- ChimeraX-users - RBVI Mailing Lists

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

2 3

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

3 7

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

2 4

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

3 5

mapping out water channels in chimerax
by Noor Agip 29 Jan '21

29 Jan '21

Hi, I am working on a membrane protein, and I am trying to map out water channels (responsible for proton conduction from one side of the membrane to another). I am currently doing this manually from one connecting water molecule to the next using the structural analysis/H-bond function. Is there an easier way to do this with 14 linked water/residues? Best wishes, Noor

2 3

Labeling canine Apolipoprotein A-I
by Moradkhan, Tiglath A 29 Jan '21

29 Jan '21

Hi I'm trying to model the N-terminus of mature canine Apolipoprotein A-I using Chimera. However the actual sequence in uniprot is not that of the mature protein. Here is the sequence: MKAALLTLAVLFLTGSQARHFWQQDEPQSPWDRVKDLATVYVDAVKDSGRDYVAQFEASA LGKQLNLKLLDNWDSLSSTVTKLREQIGPVTQEFWDNLEKETEVLRQEMSKDLEEVKQKV QPYLDDFQKKWQEEVELYRQKVAPLGSELREGARQKLQELQEKLSPLAEELRDRARTHVD ALRAQLAPYSDDLRERLAARLEALKEGGGASLAEYHARASEQLSALGEKARPALEDLRQG LLPVLESFKVSLLAAIDEATKKLNAQ The sequence of the mature form is: DEPQSPWDRVKDLATVYVDAVKDSGRDYVAQFEASA LGKQLNLKLLDNWDSLSSTVTKLREQIGPVTQEFWDNLEKETEVLRQEMSKDLEEVKQKV QPYLDDFQKKWQEEVELYRQKVAPLGSELREGARQKLQELQEKLSPLAEELRDRARTHVD ALRAQLAPYSDDLRERLAARLEALKEGGGASLAEYHARASEQLSALGEKARPALEDLRQG LLPVLESFKVSLLAAIDEATKKLNAQ According to how the sequence is labeled in uniprot the first aspartate residue of mature canine Apolipoprotein A-I starts at position 25, and this what Chimera uses. However, for the mature protein this should start at position 1. How can I change the numbering system so the first aspartate residue starts at position 1? I would be very glad for your advice. Thank you. Tiglath

2 1

Copy/combine function in ChimeraX
by Zhang, Rui 26 Jan '21

26 Jan '21

Hi, Is Copy/combine function still not available in ChimeraX? This is the command that I use on daily basis in Chimera. Thanks! Rui Zhang Washington University in St. Louis

2 1

Re: [chimerax-users] [Chimera-users] how to color an model by an attribute in chimerax
by Elaine Meng 26 Jan '21

26 Jan '21

On Jan 25, 2021, at 7:47 PM, sunyeping <sunyeping(a)aliyun.com> wrote: > > 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 Hello, Since this is a ChimeraX question, better to send to the chimerax-users(a)cgl.ucsf.edu address CC'd here instead of the chimera-users list. (1) First you need to make sure the text file is the right format. It should be tabs (not just a space) before the residue number and between the residue number and the value, e.g. as described here: <https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html> (2) Then (after the atomic structure is open), open the attribute file with the "open" command, e.g. with pathname of your file, or if you want use a file browser window to find the file, "open browse". It is easiest to first name the file ending in .defattr so that ChimeraX will know what kind of file it is supposed to be. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#defattr> (3) then the Log should report that the attribute named entropy is assigned and you are ready to do the coloring. The coloring command could be something like color byattribute entropy palette rainbow ...there are several other options, see <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

Re: [chimerax-users] windows 10 GPU acceleration?
by Tom Goddard 24 Jan '21

24 Jan '21

Hi Chuck, Glad you figured it out. I wonder what that graphics scheduling option is doing. Tom > On Jan 24, 2021, at 3:36 PM, Sindelar, Charles <charles.sindelar(a)yale.edu> wrote: > > Hey, I figured it out! There is some kind of new windows option called hardware-accelerated graphics scheduling, in the graphics settings->change default graphics settings control panel. I turned it off, and boom- ChimeraX started using the Nvidia. Thanks for the pointers- definitely helped me guess the solution. Maybe this will help someone else… cheers! > > From: Tom Goddard <goddard(a)sonic.net> > Sent: Sunday, January 24, 2021 2:38 PM > To: Sindelar, Charles <charles.sindelar(a)yale.edu> > Cc: chimerax-users(a)cgl.ucsf.edu > Subject: Re: [chimerax-users] windows 10 GPU acceleration? > > Hi Chuck! > > Yes ChimeraX and Chimera should both be using your laptop Nvidia 2080 GPU and not the Intel graphics. Chimera(X) does not choose the GPU and does not even know that there is more than one -- nothing in the OpenGL graphics library gives that information. It is up to the Windows operating system to decide what GPU used, and it usually makes the right choice. There is in fact a flag in ChimeraX that tells Windows it should use the Nvidia GPU if available. > > You can see for certain which GPU is being used in Chimera with the command > > graphics driver > > Here's what it reports in the log on my laptop > > OpenGL version: 4.1 ATI-3.10.18 > OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine > OpenGL vendor: ATI Technologies Inc. > > Yours should either save Nvidia or Intel in the output. It may say Nvidia but your 2080 GPU use does not seem to get much use. The GPU will only be used when the graphics are changing -- for instance, use the command "roll" to set the models in motion (and command "stop" to halt them). Even when the graphics is constantly changing if your model is small and lighting mode is simple, it will probably show the GPU is hardly working. Use "full" or "soft" lighting to get ambient shadows and that should load the GPU some ("lighting full", or "lighting soft"). > > The high performance graphics mode you set in Windows should certainly make the Nvidia GPU get chosen. > > If ChimeraX "graphics driver" says the Intel GPU is being used then something is clearly messed up. But it must have something to do with your Windows and graphics driver configuration. In fact are you sure you have a working Niovida graphics driver installed? Are there any other apps you use where you see the Nvidia GPU in use? > > Tom > > > > > On Jan 24, 2021, at 10:09 AM, Sindelar, Charles <charles.sindelar(a)yale.edu <mailto:charles.sindelar@yale.edu>> wrote: > > Dear Tom, Elain, Eric et al, happy new year to you and I hope all is well. > > I was wondering how much GPU acceleration I can hope for with my new Dell XPS 17, for either ChimeraX or Chimera? Right now I am noticing that when I use the programs, all the graphics load goes to my integrated Intel graphics GPU, and frame rates are not impressive. The Nvidia 2080, which should be awesome, sits idling. This is on Windows 10. I tried setting the Windows “Graphics Settings” control panel for “high performance”, which should try to make Chimera(X) use the NVidia, as far as I know, but nothing happens. > > Thanks and cheers! - Chuck > _______________________________________________ > 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://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl…>

1 0

windows 10 GPU acceleration?
by Sindelar, Charles 24 Jan '21

24 Jan '21

Dear Tom, Elain, Eric et al, happy new year to you and I hope all is well. I was wondering how much GPU acceleration I can hope for with my new Dell XPS 17, for either ChimeraX or Chimera? Right now I am noticing that when I use the programs, all the graphics load goes to my integrated Intel graphics GPU, and frame rates are not impressive. The Nvidia 2080, which should be awesome, sits idling. This is on Windows 10. I tried setting the Windows "Graphics Settings" control panel for "high performance", which should try to make Chimera(X) use the NVidia, as far as I know, but nothing happens. Thanks and cheers! - Chuck

2 1