- ChimeraX-users - RBVI Mailing Lists

ChimeraX workshop
by Jisoo Hwang 03 Jul '24

03 Jul '24

To whom it may concern, Good afternoon! I hope this email finds you well. I'm a student doing research at Johns Hopkins and was wondering if it'll be possible for us to set up a zoom meeting to ask some questions about the software. It's my first time using the software and it would be incredibly helpful if we can have a short workshop going over the features of ChimeraX. We're trying to include a 3D structure in a paper that we're planning on publishing soon. Please let me know if there's any other resource that you can point us to if we can't do a zoom meeting. Thank you so much for your help! Best, Suzie Hwang

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Request for Assistance: Selecting and Visualizing Interacting Residues in UCSF ChimeraX
by Rashmi Aggarwal 30 Jun '24

30 Jun '24

Dear UCSF ChimeraX Support Team, My name is Rashmi, and I am currently working on molecular docking studies as part of my research. I have been using UCSF ChimeraX version 1.8 for visualizing and analyzing protein structures. I am facing difficulties in performing the following tasks related to identifying interacting residues between chains A and B within 4 angstroms, similar to what I have previously done in PyMOL: 1. Select residues in chain A that are within 4 angstroms of chain B: select interactA, byres ((chain A) within 4 of (chain B)) 2. Select residues in chain B that are within 4 angstroms of chain A: select interactB, byres ((chain B) within 4 of (chain A)) 3. Combine the selections for interacting residues: select interaction_residues, interactA or interactB 4. Show interacting residues in stick representation and color them yellow: show sticks, interaction_residuescolor yellow, interaction_residues Despite attempting various commands and exploring the graphical user interface, I have been unable to achieve the desired results using UCSF ChimeraX. Could you please provide guidance on the correct commands or steps to accomplish this task in ChimeraX? Any assistance or advice would be greatly appreciated, as I have a pending deadline for my project. Thank you very much for your attention to this matter. I look forward to your prompt response. Best regards, Rashmi

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Aligning small molecules in Chimera
by Prathvi Singh 30 Jun '24

30 Jun '24

Hi Elaine, Is it possible to superimpose/align small molecules in chimera/chimeraX? I have isolated a very small part of a polypeptide chain from a PDB file (it contains a CO and NH group engaged in peptide bond formation and both the groups are flanked by C-alpha atoms such that the structure's formula becomes CH3-CO-NH-CH3). I have 10 such PDB files. I want to extract this fragment from each PDB file and superimpose them to know the differences. Thank you Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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RMSD does not make sense in a few cases
by Roden Deng Luo 29 Jun '24

29 Jun '24

Hello ChimeraX Team, In the attached screenshot, #1 and #3 are almost overlapping, but get an RMSD as 57. I occasionally encounter this. The session and log files are attached. In short, to reproduce, open 5nl2.cif and emd_3658.map; fitmap #1 in #2 search 1000; rmsd #1 to #3. This happened rarely, but in this case, it happened twice. It might be that I fit other structures first. But I indeed click "Clear List" and "close session" after each fitting. The second top hit's RMSD seems to make sense in the attached session (screenshot attached too). 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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Where has the ribbon style editor gotten to?
by Dearborn, Altaira (NIH/NIAID) [E] 28 Jun '24

28 Jun '24

I tried the NIH3D presets to prepare my structure for 3D printing. The large size of the complex, however, makes those settings still too lacey for the NIH 3D printing service. I need to edit the ribbon sizes. The youtube tutorials from the NIH 3D Printing Exchange are 7-10 years old and their instructions to open the Ribbon Style Editor no longer match chimerax. Has this feature been renamed and moved? Thank you, Altaira Dearborn

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NICE DCV graphics error
by georg.kempf＠fmi.ch 28 Jun '24

