- ChimeraX-users - RBVI Mailing Lists

ChimeraX version 1.2 released!
by Elaine Meng 28 May '21

28 May '21

UCSF ChimeraX version 1.2 has been released! Major changes since v1.1 (Aug 2020) include: - Surface Color tool - Unit Cell tool - Color Key tool and command - Crystal Contacts tool and command - volume tools: Hide Dust, Color Zone, Surface Zone - Meeting panel for multiperson VR - "fly" command for smooth motion along multiple saved views - "rmsd" command for calculating RMSD in current positions (w/o fitting) - nucleic-acid building - bond deletion/addition - UniProt fetch includes sequence feature annotations (domains, mutations, modification sites, etc.) - support for Amber netCDF trajectories - smaller session files - faster saving of sessions with maps - mouse mode for moving a clicked model without having to select it For more details, see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog Downloads: https://www.rbvi.ucsf.edu/chimerax/download.html

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Downloading Daily builds
by Moradkhan, Tiglath A 27 May '21

27 May '21

Hi, I don't know why the Fetch Additional Scores button is not returning these scores. I get the message that scores have been initiated but then nothing happens. It's annoying that I keep have to download newly released daily builds on my computer, so I can use it. Thank you Tiglath

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Web services down
by Eric Pettersen 25 May '21

25 May '21

Hi all, Due to computing cluster maintenance starting this evening (5/25) through tomorrow evening (5/26), the web services in Chimera and ChimeraX that use our cluster will be down. The frequently used web services are BLAST and Modeller for both programs, and for Chimera only: sequence realignment via Clustal Omega or MUSCLE; SAXS2; and 2D ligand depiction. --Eric Eric Pettersen UCSF Computer Graphics Lab

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Fwd: Wireframe option
by Eric Pettersen 24 May '21

24 May '21

> Begin forwarded message: > > From: "Silva, Chinthaka Mahesh" <silva228(a)llnl.gov> > Subject: Wireframe option > Date: May 24, 2021 at 12:38:13 PM PDT > To: "chimerax-bugs(a)cgl.ucsf.edu" <chimerax-bugs(a)cgl.ucsf.edu> > > Hello, > > Can you tell me how to draw pdb models using the ‘wireframe’ mode? > > Thanks! > -chinthaka

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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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