October 2020 - ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] [Chimera-users] color by zone in chimeraX
by Elaine Meng 20 Nov '20

20 Nov '20

Hi Pranav, I’m Cc'ing the chimerax-users(a)cgl.ucsf.edu list (recommended for ChimeraX questions). I believe the problem is that when coloring the chains you are using “target c” which means to color only cartoons, whereas coloring by zone uses the atom colors. Since you only colored the cartoons, the atoms probably still had heteroatom color-coding. If you use “target ac” instead (even if the atoms aren’t shown), then as long as the color zone distance is big enough, I think you will get the color zones you expect. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 20, 2019, at 10:54 AM, Pranav Shah <p.shah.lab(a)gmail.com> wrote: > > Hi Elaine and Co., > > I am trying to color a virus map with the relevant pdb file, the > series of commands I am running are as follows, > open virus.mrc > open virus.pdb > color /A plum target c > color /B lightgreen target c > color /C dodger blue target c > color zone #1 near #2 dist 3 > However, the resultant surface is rendered in splotches of red and > blue, which leads me to think the it is coloring the surface using > atom type. Could you tell me how I can get Chimera X to color the > surface using the colors of the chains only? FYI, color by zone works > flawlessly in chimera. > > Cheers, > Pranav

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New icosahedral lattices relevant for viruses
by Tom Goddard 30 Oct '20

