March 2021 - ChimeraX-users - RBVI Mailing Lists

Blast Protein not working
by Moradkhan, Tiglath A 16 Mar '21

16 Mar '21

Hi I found what the problem is. I forgot to blast my sequence. But when I run the blastprotein tool I get the following error: ValueError: not enough values to unpack (expected 2, got 1) File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\blastprotein\pdbinfo.py", line 206, in fetch_info entry, auth_cid = pcid.split('_') See log for complete Python traceback. I would be very grateful for your help. Thank you Tiglath

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Question about modelling
by Moradkhan, Tiglath A 16 Mar '21

16 Mar '21

Hi For some reason when I try to model using ChimeraX it cuts off the first two amino acid residues of the N-terminus. I'm trying to model dimeric sea otter Apo A-I using the pdb structure of 3R2P as a template. The sea otter sequence is: DEPQSPWDRVKDLATVYVDVVKDGGRDYVAQFEASA LGKQLNLKLLDNWDSLSSTVTKLREQIGPVTQEFWDNLEKETEALRQEMSKDLEEVKQKV QPYLDEFQKKWHEEVELYRQKVAPLGAELREGARQKLQELQEKLTPLGEELRDRARTHVD ALRAQLAPYSDQLRERLASRLQALK But the template does not contain the first two amino acid residues. When I model the sea otter protein, it doesn't include the first two amino acids. I'm not sure why it's doing that. I would be very grateful for your help. Thanks Tiglath

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radial coloring cryo map
by Moustafa, Ibrahim M. 15 Mar '21

15 Mar '21

Dear all, I am trying to color a cryoem map radially in ChimeraX (to get something similar to surface color by radius in chimera). I used the following comand: color radial #model However, the map is colored from one side to the other instead of radial coloring starting from the center. I tried to specify the center of the screen as 0,0,0 but that did not help. What is the correct command/options to do radial coloring in ChimeraX? Thanks for help, Ibrahim

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pause/wait read user input in chimerax script
by andrew 13 Mar '21

13 Mar '21

Greetings, I would be grateful for help with a script. I made a .cxc script. Now, I would like to show somebody the steps, one by one as in I download this [return] I select that [return] colour these [return] but I cannot see how to insert a pause/wait or something that waits on keyboard input. I did try to insert a "runscript" and put some lines in a python script that reads from the keyboard, but it looks as if chimerax has redirected the script's stdin. I have a feeling, that if I knew what I was doing, I could put another line in the python script "import chimerax.core" and read until the next newline from the command line. Is there a way to pause after each line in a script ? Many thanks for any advice.

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Placement of markers after translation
by Helge Paternoga 09 Mar '21

09 Mar '21

Dear ChimeraX team, I have a question regarding the placement of markers. I am currently trying to extract densities from cryo-EM maps for figure preparation. Therefore, I am using markers to colour any density that is not part of what I want to extract and then split the map accordingly. I noticed that when I translate a markerset, e. g. by using "view position" with "sameAsModels", new markers are not placed at the cursor position, but instead are transformed according to the translation of the whole markerset. Therefore, to move markers, I have to use the "move marker" command on each marker separately. I would like to know if this behaviour is intented and if it can be switched somehow to place markers at the cursorposition even after translation of the markerset. Ultimately, I would like to re-use defined markersets for extracting (or "cleaning") the same invariant components of my maps. But the current behaviour makes it nearly impossible to add new markers for touch-ups after opening and aligning a markerset. Best, Helge

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Volumes
by Colton Carlson 09 Mar '21

09 Mar '21

Hello, I am just wondering if ChimeraX has added the ability to colour surfaces based on the values of a different surface? That is, input 2 cube files, then colour one cube file based on the values of the other. It is available in the other version of chimera, but the only information I could find on this was from 2018 and said it was not yet implemented in ChimeraX. Thanks a bunch! Colton

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Re: [chimerax-users] ChimeraX - defattr Problems
by Elaine Meng 08 Mar '21

