April 2021 - ChimeraX-users - RBVI Mailing Lists

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.

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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> >

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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.

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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*

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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

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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.

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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.

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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

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ChimeraX-users April 2021