30 Oct '20

Hi Colin, Toni, I added your new icosahedral virus lattices to the ChimeraX hkcage command using your GitHub code. I changed your "alpha" parameter that chooses the lattice type from a number (you used 1-8) to instead a string that can be one of standard, standard-dual, rhomb, rhomb-dual, trihex, trihex-dual, snub, snub-dual. When the hkcage command is used with any of your lattices it logs a message so the user knows to cite your publication. Thanks for contributing this new feature! Tom > On Oct 30, 2020, at 12:04 PM, Colin Brown <colintravisbrown(a)gmail.com> wrote: > > Hi Tom, > > The repository is now public. Let me know if you’d like to be added as a collaborator as we continue revising the bundle. > > Thank you, > Colin Brown > From: Tom Goddard <goddard(a)sonic.net> > Sent: Friday, October 30, 2020 10:46:39 AM > To: Antoni Luque Santolaria <aluque(a)sdsu.edu> > Cc: chimera-dev(a)cgl.ucsf.edu <chimera-dev(a)cgl.ucsf.edu>; Colin Brown <colintravisbrown(a)gmail.com> > Subject: Re: [chimera-dev] question: development of a new icosahedral tool to include new lattices relevant for viruses > > Hi Toni, > > Thanks! I would like to put your improved hkcage command into ChimeraX. The github link to the hktest bundle gives a 404 error "not found" in the web browser. Maybe your repository is private? If your source code is clean and maintainable I can just put it in ChimeraX, no need for a meeting. I do not think I should be a co-author as I have contributed very little. > > Tom > > >> On Oct 30, 2020, at 6:38 AM, Antoni Luque Santolaria <aluque(a)sdsu.edu <mailto:aluque@sdsu.edu>> wrote: >> >> Dear Tom, >> >> Here are some updates and questions regarding the new hkcage bundle: >> >> 1. The new bundle now generates the 8 icosahedral lattices (hexagonal, trihexagonal, snub hexagonal, and rhombitrihexagonal), including regular and dual as published in Tawrock and Luque, 2019. Our next step is to publish the method, for example, in PeerJ Computer Science. We based our approach on your hkcage tool. Since the method underlying that tool was not published on a peer-reviewed journal, we would like you to be a co-author in the manuscript. Would you be interested in being a co-author? >> >> 2. As we polish the algorithm and the bundle's options for publication, we would like to incorporate changes that you consider adequate so the new hkcage tool can be integrated as a native tool in Chimera X in the near future. If this sounds good to you, we could set up a meeting to show you how the tool works and receive feedback from you about options that you consider essential for Chimera X. What do you think? >> >> 3. The current version of the bundle is available on GitHub: https://github.com/colintravisbrown/hktest <https://github.com/colintravisbrown/hktest>. The lattices are controlled by the new parameter alpha, which takes values from 1 to 8. We have used the tool to generate figures for research talks and a research manuscript, which is currently under review. In this google drive folder, you can see some of the images and movies (files named chimera_*): >> >> 4. Our project is funded by the National Science Foundation. Integrating our new tool in Chimera X is one of our Broader Impact goals. Accomplishing this task will help us secure additional funding to develop more computational methods for Chimera X and the scientific community. Your support on this end is greatly appreciated. >> >> Let me know if you have any questions. >> >> Thanks for your time, >> Toni >> >> On Fri, Jun 26, 2020 at 1:30 PM Antoni Luque Santolaria <aluque(a)sdsu.edu <mailto:aluque@sdsu.edu>> wrote: >> Great, thanks for the info! >> >> On Fri, Jun 26, 2020 at 9:38 AM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> Hi Toni, >> >> Ok, plan sounds good. >> >> Regarding the coloring, it is usually easy to do when you have an atomic model of the asymmetric unit, you just color each chain as needed. That requires no additional capabilities in Chimera / ChimeraX. To generate the icosahedral layout from the asymmetric unit (1/60 of capsid) use the sym command. To color a cryoEM map the easiest approach is to use the "color zone" capability to color the map according to the atomic model. It is only when you don't have an atomic model for the map that the coloring gets tricky. That is a rare case since usually the first thing that is done with these maps is to fit an atomic model. That herpes simplex virus image I sent was one of those rare cases, the researchers were studying the virus portal and did not include atomic models in their publication. So developing easier coloring may not be needed. >> >> Tom >> >> >>> On Jun 25, 2020, at 6:06 PM, Antoni Luque Santolaria <aluque(a)sdsu.edu <mailto:aluque@sdsu.edu>> wrote: >>> >>> Thanks, Tom. >>> >>> 1) The user interface will not be essential for the research that we'll be carrying out in the short term, but it's something that I think it would be beneficial in the longer run. Whenever you have a chance to port the interface from Chimera to Chimera X let us