- ChimeraX-users - RBVI Mailing Lists

Making New Bonds between two molecules in ChimeraX
by Steven Truong 25 Mar '21

25 Mar '21

Dear ChimeraX Admins and Elaine, Hello, I was wondering if ChimeraX now has a “bond” command. I saw an inquiry like this in the mailing list archives (https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-April/001029.html) but it seems like bond is still not an official functionality. When I switched over to Chimera and tried using the “bond” command, I get the error “Cannot form covalent bond joining two molecules,” even though I’ve saved all of the molecules into one PDB file. Is it because Chimera still sees these two sub-models as un-joinable? My command looks something like: "bond #0:61.A@ND2 #0.1:1222.X@C1”. For further context, we are trying to script orienting/bonding residues to glycans. We’ve been able to figure out aligning and orienting the glycans quite well with the scripts alone (.py scripts), but it seems like we’ll have to find another way to make bonds between the proteins/glycans. Do you have any suggestions? Ideally, we’d also keep as much of the pipeline in ChimeraX, but if it’s necessary, we could further pursue the ChimeraX+Chimera route. Thank you for your help! Many thanks, Steven Truong sdt45(a)cam.ac.uk<mailto:sdt45@cam.ac.uk> Cambridge University

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SwissSidechain equivalent for ChimeraX
by Madeline Grace Rollins 24 Mar '21

24 Mar '21

Hi all, I would like to mutate a serine residue to phosphoserine for one of the proteins I am working with. I have used SwissSidechain in Chimera to do this in the past, but I was wondering if there is an equivalent module like SwissSidechain but for ChimeraX? I tried downloading the SEQCROW bundle for structure editing, but I couldn't find the same range of sidechain derivatives. If not, can you use SwissSidechain in ChimeraX? I apologize in advance if this question has been asked already. Thank you, Madeline

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Questions about focal length of camera in ChimeraX
by Bin Shi 24 Mar '21

24 Mar '21

Thanks very much for your software so that I can specify the camera position and then take a snapshot. However, I can't find the information on the focal length of the virtual camera. I am using mono (default) – monoscopic with perspective (apparent size decreasing with distance from the viewer), and I didn't see any details about the camera intrinsics. Regards, Bin ----------------------------------------------------------------------------------------------- Department of Materials Science and Engineering, University of Toronto Email: binmse.shi(a)mail.utoronto.ca

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Re: [chimerax-users] VR Support
by Tom Goddard 24 Mar '21