28 Jun '24

Dear ChimeraX developers and users, we would like to use ChimeraX in a virtual session using the “NICE DCV” software. We verified that OpenGL hardware rendering is working in the virtual session (glxinfo, glxgears, nvidia-smi) but when opening a structure in ChimeraX, we get the below error. We tried it with different versions of ChimeraX (1.8.dev202311220127, 1.6.1 stable) on Ubuntu 20.04.6 LTS. Since the error doesn’t appear when using ChimeraX on the physical display of the same workstation(s) (where the DCV server is running) it must be related to the virtual session context. I was wondering if anyone knows what could be the cause of the error and in which direction to look regarding debugging? This is the traceback from ChimeraX: An error occurred in drawing the scene. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command "graphics restart" after changing the settings that caused the error. GLError( err = 1282, description = b'invalid operation', baseOperation = glDrawBuffer, cArguments = (GL_NONE,) ) Traceback (most recent call last): File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84, in draw_new_frame view.draw(check_for_changes = False) File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/view.py", line 188, in draw self._draw_scene(camera, drawings) File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/view.py", line 226, in _draw_scene shadow, multishadow = self._compute_shadowmaps(opaque_drawings, transparent_drawings, camera) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/view.py", line 626, in _compute_shadowmaps multishadow_enabled = r.multishadow.use_multishadow_map(shadow_drawings) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 1628, in use_multishadow_map self._start_rendering_multishadowmap(center, radius, size) File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 1711, in _start_rendering_multishadowmap fb = r.start_depth_render(self._multishadow_map_framebuffer, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 1356, in start_depth_render if not fb.activate(): ^^^^^^^^^^^^^ File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2309, in activate fbo = self.framebuffer_id ^^^^^^^^^^^^^^^^^^^ File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2305, in framebuffer_id self._fbo = fbo = self._create_framebuffer() ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2141, in _create_framebuffer fbo = self._create_fbo(self.color_texture or self._color_rb, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/chimerax/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2169, in _create_fbo GL.glDrawBuffer(GL.GL_NONE) File "src/errorchecker.pyx", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1282, description = b'invalid operation', baseOperation = glDrawBuffer, cArguments = (GL_NONE,) ) Many thanks! Kind regards, Georg

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ChimeraX install problems
by Alexander Hung Lee 27 Jun '24

27 Jun '24

I tried to install ChimeraX daily build on a fresh install of Ubuntu 24. When I launch the program, the log says "Available bundle cache has not been initialized yet." Another oddity I"ve noted is that tying to run a python script w/ "chimerax --nogui --silent --offscreen --script path/to/script" works but "chimerax --script path/to/script" doesn't. I just get a black screen. There also isn't a stable build for Ubuntu 24, only daily builds. Should I downgrade my OS? Alex

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induce mutations in protein structure
by Mamadou Sangare 27 Jun '24

27 Jun '24

Dear, I'm new in chimera and I wouldlike to know how to induce mutations in protein structure, in other words, how to replace one residue by another in the protein structure. Kind regards! Mamadou SANGARE, PhD student ACE-B,Mali

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Feature suggestions for the Segmentations tool
by Ricardo Righetto 27 Jun '24

27 Jun '24

Hi, Thanks a lot for adding the Segmentations mode in v1.8, this is very much welcomed for cryo-ET data! Are there any plans for expanding the capabilities of this tool? If possible, I would like to suggest some features for manual segmentation: * Segment contiguous density in 3D by clicking on it (akin to the blob selector in the "Right Mouse" options, which operates on surfaces) * Related: threshold-based segmentation i.e. segment in 3D all contiguous density between selected minimum and maximum density thresholds * 2D/3D Lasso-based segmentation * Dilation, erosion and smoothening of segmentations Some of these things are already possible by combining volume and surface operations or with external tools, but it would be very nice to have everything streamlined in one click (or a few) through the GUI. Alternatively, I would appreciate pointers on how to implement these features as a ChimeraX plugin. Happy to discuss more. Thank you and have a nice weekend! -- Ricardo Diogo Righetto

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Re: ChimeraX does not Support .stl files?
by Zach Pearson 26 Jun '24