know, and we'll adapt it for the extended hkcage. In the meantime, we'll focus on extending the hkcage tool to work through the command line. >>> >>> 2) Coloring the proteins in relation to hkcage as in the example that you shared would be ideal. In fact, for herpes, the trihexagonal lattice would show trimers that are missing in the color scheme of the image that you shared. Our initial goal is to focus on viruses deposited in viperdb because they have associated pdb files, but we would also like to include some cryo-em capsids in the analysis because there are many more capsid architectures that must to be reanalyzed. We'll follow the protocol that is described in the link that you shared with us. >>> >>> Best, >>> Toni >>> >>> On Thu, Jun 25, 2020 at 9:32 AM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >>> Hi Toni, >>> >>> That all sounds good. Yes the link you found is our svn source code for cages.py. Sorry, I accidentally gave you the https link which takes a password and allows checking in changes to the code. >>> >>> The additional options to the hkcage command should be no trouble. It will be pretty obvious how to add them in ChimeraX. In Chimera the code may be harder to fathom, but Colin can ask when stuck on anything. >>> >>> The user interface panel is the most work of what you describe. The current Icosahedron Surface tool in Chimera does not offer the hkcage options, just a plain icosahedron. The hkcage command was developed after that user interface and never got incorporated in. For that user interface window Chimera and ChimeraX will be completely different because Chimera uses the Tk window toolkit while ChimeraX uses the Qt window toolkit. I suggest giving priority to the ChimeraX version of that tool, although the plain icosahedron user interface has not been ported to ChimeraX yet. Possibly I can port it to ChimeraX making all the Tk to Qt changes as a starting point for Colin. Probably I would not have time to do that until mid-July. The Chimera icosahedron surface tool has a subdivision parameter that divides the facets into smaller triangles. The current hkcage does not support that and some extra code would be needed to compute such subdivisions of the hexagons, pentagons, .... >>> >>> It may also be interesting to think about how to color electron microscopy maps to show the virus capsomere arrangement, for example as in this image >>> >>> https://www.cgl.ucsf.edu/chimera/ImageGallery/entries/herpes/herpes.html <https://www.cgl.ucsf.edu/chimera/ImageGallery/entries/herpes/herpes.html> >>> <emd1307.jpg> >>> ChimeraX hkcage docs >>> >>> https://www.cgl.ucsf.edu/chimerax/docs/user/commands/hkcage.html <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/hkcage.html> >>> >>> Chimera hkcage docs >>> >>> https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hkcage.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hkcage.html> >>> >>> Chimera icosahedron surface docs >>> >>> https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/icosahedron/icosa… <https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/icosahedron/icosa…> >>> >>> Tom >>> >>> >>>> On Jun 25, 2020, at 9:02 AM, Antoni Luque Santolaria <aluque(a)sdsu.edu <mailto:aluque@sdsu.edu>> wrote: >>>> >>>> Hi Tom, >>>> >>>> 1. Thank you for the quick response and clear instructions. I wasn't aware of ChimeraX. I just installed it, and it looks fantastic. >>>> >>>> 2. Colin Brown (in CC) is a master student in the lab who will be leading the efforts to develop the new icosahedral tool over the summer. He will contact you if we have any questions during the development process. >>>> >>>> 3. I wasn't able to access the second link that you shared with us. It requires a username and password. But I found the cages.py in this other link: http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/contrib/IcosahedralCag… <http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/contrib/IcosahedralCag…> Is it the same code? >>>> >>>> 4. The extension that we have in mind would include an option, as you suggest, to identify the lattice (h, t, s, r,...), an option to indicate if the construction uses the regular (hexagons, pentagons) or dual (single tile) blocks, and a third parameter for lattices that have a degree of freedom (see for example Figure 5a in Twarock and Luque, 2019). We would also like to add a panel to control the options manually like in the icosahedron tool. The goal of this gui panel would be to facilitate users to modify the radius, sphere factor, and other options on the fly to obtain a good visual agreement with the viral structure or macromolecular complex of study. Let us know if this would be reasonable. >>>> >>>> Best, >>>> Toni >>>> >>>> On Wed, Jun 24, 2020 at 2:30 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >>>> Hi Toni, >>>> >>>> Neat! I wrote the hkcage code and I think adding your 3 additional series t,s,r to that command would be the way for researchers to get the most use out of it. It could simply be adding one more option to that command that