24 Mar '21

Hi Gökhan, Your Nvidia RTX 3090 should give the best performance possible with current GPUs. There was a shortage of high-end graphics card in 2020 and supply continues to far outpace demand with popular cards priced 2 to 3 times their suggested retail price. For instance your RTX 3090 has a suggested price of $1500 but currently is priced over $3000. This may not improve until 2022 according to news reports. This may be the biggest problem in getting a new molecular visualization computer setup for VR. https://www.theverge.com/2021/3/23/22345891/nvidia-amd-rtx-gpus-price-scalp… <https://www.theverge.com/2021/3/23/22345891/nvidia-amd-rtx-gpus-price-scalp…> I have not tried the HP Reverb G2 virtual reality headset. I know people were excited about the 2160 by 2160 pixels per eye resolution -- for comparison a Valve Index headset has 1440 by 1600 pixels. But reports said the hand-controller tracking with the Reverb G2 was below current VR standards. ChimeraX and any SteamVR application will work with any hand controllers. I have used ChimeraX VR with other Windows Mixed Reality controllers with a Samsung Odyssey headset with no problems. I've also used it with various other controllers with no problem: Vive Pro, Vive, Oculus Rift S, Oculus Rift, Oculus Quest. ChimeraX won't take advantage of the many extra inputs on Valve Index hand controllers. Nanome is a VR molecular visualization application funded by venture capital -- so they of course will need to charge plenty of money once that VC money runs out. I expect they will mostly be aiming their features at pharmaceutical company needs. I don't know if Nanome has any atomic model refinement capabilities. Tom > On Mar 23, 2021, at 12:11 AM, <tolung.bio(a)gmail.com> <tolung.bio(a)gmail.com> wrote: > > Hi Tom, > > Thanks for the prompt response. > > My responses are below. > > Cheers, > > Gökhan > > > > From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > Sent: Tuesday, 23 March 2021 5:49 PM > To: tolung.bio(a)gmail.com <mailto:tolung.bio@gmail.com> > Cc: Tristan Croll <tic20(a)cam.ac.uk <mailto:tic20@cam.ac.uk>>; ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>>; Simon Brown <simonb(a)uow.edu.au <mailto:simonb@uow.edu.au>>; James Bouwer <jbouwer(a)uow.edu.au <mailto:jbouwer@uow.edu.au>> > Subject: Re: [chimerax-users] VR Support > > Hi Gökhan, > > ISOLDE works in VR in a minimal way -- you can tug on atoms. Here's a little video showing that in ChimeraX 1.1. > > https://www.rbvi.ucsf.edu/chimerax/data/isolde-vr-mar2021/isolde_vr.mp4 <https://www.rbvi.ucsf.edu/chimerax/data/isolde-vr-mar2021/isolde_vr.mp4> > > I turned off depth cue and clipping with commands "light depthcue off" and "clip off" otherwise it clips to a slab which keeps moving as I move my head. I click a VR button on the ISOLDE panel tug atoms mouse mode icon to assign the VR button. I wouldn't say this makes ISOLDE usable in VR. For instance I don't have a way to move the roaming contour mesh region which normally stays in the middle of the screen. But it is enough to play around a bit. I was using a GTX 1080 Ti graphics card. Both the VR and ISOLDE molecular dynamics are running on the graphics card so this puts heavy demand on the card. For simulating just a region around a residue it was reasonably smooth. > > Thanks for the tips to get it to work with ISOLDE. I have a 3090 to play with (which recently replaced my trusty 1080) that should have significantly better performance than the 1080 Ti. Let’s see how it goes… > > I would like to make ISOLDE work well in VR. I think it is the perfect VR application where you really benefit from the best 3D perception possible and the 6-degree-of-freedom hand controllers for moving atoms around is much better suited than a mouse. > > ABSOLUTELY, and I cannot wait for that day that I’ve been waiting for since I started working on structures, to come… > > VR resolution has not been a major issue for use in molecular visualization. We have been using Vive Pro headsets that have adequate resolution for a few years now. A Valve Index headset is probably the best choice for molecular visualization right now. People also use Quest 2 with link cable. > > I have an HP Reverb G2 that recently replated my original HTC Vive. I am quite disappointed with it so far, and was wondering whether I should’ve gone for an Index. However, Index is not sold in Australia (and therefore would have required having one shipped from the US, which means no warranty here and expensive shipping). That was one of the reasons for going for the G2, and I have already used that warranty, since the first unit they sent died after minutes of first use! > > Do you think ChimeraX+ISOLDE should work with the WMR controllers that come with the G2, or is the current code specific to the Vive controllers? > > The big problem is it would take many developer years of effort to have decent user interfaces in VR. The furthest along on this for molecular visualization is Nanome -- you should check out their molecular VR. We continued to develop ChimeraX VR including multi-person VR. > > I have used Nanome’s one of the earliest versions, but it looks like they’re locking more and more of its features for free users based on my most recent try. ☹ Does it work as well as ChimeraX+ISOLDE in refining models? > > Tom > > > > >> On Mar 22, 2021, at 9:18 PM, <tolung.bio(a)gmail.com <mailto:tolung.bio@gmail.com>> <tolung.bio(a)gmail.com <mailto:tolung.bio@gmail.com>> wrote: >> >> Hello Tristan and the Chimera team, >> >> I have been using ChimeraX in VR: fantastic! >> >> However, ISOLDE was not working in VR, unfortunately. >> >> Is there a fix/workaround currently available to get ISOLDE running in VR? >> >> Is there ongoing work on making ISOLDE VR compatible? >> >> Also: 1) are there any advantages of using a Quadro card over a consumer-line card for ChimeraX VR? and 2) is there a recommended minimum system spec for getting high-enough frame rates in VR with large models? We are planning to put together a new system soon for molecular visualization and modelling, hence the questions. >> >> Now that there are VR headsets with high-enough resolution (such as the HP Reverb G2) that allow reading smaller text and finer details in VR, I am hoping that the molecular visualization and modelling software will start providing built-in easy-to-use support for these devices. I applaud ChimeraX team for leading in this space (no pun intended 😊). >> >> Best, >> >> Gökhan >> >> _______________________________________________ >> 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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Re: [chimerax-users] movie in ChimeraX
by Elaine Meng 24 Mar '21

