February 2021 - ChimeraX-users - RBVI Mailing Lists

Identifying symmetry of a model
by Y. Mutum 06 Feb '21

06 Feb '21

Hi I am working with pdb id: 3cx5. This model is roughly C2 symmetric. Is there a way to identify the symmetry (or rough symmetry of a not-so symmetric model) of a pdb/ mmcif model and orient the symmetry axis to the axis perpendicular to the screen? On a similar note, say we select a 4 somewhat symmetry-related residues in this model and make 2 intersecting lines, is there a way to align these lines perpendicular to the perpendicular screen axis? Thanks Yaikhomba

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error when using Blast Protein
by Elghobashi-Meinhardt, Nadia 05 Feb '21

05 Feb '21

Dear ChimeraX forum, I am trying to do a sequence search with the Blast Protein tool (MacOS). I have tried using various pdb structures/chains but am repeatedly getting the following error: "ValueError: not enough values to unpack (expected 2, got 1)" from ".../blastprotein/pdbinfo.py", line 206, in fetch_info entry, auth_cid = pcid.split('_') What is the correct usage of Blast Protein? Thank you! Nadia

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ChimeraX tool installationg
by Yongcheng MU 04 Feb '21

04 Feb '21

Hello, Hope you are doing well. This is Yongcheng. I am writing this email because I am trying to install a Deep learning tool in ChimeraX, but I have some issues about it. I built and installed my code following the steps on the Chimera Guide website. I installed my code successfully, but when I run using command that I created, it hold some errors: *"RuntimeError: delayed command registration for 'CL_Tensorflow' failed (register_command() failed for command CL_Tensorflow in bundle ChimeraX-CL-Tensorflow:* *cannot import name 'cmd' from 'chimerax.CL_Tensorflow' (/Users/jackmu/Library/Application Support/ChimeraX/1.1/site-packages/chimerax/CL_Tensorflow/__init__.py))File "/Users/jackmu/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2142, in lazy_register* *raise RuntimeError("delayed command registration for %r failed (%s)" % (cmd_name, e))"* *"During handling of the above exception, another exception occurred:* *Traceback (most recent call last): File "/Users/jackmu/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/cmd_line/tool.py", line 275, in execute cmd.run(cmd_text) File "/Users/jackmu/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2746, in run self._find_command_name(final, used_aliases=_used_aliases) File "/Users/jackmu/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2489, in _find_command_name what.lazy_register(cmd_name) File "/Users/jackmu/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2142, in lazy_register raise RuntimeError("delayed command registration for %r failed (%s)" % (cmd_name, e))RuntimeError: delayed command registration for 'CL_Tensorflow' failed (register_command() failed for command CL_Tensorflow in bundle ChimeraX-CL-Tensorflow:cannot import name 'cmd' from 'chimerax.CL_Tensorflow' (/Users/jackmu/Library/Application Support/ChimeraX/1.1/site-packages/chimerax/CL_Tensorflow/__init__.py))RuntimeError: delayed command registration for 'CL_Tensorflow' failed (register_command() failed for command CL_Tensorflow in bundle ChimeraX-CL-Tensorflow:cannot import name 'cmd' from 'chimerax.CL_Tensorflow' (/Users/jackmu/Library/Application Support/ChimeraX/1.1/site-packages/chimerax/CL_Tensorflow/__init__.py))File "/Users/jackmu/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2142, in lazy_register* *raise RuntimeError("delayed command registration for %r failed (%s)" % (cmd_name, e))"* I wonder if you know what's going on here, and how to fix it. Thank you so much for your time. Best regards, Yongcheng

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Re: [chimerax-users] [Chimera-users] how to color an model by an attribute in chimerax
by Elaine Meng 03 Feb '21

