before the calculation. In addition, from the attached screenshot (matching https://alphafold.ebi.ac.uk/files/AF-P32565-F1-model_v4.cif to 5wvi chain N), I expect most of the atoms should not be pruned, which is not the case. I wonder if there is a command or tool to calculate the RMSD between the not-moved nonidentical atomic models. Thanks, Roden -- 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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ChimeraX opening failure
by gianmarco.elisi＠gmail.com 25 Nov '24

25 Nov '24

Dear users, ChimeraX fails to open with multiple installation versions. The error with debug option that is shown is the following: Starting main interface Toolshed: find_bundle ChimeraX-Toolbar True None Toolshed: find_bundle ChimeraX-Toolbar True None Toolshed: find_bundle ChimeraX-Toolbar True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-SelInspector True None Toolshed: AvailableBundleCache.load: toolshed_url https://cxtoolshed.rbvi.ucsf.edu Toolshed: AvailableBundleCache.load: url https://cxtoolshed.rbvi.ucsf.edu/bundle/?uuid=e42ced0f-7162-57b1-9d35-4f49e… Toolshed: find_bundle ChimeraX-Core True None Windows fatal exception: access violation Thread 0x00004b9c (most recent call first): File "C:\Program Files\ChimeraX 1.8\bin\Lib\socket.py", line 836 in create_connection File "C:\Program Files\ChimeraX 1.8\bin\Lib\http\client.py", line 945 in connect File "C:\Program Files\ChimeraX 1.8\bin\Lib\http\client.py", line 1451 in connect File "C:\Program Files\ChimeraX 1.8\bin\Lib\http\client.py", line 979 in send File "C:\Program Files\ChimeraX 1.8\bin\Lib\http\client.py", line 1041 in _send_output File "C:\Program Files\ChimeraX 1.8\bin\Lib\http\client.py", line 1281 in endheaders File "C:\Program Files\ChimeraX 1.8\bin\Lib\http\client.py", line 1332 in _send_request File "C:\Program Files\ChimeraX 1.8\bin\Lib\http\client.py", line 1286 in request File "C:\Program Files\ChimeraX 1.8\bin\Lib\urllib\request.py", line 1348 in do_open File "C:\Program Files\ChimeraX 1.8\bin\Lib\urllib\request.py", line 1391 in https_open File "C:\Program Files\ChimeraX 1.8\bin\Lib\urllib\request.py", line 496 in _call_chain File "C:\Program Files\ChimeraX 1.8\bin\Lib\urllib\request.py", line 536 in _open File "C:\Program Files\ChimeraX 1.8\bin\Lib\urllib\request.py", line 519 in open File "C:\Program Files\ChimeraX 1.8\bin\Lib\urllib\request.py", line 216 in urlopen File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\core\toolshed\available.py", line 62 in load File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\core\toolshed\__init__.py", line 467 in reload_available File "C:\Program Files\ChimeraX 1.8\bin\Lib\threading.py", line 975 in run File "C:\Program Files\ChimeraX 1.8\bin\Lib\threading.py", line 1038 in _bootstrap_inner File "C:\Program Files\ChimeraX 1.8\bin\Lib\threading.py", line 995 in _bootstrap Current thread 0x00005d04 (most recent call first): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\ui\gui.py", line 315 in event_loop File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\core\__main__.py", line 1003 in init File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\core\__main__.py", line 1166 in <module> File "<frozen runpy>", line 88 in _run_code File "<frozen runpy>", line 198 in _run_module_as_main Any suggestion? Thanks

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Overlay of specific chains
by Reza Khayat 25 Nov '24

25 Nov '24

Hi, We have multiple structures of a homo-hexamer (chains A-F). We'd like to overlay limited regions of each chain onto equivalent chains (e.g. residues 200-452 of chain A onto residues 200-452 of chain A). We're having difficulty identifying the correct syntax. Some of our structures align as desired while others are aligned according to the chain combinations that produce the lowest RMSD (e.g. residues 200-452 of chain A align onto residues 200-452 of chain C. Is it possible to restrict which chains align to which? Best wishes, Reza

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