26 Jun '24

Hi Kevin, Please direct questions about ChimeraX to our mailing list, chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> — others on the team or even in the community may have more experience or more recent experience in a given subject than I or any other developer has at the moment. Eric (CC’ed) has been working on the NIH 3D pipeline; part of that pipeline is adding struts to delicate objects for 3D printing. He may be able to help you better than I can. — Zach > On 26 Jun 2024, at 14:55, Maroney, Kevin James <kmaroney(a)uab.edu> wrote: > > Hello Dr. Pearson, > Despite doing more Immunology research and really no proteomics, I have had a hobby interest in fooling around with Pymol and ChimeraX. I just recently got a very nice 3D Printer and was hoping to print out a model of the epitope of my PhD complexed between HLA-B57 and TCR that is publically available. I was going to use UCSF Chimera, but it does not seem like it is capable of representing space-filling diagrams and only gives me errors. I obviously can’t print the complex and delicate ribbon or atomic representations and like ChimeraX better anyway. But the guide from the NIH suggests passing PDB models through Chimera to generate .stl files which I can easily then pop into my Studio software to 3D print and resize etc. Problem is, I don’t see that there is any way to actually export as .stl in ChimeraX. Is there any way you could add this feature? Thank you very much. Lovely program. > > Sincerely, > Kevin Maroney > M.S. Biotechnology > University of California, Irvine > PhD Student > University of Alabama at Birmingham

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transparency using in movie making
by Yanhe Zhao 26 Jun '24

26 Jun '24

Dear ChimeraX team, I have a map with model docking and am making movie. My plan is to fade away the map to show the docked model for next step. I tried the crossfade which works. But I want to use the transparency command for this purpose because I want to keep the map at specific transparency level, like 80%. The chimera has command like 'surftransparency 80 #1 50'. I was wondering what is the similar command in ChimeraX? Thanks and cheers, Yanhe

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Sequence based selections
by Kumpula, Esa-Pekka 26 Jun '24

26 Jun '24

Dear ChimeraX team, Two selection-related questions: 1. I'm looking for a way to combine multiple sequence based selections into one selection but I wasn't able to find a way to do this. The use case is, I have a lot of models that have these two proteins and I would like to use them together for superposition (via align command against Calphas). I would normally refer to them by chain ID, but here these are not consistently assigned so I need to use the sequence for selection. 1. Is it possible to have a named, sequence-based selection that, when called, would perform the selection? This would save a lot of pain when writing scripts for sequence based selections. Cheers, EP -- Esa-Pekka Kumpula, PhD Senior Postdoctoral Researcher Laboratory of Structural Biology Institute of Biotechnology Helsinki Institute of Life Science HiLIFE University of Helsinki www.helsinki.fi/lsb<http://www.helsinki.fi/lsb>

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Generic Linux installation package for ChimeraX 1.8
by Kumpula, Esa-Pekka 26 Jun '24

26 Jun '24

Dear ChimeraX team, I noticed that version 1.8 no longer comes with a "Generic Linux" installation package (unlike 1.7). I have been using this for a centralised installation on a network drive that has so far worked very well. Is this coming to 1.8 or is it discontinued? Cheers, Esa-Pekka -- Esa-Pekka Kumpula, PhD Senior Postdoctoral Researcher Laboratory of Structural Biology Institute of Biotechnology Helsinki Institute of Life Science HiLIFE University of Helsinki www.helsinki.fi/lsb<http://www.helsinki.fi/lsb>

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Bundles with dependencies
by Vincent Mallet 24 Jun '24

24 Jun '24

Hello, Thanks for the tool and the tutorials. I have a machine learning tool based on pytorch to analyse cryo-EM data. I was hoping to package (bundle) it for Chimerax and started to follow tutorials, but I don't think you mention the right way to set up a code environment with depencies. I see a numpy import in the save_new_format tutorial, but it's not listed in the "dependencies" section of the xml file. I guess my question is : can I add arbitrary packages in a bundle ? Is there a way to install pip packages only ? Should I copy all source code in the folder and deal with my imports like that ? In particular, I am thinking of torch that is not so easy to replace... I am hoping you can help me, thanks in advance for the help ! Best, Vincent

