- ChimeraX-users - RBVI Mailing Lists

moving map with model in chimerax
by Fabian Glaser 20 May '21

20 May '21

Dear experts, I am preparing figures for a paper, and I would like to color several structures using apbs dx maps. I manage todo that, but I need to move or align the coordinates of the pdb in order to map several different maps, and when I save the chimerax session and reopen, the map is not aligned with the new coordinates of the pdb, so the colouring fails. So is there a way to move or associate the map with a certain model, and move it together with it? Tahnks a lot, Fabian ---------------------------------------------------------------------------- Fabian Glaser PhD Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel Web https://lokey.technion.ac.il/bioinformatic-knowledge-unit/ <https://lokey.technion.ac.il/bioinformatic-knowledge-unit/> Tel +972 (0) 4 8293701

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Questions:how to clean the dashed lines in chimeraX?
by 段泽林 20 May '21

20 May '21

Dear ChimeraX developers, When I opened my structure in chimeraX, I see dashed lines inside my model,those dashed lines represent the gap inside the model because I cannot model these gaps due to bad density. Now I want to clean these dashed lines, I can use the inspect selection panel to clean these dashed lines in chimera, but I cannot do that in chimeraX, would you please tell me how to do that? either in command line or GUI many thanks Zelin

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Colour residues by local resolution estimation map
by Ioannis Skalidis 20 May '21

20 May '21

Dear all, I am trying to color a protein model based on the local resolution of the corresponding map. I can color the overall surface of the model, but not the residues themselves. Is there a way to do this, e.g, color the model backbone somehow? Thanks a lot for your help! Cheers, Yiannis -- Skalidis Ioannis, MSc Biochemistry & Cryo-EM Scientist PhD Candidate Kastritis Laboratory for Biomolecular Research Cryo-Electron Microscopy & Computational Structural Biology ________________________________________________ Martin-Luther-Universität Halle-Wittenberg Biozentrum, Room A.2.21 IWE ZIK HALOmem NWG III "Kryo-Elektronenmikroskopie an Membranproteinkomplexen" Weinbergweg 22, 06120 Halle tel: +49 345 5524986 web (Lab): https://blogs.urz.uni-halle.de/kastritislab/ web (HALOmem): https://www.halomem.de/en/

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Measuring surface area of a colored portion of the map
by Y. Mutum 19 May '21

19 May '21

Hi This problem relates to surface area of a low-resolution EM map using ChimeraX I have opened the following map and the corresponding model using the following commands in ChimeraX. >>> open 4uq8; open 2676 from emdb >>> color #1 green; color zone #2 near #1 dist 4 As many parts of the map are unmodelled, I am interested 'how much of the map is unmodelled' in terms of surface area. This is mainly because the model is not accurate and I am trying to only use the raw-data (map) to estimate the surface area and avoid using the model. Is there a way to figure out how much of the map is unmodelled in terms of surface area? In this case, count the number of 'outer pixels of a map' that are colored green or gray, at a given map contour? Could you please help with a way to measure this without using the 'volume splitbyzone' command? Thanks Yaikhomba [cid:71184965-9ba5-4374-82b3-bd2b264b4b0c]

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Re: [chimerax-users] How to change the palette of hydrophobicity in ChimeraX
by Le Han 19 May '21

19 May '21

Hi Elaine, Thank you so much for your help. I managed to change it. Have a nice day! Han From: Elaine Meng<mailto:meng@cgl.ucsf.edu> Sent: Tuesday, 18 May 2021 18.12 To: Le Han<mailto:han.le@aalto.fi> Cc: chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] How to change the palette of hydrophobicity in ChimeraX Hi Han, Although the icon just uses the "mlp" command with the default palette, you can use the "mlp" command with any palette that you want. The "palette" option specifies palette and "range" specifies value range. Instructions on "mlp" command and how to specify palettes: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/mlp.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options> The hydrophobic coloring icon in the Toolbar "Molecule Display" tab uses command: mlp ...which is same as: mlp palette lipophilicity range -20,20 To use the same value range but get blue for hydrophilic and red for hydrophobic, you could use, for example, command: mlp palette blue-white-red range -20,20 Since red-white-blue is traditionally used for electrostatic coloring, however, you will have to be sure to explain the image so that people understand it is showing hydrophobicity instead. In the "mlp" instructions linked above, you can see there are several other options of the command that may interest you. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 18, 2021, at 6:55 AM, Le Han <han.le(a)aalto.fi> wrote: > > Hi, > I’d like to change the colour palette of hydrophobicity to red (most hydrophobic) – white – blue (most hydrophilic). Is it possible to do so in ChimeraX and how can I change? > Thank you in advance, > Han

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Proxy setting with user authentication
by fukamitka＠chugai-pharm.co.jp 18 May '21

18 May '21

Dear ChimeraX developers, I’m a new user of ChimeraX. How can I set username/password for HTTP/HTTPS proxy settings? Our firewall is strict and requires username/password authentication. I’d like to install ISOLDE (we purchased the license), but I can’t install it via Tools > More Tools... I downloaded the .whl file for ISOLDE from the ChimeraX Toolshed page (https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxisolde) and tried the command below in ChimeraX windows, toolshed install /path/to/the/ChimeraX_ISOLDE-1.2.0-cp38-cp38-manylinux_2_17_x86_64.whl but failed during pip install (by SSLError, which means proxy was not set correctly). Enviroment variables http_proxy and https_proxy were set when ChimeraX executed, but not worked. Best regards, Takaaki ----- Dr. Takaaki Fukami (mailto:fukamitka@chugai-pharm.co.jp) Protein Science Dept. (Protein Science 2 Gr.) Chugai Pharmaceutical Co.,Ltd. 200 Kajiwara, Kamakura, 247-8530 Japan Tel: +81-467-47-6178

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How to change the palette of hydrophobicity in ChimeraX
by Le Han 18 May '21

18 May '21

Hi, I’d like to change the colour palette of hydrophobicity to red (most hydrophobic) – white – blue (most hydrophilic). Is it possible to do so in ChimeraX and how can I change? Thank you in advance, Han

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Pseudobond in Metalloproteins
by Rachael Coleman 17 May '21

17 May '21

Hello! I have recently switched over to using ChimeraX from PyMol and I'm really enjoying it a lot! My one question that I haven't been able to figure out is how to deal with pseudobonds in a heme-containing protein. I want ChimeraX to treat the bond between the porphyrin N atoms and the Fe atoms like a bond and not a pseudobond (so I want it to be half blue and half orange to correspond to the colors of those atoms). Is there an easy way to tell the program that a pseudobond is a bond? Best, Rachael Coleman -- *Rachael E. Coleman* PhD Candidate, Lancaster Group Department of Chemistry and Chemical Biology Cornell University Ithaca, NY 14853 Pronouns: She, her, hers

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How to Color Each Atom (TAD) According to Its Gene Expression Level
by Cardiff Jiang 15 May '21

15 May '21

Dear ChimeraX Users Help, I want to color each atom, which is a TAD, according to its genes’ expression value. My code writes a Chimera marker file because it has RGB variables (shown below, the lower the gene expression, the lighter the shade of green). However, ChimeraX shows the entire model in the same color. How should I color each atom (TAD) according to its gene expression level? [image: image.png] Thank you. Best regards, Zichen “Cardiff” Jiang -- Best regards, Zichen “Cardiff” Jiang

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where is my saved image
by Kang, Yanyong 13 May '21

13 May '21

Hello, I am saving image using the command below. Do you know where the saved image is? Thanks save a.png transparentBackground true Yanyong The content of this email and of any files transmitted may contain confidential, proprietary or legally privileged information and is intended solely for the use of the person/s or entity/ies to whom it is addressed. If you have received this email in error you have no permission whatsoever to use, copy, disclose or forward all or any of its contents. Please immediately notify the sender and thereafter delete this email and any attachments.