08 Mar '21

Hi Harsh, Sorry, I don't know the answer, so I'm CC'ing the chimerax-users(a)cgl.ucsf.edu list. In general, please use the chimerax-users(a)cgl.ucsf.edu address to ask us questions unless your message contains private data. It allows others to answer or to learn from the answers, serves as a record of our service, and is searchable later. Also, when you get a traceback, it is sometimes better (than sending mail directly) to use the menu: Help... Report a Bug and attach any files needed to reproduce the problem, as well as including a short description of what you did and your e-mail address if you want feedback. That will automatically send us information about platform, version, etc. Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 6, 2021, at 7:25 PM, Harsh Srivastava <hrs4853(a)rit.edu> wrote: > > Hello Dr. Meng, > > I hope this message finds you well. I am receiving the following error when attempting to load an external attribute file into ChimeraX using the defattr command as follows: > > defattr /Users/harsh/Downloads/attfile.defattr > > 1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/atomic/attr_registration.py", line 90, in register > type_str(prev_attr_type), type_str(attr_type))) > chimerax.atomic.attr_registration.RegistrationConflict: Registration of attr 'deltaKL' with Residue by defattr command conflicts with previous registration by defattr command due to differing value types (int vs. float) > > chimerax.atomic.attr_registration.RegistrationConflict: Registration of attr 'deltaKL' with Residue by defattr command conflicts with previous registration by defattr command due to differing value types (int vs. float) > > File "/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/atomic/attr_registration.py", line 90, in register > type_str(prev_attr_type), type_str(attr_type))) > > Below is an excerpt of the attribute file following the rules outlined on the web documentation. It might not be apparent on email, but the format of the values is (tab)(residue)(tab)(value). > > attribute: deltaKL > recipient: residues > :1 0.23 > :2 0.23 > :3 0.23 > :4 0.27 > :5 0.19 > :6 0.06 > :7 0.1 > :8 0.46 > :9 -0.44 > :10 0.15 > :11 0.32 > :12 0.05 > :13 -0.6 > :14 -0.4 > :15 -0.35 > :16 0.2 > :17 0.14 > > I receive the same error consistently where ChimeraX tells me there is a conflict when registering the attribute despite having never registered a deltaKL attribute to the structure. > > Would you kindly be able to advise? > > Kindly, > Harsh > -- > Harsh Srivastava > Rochester Institute of Technology > Bioinformatics and Computational Biology > hrs4853(a)rit.edu > >

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Getting rid of a gap in a helix ribbon
by Luca Pellegrini 08 Mar '21

08 Mar '21

Hi, The cartoon drawing of one helix in my structure has a gap in the middle, where it is drawn as a coil. I would like to draw the whole helix as a continuous ribbon. If I select the two consecutive residues at the gap and type: 'setattr sel res ss_type 1' the gap remains. So it looks like the residues at the gap are already helical, as the C-end and N-end residues of two consecutive helices. This looks trivial to fix but I can’t figure it out at the moment… Thanks for your help. Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK

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Displaying multiple sequences during alignment
by Y. Mutum 08 Mar '21

08 Mar '21

Hi I have a very quick query. I opened up 3 models - 3cx5, 2qjp and 1zrt in ChimeraX. I was thinking of aligning on one of the chains and looking at the global-sequence-alignment. >>> match #3/C #2/A to #1/C showAlignment true The sequence alignment opens up as pairwise sequence alignement, in 2 separate windows for each of the 2 pairs. Picture attached. Rather, is there a way to get all 3 sequences aligned together, not separately? I tried looking up at other options, but I think I am missing out something somewhere. Thanks Yaikhomba

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Re: [chimerax-users] Map Coloring in ChimeraX
by Tom Goddard 06 Mar '21

06 Mar '21

Hi Jagannath, Here's a video showing how to use the ChimeraX color zone tool to color a cryoEM so each protein has a different color. https://youtu.be/zU3Xb6LRFco <https://youtu.be/zU3Xb6LRFco> Tom > On Mar 5, 2021, at 11:09 AM, Jagannath Maharana <jmbhu7(a)gmail.com> wrote: > > Dear Tom, > Greetings of the Day. I'm Jagannath, a PhD student, IIT Kanpur, India. I'm truly a fan of your program and it's amazing potential in creating beautiful illustrations. Specially the CryoEm maps. I had a query regarding that. I wanted to colour different domains differently in a single map. I've been trying hard for this but unable to figure it out. I'd really appreciate if you could extend your help regarding this. For your reference I've provided a picture. > > Looking forward to hearing from you > Best Regards > Jags. > PhD Student > GPCR biology lab > IIT kanpur, India > > > <Screenshot_2021-03-06-00-37-33-325_com.android.chrome.jpg>