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Troubleshooting MOLE Channel Visualizations
by Josh Gonzalez 24 Jun '24

24 Jun '24

Hello, I am a newer user of ChimeraX and am having some trouble creating visualizations to characterize a channel of interest. I began by following the procedure outlined in the tutorial "MOLE Channel Coloring by Property" but quickly ran into some issues with my own channel. This led me to try the click-to-execute links for the example in the tutorial and I ran into the same problem. It seems ChimeraX cannot accept .json files that are not Alphafold PAE maps, meaning there is no way to visualize the results of the MOLEsever analysis. I have attempted parsing data from the .json into a usable file format such as a .bild or a .pdb in a separate anaconda kernel, and while I am able to get coordinates for a superimposed visualization, they are not selectable atoms that can be color-coded or manipulated as they are in the procedures following the "open molepore-1bl8.json" command. I know this is because I have not found a way to parse all of the useful data from the .json file into another format, but I do not see exactly how I would go about doing so. Is there a way to get ChimeraX to accept a .json file that is not a PAE plot without the need for parsing data or changing format? Thank you so much for the help!

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Question
by Suwisanto, Natasha 24 Jun '24

24 Jun '24

Hello, My name is Natasha Suwisanto. I’ve been using UCSF Chimera X and AlphaFold servers for a personal research project to mutate a GPCR protein. I just had a quick question. I was mutating a structure using the Rotamer tool on ChimeraX. I mutated a single amino acid (Tyrosine) to a Proline using the Richardson Common Atom library. However, when I ran AlphaFold on it, the predicted 'best model' structure they gave me had a different amino acid (Leucine) on the position I previously mutated the Tyrosine to the Proline. I was just wondering if I did something wrong or if AlphaFold/ChimeraX works differently than I thought. Best, Natasha Suwisanto

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Installing ChimeraX on Linux without sudo
by Ricardo Righetto 24 Jun '24

24 Jun '24

Dear ChimeraX team, Is there any way to install ChimeraX >= 1.8 on Linux without admin rights, like a generic Linux version that I can unpack at an arbitrary location? Our system is running Ubuntu 22.04 more specifically. Thank you! -- Ricardo Diogo Righetto

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Help_saving
by Noriega, Heather 22 Jun '24

22 Jun '24

Hello, I have a question. I created this sphere nanoparticle and have been trying to save it as a PDB (the whole sphere). But when I save "selected atoms, " I try to re-open the PDB file. It only shows the original single Span-60 that was used. Is there a way to save the copies and nanoparticles as a whole so I can minimize them altogether? I attached the session below for your reference. Thanks, Happy Friday! Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883

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Re: Help_saving
by Elaine Meng 21 Jun '24