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Release of ISOLDE 1.2
by Tristan Croll 13 May '21

13 May '21

Hi all, I'm very happy to announce the release of ISOLDE 1.2, now available for installation into the ChimeraX 1.2 release. To get it, first download and install ChimeraX 1.2 from https://www.rbvi.ucsf.edu/chimerax/download.html, then go to "Tools/More Tools..." in the menu and follow the links to install ISOLDE. Key new features include: * The ability to add residues to the ends of protein chains (see https://twitter.com/CrollTristan/status/1391747032579289089?s=20; support for nucleic acid chain extension still in development) * Lower-fidelity simulation modes for greatly improved performance on lower-end GPUs (see https://twitter.com/CrollTristan/status/1390709520876331009?s=20) * Commands to write input files for phenix.refine and phenix.real_space_refine with recommended settings for refining models from ISOLDE * Command to write a ProSMART-like restraint definition file to softly restrain the model to its current geometry in Refmac * Improvements to stability and performance of bulk solvent/scaling in crystallographic datasets * Short aliases for commonly-used commands to make life easier for power users. Please enjoy! Best regards, Tristan

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BLAST fix
by Eric Pettersen 12 May '21

12 May '21

Hi all, The RCSB switching off http access and only allowing https (which had been announced) unfortunately broke the fetching of PDB info associated with BLAST results, basically breaking the BLAST tools in both Chimera and ChimeraX. Fixes have been applied and will be available in tomorrow's daily builds. For ChimeraX, also available in the 1.2.3 release candidate -- hopefully also out tomorrow. --Eric Eric Pettersen UCSF Computer Graphics Lab

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Generating map from structure
by Eric Pettersen 11 May '21

11 May '21

> Begin forwarded message: > > From: "Azad, Roksana" <razad(a)gc.cuny.edu> > Subject: Re: [ChimeraX] #4622: save dialog: 'SaveModelOptionWidget' object has no attribute '_name' > Date: May 11, 2021 at 9:00:00 AM PDT > To: "ChimeraX-bugs(a)cgl.ucsf.edu" <ChimeraX-bugs(a)cgl.ucsf.edu> > > Dear Eric, > Thank you so much for your reply. > > I have a model of my protein in pdb format, which I am trying to save as .mrc or any sort of volume file on chimera. However, since its a model and do not have any coordinate in the file like xtal or NMR structure, it won’t save it as .mrc or volume file and was giving me the error. > > I want to create a volume file from the model to load on cryoSPARC or relion and create 2D projections to help me pick better 2D classes from my raw data. Do you think there is an option to do something like this on chimera? > > Thank you again for your time and help in advance – very much appreciated. > > Sincerely, > Roksana > >> On May 11, 2021, at 11:50 AM, ChimeraX <ChimeraX-bugs-admin(a)cgl.ucsf.edu> wrote: >> >> #4622: save dialog: 'SaveModelOptionWidget' object has no attribute '_name' >> -----------------------------------+---------------------------- >> Reporter: razad@… | Owner: Eric Pettersen >> Type: defect | Status: closed >> Priority: normal | Milestone: >> Component: Input/Output | Version: >> Resolution: duplicate | Keywords: >> Blocked By: | Blocking: >> Notify when closed: | Platform: all >> Project: ChimeraX | >> -----------------------------------+---------------------------- >> Changes (by Eric Pettersen): >> >> * status: accepted => closed >> * resolution: => duplicate >> >> >> Comment: >> >> Hi Roksana, >> Thanks for reporting this problem. ChimeraX was trying to tell >> you that you hadn't selected anything to save in the save dialog, but >> there was an error in the code that generates that message, which is what >> you saw. So the error is easy to avoid. Nonetheless, if you want to >> always avoid it in the future you could use the current daily build or the >> 1.2.2 release candidate, both of which have this problem fixed. >> >> --Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> >> -- >> Ticket URL: <https://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_tra… > >> ChimeraX <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chime… > >> ChimeraX Issue Tracker > >

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job opening for ChimeraX developer
by Elaine Meng 06 May '21

06 May '21

Hello everybody, We're looking for somebody to join the ChimeraX development team! Please see this posting for details: <https://sjobs.brassring.com/TGnewUI/Search/Home/Home?partnerid=6495&siteid=…> On behalf of the team, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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DAE format
by Giorgio Luciano 06 May '21

06 May '21

Hello to all, I'm writing for a feature request. The old chimera had the option to export models (surfaces, ball and stickers etc) in DAE format which is the most "trustful" for importing the model in 3D software (blender for me now). Will it be possible to "revamp" it or include format as .abc ? (I don't know if .usd can be an idea also since I think its specifications are open). Thanks

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ChimeraX not starting up using win10
by Bernd M. Schmidt 05 May '21

05 May '21

Dear ChimeraX users and coders, Thanks for the hard work and for providing the community with such great program. I cannot run Chimera on my desktop PC. After clicking in win10, the cursor indicates something is happening for three seconds, then nothing happens and also no error message or anything appeares Before that, I ran Chimera 1.14rc successfully, since installation of ChimeraX and also with ChimeraX 1.2, this happens. I deinstalled everything and installed first the latest python release (3.9.5), then ChimeraX 1.2. But no change, nothing. Reading the newsgroup suggested running debug mode, finally giving some error message, as seen below. C:\Program Files\ChimeraX 1.2\bin\lib\site-packages\win32\lib\pywintypes.py:2: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses import imp, sys, os Windows fatal exception: access violation Current thread 0x000023f8 (most recent call first): File "C:\Program Files\ChimeraX 1.2\bin\lib\site-packages\chimerax\ui\gui.py", line 157 in __init__ File "C:\Program Files\ChimeraX 1.2\bin\lib\site-packages\ChimeraX_main.py", line 577 in init File "C:\Program Files\ChimeraX 1.2\bin\lib\site-packages\ChimeraX_main.py", line 1015 in <module> File "C:\Program Files\ChimeraX 1.2\bin\lib\runpy.py", line 87 in _run_code File "C:\Program Files\ChimeraX 1.2\bin\lib\runpy.py", line 194 in _run_module_as_main C:\Program Files\ChimeraX 1.2\bin> Happy for some help. Many greetings bernd

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Saving name attribute
by David Leeming 04 May '21

04 May '21

Hi, I'm attempting to use a python script to save the names of each residue in a protein The code I have is as follows: import chimerax, sys from chimerax.core.commands import run cwd = (str(sys.argv[0][:-17])) prot = "/A" run(session, "open 3GDM") run(session, "save " + str(cwd) + "/script_content/sasa/name.defattr " + str(prot) + " & protein attrName r:name format defattr") The command being input into the command line of ChimeraX by the script is as follows: "save [file path]/name.defattr /A & protein attrName r:name format defattr" I've also tried using: "save [file path]/name.defattr attrName r:name format defattr models /A & protein" However, both commands give me a file with all the residues and all the names contained within the model rather than just the chain I'm interested in. Could you advise on how I can better use this command to save a file with the residue positions and corresponding amino acid for each residue from a single chain only? I've attached the resultant file to this email. Kind regards, David

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assigning 3.10 helices to a pdb
by Sheena Vasquez 03 May '21

03 May '21

Hi everyone, I was wondering if there's a way to reassign alpha-helices to 3.10 helices in chimeraX? I've been using the setattr /A:###-### res ss_type 1 command, but it seems as if there's only the option to assign alpha helices (ss_type 1). If I try ss_type 5 (5 is the assigned number for 3.10 helices in the pdb), the helix is lost. Any help with this is greatly appreciated! Take care, Sheena

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ChimeraX Cheat Sheet/List
by André Graça 30 Apr '21

30 Apr '21

Hi everyone, There is no doubt that we have a very good documentation on the different functions of ChimeraX as well as for Chimera. Nevertheless, sometimes it is easy to have a summarized sheet with the most used functions and options. I plan to start doing a cheat sheet for me, and it would be great to make it open source. However I might not be aware of the existence of one already. Does anyone know/have one and would be willing to share with the community, or point me to one available online? Or has the ChimeraX team any plans to do one in the near future? Thank you, André

