September 2021 - ChimeraX-users - RBVI Mailing Lists

Flat transparency setting absent
by David William Kastner 27 Sep '21

27 Sep '21

ChimeraX community, I noticed that in ChimeraX, the “flat” transparency option that was present in Chimera has been either moved or renamed in ChimeraX. This setting made it so the transparency setting wasn’t overwhelming/distracting when focusing on details. In Chimera, it is accessed with Tools > Viewing controls > Effects > transparency > flat. Does anyone know how to achieve this effect in ChimeraX? I find the default ChimeraX transparency option to be disorienting when visualizing details. Here is a rendering comparing the two rendering styles with and without “flat” option. I look forward to your thoughts! https://www.dropbox.com/s/xrjyjnzegeeltap/transparency_comparison.png?dl=0 David --- David Kastner Ph.D. student | Bioengineering MIT | Kulik Lab kastner.io

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Error on installing isolde
by benhaijing＠sina.com 27 Sep '21

27 Sep '21

Hi all！ I can’t install the plugin isolde using command 'toolshed install isolde'. Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Requirement already satisfied: ChimeraX-ISOLDE==1.2.2 in c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages (1.2.2) Requirement already satisfied: ChimeraX-AtomicLibrary~=3.1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (3.1.3) Requirement already satisfied: ChimeraX-Core~=1.2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (1.2.5) Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (1.0) Requirement already satisfied: ChimeraX-Clipper~=0.16.0 in c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages (from ChimeraX-ISOLDE==1.2.2) (0.16.0) Requirement already satisfied: ChimeraX-Atomic~=1.13.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (1.13.2) Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0.1) Requirement already satisfied: ChimeraX-mmCIF~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.3) Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0) Requirement already satisfied: ChimeraX-Geometry~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.1) Requirement already satisfied: ChimeraX-Graphics~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0) Requirement already satisfied: ChimeraX-PDB~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.4.1) Requirement already satisfied: ChimeraX-AtomSearchLibrary~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ConnectStructure~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0) Requirement already satisfied: ChimeraX-DataFormats~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.1) Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.5) Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0.1) Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.4) Requirement already satisfied: ChimeraX-IO~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-DataFormats~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0.1) Requirement already satisfied: ChimeraX-Surface~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0) Requirement already satisfied: ChimeraX-UI~=1.0 in c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.2.1) INFO: pip is looking at multiple versions of chimerax-pdblibrary to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-pdb to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-opencommand to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-nucleotides to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-io to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-dataformats to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-mmcif to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-graphics to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-geometry to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-core to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-atomsearchlibrary to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-connectstructure to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-clipper to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-atomiclibrary to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-atomic to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-arrays to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-isolde to determine which version is compatible with other requirements. This could take a while. The conflict is caused by: chimerax-nucleotides 2.0.1 depends on ChimeraX-UI~=1.0 chimerax-opencommand 1.5 depends on ChimeraX-UI~=1.0 chimerax-savecommand 1.4 depends on ChimeraX-UI~=1.4 To fix this you could try to: 1. loosen the range of package versions you've specified 2. remove package versions to allow pip attempt to solve the dependency conflict ERROR: Cannot install chimerax-nucleotides==2.0.1, chimerax-opencommand==1.5 and chimerax-savecommand==1.4 because these package versions have conflicting dependencies. ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/user_guide/#fixing-conflicting-dependencies WARNING: You are using pip version 21.0.1; however, version 21.2.4 is available. You should consider upgrading via the 'C:\Program Files\ChimeraX\bin\ChimeraX.exe -m pip install --upgrade pip' command. Thanks, Haijing Ben

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Compound Docking in UCSF Chimera
by Ayush Patel 25 Sep '21

25 Sep '21

Sir or Madam; Recently, I was having issues with docking a ligand into a receptor due to surface calculation failures. A quick search told me to use ChimeraX. However, I am not sure how to carry out docking in ChimeraX. Could you please explain how to do this? As a side note, I do currently have AutoDock Vina. Thank you so much, Ayush Patel

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Hi. I have a question about Chimera X program
by dongyoung kim 24 Sep '21