specifies the series. The code that would be needed is Python that computes the vertex coordinates, a triangulation (a list of 3-tuples of vertex indices), and an edge mask that says which of the triangle edges should be hidden (one integer per triangle with 3-bits 0x1, 0x2, 0x4 indicating if the triangle edge should be shown). I could incorporate your code into the Chimera and ChimeraX distributions and we would credit you cite your paper in the documentation. I think it would be quite easy for you to simply modify the cage.py code in your Chimera or ChimeraX distribution, do all the testing, write a bit of documentation describing the new option -- send that to me and I will get it into the daily builds and subsequent releases. >>>> >>>> ChimeraX is the successor of Chimera and ChimeraX 1.0 was just released. Most researchers are still using Chimera instead of ChimeraX but we expect that to transition over the next few years, so I would suggest making your addition to the ChimeraX code. But you can make the additions to ChimeraX or Chimera and I can move it to the other if you like, the hkcage code for the two is nearly identical. ChimeraX uses Python 3 while Chimera uses Python 2. >>>> >>>> https://www.rbvi.ucsf.edu/trac/ChimeraX/browser/src/bundles/hkcage/src/cage… <https://www.rbvi.ucsf.edu/trac/ChimeraX/browser/src/bundles/hkcage/src/cage…> >>>> >>>> https://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/IcosahedralCage/… <https://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/IcosahedralCage/…> >>>> >>>> Tom >>>> >>>> >>>>> On Jun 24, 2020, at 8:49 AM, Antoni Luque Santolaria <aluque(a)sdsu.edu <mailto:aluque@sdsu.edu>> wrote: >>>>> >>>>> Dear Chimera development team, >>>>> >>>>> My lab is interested in developing (or extending) a new version of the hkcage command in cages.py to include the different icosahedral lattices that have been recently discovered and have important implications for viral structures (see Twarock and Luque, Nature Communications, 2019). We would like to receive advice on what would be the best approach to help integrate the tool to be used and shared with the Chimera community. Would it be better to extend hkcage? Generate a new function? Integrate the function in cages.py? Generate a different python script? >>>>> >>>>> My lab (https://www.luquelab.com/ <https://www.luquelab.com/>) is part of the Viral Information Institute at San Diego State University (https://viralization.org/ <https://viralization.org/>) and recently discovered, in collaboration with Prof. Reidun Twarock (The University of York), a new set of icosahedral lattices that describe previously uncharacterized viral capsid structures (https://www.nature.com/articles/s41467-019-12367-3 <https://www.nature.com/articles/s41467-019-12367-3>). My lab's goal is to develop a tool in Chimera that reflects these new geometries and helps us analyze viral capsids and other complexes with icosahedral symmetry. We would also like to facilitate the scientific community to use this tool in Chimera. This project will be developed as part of an NSF award. >>>>> >>>>> Please let us know the best way to proceed. >>>>> >>>>> Thanks, >>>>> Toni >>>>> >>>>> >>>>> -- >>>>> Antoni Luque, PhD >>>>> http://luquelab.com <http://luquelab.com/> >>>>> Assistant Professor >>>>> Department of Mathematics and Statistics >>>>> Viral Information Institute >>>>> San Diego State University >>>>> >>>>> Office: GMCS 514 >>>>> Phone: 619 594 7244 >>>>> email: aluque(a)sdsu.edu <mailto:aluque@sdsu.edu>_______________________________________________ >>>>> Chimera-dev mailing list >>>>> Chimera-dev(a)cgl.ucsf.edu <mailto:Chimera-dev@cgl.ucsf.edu> >>>>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-dev <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-dev> >>>> >>>> >>>> >>>> -- >>>> Antoni Luque, PhD >>>> http://luquelab.com <http://luquelab.com/> >>>> Assistant Professor >>>> Department of Mathematics and Statistics >>>> Viral Information Institute >>>> San Diego State University >>>> >>>> Office: GMCS 514 >>>> Phone: 619 594 7244 >>>> email: aluque(a)sdsu.edu <mailto:aluque@sdsu.edu> >>> >>> >>> -- >>> Antoni Luque, PhD >>> http://luquelab.com <http://luquelab.com/> >>> Assistant Professor >>> Department of Mathematics and Statistics >>> Viral Information Institute >>> San Diego State University >>> >>> Office: GMCS 514 >>> Phone: 619 594 7244 >>> email: aluque(a)sdsu.edu <mailto:aluque@sdsu.edu> >> >> >> -- >> Antoni Luque, PhD >> http://luquelab.com <http://luquelab.com/> >> Assistant Professor >> Department of Mathematics and Statistics >> Viral Information Institute >> San Diego State University >> >> Office: GMCS 514 >> Phone: 619 594 7244 >> email: aluque(a)sdsu.edu <mailto:aluque@sdsu.edu> >> >> -- >> Antoni Luque, PhD >> http://luquelab.com <http://luquelab.com/> >> Assistant Professor >> Department of Mathematics and Statistics >> Viral Information Institute >> San Diego State University >> >> Office: GMCS 514 >> Phone: 619 594 7244 >> email: aluque(a)sdsu.edu <mailto:aluque@sdsu.edu>