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Re: [chimerax-users] ChimeraX-Deeplearning plugin
by Yongcheng MU 29 Apr '21

29 Apr '21

Hello Tom, Hope you are doing well. I am creating a GUI, and I have some problems. At the right bottom DL Struct window, I want to click the browse button and select a file, but it holds this error. I wonder if you know what's the problem? (My goal is let users find or input the path of a file, and use this path to submit jobs) Best regards, Yongcheng [image: Screen Shot 2021-04-29 at 1.24.02 PM.png] On Fri, Apr 23, 2021 at 7:20 PM Yongcheng MU <ymu004(a)odu.edu> wrote: > Hello Tom, > > Thank you for the information. I will check these documents you have > provided. > > Best regards, > Yongcheng > > On Fri, Apr 23, 2021 at 7:01 PM Tom Goddard <goddard(a)sonic.net> wrote: > >> Hi Jing, Yongcheng, >> >> ChimeraX requires all different code from Chimera so I suggest not >> looking at a Chimera example, that will only confuse you as none of it is >> right for ChimeraX. There are simple examples of Python scripts for >> ChimeraX at the ChimeraX recipes site >> >> https://rbvi.github.io/chimerax-recipes/ >> >> For packaging up a plugin there are examples in the ChimeraX programming >> manual >> >> https://www.rbvi.ucsf.edu/chimerax/docs/devel/index.html >> >> And it can also the packaging for plugins using a bundle_info.xml is used >> by each of the tools in ChimeraX and you can look at any of those as >> examples at the ChimeraX GitHub code repository >> >> https://github.com/RBVI/ChimeraX/tree/develop/src/bundles >> >> Let me know if you run into trouble. >> >> Tom >> >> >> >> >> On Apr 23, 2021, at 2:53 PM, He, Jing <jhe(a)cs.odu.edu> wrote: >> >> Hi Tom, >> >> Yongcheng has been setting up the bundle of a PyTorch-based deep learning >> method to detect secondary structures from medium-resolution density maps. >> He is able to install the bundle on Mac and PC and it looks like working. >> He started to create a GUI. I passed him our previous code for a Chimera >> plugin. Below he shows a few snapshots for that code. We are wondering if >> ChimeraX has similar functions to be called. Previously our code uses >> Chimera's functions to do input, output, and any display of some calculated >> results. How do we do this in ChimeraX? >> >> Jing >> >> ------------------------------ >> *From:* Yongcheng MU <ymu004(a)odu.edu> >> *Sent:* Friday, April 23, 2021 2:04 PM >> *To:* He, Jing <jhe(a)cs.odu.edu> >> *Subject:* ChimeraX-Deeplearning plugin >> >> Dear Dr. He, >> >> I am trying to create a GUI for the bundle. When I check the previous >> work, I find some codes were called such as chimera.extension. I wonder if >> ChimeraX needs this kind of code or package as well, and where I can search >> and find this useful information. >> >> Best regards, >> Yongcheng >> >> [image: Screen Shot 2021-04-23 at 1.55.24 PM.png] >> [image: Screen Shot 2021-04-23 at 1.55.40 PM.png] >> [image: Screen Shot 2021-04-23 at 1.56.01 PM.png] >> >> >>

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Display chain annotations w/o having to reopen files
by Alexander Julian 28 Apr '21

28 Apr '21

Good afternoon, I was wondering if there was any built-in functionality to show the chain annotations that are shown when the file is first open? When I save a session (.cxs) and reopen it later, this information is missing. Best, Alexander -- *Alexander T. Julian* PhD Student, Department of Biology, Microbiology Bachelor of Science, Biomedical Engineering, Cell and Tissue Specialization 2021 Master of Advanced Study, Chemical Engineering 2021 Illinois Institute of Technology Chicago, IL 60616 *Phone (727)-735-7104*

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Hide dashed lines (chain breaks)
by Gabriele Cerutti 28 Apr '21

28 Apr '21

Hello, I am displaying a protein molecule in cartoon representation and chimeraX automatically shows dashed lines for chain breaks (see attached). Is there a way to hide these dashed lines? Best, Gabriele [image: Screen Shot 2021-04-28 at 9.50.54 AM.png]

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Scale bar in ChimeraX
by Sen, Anindito 27 Apr '21

27 Apr '21

Dear All, How to put a scale bar in a ChimeraX session depicting a density map ( as in Chimera Tools - High-Order structure -Scale Bar). Stay safe & Regards Anindito Sen. Ph.D Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257 Office: ILSB Room 1133 <http://microscopy.tamu.edu/>Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu<http://microscopy.tamu.edu/>

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Adding amino acids to end of chain
by Tom Goddard 26 Apr '21

26 Apr '21

Alexis Rohou asked on Twitter In @UCSFChimeraX <https://twitter.com/UCSFChimeraX> 1.1.1 and #Isolde <https://twitter.com/hashtag/Isolde?src=hashtag_click> by @CrollTristan <https://twitter.com/CrollTristan> is there an easy way to add aa residues to the end of a chain? https://twitter.com/AlexisRohou/status/1386171500604977152 <https://twitter.com/AlexisRohou/status/1386171500604977152> Elaine says: There isn't an "add amino acid" yet in ChimeraX, only Chimera.... unless ISOLDE can do it (I don't know). So maybe it's an ISOLDE question. ChimeraX itself has building peptides from scratch but not sticking them on to the end of an existing peptide. Build Structure, Start Structure: peptide <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#start <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#start>> or command "build start peptide" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/build.html#start <https://rbvi.ucsf.edu/chimerax/docs/user/commands/build.html#start>> Elaine

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Re: [chimerax-users] Cannot install
by Tom Goddard 26 Apr '21

26 Apr '21

Volodymyr says it is necessary to choose "save" when downloading the Linux ChimeraX, not "open". > On Apr 25, 2021, at 5:30 AM, Volodymyr Dvornyk wrote: > > Dear Tom, <> > > Fixed. That was my error: I selected “open” when downloading instead of “save”. > > Best, > > Volodymyr >

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z-slice movie making
by Stapleton kevin2017/4/3 26 Apr '21

26 Apr '21

Greeting everyone in the ChiX community. Long time listener first time caller :-) I was wondering if anyone could help me with making a movie that is essentially slicing (clipping) through a given volume. I am pretty comfortable with the movie making movie parameters and I have read through the sections 1) help:user/movies.html 2) help:user/commands/clip.html However the command parameters explanation is juuuuust a smidgen beyond my limits (almost there...damn!) and cant seems to get this into a working movie (if possible at all). So, using the emdb entry: 22910 for example case, how can I make a movie that is 10 seconds long and extends through the clipping plane of a given volume, moving front to back (from the "view orient" perspective; the clipping plane will extend forward through the volume, and back again) Thanks for all your help in this specific case, and for all of the efforts put into to this mailing list. It has been a well spring of fun learning for me over the years. SO many cool tips and tricks to make macro-molecular structures look top notch and cool. THANKS CHIMERA TEAM!! All the best and well wishes from Japan, Kako PS. apologies if this was covered in a previous thread. I must have missed it.