03 Feb '21

Hi Yeping, **Please send ChimeraX questions to the chimerax-users(a)cgl.ucsf.edu address, *not* to chimera-users(a)cgl.ucsf.edu, because that makes people confused about which program we are talking about. Two more thoughts about your file: (1) you need to make sure the residue numbers in the file all match to your structure. I don't know which structure you are using so when I test it on some other structure that doesn't have all the same residue numbers, it does not work unless I change the match mode from "1-to-1" to "any". You might want to try using match mode "any". (2) looks like one residue has a high value 0.788 and all the others are very close to zero, so when I color the whole range the structure is all the same color (used for the low end) except for the one high-value residue. E.g. coloring by attribute entropy using palette blue-white-red makes the whole structure blue except for one residue red. Elaine > On Jan 27, 2021, at 8:25 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Hi Sun Yeping, > To use the "open" command to open defattr format you need ChimeraX daily build from Oct 30, 2020 or newer. Or if you are using ChimeraX 1.1, you can use the "defattr" command to open the file. Older ChimeraX than version 1.1 cannot read this file type at all. Changes and approximate dates are given in the Change Log: > > <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> > > The format is described here: > <https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > >> On Jan 27, 2021, at 1:04 AM, sunyeping <sunyeping(a)aliyun.com> wrote: >> >> Dear Elaine, >> >> Thank you for your reply. The attribute file entropy.txt is available at >> >> https://drive.google.com/file/d/1oG0O4zKqw-uD5SeLTrAu16c3Jh8m3LG5/view?usp=… >> >> Could you please help check whether the format is correct"? >> >> I cannot figure out how to open this attribure file in chimera. When I input "open entropy.txt format defattr" in chimerax, I get the following error message: >> >> Invalid "format" argument: Should be one of 'aln', 'amira', 'apbs', 'bild', 'brix', 'ccd', 'ccp4', 'cellpack', 'cmap', 'cmd', 'collada', 'compiled python', 'cube', 'dcd', 'delphi', 'dicom', 'dock', 'dsn6', 'dv', 'emanhdf', 'fasta', 'fsc', 'gltf', 'gopenmol', 'hdf', 'hssp', 'html', 'ihm', 'images', 'imagic', 'imod', 'imodmap', 'ims', 'macmolplt', 'markers', 'mmcif', 'mmtf', 'mol2', 'mrc', 'msf', 'netcdf', 'obj', 'pdb', 'pdbqt', 'pfam', 'pif', 'pir', 'positions', 'priism', 'profec', 'pseudobonds', 'python', 'rsf', 'sdf', 'segger', 'session', 'sff', 'situs', 'smiles', 'spider', 'stl', 'stockholm', 'storm', 'swc', 'tom_em', 'trr', 'uhbd', 'uniprot', 'vtk', 'web fetch', 'xplor', or 'xtc' >> >> Could you tell me what is the correct way to open the file? >> >> Thank you, >> Best, >> Yeping >> ------------------------------------------------------------------ >> From:孙业平 <sunyeping(a)aliyun.com> >> Send Time:2021年1月26日(星期二) 11:53 >> To:chimera-users <chimera-users(a)cgl.ucsf.edu> >> Subject:[Chimera-users] how to color an model by an attribute in chimerax >> >> Dear all, >> >> I wish to color an model by an attribute in chimerax. The attribute is the entropy which is calculted by an external software. I wrote the entropy values of each residue in a text file (attr.txt) like the following: >> >> attribute: entropy >> match mode: 1-to-1 >> recipient: residues >> :1 0.0 >> :2 0.0014948 >> :3 0.0090952 >> :4 0.0004805 >> :5 0.1102497 >> :6 0.0095258 >> :7 0.0008226 >> :8 0.0042205 >> :9 0.0037255 >> :10 0.0006678 >> :11 0.0027988 >> :12 0.0193925 >> :13 0.0153925 >> :14 0.0052115 >> :15 0.0020136 >> .......... >> >> However, when I input the command "color byattr attr.txt", I get the following error information: >> "No known/Registered attribute attr.txt" >> >> Could anyone tell me what is the correct way to do this? >> >> With many thanks. >> >> Best regards >> > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users > ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Reading cube file from Quantum Espresso pp.x
by Zack Gainsforth 02 Feb '21

02 Feb '21

Hi, I produced some projected wavefunctions in a crystal that I'm working with using Quantum Espresso (DFT). I output these projections to a gaussian cube file using the pp.x program (built into Quantum Espresso). I'm able to read these into ChimeraX but I'm unable to see the atoms -- only the volumetric data. I tried Actions - Atoms/Bonds - Show, but I still don't see the atoms. Is there another step I should take to make them visible? I see something like this: (very nice!) I'm attaching a link to the cube file below -- I can't include it because it is 600 MB. Thanks, Zack https://www.dropbox.com/s/ehhli8h3qr7vd4y/wfc_k001_b329wfc.cube?dl=0

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