- ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] [Chimera-users] chimera, H-bonds
by Elaine Meng 18 Nov '21

18 Nov '21

> On Nov 18, 2021, at 11:37 AM, Rio Aquarius via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear Developer, > I have a specific task for ChimeraX. I want to show H-bonds and hide all amino acid residues. But when I hide amino acid residues, all H-bonds I need disappear. Is there a way to do what I want? Dear Rio, The H-bond displays are lines (pseudobonds) drawn between atoms. When you hide those atoms, the H-bonds are also hidden. I don't understand why you would want to display a bunch of lines in space without any atoms, as you won't be able to see most of the valuable information from the calculation. However, I will explain how to do it: In ChimeraX, there is no pseudobond option to display even when its atoms are hidden. The only way to make it look like the H-bond lines are shown when you can't see the atoms (and/or ribbons) is to make the atoms (and/or ribbons) 100% transparent with the "transparency" command. Example commands: open 2gbp hbonds reveal true transparency 100 target ar <https://rbvi.ucsf.edu/chimerax/docs/user/commands/transparency.html> 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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getting sequences into the Structure Prediction
by Marc Pusey 17 Nov '21

17 Nov '21

Hi - I may be missing something very obvious, but... I am trying to input and use protein sequences for structure predictions using the AlphaFold feature of ChimeraX. I've not had any problems when the sequence can be obtained from a UniProt file, but several of the proteins I'm working with do not have such a file available. Additionally, there is going to come a time where I will want to see what the consequences are from making mutations to those sequences that are available from UniProt. The input gives the option of either Paste or UniProt, but I've not found a way to do a simple cut and paste to put in the sequence. I'm using a Mac running Mojave, version 10.14.6. Thanks! Marc Pusey -- Marc Pusey

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Viewing all frames of trajectory at once
by German Barcenas 17 Nov '21

17 Nov '21

Hello, I've made a trajectory of some similar frames that are stored as an .xtc file. I can upload this with my defined topology file (.pdb) and see each frame individually. Currently I can create a picture of each frame with the frame centered on some residue (SQA) with: perframe "save ~\snapshot_$1.png" frames 10;coordset #1 holdSteady /A:SQA This creates individual pictures for each frame which is nice. I was wondering how one makes a picture with all 10 frames superimposed on each other. I'd also like to change all but the 1st frame to be transparent. I'm aware of the transparent command, which I presume I'd apply to all frames except the 1st, but I'm not sure how to display all frames at once. I'm also struggling on the 1st frame only condition. This is my current attempt: perframe "transparency 0 ALL" frames 1;perframe "transparency 25 ALL" frames 9;coordset #1 holdSteady /A:SQA Thanks, -- German Barcenas Ph.D Candidate | Materials Science and Engineering Materials Modeling and Theory Group Boise State University

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Model info editing
by Eric Pettersen 16 Nov '21

16 Nov '21

Hi all, The current daily build (not 1.3 release candidate) has a new feature that may be of general interest. You can change the name/ID of a model in the Model Panel by double clicking on the corresponding field and entering a new value. --Eric Eric Pettersen UCSF Computer Graphics Lab

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Feature request regarding clipping planes
by Pranav Shah 15 Nov '21

15 Nov '21

Hi Team, Chimera has really nice clipping planes visibility and UX in comparison to ChimeraX. While it may take some effort to include the middle-click based riflling through planes shortcut, in the short term would it be possible to change the color of the clipping planes to a color that isnt gray? Currently, it is quite hard to see the clipping planes in the default view (see attached image). Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

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Re: [chimerax-users] Any interest in reading ModelArchive metadata from mmCIF files?
by Tom Goddard 12 Nov '21