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rmsd no fitting
by Fabian Glaser 26 Apr '21

26 Apr '21

Dear all, I want to perform rmsd calculation but without fitting to compare docking poses results. In chimera I used rmsd, but in chimeraX no rmsd and no align works for me. Can you please advice? thanks! Best, Fabian Fabian Glaser PhD Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel Web https://lokey.technion.ac.il/bioinformatic-knowledge-unit/ Tel +972 (0) 4 8293701

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rmsd with no fitting
by Fabian Glaser 26 Apr '21

26 Apr '21

ear all, I want to perform rmsd calculation but without fitting to compare docking poses results. In chimera I used rmsd, but in chimeraX no rmsd and no align works for me. Can you please advice? thanks! Best, Fabian Fabian Glaser PhD Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel Web https://lokey.technion.ac.il/bioinformatic-knowledge-unit/ <https://lokey.technion.ac.il/bioinformatic-knowledge-unit/> Tel +972 (0) 4 8293701 Best, Fabian Fabian Glaser PhD Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel Web https://lokey.technion.ac.il/bioinformatic-knowledge-unit/ Tel +972 (0) 4 8293701

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Errors hold when Plugin a bundle into ChimeraX toolshed
by Yongcheng MU 23 Apr '21

23 Apr '21

Hello, Hope this email finds you well. I'm trying to Plugin a bundle into ChimeraX. I have successfully installed a bundle on macOS, now I'm trying to install the bundle on a Window Desktop. It holds some errors, I searched a lot and I failed to fix this issue. I wonder if you have any suggestions? Best regards, Yongcheng [toolshed install Z:/Plugin_dl\dist\ChimeraX_DLStruct-0.1-py3-none- any.whl](cxcmd:toolshed install Z:/Plugin_dl\\dist\\ChimeraX_DLStruct-0.1-py3-none-any.whl) Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\toolshed_utils\__init__.py", line 489, in _pip_install results = _run_pip(command, logger) File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\toolshed_utils\__init__.py", line 540, in _run_pip *raise RuntimeError(s)RuntimeError: Looking in indexes: https://pypi.org/simple <https://pypi.org/simple>, https://cxtoolshed.rbvi.ucsf.edu/pypi/ <https://cxtoolshed.rbvi.ucsf.edu/pypi/> * Processing z:\plugin_dl\dist\chimerax_dlstruct-0.1-py3-none-any.whl Requirement already satisfied: ChimeraX-Core~=1.0 in c:\program files\chimerax 1.1\bin\lib\site-packages (from ChimeraX-DLStruct==0.1) (1.1) Requirement already satisfied: numpy~=1.16.4 in c:\users\ymu\appdata\local\ucsf\chimerax\1.1\site-packages (from ChimeraX-DLStruct==0.1) (1.16.6) Requirement already satisfied: torch~=1.7.1 in c:\users\ymu\appdata\local\ucsf\chimerax\1.1\site-packages (from ChimeraX-DLStruct==0.1) (1.7.1) Requirement already satisfied: numpy~=1.16.4 in c:\users\ymu\appdata\local\ucsf\chimerax\1.1\site-packages (from ChimeraX-DLStruct==0.1) (1.16.6) Requirement already satisfied: typing-extensions in c:\users\ymu\appdata\local\ucsf\chimerax\1.1\site-packages (from torch~=1.7.1->ChimeraX-DLStruct==0.1) (3.7.4.3) Collecting quadprog~=0.1.7 Using cached quadprog-0.1.8.tar.gz (269 kB) Requirement already satisfied: Cython in c:\program files\chimerax 1.1\bin\lib\site-packages (from quadprog~=0.1.7->ChimeraX-DLStruct==0.1) (0.29.20) Collecting importlib-metadata~=0.17 Using cached importlib_metadata-0.23-py2.py3-none-any.whl (28 kB) Requirement already satisfied: zipp>=0.5 in c:\users\ymu\appdata\local\ucsf\chimerax\1.1\site-packages (from importlib-metadata~=0.17->ChimeraX-DLStruct==0.1) (3.4.1) *Building wheels for collected packages: quadprog Building wheel for quadprog (setup.py): started Building wheel for quadprog (setup.py): finished with status 'error' Running setup.py clean for quadprog Failed to build quadprog * Installing collected packages: quadprog, importlib-metadata, ChimeraX-DLStruct Running setup.py install for quadprog: started Running setup.py install for quadprog: finished with status 'error' *ERROR: Command errored out with exit status 1: * command: 'C:\Program Files\ChimeraX 1.1\bin\ChimeraX.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\ymu\\AppData\\Local\\Temp\\pip-install-xakoctiw\\quadprog_7cb25d8bb3904ea3b64643e58389ec80\\setup.py'"'"'; __file__='"'"'C:\\Users\\ymu\\AppData\\Local\\Temp\\pip-install-xakoctiw\\quadprog_7cb25d8bb3904ea3b64643e58389ec80\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d 'C:\Users\ymu\AppData\Local\Temp\pip-wheel-gloxcthl' cwd: C:\Users\ymu\AppData\Local\Temp\pip-install-xakoctiw\quadprog_7cb25d8bb3904ea3b64643e58389ec80\ Complete output (6 lines): running bdist_wheel running build running build_ext *skipping 'quadprog\quadprog.cpp' Cython extension (up-to-date) building 'quadprog' extension error: Microsoft Visual C++ 14.0 is required. Get it with "Build Tools for Visual Studio": https://visualstudio.microsoft.com/downloads/ <https://visualstudio.microsoft.com/downloads/> * ---------------------------------------- *ERROR: Failed building wheel for quadprog DEPRECATION: Could not build wheels for quadprog which do not use PEP 517. pip will fall back to legacy 'setup.py install' for these. pip 21.0 will remove support for this functionality. A possible replacement is to fix the wheel build issue reported above. You can find discussion regarding this at https://github.com/pypa/pip/issues/8368 <https://github.com/pypa/pip/issues/8368>. ERROR: Command errored out with exit status 1: * command: 'C:\Program Files\ChimeraX 1.1\bin\ChimeraX.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\ymu\\AppData\\Local\\Temp\\pip-install-xakoctiw\\quadprog_7cb25d8bb3904ea3b64643e58389ec80\\setup.py'"'"'; __file__='"'"'C:\\Users\\ymu\\AppData\\Local\\Temp\\pip-install-xakoctiw\\quadprog_7cb25d8bb3904ea3b64643e58389ec80\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record 'C:\Users\ymu\AppData\Local\Temp\pip-record-gcrsp7lk\install-record.txt' --single-version-externally-managed --user --prefix= --compile --install-headers 'C:\Users\ymu\AppData\Local\UCSF\ChimeraX\Python37\Include\quadprog' cwd: C:\Users\ymu\AppData\Local\Temp\pip-install-xakoctiw\quadprog_7cb25d8bb3904ea3b64643e58389ec80\ Complete output (6 lines): running install running build running build_ext skipping 'quadprog\quadprog.cpp' Cython extension (up-to-date) building 'quadprog' extension error: Microsoft Visual C++ 14.0 is required. Get it with "Build Tools for Visual Studio": https://visualstudio.microsoft.com/downloads/ ---------------------------------------- ERROR: Command errored out with exit status 1: 'C:\Program Files\ChimeraX 1.1\bin\ChimeraX.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\ymu\\AppData\\Local\\Temp\\pip-install-xakoctiw\\quadprog_7cb25d8bb3904ea3b64643e58389ec80\\setup.py'"'"'; __file__='"'"'C:\\Users\\ymu\\AppData\\Local\\Temp\\pip-install-xakoctiw\\quadprog_7cb25d8bb3904ea3b64643e58389ec80\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record 'C:\Users\ymu\AppData\Local\Temp\pip-record-gcrsp7lk\install-record.txt' --single-version-externally-managed --user --prefix= --compile --install-headers 'C:\Users\ymu\AppData\Local\UCSF\ChimeraX\Python37\Include\quadprog' Check the logs for full command output. WARNING: You are using pip version 20.2.2; however, version 21.0.1 is available. You should consider upgrading via the 'C:\Program Files\ChimeraX 1.1\bin\ChimeraX.exe -m pip install --upgrade pip' command.