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Request for technical clarification on your software to enhance for 3D Visualization
by rameshsj＠ideasahead.in 30 Oct '20

30 Oct '20

Hi, Greetings from Ideas Ahead AV Solutions Pvt. Ltd. We are working on a project to provide a solution for 3D Visualization on a CAVE environment to one of our customer in India who are working on molecular structure and Genomics. We have few queries w.r.t to the functionality of your software. Hence kindly request you to please clarify on the same for us to proceed further. 1. Does your software files supports 3D stereoscopic visualization and the CAVE environment (multiple projection system)? 2. Please let us know what are the minimum hardware specification that is required along with the graphics card to run your software models? 3. Does your software support ART Tracking environment? 4. For visualization does the software needs TechViz 3D Real Time Visualization software or can it run independently on the cable? ____________________________________________________________________________ __________________________________________ Ideas Ahead AV Solutions Pvt. Ltd. the India's leading Audio Visual systems integrator and the right technical Solution provider along with technical support & service. The Ideas Ahead team has an unrivalled knowledge of providing turn-key solutions for VR/AR/MR, Visual Simulation, 3D theatre & Auditorium, audio visual technology. Ideas Ahead specifies designs, installs, integrates, maintains and operates complex audio visual systems for Corporates, OEMs, Defence labs, Educational institutions, Department of Space and Public sector Organizations in India. We have been an established and popular company with an excellent track record for the best customer satisfaction. We have never compromised on the quality and the services provided to the customer. Please find the business areas of Ideas Ahead is mentioned below. Business Verticals: * Virtual Reality & 3D Visualization with CAVE * Audio-Visual & Controls * Visual Simulation in Aerospace, Military & Marine Engineering * 3D theatre & Auditorium * Customer Experience Centers * Services & AMCs ____________________________________________________________________________ _______________________________________________ Your assistance would definitely help us to understand the software better for further projects and contribute back to the ecosystem. Looking forward to your kind clarifications on the requested queries. Thanks, With Best Regards, S J Ramesh Kumar I General Manager - Key Accounts Ideas Ahead AV Solutions Pvt. Ltd. #436, 9th Main, HRBR Layout Kalyan Nagar 1st Stage, Bangalore - 560 043. India (M)+91 81979 66677 / (Off) +91 80 4098 0201/202/203 Skype id: rameshsj Website: www.ideasahead.in <http://www.ideasahead.in/> "Ideas Ahead India's leading Audio Visual Systems Integrator & Service Provider excels at complex requiring converged AV & IT Solutions" <https://tc3.shftrk.com/e/3k5GdZEo0oPD6PEm/KY5nl8znAEr8bNg1/9GO6XdBNgPedZQM0 >

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Deleting unmodelled termini
by mailman-bounces＠cgl.ucsf.edu 29 Oct '20

29 Oct '20

From: "Moradkhan, Tiglath A" <tmoradkhan(a)csus.edu <mailto:tmoradkhan@csus.edu>> Subject: Deleting unmodelled termini Date: October 29, 2020 at 4:48:14 PM PDT Hi I've read the delete command documentation to delete unmodelled termini and rerun Modeller, but I'm having a hard time trying to delete the C-terminal end of the models. Say that the first time Modeller wasn't able to model residues 1-67 and 209-267 because these regions don't align with the template structures. Here is the command (all the returned models are labeled as 3.1-3.4) delete #3/A-B: 1-67,209-267 Is this right? I also tried deleting these residues before running Modeller with no success. I'll be very glad for some help. Thanks Tiglath

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Set atom coordinates by command?
by Jeschke Gunnar 29 Oct '20