12 Nov '21

Hi Elaine, This is related but a little different from what Ben was asking. It is different because the template and scoring data in the mmCIF tables could be shown no matter how the mmCIF file is loaded -- it would not be limited to fetching from ModBase. Maybe Ben has an opinion about how desirable it is to put the Chimera ModBase fetch capability into ChimeraX, and whether it is more or less desirable than making the new mmCIF tables accessible in ChimeraX, to help figure out priorities. Tom > On Nov 12, 2021, at 3:05 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Chimera had a ModBase Fetch: > > "a SwissProt, TrEMBL, GenPept or PIR accession code will be used to fetch comparative models in PDB format from ModBase (associated information will be shown in a model list)" > > https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modbase.html <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modbase.html> > > ...where "model list" is the same dialog as used to show Modeller results. Now that ChimeraX has a Modeller Results dialog for displaying the output from Comparative Modeling and Model Loops, could consider adding analogous Modbase fetch capability. > > I can make a ticket if anybody thinks that's a good idea. > > Elaine > > >> Begin forwarded message: >> >> From: Tom Goddard via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> >> Subject: Re: [chimerax-users] Any interest in reading ModelArchive metadata from mmCIF files? >> Date: November 12, 2021 at 2:56:49 PM PST >> To: Ben Webb <ben(a)salilab.org <mailto:ben@salilab.org>> >> Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> >> Reply-To: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> >> >> >> So it looks like only ModBase would currently benefit from ChimeraX reading template sequences and alignments. I do not think it would be too hard to implement it. I've made a ChimeraX feature request for that >> >> https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5601 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5601>

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Any interest in reading ModelArchive metadata from mmCIF files?
by Ben Webb 12 Nov '21

12 Nov '21

Do you have any plans to extend ChimeraX's mmCIF reader to parse and display metadata on theoretical models, such as quality scores or the alignments to template structures? The folks at PDB have recently done a lot of work to standardize this metadata in the MA mmCIF dictionary: https://mmcif.wwpdb.org/dictionaries/mmcif_ma.dic/Index/ The dictionary has already been adopted by ModelArchive (e.g. AlphaFold2 models) and by ModBase (Modeller models) and I believe that other repositories such as SwissModel are also moving in that direction. See e.g. mmCIF downloads at https://www.modelarchive.org/doi/10.5452/ma-bak-cepc-0250 https://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?databaseID=Q1… (My ulterior motive: we've previously built Chimera web data files to download a ModBase model and the accompanying alignment, and display them in Chimera; now that this data is embedded in the mmCIF file, in principle ChimeraX could do this itself in a less clunky and not ModBase-specific fashion.) Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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Fit in map sequentially with global search?
by Oliver Clarke 12 Nov '21

12 Nov '21

Hi, I frequently use the "global search" option of fitmap in chimera to identify the orientation of proteins or fragments in my map. Fitmap has an option, "sequence", allowing the sequential fitting of multiple structures to a map, after subtracting the density corresponding to the previous fit, but this is not compatible with global search. Would it be possible to add an option to fitmap in ChimeraX such that it considers clashes with designated existing models? This would be useful when one is trying to fit the density of a weakly occupied binding partner in the context of a larger known structure. Presently, when one uses fitmap with global search in such a case, the binding partner frequently gets sucked in to the stronger density for the host protein, even when the density for the binding partner is visually clear. Cheers Oli

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chimera x : how to increase font size of the command line display?
by Rangarajan, Amith 12 Nov '21

12 Nov '21

Dear All, I am wondering if there is a way to increase the font size of the command line display? I found this post with tom's comment https://www.cgl.ucsf.edu/pipermail/chimera-users/2020-April/016776.html [Chimera-users] Make command-line text bigger<https://www.cgl.ucsf.edu/pipermail/chimera-users/2020-April/016776.html> Hi Lothar, I don't know what problem you are encountering using ReadStdin on Windows. It may have something to do with Windows not allowing stdin/stdout for GUI apps. www.cgl.ucsf.edu not sure if things have changed after that. thanks , amith

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saving PDB
by Noriega, Heather 11 Nov '21