3 5

Fwd: [Ext] Session Initiation Error
by Tom Goddard 22 Apr '21

22 Apr '21

> From: Alexander Julian > > That did the trick. > > Thank you so much. > > On Thu, Apr 22, 2021 at 11:37 AM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > Hi Alexander, > > Your error says it can't import libpython3.7m.so <http://libpython3.7m.so/> the Python language system library. That suggests that you ran your test.py script in a strange way. A few ways to run your Python script are > > $ chimerax test.py > > Don't start a graphical user interface. > > $ chimerax --nogui.py > > Start ChimeraX and after it starts use a ChimeraX command to open the script > > $ chimerax > ChimeraX command "open test.py" > > Tom > > > >> On Apr 22, 2021, at 8:34 AM, Alexander Julian <ajulian(a)hawk.iit.edu <mailto:ajulian@hawk.iit.edu>> wrote: >> >> Good morning, >> >> I am currently trying to create a python script that hides atoms and shows ribbons in a .pdb file. >> >> However, I am getting an error while trying to initialize a session. I've been trying to debug the problem to the best of my ability, but I am unable to figure out the issue. >> >> My code: >> ``` >> import chimerax.core.session as cxsession >> session = cxsession.Session('name') >> ``` >> >> My error: >> ``` >> File "./test.py", line 15, in <module> >> session = cxsession.Session('name') >> File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/session.py", line 437, in __init__ >> self.app_name = app_name >> File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/session.py", line 508, in __setattr__ >> if not name.startswith('_') and self.snapshot_methods(value, base_type=StateManager) is not None: >> File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/session.py", line 535, in snapshot_methods >> from .serialize import PRIMITIVE_TYPES >> File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/serialize.py", line 42, in <module> >> from ._serialize import msgpack_serialize_stream, msgpack_deserialize_stream, PRIMITIVE_TYPES >> ImportError: libpython3.7m.so.1.0: cannot open shared object file: No such file or directory >> ``` >> >> I look forward to your assistance. >> >> Best, >> Alexander >> >> -- >> Alexander T. Julian >> PhD Student, Department of Biology, Microbiology >> Bachelor of Science, Biomedical Engineering, Cell and Tissue Specialization 2021 >> Master of Advanced Study, Chemical Engineering 2021 >> Illinois Institute of Technology >> Chicago, IL 60616 >> Phone (727)-735-7104 >> _______________________________________________ >> 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> >

1 0

Cannot install
by Volodymyr Dvornyk 22 Apr '21

22 Apr '21

Hi, Downloaded and tried to install the package for Ubuntu 20.04 (Linux) 64-bit from your site following the recommendations. My system is Ubuntu 20.04.2 LTS. The system generates an error: "unsupported file ... given on commandLine". Any ideas how to fix this? ________________________________ DISCLAIMER: This electronic mail transmission contains confidential information intended only for the person(s) named. Any use, distribution, copying or disclosure by any other person is strictly prohibited. If you received this transmission in error, please notify the sender by reply e-mail and then destroy the message. Opinions, conclusions, and other information in this message that do not relate to the official business of Alfaisal University shall understand to be neither given nor endorsed by Alfaisal University. The contents of any attachment to this e-mail may contain software viruses, which could damage your own computer system. While "Alfaisal University" has taken every reasonable precaution to minimize this risk, we cannot accept liability for any damage which you sustain as a result of software viruses. You should carry out your own virus checks before opening the attachment.

2 1

Session Initiation Error
by Alexander Julian 22 Apr '21

22 Apr '21

Good morning, I am currently trying to create a python script that hides atoms and shows ribbons in a .pdb file. However, I am getting an error while trying to initialize a session. I've been trying to debug the problem to the best of my ability, but I am unable to figure out the issue. My code: ``` import chimerax.core.session as cxsession session = cxsession.Session('name') ``` My error: ``` File "./test.py", line 15, in <module> session = cxsession.Session('name') File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/session.py", line 437, in __init__ self.app_name = app_name File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/session.py", line 508, in __setattr__ if not name.startswith('_') and self.snapshot_methods(value, base_type=StateManager) is not None: File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/session.py", line 535, in snapshot_methods from .serialize import PRIMITIVE_TYPES File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/serialize.py", line 42, in <module> from ._serialize import msgpack_serialize_stream, msgpack_deserialize_stream, PRIMITIVE_TYPES ImportError: libpython3.7m.so.1.0: cannot open shared object file: No such file or directory ``` I look forward to your assistance. Best, Alexander -- *Alexander T. Julian* PhD Student, Department of Biology, Microbiology Bachelor of Science, Biomedical Engineering, Cell and Tissue Specialization 2021 Master of Advanced Study, Chemical Engineering 2021 Illinois Institute of Technology Chicago, IL 60616 *Phone (727)-735-7104*

2 1

specify pseudobonds
by Ruchika Bajaj 17 Apr '21

17 Apr '21

Hi Elaine I am using the contact tool from the structure analysis tool. It is giving me a few pseudobonds and I want to delete a few of them for the picture I am working on. I also tried checking the pseudobond command. So, could you please help me in specifying pseudo bonds and how to delete or hide specified pseudobonds in the figure, instead of all of them. Thanks a lot !! Regards Ruchika

2 3

Exporting DNA Molecules from Chimera X
by AQUILINA Matthew 15 Apr '21

15 Apr '21

Dear ChimeraX users, I’ve recently started using ChimeraX to produce rendered 3D models of DNA nanostructures. I do this through the following process: * Prepare nanostructure as a PDB file. * Import this into ChimeraX. * Arrange visualization settings such as nucleotide representation shape, width etc. * Export .x3d file into Blender for downstream processing. However, there is one issue - the 3D models exported by ChimeraX aren’t grouped into individual objects per nucleotide, so I am not able to easily select nucleotides and colour them in according to their type (A, T, G or C). With the older version of Chimera, these nucleotides are exported as individual objects, but then are given identical names with randomized IDs. This means that setting the nucleotide types is a long manual process of clicking on each resulting nucleotide and naming them individually. Does anyone know of a way to export a 3D model of a DNA structure which also exports the IDs of each nucleotide? This would greatly speed up the process for me to produce and render a DNA structure. Many thanks for your help! Best wishes, Matthew Aquilina -- Matthew Aquilina Precision Medicine PhD Student College of Medicine and Veterinary Medicine & School of Engineering | University of Edinburgh Profile<https://www.ed.ac.uk/profile/matthew-aquilina> | LinkedIn<https://www.linkedin.com/in/matthewaq/> | Twitter<https://twitter.com/matt_aqui> [cid:3C793866-9668-486C-B3DC-D0346CD79675@Home] Mary Brück Building | Colin Maclaurin Rd | EH9 3DW | Scotland | UK The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.

2 1

MCCOY - coloring a map by local resolution - Rnd 2
by McCoy, William 14 Apr '21

14 Apr '21

Dear Elaine and other Chimera support staff, Thank you for your explanation. Unfortunately, my problem is that I cannot find the tool "Surface Color" in ChimeraX-1.1.1. Here is a screenshot of what I see when I look for it with both .mrc files loaded. From the hyperlink that you provided (https://rbvi.ucsf.edu/chimerax/docs/user/tools/surfacecolor.html) it appears that I could also access "Surface Color" from "Depiction" within tools, but I also cannot find "Depiction" as an option. Is there somewhere else that I should be looking for the "Surface Color" tool? Thanks ahead of time for the help. Sincerely, Bill McCoy William H. McCoy IV, MD, PhD Research Instructor in Medicine Department of Medicine, Division of Dermatology Washington University School of Medicine Saint Louis, MO 63110 The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone at (314) 540-1512 or by return email. ________________________________ From: Elaine Meng <meng(a)cgl.ucsf.edu> Sent: Tuesday, April 13, 2021 6:47 PM To: McCoy, William <mccoyw(a)wustl.edu> Cc: Elaine Meng <meng(a)cgl.ucsf.edu> Subject: Re: [chimerax-users] coloring a map by local resolution * External Email - Caution * I just sent the question to the whole list already, right above my response (below), so you didn't need to do it.... the reason I gave the address is for your future reference and future correspondence. The moderator is deleting the duplicate question so that people don't have to read the same exact question again. Elaine > On Apr 13, 2021, at 4:40 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > >> On Apr 13, 2021, at 4:17 PM, William.H.McCOy.IV(a)cgl.ucsf.edu wrote: >> >> I can't get the following from relion 3.1 to work: The output is a file called LocalRes/polished/relion_locres.mrc that may be used in UCSF chimera to color the Postprocess/polished/postprocess.mrc map according to local resolution. # This is done using Tools -> Volume data -> Surface color, and then select by volume data value and browse to the resmap file. > > Dear William, > We have a mailing list that is recommended for asking questions, chimerax-users(a)cgl.ucsf.edu (CC'd on this message). > <https://www.rbvi.ucsf.edu/chimerax/docs/contact.html> > > Coloring by local resolution is a fairly common task and I don't know of any reason it wouldn't work. It is not clear what you mean by not working. If you are more specific with your question, we can give more targeted answers. > > First you have to open both mrc files in ChimeraX. Say you opened the map that you want to show as a surface as model #1 and the map with locres values for coloring as model #2. Then in Volume Viewer, you can adjust the isosurface level of map #1 and hide the isosurface of map #2 (or you can hide it using Model Panel, same thing). In Surface Color you would choose the (already open) models: the surface to color is model #1, you want to color it by "volume data value," and the map with values to use for coloring is #2. You can see the help for the tool by clicking its Help button, or view the copy on our website here: > > <https://rbvi.ucsf.edu/chimerax/docs/user/tools/surfacecolor.html> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > > > _______________________________________________ > ChimeraX-users mailing list > ChimeraX-users(a)cgl.ucsf.edu > Manage subscription: > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

