April 2021 - ChimeraX-users - RBVI Mailing Lists

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.

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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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