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Re: [chimerax-users] trouble with importing chimerax module
by Tom Goddard 06 Mar '21

06 Mar '21

Hi Greg, ChimeraX like Chimera includes Python within the application. So the normal way to run a ChimeraX Python script is to just open it in ChimeraX for example with the open command "open myscript.py" or you can run ChimeraX from a shell without a graphical user interface and have it run the script chimerax --nogui myscript.py With Chimera there is a pychimera PyPi module (https://pypi.org/project/pychimera/ <https://pypi.org/project/pychimera/>) created by Jaime Rodriguez-Guerra outside our lab to use Chimera with your own Python 2 installation. There currently is not a PyPi module to use ChimeraX in your own Python 3. I made a ChimeraX PyPi module (a "wheel") a few months ago as a test but it only partly works and we have not released it. Various initializations in the ChimeraX code need to be fixed to work outside the ChimeraX application. We proposed doing that work in a grant application to Chan-Zuckerberg Initiative last month, their Visual Proteomics call for proposals (https://chanzuckerberg.com/rfa/visual-proteomics/ <https://chanzuckerberg.com/rfa/visual-proteomics/>). We will not know whether we get funding to pursue that until at least May 2021. Is it essential to your use of ChimeraX that you run Python scripts in your own Python? If so we could try to get something rigged up that would work for you. If the main issue is you need other PyPi packages that are not in ChimeraX for your Python scripts, you can install those packages easily into ChimeraX using chimerax -m pip install <NameOfPyPiPackage> Tom > >> On Mar 5, 2021, at 12:49 PM, Gregory Babbitt <gabsbi(a)rit.edu> wrote: >> >> Hi Dr. Meng >> >> Some of us at RIT are having trouble importing chimerax.core.commands to python3 so we can write a script to run things in chimerax. >> >> Does debian have it? I also noticed my pip list does not show the older chimera module even though we call it alot in python. Does it have a different name like midas or pychimera? >> >> What is chimeraX equivalent...how do we install it via pip/pip3? >> >> thx >> >> Greg B >> >> Dr. Gregory A Babbitt >> Associate Professor >> T.H. Gosnell School of Life Sciences >> Rochester Institute of Technology >> Rochester NY USA >> website: http://people.rit.edu/gabsbi >> >> > >

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chimera X troubles
by Dorian Armando Acevedo Castro 05 Mar '21

05 Mar '21

Good morning, I tried to install chimera X for Ubuntu 16 but I have the following problem. (base) da.acevedo10@colab14:~$ sudo apt-get install /home/UANDES/da.acevedo10/chimerax-daily.deb Reading package lists... Done Building dependency tree Reading state information... Done Note, selecting 'ucsf-chimerax-daily' instead of '/home/UANDES/da.acevedo10/chimerax-daily.deb' Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: ucsf-chimerax-daily : Depends: ffmpeg but it is not installable E: Unable to correct problems, you have held broken packages. I really appreciate if you can tell me why I can't install chimera x Cordialmente, Dorian Armando Acevedo Castro COBO - Computational Bio- Organic Chemistry Bogotá cobo.uniandes.edu.co<http://cobo.uniandes.edu.co/> Estudiante Doctorado Ciencias-Química. M. Sc. Química, U. de los Andes. Químico, U. Nacional. <mailto:daacevedoc@bt.unal.edu.co> <mailto:dorian.acevedo@gmail.com>

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An urgent question about Chimera (need help)
by 陆萌 05 Mar '21

05 Mar '21

Dear developers: I have always failed to minimize my structure in Chimera, even if I reinstalled my Chimera or tried another version of Chimera. I can not fix this bug by myself, so I have to ask for help to you. I'll appreciate very much if you can help me solve the problem. Thank you very much! Sincerely! Meng Lu 2021.3.5

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Attribute files in ChimeraX
by David Leeming 04 Mar '21