21 Jun '24

Sure, if you tell me that works. I wasn't sure if #2 had all 60 or just the other 59 and it would have been another several minutes experimenting. Elaine > On Jun 21, 2024, at 1:53 PM, Tom Goddard <goddard(a)sonic.net> wrote: > > How about execute the second sym command with copies true on model #2 which has the first 60 copies? > > Tom > > >> On Jun 21, 2024, at 1:50 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> >> Sigh, I was trying to enlist help in answering the question directly considering I've already spent hours messing around with it... especially if you think it is simple to explain. I don't think it is obvious to expect different numbers of copies just because you wanted them to be atomic instead of graphical. >> >> If she wants 3600 full atomic copies how would she do that?? >> >> Elaine >> >>> On Jun 21, 2024, at 1:35 PM, Tom Goddard <goddard(a)sonic.net> wrote: >>> >>> Hi Elaine, >>> >>> If you don't use copies true, then the first sym command changes model #1 rendering to include 60 graphical clones, and then the second sym command also on model #1 makes 60 graphical clones of the previous 60 graphical clones, so you now have 3600 graphical clones in model #1. You can see this with "info #1" which says "3600 instances". >>> >>> If you use the "copies true" option then the sym command makes a new model #2 with 60 copies. The second sym command on #1 with copies true makes 60 more copies as model #3. Of course that is a very different result then the sequence without copies true because the copies true version makes new models instead of modifying the original model. >>> >>> This all makes sense to me. >>> >>> Tom >>> >>> >>>> On Jun 21, 2024, at 1:25 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >>>> >>>> Hi Tom, maybe you can figure it out?? >>>> >>>> OK I give up, I did extensive tests and can't figure it out either. I regenerated the original starting molecule (I think), attached as temp.pdb >>>> >>>> Then the overall result visible with the following, which is what she apparently wants (except with real atomic copies) although I worry it may have double copies in places, is a very packed-looking sphere: >>>> >>>> sym #1 i,2n5 center 20,20,20 >>>> sym #1 i,2n3 center 20,20,20 >>>> >>>> However if you start over with temp.pdb and then do the following, you get something much more patchy/holey >>>> >>>> sym #1 i,2n5 center 20,20,20 copies true >>>> sym #1 i,2n3 center 20,20,20 copies true >>>> >>>> I thought it might have something to do with copies replacing other copies but I tried with newModel true and still had seemingly the same issues. >>>> >>>> Maybe the more-packed appearance is actually a bug if sym w/o copies true makes more graphical copies of ones that are already graphical copies. >>>> >>>> Elaine >>>> >>>> <temp.pdb> >>>> >>>> >>>> >>>>> Begin forwarded message: >>>>> >>>>> From: "Noriega, Heather via ChimeraX-users" <chimerax-users(a)cgl.ucsf.edu> >>>>> Subject: [chimerax-users] Re: Help_saving >>>>> Date: June 21, 2024 at 12:14:50 PM PDT >>>>> To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> >>>>> Reply-To: "Noriega, Heather" <heather.noriega(a)bison.howard.edu> >>>>> >>>>> Hello, >>>>> >>>>> It is quite baffling to me why it does this. I am going to add different sessions to show you what I see. I have included each session to try and separate to explain myself and not confuse. Three of the sessions do not include the copies true command: (sym_2n3, sym_2n5, sym_both). The one with both (sym_2n3 and sym_2n5) gives me the niosome I am quite interested in with an aqueous and lipophilic compartment. I want to do a simple measure of the volume inside the large compartment, but would like to minimize the niosome as a whole first, hence needing a pdb file. However, I have done the same with the next three sessions, but adding copies true command and it is not coming up with the same result for sym_both_copiestrue. >>>>> >>>>> I