3 3

coloring a map by local resolution
by Elaine Meng 13 Apr '21

13 Apr '21

> On Apr 13, 2021, at 4:17 PM, William.H.McCOy.IV(a)cgl.ucsf.edu wrote: > > I can't get the following from relion 3.1 to work: The output is a file called LocalRes/polished/relion_locres.mrc that may be used in UCSF chimera to color the Postprocess/polished/postprocess.mrc map according to local resolution. # This is done using Tools -> Volume data -> Surface color, and then select by volume data value and browse to the resmap file. Dear William, We have a mailing list that is recommended for asking questions, chimerax-users(a)cgl.ucsf.edu (CC'd on this message). <https://www.rbvi.ucsf.edu/chimerax/docs/contact.html> Coloring by local resolution is a fairly common task and I don't know of any reason it wouldn't work. It is not clear what you mean by not working. If you are more specific with your question, we can give more targeted answers. First you have to open both mrc files in ChimeraX. Say you opened the map that you want to show as a surface as model #1 and the map with locres values for coloring as model #2. Then in Volume Viewer, you can adjust the isosurface level of map #1 and hide the isosurface of map #2 (or you can hide it using Model Panel, same thing). In Surface Color you would choose the (already open) models: the surface to color is model #1, you want to color it by "volume data value," and the map with values to use for coloring is #2. You can see the help for the tool by clicking its Help button, or view the copy on our website here: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/surfacecolor.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

Re: [chimerax-users] ChimeraX reading cube files
by Elaine Meng 10 Apr '21

10 Apr '21

> On Apr 10, 2021, at 7:54 AM, Carles Serrat Jurado <carles.serrat-jurado(a)upc.edu> wrote: > > Dear Elaine, > Thank you very much for your help. These instructions will certainly be very important for my work. > > There is still something that is not clear to me. My cube files, produced by the NWChem package, include information about the differential density. This appears by default when I open one of these files with the VESTA visualization software (https://jp-minerals.org/vesta/en/) Here I attach the 10 cube files I sent to you just converted to tif images after opening them with VESTA. As you can see, it is not the position of the atoms what evolves, as you already observed, but the differential charge density. > > I don’t know why ChimeraX does not produce the differential densities. If it would do it, then following your kind indications I could make now a movie to see that evolution (I have thousands of cube files to see a quite long time evolution - 5 femtoseconds, actually :-), which is what I am looking for. > > Again, I sincerely thank you for your answers and indications. I understand that probably ChimeraX is not able to read this information from my cube files. > > Best regards, > Carles > > PS: Please no worries about the data I am sending, it is not private so to say, these are tests I am doing at the moment. > PS2: I subscribed to the ChimeraX mailing list, but I don’t manage yet to answer there and attach files, please be free to share my mails however. Dear Carles, From your first message, I mistakenly thought you only wanted to see the atomic coordinates, so I ignored the density part. The instructions I sent before were how to make an atomic trajectory. If the atoms don't change position, then you can ignore most of those long instructions and just make one atomic model and keep showing it at the same time you show the changing density. For example, just open the attached PDB file, carles1.pdb. By default, ChimeraX does show the density from the cube files... that is the blob you see as soon as you open the file. If you mean that you want to see the densities as a series that changes over time, you just need to use the "open" command "vseries" option to tell ChimeraX that it is a volume series. For example, you previously sent a folder containing 10 files named density_subgs.0000030000.cube .... density_subgs.0000039000.cube (numbering increments of 1000). In ChimeraX, the following command opens the 10 files as a single volume series (time series): open [folder location]/density*cube vseries true Now you have a slider to play the series, or you can use the "vseries" command. Screen shot below. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/vseries.html> More about atomic trajectories and volume series: <https://rbvi.ucsf.edu/chimerax/docs/user/trajectories.html> The blob is probably bigger than what you are used to seeing in Vesta. This is just the contour level. To change contour level, you can move the vertical bar on the volume viewer (density map) histogram that automatically appears when you open the data in ChimeraX. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html> Your cube files are signed data, so there are two vertical bars, one for the positive contour level and one for the negative contour level. You can drag either bar, and change the color by then clicking on the small color square above the histogram. In the attached screenshot I made the negative one greenish and the positive one magenta. I only see a very small change in these densities as I play the 10 frames. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > > >> On Apr 10, 2021, at 3:10 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> >> Hi Carles, >> Attached is the PDB file from step #3 that you can open as a trajectory as described in step #4. >> Best, >> Elaine >> >> <carles-atomic.pdb> >> >> >> >>> On Apr 9, 2021, at 6:07 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >>> >>> Dear Carles, >>> It took me a couple of days to try that recipe script on your data, sorry about the slow reply. Now I realize there are a few extra steps to convert your data to a trajectory (e.g. with slider to play as movie), so I thought I should share the details with the list: >>> >>> (1) In ChimeraX, I opened your 10 cube files, and then I used the python file in the ChimeraX recipe to create 10 atomic models. >>> <https://rbvi.github.io/chimerax-recipes/gaussian_cube_atoms/gcatoms.html> >>> >>> (2) Then I saved the 10 atomic models as a single PDB file (using ChimeraX menu: File... Save), File type PDB, relative to the first atomic model. Doesn't matter which one you choose as the "relative to" model, however. >>> >>> (3) Then I was going to open that single PDB file as a trajectory. However, there is a bug in the saving that currently prevents it. The bug puts "END" after each atomic structure in the file. So I first needed to text-edit the PDB file to remove all of the "END" lines (but not "ENDMDL"). >>> >>> **I will send you the resulting PDB file in a separate message in case it is private data.** >>> >>> (4) In ChimeraX, I closed all the other models and then opened the new edited multi-model PDB file with the "coordsets" option to make it into a trajectory, for example, command: >>> >>> open carles-atomic.pdb coordsets true >>> >>> However, 10 frames of the trajectory all look exactly the same to me, but far as I know that is a correct conversion of the data from the 10 cube files you sent me. >>> >>> When the bug is fixed (#4487 <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4487>), step #3 would not be necessary. >>> >>> I hope this helps, >>> Elaine >>> ----- >>> Elaine C. Meng, Ph.D. >>> UCSF Chimera(X) team >>> Department of Pharmaceutical Chemistry >>> University of California, San Francisco >>> >>> >>>> On Apr 7, 2021, at 9:33 AM, Anthony James Schaefer <tony.schaefer(a)uga.edu> wrote: >>>> >>>> ChimeraX does actually store the atom info in the cube file. Someone asked about this a while ago, and it was mentioned that there's some limitation where the stuff for opening volume data can't load atomic structures or something. I can't find the thread, but Tom Goddard wrote a script to load those atoms into ChimeraX: https://rbvi.github.io/chimerax-recipes/gaussian_cube_atoms/gcatoms.html >>>> >>>>> >>>>>> On Apr 7, 2021, at 7:25 AM, Carles Serrat Jurado <carles.serrat-jurado(a)upc.edu> wrote: >>>>>> >>>>>> Dear Elaine, >>>>>> >>>>>> I am writing because I have problems to plot a cube file with ChimeraX. I would greatly appreciate your assistance. Here I send the only figure I get when I open the cube file with ChimeraX. Also I attach what I would more expect, which is obtained with the software VESTA. >>>>>> >>>>>> My ultimate goal is to make a movie with using different frames. I also send a zipped file with the frames, so that you can see the kind of cube files I am working on. >>>>>> >>>>>> Thank you very much in advance for your support. >>>>>> >>>>>> Best regards, >>>>>> >>>>>> Carles >>>>>> >>>>>> <ChimeraX.png> >>>>>> >>>>>> <VESTA.png> >>>>>> <cube_files.zip> >>>>>> —————————-————————— >>>>>> Prof. Carles Serrat (PhD) >>>>>> Department of Physics >>>>>> UPC - Polytechnic University of Catalonia >>>>>> Colom 11, 08222 - Terrassa >>>>>> Phone: +34 93 739 8137 >>>>>> Mobile: +34 696 738 728 >>>>>> https://donll.upc.edu >>>>>> ——————————————————- >>>>> >>>>> >>>>> _______________________________________________ >>>>> ChimeraX-users mailing list >>>>> ChimeraX-users(a)cgl.ucsf.edu >>>>> Manage subscription: >>>>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >>>>> >>>> >>>> >>>> _______________________________________________ >>>> ChimeraX-users mailing list >>>> ChimeraX-users(a)cgl.ucsf.edu >>>> Manage subscription: >>>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >>>> _______________________________________________ >>>> ChimeraX-users mailing list >>>> ChimeraX-users(a)cgl.ucsf.edu >>>> Manage subscription: >>>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >>> >>> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu >>> Manage subscription: >>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >>> >> > > —————————-————————— > Prof. Carles Serrat (PhD) > Department of Physics > UPC - Polytechnic University of Catalonia > Colom 11, 08222 - Terrassa > Phone: +34 93 739 8137 > Mobile: +34 696 738 728 > https://donll.upc.edu > ——————————————————- > > > > > > > > > > > > > > > > >