29 Oct '20

Hi all, is there a way to set atom coordinates by a command? setattr spec atoms coord value appears to accept only one double argument and sets x, y, and z to this number. Neither space-separated nor comma-separate lists of three values appear to work. Kind regards Gunnar --- Prof. Dr. Gunnar Jeschke ETH Zurich Department of Chemistry and Applied Biosciences Vladimir-Prelog-Weg 2 CH-8093 Zurich Switzerland www.epr.ethz.ch

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Worms?
by Boris Steipe 28 Oct '20

28 Oct '20

Worm plots is one of the still missing features. I probably have the following options (though I haven't actually tried any): - compute my own spline and place a dense string of spheres - compute my own spline and place alternating spheres and cones - place pseudoatoms and compute a surface with a small probe radius - wait until Chimera's worm plot arrives in ChimeraX. Or is there a better way? Thanks! Boris

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Set different colors for each letter like in chimera
by Siyu Chen 28 Oct '20

28 Oct '20

Dear chimerax developers, I was trying to color my labels in chimerax using commands, but it will be too tedious for me to create different labels for each letters, color them differently then align them by fine-tuning the x/y positions. I remember in chimera I was able to call out an window and within that, I can conveniently edit my texts and colors, and save it as a label file. Does chimerax still offer the similar function? Or if there is any equivalent way to achieve that easily? Thanks a lot for your help! Best, Siyu

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Using ChimeraX Modeller interface
by Moradkhan, Tiglath A 26 Oct '20

26 Oct '20

Hi My name is Tiglath and I'm trying to use ChimerX Modeller interface to build a dimer model of a protein I'm currently studying. I first tried to run a BLASP search to find templates but it seems that in ChimeraX, this works differently than in Chimera. In the user guide it says that if the query is a sequence whose structure hasn't been determined, then it's not necessary to specify particular chains. However, when I try running the BLAST search it doesn't do anything. It seems that it is necessary to specify a chain number. But how is this possible if I don't know the template for the target sequence? Am I missing something? Also, I'm a little bit unsure how the Modeller interface works for building dimers. I would be very glad for your help. Thank you Tiglath

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Markers from CMM
by Scott, Brandon L. 26 Oct '20

26 Oct '20

Hello all, When loading markers from a cmm file (example attached), is there a way to specify which submodel the marker goes to rather than it creating a new id? I've added the id_string to the cmm file when I created a new one which is the desired model. I hacked the following, which works, but there are hundreds of tracks so I would like to come up with an automated (and proper) way to do this. perframe "rename #2.$1 track_1 id #1.$2.2;" ranges 1,113 ranges 4,116 perframe "rename #2.$1 track_2 id #1.$2.3;" ranges 114,259 ranges 5,150 Brandon Scott, PhD CZI Imaging Scientist, Research Assistant Professor Nanoscience & Nanoengineering South Dakota Mines 501 E. Saint Joseph St., Rapid City, SD 57701 724.510.1253 | Brandon.Scott(a)sdsmt.edu<mailto:Brandon.Scott@sdsmt.edu> [South Dakota Mines]<https://www.sdsmt.edu/> [South Dakota Mines on Facebook]<https://www.facebook.com/SouthDakotaMines/>[South Dakota Mines on Instagram]<https://www.instagram.com/southdakotamines/>[South Dakota Mines on Twitter]<https://twitter.com/sdsmt>[South Dakota Mines on Snapchat]<https://www.snapchat.com/add/sdsmt>

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Re: [chimerax-users] ISOLDE on Chimerax on centos8.0
by chimera-users-owner＠cgl.ucsf.edu 23 Oct '20

23 Oct '20

Hi I have just recently installed Chimerax 1.1 on my centOS 8.0 workstation and am trying to install the ISOLDE bundle thru Toolshed but I get the message "no download available for Cimerax 1.1 on Linux." how do I get around this problem Cheers Shabir Najmudin

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ChimeraX-users October 2020