hope this helps to try and understand what I am looking for, and maybe you have an answer as to why there are different results for Sym_both and Sym_both_copiestrue. >>>>> >>>>> Thank you, >>>>> >>>>> Heather Noriega >>>>> PhD-Pharmaceutical Science student >>>>> Howard University >>>>> heather.noriega(a)bison.howard.edu >>>>> 520-203-1883 >>>>> >>>>> >>>>> On Fri, Jun 21, 2024 at 2:33 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >>>>> Hi Heather, >>>>> >>>>> I don't really understand why you needed two sym commands instead of one (must be something specific about your structure(s)), but whenever you want to actually save the PDB of any parts that "sym" adds you would need to include "copies true" when you add them. >>>>> >>>>> You could just do the experiment with and without it yourself and see what you get. Or save two separate PDB files, one from each command, to make sure you aren't getting duplicates of the same atoms exactly on top of each other from using sym twice. >>>>> >>>>> Elaine >>>>> >>>>>> On Jun 21, 2024, at 9:45 AM, Noriega, Heather via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>>>>> >>>>>> Hello, >>>>>> >>>>>> I do not want to save the shape of a sphere. I was using that for something else while creating the nano. >>>>>> >>>>>> Ok, that is what I did wrong. I did not include the copies true command. I have a question. I used the commands: >>>>>> >>>>>> Sym #1 i,2n3 center 20,20,20 and Sym #1 2n5 center 20,20,20 to create the sphere. Would I have to add copies true to both commands? >>>>>> >>>>>> sym#1 i,2n3 center 20,20,20 copies true >>>>>> sym#1 i,2n5 center 20,20,20 copies true >>>>>> >>>>>> And then continue with the saving process for PDB >>>>>> >>>>>> >>>>>> Thank you, >>>>>> >>>>>> Heather Noriega >>>>>> PhD-Pharmaceutical Science student >>>>>> Howard University >>>>>> heather.noriega(a)bison.howard.edu >>>>>> 520-203-1883 >>>>>> >>>>>> >>>>>> On Fri, Jun 21, 2024 at 12:37 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >>>>>> Hi Heather, >>>>>> I can't tell what you are trying to save exactly but here are two issues: >>>>>> >>>>>> (1) when you used "sym" the Log said it was making graphical clones. (The log contents are included in the session file.) If you want full atomic copies instead of graphical clones you have to use "copies true" as explained in the help: >>>>>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#copies> >>>>>> >>>>>> (2) The big sphere seems to be a surface model, and you can't save a surface model as PDB format. Maybe you used the "shape" command, which creates surface models. But I can't tell from your message whether you are trying to save that in the file or not. >>>>>> >>>>>> 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 Jun 21, 2024, at 9:16 AM, Noriega, Heather via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>>>>>> >>>>>>> Hello, >>>>>>> >>>>>>> I have a question. I created this sphere nanoparticle and have been trying to save it as a PDB (the whole sphere). But when I save "selected atoms, " I try to re-open the PDB file. It only shows the original single Span-60 that was used. Is there a way to save the copies and nanoparticles as a whole so I can minimize them altogether? >>>>>>> >>>>>>> I attached the session below for your reference. >>>>>>> >>>>>>> Thanks, Happy Friday! >>>>>>> >>>>>>> Thank you, >>>>>>> >>>>>>> Heather Noriega >>>>>>> PhD-Pharmaceutical Science student >>>>>>> Howard University >>>>>>> heather.noriega(a)bison.howard.edu >>>>>>> 520-203-1883 >>>>>>> <nano_span_60.cxs> >>>>> >>>> <sym_2n5_copiestrue.cxs> >>>> <sym_2n3_copiestrue.cxs> >>>> <sym_2n5.cxs> >>>> <sym_2n3.cxs> >>>> <sym_both.cxs> >>>> <sym_both_copiestrue.cxs> >>>>> _______________________________________________ >>>>> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu >>>>> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu >>>>> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >>>> >>> >> >> > >