24 Mar '21

> On Mar 23, 2021, at 5:04 AM, Ruchika Bajaj <phd.ruchika(a)gmail.com> wrote: > > Hi Elaine > I am trying to figure out two things. Could you please help me with this? I would appreciate your help. > 1. I have two structures. The first one doesn't have a ligand and the second one has two ligands. I am trying to make a movie with these steps. 1) first structure, 2) two ligands are coming or flying in the picture, 3) then the 2nd structure with two ligands. However, when I am trying to make the morph between the first and second structure, it doesn't show any ligand. I did check the following link, where it discusses that both structures should have ligands to include it in the morph. So, my question is how should I include the ligand ? Could you please explain me with command usage? Thanks !! > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing> > 2. I heard that frames/sec rate could be increased to smoothen steps in movies. I checked the maxFrameRate command. However, I don't know the usage. Could you please help me with that ? > Thanks a lot for your help !! Your prompt response would help me to proceed further. > Regards > Ruchika Hi Ruchika, Please send questions to chimerax-users(a)cgl.ucsf.edu (if you are using ChimeraX) or chimera-users(a)cgl.ucsf.edu (if using Chimera) rather than my individual address, or else they may not get answered. (1) as explained here <https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing> morph only contains the atoms that are the same in both start and end structures. You can show ligands but because they are not included in the morph model, you have to display the ligand(s) from the original model (or an additional copy of the original model) along with the protein in the morph model. Moving them to different positions is even more complicated than showing/hiding. There is a Chimera tutorial that covers this, and what you would do with ChimeraX is similar except that ChimeraX "view" is used to save and restore positions instead of the Chimera commands "savepos" and "reset": <https://www.rbvi.ucsf.edu/chimera/data/tutorials/movies08/moviemaking.html> (2) if you mean you want more steps in the morph (more gradual change) then you would use the "frames" option in the morph command. Probably that is what you want. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#top> However, if you really mean you wanted movie framerate, then it is the "framerate" option of the "movie encode" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/movie.html#encode> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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VR Support
by tolung.bio＠gmail.com 23 Mar '21

23 Mar '21

Hello Tristan and the Chimera team, I have been using ChimeraX in VR: fantastic! However, ISOLDE was not working in VR, unfortunately. Is there a fix/workaround currently available to get ISOLDE running in VR? Is there ongoing work on making ISOLDE VR compatible? Also: 1) are there any advantages of using a Quadro card over a consumer-line card for ChimeraX VR? and 2) is there a recommended minimum system spec for getting high-enough frame rates in VR with large models? We are planning to put together a new system soon for molecular visualization and modelling, hence the questions. Now that there are VR headsets with high-enough resolution (such as the HP Reverb G2) that allow reading smaller text and finer details in VR, I am hoping that the molecular visualization and modelling software will start providing built-in easy-to-use support for these devices. I applaud ChimeraX team for leading in this space (no pun intended 😊). Best, Gökhan

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Move model to specific coordinates of reference model
by Vorländer,Matthias Kopano 19 Mar '21

19 Mar '21

Hi there, I am trying to place a model (volume) at specific coordinates of a second volume (the first model is a map and the second model is a tomogram). I have managed to place a sphere at the desired position, but I can’t figure out how do this with a volume file. Example for placing the sphere: shape sphere radius 100 center 5243.80,3103.88,1086.01 coordinateSystem #1 How can I achieve the same but placing a volume at the desired location? Thanks a lot, Best, Matthias

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building peptides in Chimera/ChimeraX
by Elaine Meng 18 Mar '21