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ChimeraX reading cube files
by Elaine Meng 09 Apr '21

09 Apr '21

Hi Carles, We recommend using the chimerax-users(a)cgl.ucsf.edu address (CC'd here) for questions about ChimeraX, unless you have attached data that needs to stay private. ChimeraX reads cube format but only as maps (e.g. density maps, electron localization functions, ...) with values on a grid. It does not read atomic coordinates from the cube format. This is a list of the atomic formats ChimeraX can read -- can you output any of those atomic formats instead of cube? (pdb, mol2, mol, sdf) <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#formats> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#atomic> You can see that "cube" is in the list for volume (map) formats, but not as an atomic format. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#volume> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 7, 2021, at 7:25 AM, Carles Serrat Jurado <carles.serrat-jurado(a)upc.edu> wrote: > > Dear Elaine, > > I am writing because I have problems to plot a cube file with ChimeraX. I would greatly appreciate your assistance. Here I send the only figure I get when I open the cube file with ChimeraX. Also I attach what I would more expect, which is obtained with the software VESTA. > > My ultimate goal is to make a movie with using different frames. I also send a zipped file with the frames, so that you can see the kind of cube files I am working on. > > Thank you very much in advance for your support. > > Best regards, > > Carles > > <ChimeraX.png> > > <VESTA.png> > <cube_files.zip> > —————————-————————— > Prof. Carles Serrat (PhD) > Department of Physics > UPC - Polytechnic University of Catalonia > Colom 11, 08222 - Terrassa > Phone: +34 93 739 8137 > Mobile: +34 696 738 728 > https://donll.upc.edu > ——————————————————-

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Surface caps only colored interactively
by Daniel Asarnow 09 Apr '21

09 Apr '21

Hi, I'm trying to generate a figure using several surfaces colored by map values. If I clip a surface, and then color it, the caps have the correct colors. However, when I do the same thing non-interactively, the caps are uncolored. Am I doing something wrong? view front.cut color sample #1.1 map #1.2 palette cyanmaroon range 2.25,7.0 #surface dust #1.1 size 100 save front_cut.png pixelSize 0.1 transparentBackground true Best, -da

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chimerax python module - LigParGen tutorial
by mdigennaro＠uliege.be 07 Apr '21

07 Apr '21

Dear ChimeraX users, I am trying to follow this tutorial to get the proper residues: http://zarbi.chem.yale.edu/ligpargen/gmx_tutorial.html I have found chimera (0.4.7) as pip module, but it's written in python2 and therefore no longer maintained. Is there a chimerax module I can import? Pychimera is also available and could install it with python2, but it also show compatibility problems with python3 Is DockPrep a separate module? I have found this thread on the chimera forum which doesn't really answer the question: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-July/010115.html Generally, how do I get unknown/custom residues (from LigParGen in this case) for Gromacs input files. Thank you for your support Marco ------------------- Marco Di Gennaro University of Liege

3 2

Use symmetry information in Isolde
by Sean Connell 06 Apr '21

06 Apr '21

Hello I have a naive question about using Isolde to build a model into a cryoEM map generated with symmetry (ie. D4). Basically I don't understand how to rebuild a chain and have the changes reflected in the symmetry related chains when using a cryoEM map. Is it possible to use, for example, a NCS file (like symmetry_from_map.ncs_spec) generated by phenix in order to get Isolde to build simultaneously the NCS related chains? Or is there another way build symmetry related chains into a symmetrical cryoEM map? Thanks for any tips you have.

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An issue about chimeraX
by 祗俊生 02 Apr '21

02 Apr '21

Dear expert： I used "chimeraX 1.1 for windows 10 64-bit" to make animation. As can be seen in the figure provided in the attachment, the labels of hydrogen bonding distance overlapped when I played the animation. However, when I used "Tools-Structure Analysis-Contacts" to show the labels of "Contacts", these labels did not exhibit the above-mentioned problem when I played the animation. I wonder how to solve the problem of the label overlap regarding hydrogen bonds because I want to make a movie to show all of the hydrogen bonds. Moreover, I want to download "chimeraX 1.0 for windows 10 64-bit", but I can't find the download address of the old version. Many thanks!

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Re: [chimerax-users] Displaying silhouette around specific visual elements
by Tom Goddard 31 Mar '21