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Sequence viewer colour by B factor
by isaphan＠uw.edu 21 Jun '24

21 Jun '24

How do I colour a sequence by B factor? There's an option to 'Load a sequence coloring file'. Sounds good, but how do I produce an .scf file from a structure coloured by B-factor ? There's a format explanation, but how do I get the actual data ? Grateful for any hints.

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question about coloring
by Artur Biela 21 Jun '24

21 Jun '24

dear all, I would like to color my structure (atoms) according to the LocalResolution of the map that the model is fitted in. There is a simple way to color a map according to the colors of the molecular model, but can it be done the other way around? best Artur =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Artur BIELA, PhD tel: +48-518-459-652 @: artur.biela(a)uj.edu.pl [cid:ced8e93e-4e29-47d8-b709-419b04837a3b] cryoEM faciliy manager SOLARIS National Synchrotron Radiation Centre Jagiellonian University Czerwone Maki 98, 30-392 Kraków www.synchrotron.pl<http://www.synchrotron.pl/> https://synchrotron.uj.edu.pl/en_GB/linie-badawcze/cryo-em

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Adjusting Torsion Angles
by Eleanor Streeper 20 Jun '24

20 Jun '24

Hi Chimera X, I hope you are well. I am a student at Swarthmore College and am currently trying to use Chimera X to adjust the torsion angles of glycans on a protein I have glycosylated. I tried using the same notation in your user guide, but the program says I am only entering 3 atom into the command bar. I attached images of the command and the numbering of those atoms (2nd entry in the angle/torsion measurement picture). I am trying to get the 2nd entry torsion to be 178.6 degrees. Can you let me know what I am doing wrong and how to adjust the torsion angle. Best, Ellie Streeper [image: Screenshot 2024-06-20 at 1.28.34 PM.png][image: Screenshot 2024-06-20 at 1.28.24 PM.png] [image: Screenshot 2024-06-20 at 1.35.46 PM.png]

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Re: CHimeraX and Chimera website down
by Elaine Meng 19 Jun '24

19 Jun '24

Hi Yaikhomba, Yes, we had a planned outage for server maintenance the last few days. Usually our email is out at the same time so it will not help to send email either, sorry! There was an announcement about it to this chimerax-users email list and also a news item on the ChimeraX home page, although of course you can't see the home page when the website is down. You can change the map origin with the ChimeraX "volume" command option "origin" or "originIndex", see the help for what these mean and how to use them: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dimensions> 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 Jun 19, 2024, at 8:49 AM, M Y <yai25ram(a)gmail.com> wrote: > > Hi Elaine > > I hope you are well. > > I had trimmed the box size of a cryoEM-map using the RELION software (to 375 pixels from 600 pixels). To fit in a PDB model to the trimmed map, I also rescaled the trimmed map to 1.048 A/pixel from 1.07 A/pixel. However, these 2 maps do not overlay with one another (image attached). > > I wanted to change the origin of the trimmed map such that 2 maps overlay with one another. How could I do this in ChimeraX? > > I tried looking at the Chimera or the ChimeraX website. But, the website is either down or I am not able to access it (Screenshot attached). > > Your suggestions will be helpful. > > Many thanks > Yaikhomba > <image.png> > <image.png>

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Creating bond between two selected atoms
by Eleanor Streeper 17 Jun '24

17 Jun '24

Hi Chimera X, I hope you are well. I am a student at Swarthmore College and am currently trying to use Chimera X to covalently attach glycans to asparagine residues. I was able to get 3 out of 5 of the glycans attached by selecting both atoms > structure editing > build structure > adjust bonds > add reasonable bonds. I did the same process for the other 2 glycans and no bond was made. The log says bond sel, 0 bonds. The glycans are combined with the protein using the combine command. I believed it may be an issue with an unreasonable binding distance but when I moved the glycan closer, the bond still didn't work. What else should I try? Also, do you know why it is working for some glycans but not others? Best, Ellie Streeper

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Updating pdb SEQRES record with a loaded .fasta file
by Samuel Haysom 14 Jun '24

14 Jun '24

Hello, I would like to use a .fasta file that I have loaded into ChimeraX to update the SEQRES records of a PDB file that is also loaded into ChimeraX. Currently the loaded PDB file only has SEQRES records for the residues that are modelled, while the .fasta file has the full, sequence with no gaps. I have tried loading in the .fasta file and then using the $ sequence associate command to associate it with the relevant pdb chain. However, when I then save out the pdb file (using the $ save command) and then examine the pdb file it still only records the modelled residues. Is there any way to force the written pdb file to have the full sequence as uploaded in the .fasta file? I am running chimeraX version 1.7 (2023-12-19). Thanks for your help, Sam Samuel Haysom Research Scientist • Biophysics Nxera Pharma UK Limited +44 (0)1223 949201 • Steinmetz Building, Granta Park, Great Abington Cambridge, CB21 6DG, United Kingdom The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Contact and registered office address: Nxera Pharma UK Limited, Granta Park, Great Abington, Cambridge, CB21 6DG. Company No: 06267989.

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