18 Mar '21

Hello Ishita, Your question was forwarded. I'm CC'ing chimerax-users(a)cgl.ucsf.edu (which is the recommended address for asking ChimeraX questions, for future reference). Peptide-building in ChimeraX (and Chimera) does not predict the structure, it simply uses whatever angles you choose in the Build Structure tool. So the reason it looks like a helix is that you told it to use the helix phi,psi angles. ChimeraX build structure: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#start> In the paper figure, it says that the indolicin structure is PDB 1g89 ... so if you want it to look like that, just open 1g89. In the legend it says structures generated by Chimera, but apparently they just mean that images of the structures (from the PDB) were generated by Chimera. 1g89 is an NMR ensemble of 16 structures, so they apparently just chose one of the structures to show and hid the others. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > -------- Forwarded Message -------- > Subject: Request regarding ChimeraX (From UC Davis) > Date: Wed, 17 Mar 2021 02:04:17 +0000 > From: Ishita M Shah <imshah(a)ucdavis.edu> > > Dear Dr. Ferrin, > I’m a Project Scientist at UC Davis and the newest user of ChimeraX. > I have a few questions regarding peptide secondary structure generation using ChimeraX. Would you please connect me to someone who could spare a few minutes to walk me through? > > Specifically, when I look up the secondary structure of Indolicidin (generated using Chimera) _ image attached from publication (it shows an extended structure), whereas, using Tools -> Structure editing -> Build Structure -> Start Structure -> Peptide/ Input sequence, the image I get is completely different (attached .bmp file). I really have basic requirements of prediction of secondary structures of peptides (and was using Indolicidin as an control) prior to exploring more. > > I apologize if this information regarding the use of ChimeraX for this purpose is readily available and that I could just be unaware of it. Any advice you can offer is highly appreciated. > > Best, > ishita. > > Ishita M. Shah, PhD > Associate Project Scientist > Associate Director, Microbial Programs > Foods for Health Institute > Department of Food Science and Technology > University of California Davis > 1221 Robert Mondavi Institute, South > Davis, CA 95616 > Phone: (530) 754-7962 > > https://ffhi.ucdavis.edu/people/ishita-shah > https://www.linkedin.com/in/ishita-m-shah-ph-d-a6a9664/ >

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Re: [chimerax-users] Global Diffusion Tensor Models
by Tom Goddard 17 Mar '21

17 Mar '21

Hi Arun, I see from the image you sent that the diffusion ellipsoid script I sent you gave the wrong ellipsoid orientation -- it was using the inverse of the rotation. Here is the correct ChimeraX script which I have also put on the ChimeraX Recipes web site: https://rbvi.github.io/chimerax-recipes/ellipsoid/ellipsoid.html <https://rbvi.github.io/chimerax-recipes/ellipsoid/ellipsoid.html> Tom > On Mar 17, 2021, at 12:23 PM, Gupta, Arun <Arun.Gupta(a)warwick.ac.uk> wrote: > > Dear Tom, > > I think this is what you referring w.r.t to orientation. I have also overlaid the ROTDIF generated output " Tensor axes " on the protein PDB in the attached pic. Although, the ellipsoid shape model representation doesn't looks great. > > Best Regards > > Arun >

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How to produce a multiple sequence alignment
by Luca Pellegrini 17 Mar '21

17 Mar '21

Hello, I have superposed several similar structures with Matchmaker, and now would like to obtain a structure-based multiple sequence alignment. In Chimera, Matchmaker has a nice button ‘After superposition, compute structure-based multiple sequence alignment’. ChimeraX produces all pairwise alignments with the reference structure, but how do I obtain a single alignment with all my sequences? Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK

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Global Diffusion Tensor Models
by Gupta, Arun 17 Mar '21

17 Mar '21

Dear ChimeraX team, I am interested in generating Global diffusion tensor geometry models such as Prolate, Ellipsoid, Oblate or Sphere with overlaid protein PDB or structure of my interest. (As shown in attached pic). I am using diffusion tensor prediction module provided in ROTDIF software (http://gandalf.umd.edu/FushmanLab/pdsw.html) to generate an ellipsoid diffusion tensor of a protein molecule of my interest. Is it possible that I can use ROTDIF generated output (Which is in Pymol output format, please find attached ) to open in ChimeraX with my protein PDB, to render such representative figure ? Thanks!!! Arun Arun Gupta PhD, MRSC Research Fellow Challis & Lewandowski Group Chemistry Department University of Warwick Gibbet Hill Road Coventry CV4 7AL United Kingdom

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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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