24 Sep '21

Hi. I'm researching protein 3D structure to develop the new drug. In recent, I'm using the Alphafold function in Chimera X daily version. I have 4 questions. First, if I use Alphafold to predict my important project data, is it keep secure privately? I want to keep my data secret. It shouldn't be open to anybody without me. Second, when I using Alphafold in ChimeraX, I faced some error messages that mean 'Not enough disk volume. please remove past data.'. I'm not familiar with google colab...how can I manage the disk to remove past data or expand disk volume? Third, how can I improve the speed of alphafold prediction? ChimeraX shows some resources like ram, disk. fourth, I want to operate simultaneously Alphafold prediction to predict 2 or more structures. Is it possible? If there need some pay to improve the second, third, fourth question, please let me know methods. Many thanks. -from KDY

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Finding Continuous Residue Stretches
by Daniel Wells 23 Sep '21

23 Sep '21

Dear Chimerax Users: I need to find Continuous Residue Stretches between 15-25 amino acids in length on the surface of these two molecules: https://www.rcsb.org/3d-view/4MYV/1 https://www.rcsb.org/structure/3U82 Could anyone here help me perform that function on Chimerax? Thank you for your time. Sincerely, Dan Wells

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Error on save
by Christophe Leterrier 23 Sep '21

23 Sep '21

HI, When I'm saving a session displaying 3D image stacks as surfaces into a csx file, I get this error: TypeError: object of type 'SurfaceUpdaters' has no len() File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/session.py", line 242, in discovery if sm is None and len(value) == 0: However if I switch the displayed stacks as volume, then there is no error on save. This is with the daily build 1.3.dev202109160803 (2021-09-16) on OSX Big Sur (Intel architecture). Thanks, Christophe

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A couple questions about programming in ChimeraX
by William Hofsøy 22 Sep '21

22 Sep '21

Hi, I'm currently working on a plugin that deals with a cmm-file model and have a few questions about how to do certain things. Mainly I would like to be able to modify the model by adding new markers and links to the model. I have managed to figure out how to make new markersets and add them to the session but not how to alter existing ones aka the model that I load from the cmm file. Additionally I am making use of the marker_extra_attributes info since the cmm file im reading has attributes there that I need, but as I read in the documentation these aren't saved in sessions and I wondered if there is a way to do just that. Lastly, I was wondering if it is possible to place any mesh in the scene, for instance a cube. -William

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Re: [chimerax-users] Adding a custom preset question
by Elaine Meng 22 Sep '21

22 Sep '21

Hi Boaz, Just download the file using your standard browser mechanism. When I ctrl-click on the link "kyte-doolittle_hydrophobicity.cxc" in this page: <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup> ...when viewed in Firefox on Mac, I get a menu that includes "Save link as..." Choosing that brings up a little dialog that I use to save the file (without changing the name, but you can change it if you keep the cxc part) to my desired download location. On other platforms or different browsers it might be slightly different how to get the context menu with the choice to save the file, but should be similar. Or since it is a plain text file, like you said, you can also view contents and then paste them as plain text in a text-editor to create your own cxc file. However it is usually easy just to save the file from the browser as described above. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 21, 2021, at 10:13 PM, Boaz Shaanan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hi, > You give a nice example of adding the kyte-doolittle_hydrophobicity.cxc to the custom_presets folder that I created, but where can I find this file? Or, should I paste the content of the file which is opened by pressing the link in the user guide into a file by this name ( I doubt it but nevertheless suggest it as a possibility). > Excuse my naive question, please. > Thanks, > Boaz

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color zone colors by atom type
by vincent Chaptal 21 Sep '21

21 Sep '21

Dear ChimeraX users, I just subscribed so apologies if this has been asked before. When is type the command: color zone #2 near #1/A distance 5 sharpEdges false farColor blue I have the volume #2 in blue with chain A colored by atom type: i.e. with carbons in sand, oxygens in red, nitrogens in blue. I tried to follow the tutorial on youtube, downloading the model and emdb like in the tutorial, and it does work like the tutorial, meaning colored by chain. I am wodering what is going on and how to fix it? I've seen this behavior for my protein, on a PDB refined from Phenix, or from a download from the rcsb. I don't see anything special on the PDB, all the atoms are listed normally. Is it possible to assign a specific color per chain using this command? Thank you for your help. best Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

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Download Speed
by Gulzar Singh 21 Sep '21

21 Sep '21

Dear Chimera Teach team, The download speed of software is less than 200KB/s (mostly 160 KB/s). I tried both Firefox and wget. We have download limit of 11MB/s My location is Pune, India Please have a look at the issue. Regards, Gulzar Singh

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ChimeraX-users September 2021