31 Mar '21

Hi Gustavo, Glad you noticed the smoothness of the surface. I made it smoother than the default. The surface came from the molmap command which computes a density map from the atomic model. That command uses a density map grid spacing of 1/3 the requested resolution by default, but I specified an extra option that used a grid spacing 1/8 of the resolution: open 2gbp molmap #1 8 gridSpacing 1 Also if you are doing this with a big molecule (100,000 atoms) the density map created may be very large and may be shown subsampled so the surface looks coarser. Make sure to set the "step" to 1 in the Volume Viewer panel so that it uses the full resolution of the computed map instead of step 2 which would use only every other grid point. One more pro tip about that image composition example. It only worked nicely because the atomic structure was completely behind the surface, so I could layer the surface on top. If part of the atomic model was behind and part in front (for example with a cryoEM map surface), then the layering would not work well -- the composite image would have the surface in front everywhere. Elaine's selection highlight approach can handle that situation with correct occlusions but the edging is not as nice as silhouettes. Tom > On Mar 31, 2021, at 1:00 PM, de Miranda Seabra, Gustavo <seabra(a)cop.ufl.edu> wrote: > > Hi Tom, > > This looks beautiful! Just one tangential question: How do you get such a smooth surface? Can you share the exact commands you gave? > > Thanks! > > -- > Gustavo Seabra > Assistant Scientist > Center for Natural Products, Drug Discovery and Development (CNPD3) > Department of Medicinal Chemistry > College of Pharmacy > University of Florida, Gainesville, FL, USA > From: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> on behalf of Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > Sent: Tuesday, March 30, 2021 8:55 PM > To: Andre LB Ambrosio <andre(a)ifsc.usp.br <mailto:andre@ifsc.usp.br>> > Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> > Subject: Re: [chimerax-users] Displaying silhouette around specific visual elements > > [External Email] > Hi Andre, > > If you are willing to go to a little trouble you can get silhouettes on an atomic model beneath a transparent surface that has no silhouettes. You first save an image of the atomic model with silhouettes with no surface, then save an image of the transparent surface with no atomic model and no silhouettes, then overlay the second image on the first in a photo editor like Gimp. Below is Elaine's example done this way. The command to save the surface image with transparency for overlaying is "save transpsurf.png transparentBackground true". > > Tom > > Overlay of two images. > > > Atomic model image > > > Transparent surface image > > >> On Mar 30, 2021, at 3:11 PM, Andre LB Ambrosio <andre(a)ifsc.usp.br <mailto:andre@ifsc.usp.br>> wrote: >> >> Dear Elaine, that is excellent! It is the visual effect I was looking for indeed. >> Thank you very much for this and thank you Tom for the very detailed response and for the feature request ticket. >> Andre. >> >> Em ter., 30 de mar. de 2021 às 15:59, Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> escreveu: >> Hi Andre, >> Sometimes you can approximately "fake" this effect by using the selection outline. It is not the same, however, as silhouettes; it will only go around the outside perimeter of the selected item(s). For example, if I have a molecule inside a map surface, I can make the surface transparent, select the atomic structure, and make the selection outline color black etc. as in these commands, resulting in the appearance in the attached image. >> >> open 2gbp >> molmap protein 8 >> trans 70 >> view >> set bgColor white >> select @* >> graphics selection color black >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> >> >> >>> On Mar 25, 2021, at 8:23 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >>> >>> Hi Andre, >>> >>> It is not currently possible to display silhouettes on some models and not others. >>> >>> Several people have wanted this but I think it is complex to achieve. The silhouettes show boundaries where the depth in the entire scene changes abruptly. In order to have per-model silhouettes the ChimeraX GPU shader programs would need to compute an additional depth buffer separately for each model. Also the silhouette edges are not currently drawn at a specific depth. If per-model silhouettes were supported a stick model with silhouettes beneath a transparent surface needs to draw the silhouettes under the transparent surface so knowing the depth of the silhouette edge becomes important. When not using silhouettes the shader programs need to not compute the extra per-model depth buffers otherwise it would slow down rendering even when not being used. Adding these additional complexities to already complex graphics rendering shader programs have so far made this feature out of reach for our one graphics rendering developer (me). >>> >>> I made a feature request for per-model silhouette edges and perhaps in the future we will find a simpler way to implement it that makes it feasible. >>> >>> https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4420 <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_trac…> >>> >>> Tom >>> >>>> On Mar 25, 2021, at 10:09 PM, Andre LB Ambrosio <andre(a)ifsc.usp.br <mailto:andre@ifsc.usp.br>> wrote: >>>> >>>> Dear all, >>>> >>>> I wonder if it's possible to display silhouettes selectively in the same figure; for instance, displaying silhouettes only on structure representation (around sticks, spheres, cartoons and so on), but not around the maps or volumes that surround them. >>>> Many thanks in advance, >>>> >>>> Andre >>>> _ >> >> >> -- >> Andre LB Ambrosio >> Associate Professor, IFSC/USP - Brazil >> www.ifsc.usp.br/alba <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ifsc.usp.br_alba&d=…> >> _______________________________________________ >> 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://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_mai…>

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Displaying silhouette around specific visual elements
by Andre LB Ambrosio 30 Mar '21

30 Mar '21

Dear all, I wonder if it's possible to display silhouettes selectively in the same figure; for instance, displaying silhouettes only on structure representation (around sticks, spheres, cartoons and so on), but not around the maps or volumes that surround them. Many thanks in advance, Andre

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Re: [chimerax-users] [Chimera-users] Debug
by 안예림 30 Mar '21

30 Mar '21

As soon as I start Chimera, the error message appears. I don't know how to report a bug to you. help me -----Original Message----- From: "Eric Pettersen"<pett(a)cgl.ucsf.edu> To: "안예림"<cp7617(a)naver.com>; Cc: <chimera-users(a)cgl.ucsf.edu>; Sent: 2021-03-30 (화) 03:36:23 (GMT+09:00) Subject: Re: [Chimera-users] Debug You should start Chimera and immediately use Help→Report A Bug to send a bug report to us, with a short description of the problem like you provided here. That will automatically provide us with many details about the machine you are using and the version of Chimera you are running. We can carry on from there, since I imagine this problem is only affecting you and therefore other people on this mailing list wouldn't want to get mail about all the details of this problem. --Eric Eric Pettersen UCSF Computer Graphics Lab On Mar 28, 2021, at 10:28 PM, 안예림 <cp7617(a)naver.com> wrote: Hi I have tried to make a movie of MD simulation by Chimera. I could be done one time, then for other MD’s it exits abnormally with the code -1073741819. Even I have decreased the size of .xtc file, it exits abnormally yet. Please check my capture picture. I have reinstalled chimera, but the problem did not resolve.What should I have to do ? I need your assistant. Thanksbe <20210329_142325.png>_______________________________________________ Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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xchimera multiscale model
by Ana Sofia Ramos 29 Mar '21

29 Mar '21

Hi, I am having some difficulties in using xchimera, and I would like to ask you if you could help me. I want to make a representation of a virus-like nanoparticle using the pdb 1HQK. I have searched in the tutorial of xchimera but I could not find the general instructions, but I found them in the tutorial of chimera (multiscale model), however, the options are not present in my installation xchimera (and also in my installation of chimera). Then, I thought that maybe you could tell me how to make it in xchimera. Thank you very much for your attention. Kind regards, Ana

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Rotate PDB file around euler angles in ChimeraX
by Vorländer,Matthias Kopano 26 Mar '21

26 Mar '21

Dear all, So, I am working with a tomogram and refined subtomogram average and would like fit all copies of the molecule, represented as a pdb file, back into the tomogram at all positions where it was found. In practice this means to translate the pdb file to specific coordinates of a reference volume (tomogram) and then rotate it around 3 euler angles defined in a relion star file. I figured out the translation part (thanks to your help), but for the rotation I could only find this script (https://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/eulermove.py) for chimera which allows to rotate a volume around the euler angles and then resample the transformed volume and save it. While a workaround would be to do the operation with the volume in chimera, then fit the pdb file in the transformed volume, and then save the transformed pdb file, and then load everything back in chimera, the manual fitting of the pdb would become very laborious for several hundred copies. So ideally, I would like to adapt the eulermove.py script that I linked to i) work in ChimeraX and ii) work with pdbs instead of volumes. Unfortunately I have zero coding experience… Any help would be much appreciated! Best, Matthias

2 1

RR distance maps
by William S Wang 26 Mar '21

26 Mar '21

Is there implementation of RR distance maps from chimera?

2 1

generating icosahedron from pentamer
by Moustafa, Ibrahim M. 25 Mar '21

25 Mar '21

Dear all, I want to generate icosahedral structure from a pentamer (chains A-E). When I use the command: sym #1 i,222 coordinateSystem #2 center #2 It generated 5 copies, icosahedron for each chain. What I'd like to build is just 12 copies of the pentamer in an icosahedral sym. How to do that in ChimeraX? Thanks, Ibrahim

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Custom Palette
by Abhilash Padvannil 25 Mar '21

25 Mar '21

Hi, I am wondering if there is a way to create custom palettes for use in ChimeraX. Please suggest. Thanks Regards Abhilash.

3 2