May 2021 - 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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