04 Mar '21

Dear ChimeraX users, I'm trying to write a script that will export an attribute file in ChimeraX, (specifically the attribute sasa) I'm looking for a similar output to that of the attribute calculator function in Chimera (see image below) [cid:9fd01eec-1765-4ec9-8172-dec4315fa1d6] I'm currently trying to run the command below to export the attribute file: [cid:6e286ca4-a133-49bc-a34e-1a2f39bb7243] However, when I run this script, it produces the error: "No known data format for file suffix '.defattr'" Any advice on how I can better go about producing this file or how I can modify my script to prevent this error would be greatly appreciated. Thank you for your time. Kind regards, David

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Re: [chimerax-users] How to expand the RAN in ChimeraX?
by Tom Goddard 03 Mar '21

03 Mar '21

Hi Andrea, The volume command dataCacheSize option will do this. For example for 32 Gbytes of memory cache for volume data use command volume dataCacheSize 32000 The default is to set it to half the physical memory of the computer. https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#sampling <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#sampling> I would not suggest changing it because surface and image rendering typically use an amount memory for the graphics similar to the data size. The cache is only for the volume data, so with graphics, the current setting can utilize all your memory. Increasing it can cause data to be paged out to disk with horrible performance. The above setting is not saved. If you did want to change it for every ChimeraX session you would use Preferences / Startup / Execute these commands at startup. Tom > On Mar 3, 2021, at 9:04 AM, Andrea Fera <andrea.fera(a)revealgc.com> wrote: > > Dear Mr. Goddard, > > This is Andrea. I am not sure that you remember me, but we met in 2013 or so in S. Francisco and Berkeley. > > I am a strenuous fan of your software! Especially for volume rendering of cryo-type tomograms. > I do have a tomogram pf a few Gb that I would like to render with your software. I use a Lynux server with LOTS of RAM. How can I increase the RAM allocated by ChimeraX? > > Thank you and all best… > Andrea Fera > > -- > Andrea Fera, PhD > Senior Data Scientist > <image003.jpg>

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Accessing shapes created through a .BLD script
by Tanmoy Sanyal 03 Mar '21

03 Mar '21

Hi, I have a bunch of shapes (spheres and cylinders) created through a .bld script. I'd like to load this script once, and then be able to change the colors of said shapes in successive operations. It is possible to set the colors directly in the .bld script, but I need to make an animation out of this. E.g: if my .bld script contains lines that draws shapes like so: .sphere 0 0 -1 5.0 .cylinder 0 0 0 1 1 1 1.0 I want to be able to later have a bunch of scripts called 1.cxc, 2.cxc, 3.cxc, .... each of which change the color of the sphere and cylinder. This way, I can load these scripts in the per-frame mode, to create an animation out of the color changes. Alternatively, I tried doing this with just the shape command and without a .bld script, but I have over ~10000 shapes; the shape command interprets each as a different model, and my computer hangs. ----- Thanks, Tanmoy Tanmoy Sanyal Postdoctoral scholar, Sali lab <https://salilab.org/>, Department of Bioengineering and Therapeutic Sciences <https://bts.ucsf.edu/>, University of California San Francisco Phone:- (+1) 805-637-0375

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Help with surfaces
by Eoin Winston 02 Mar '21

02 Mar '21

Hello, I create molecular animations and use ChimeraX to import PDB files and convert them to surfaces which I then export for use in Autodesk 3dsmax. I have a very limited understanding of this fantastic software however I am wondering if there is a quick way to solve my problem. I have a PDB file I was sent containing a trimer. When I use a command such as: *molmap #13,1 20 *(I found this on a YouTube video BTW) It creates a surface model of the entire PDB file. How do I create separate surface models for each of the trimers? So the PDB exports with three meshes as opposed to a single mesh. Hope that makes sense. Best regards, Eoin *Eoin Winston, *Head of Design *Phone:* +353 877991603 | Email <eoin(a)nexucreative.com> | Web <http://www.nexucreative.com/> | Instagram <https://www.instagram.com/NEXU.creative/> | Twitter <https://twitter.com/NEXU_Science> Raptech Ltd. t/a *NEXU* Science Communication is registered in Ireland as a private company limited by shares. Registration No. 610585. Registered business address: 3 Mruigtuaithe, Ratoath, County Meath, Ireland. A85 Y883

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