11 Nov '21

Hello, I am going to attach my command line. OK, so I created a specific capsid that is not all one monomer. It has 3 different monomers in a specific ratio. I have toggled around with different options below to try to save in PDB, the save option from my understanding should be the selected only because this capsid was created using the matchmaker. I tried display only as well just to try to see if that worked. I also have used the relative model from biological assembly of 1LP3 and tried to save or not save options and have kept all consistent with hybrid 36 (default). All these options say "saved", however when i go to open any of them, they do not at all. My objective is to save the whole capsid so when I open it I can perform the density map to measure the volume inside. The weird part of this is when I open these saved creations in Chimera they will open how I want them to, but not in ChimeraX. I am not too sure why. Please help me and I hope everyone is well, have a good night. UCSF ChimeraX version: 1.3.dev202110160902 (2021-10-16) © 2016-2021 Regents of the University of California. All rights reserved. open "C:\Users\Haten\Documents\AAVgene\AAV 3B VP1 VP2 VP3 118.cxs" format session Log from Mon Nov 1 22:55:58 2021opened ChimeraX session save "C:/Users/Haten/Documents/AAVgene/why wont you open.pdb" models #2-61 displayedOnly true relModel #1 close session open "C:\Users\Haten\Documents\AAVgene\why wont you open.pdb" format pdb UCSF ChimeraX version: 1.3.dev202110160902 (2021-10-16) © 2016-2021 Regents of the University of California. All rights reserved. open "C:\Users\Haten\Documents\AAVgene\AAV 3B VP1 VP2 VP3 118.cxs" format session Log from Mon Nov 1 22:55:58 2021opened ChimeraX session save "C:/Users/Haten/Documents/AAVgene/why wont you open 2.pdb" models #2-61 selectedOnly true close session open "C:\Users\Haten\Documents\AAVgene\why wont you open 2.pdb" format pdb Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883

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An inquiry
by Victor Ejigah 11 Nov '21

11 Nov '21

Hi Elaine, I am using chimeraX for protein analysis and simulations and recently, we have a question we want to explore by first simulating before going to the wet lab. We want to conjugate a polymer of different molecular weight to an antibody and thereafter determine the impact of the MW of each polymer on the binding affinity of the mAB to its ligand. Therefore, we want to know 1) Can we create polymers of different sizes with chimera? If not, can you recommend alternatives? 2) What tool can we use for conjugation( assuming chimera can be of help)? 3) Can such conjugates be exported to Chimera1.5 for MD ensemble since Chimera X does not have this feature? I will be most glad to hear from you soon. Kind regards, Victor (PhD student @Howard University)

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vop min/max threshold
by Stapleton kevin2017/4/3 10 Nov '21

10 Nov '21

Hello everyone! just trying to get my head around a small problem, but one my brain turns into spaghetti. I am trying to save a density from molmap with a threshold range of given values. for example: open 2gbp molmap #1 10 >From the resulting density (now ID #2) I want to save the map at a very narrow threshold range. for example the current range is 0.0-0.528. But I would like to save the map with a "restricted" level of 0.26-0.27. I have been playing with the vop min/max threshold xxx set 0/1 commands but I keep getting turned around. here is what I did: open 2gbp molmap #1 10 - produces a new map ID #2 vop threshold #2 minimum 0.26 set 0 vop threshold #3 maximum 0.27 set 1 I used the set 0/1 because I want the range 0.26-0.27 to have the density values and anything outside of that to have zero. Like a mask in relion. But for my specific case relion_mask wont work as well. Somewhere I am turning the options around and it has my brain flattened. Any help is appreciated. All the best and thanks for making my science life 1Million times easier with your wonderful program :-) Kako

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Improved VR support in ChimeraX
by tolung.bio＠gmail.com 09 Nov '21

09 Nov '21

Hi, The VR support in ChimeraX and meeting functionality has a great potential especially for teaching and educational purposes. Are you planning to improve that to bring it to the same level as Nanome (or close)? For example, a dedicated VR GUI interface for better VR usability? Cheers, Gökhan

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Labelling w.r.t Secondary structure elements
by Gupta, Arun 09 Nov '21

09 Nov '21

Hello, I was wondering is there a quick fix way around by which we can define in an automated fashion the numbering and further labelling of secondary structural elements labels, alongside the structure, based on “dssp” described symbol notation "for example starting from α1/β1-α10/β14 " for any protein instead of manually labelling later in Power point. Thanks a lot! 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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Removing and Testing Bundles
by Zeng, Jingrou 09 Nov '21

09 Nov '21

Hello, I am working on a selector bundle and need to actively reload it into ChimeraX every time I make changes to the code. I have followed the instructions on the tutorials and successfully loaded my bundle into ChimeraX using 'devel install [path]'. I then tried to reload the bundle after I have made changes to the code with commands 'devel clean [path]' followed by 'devel install [path]'. But ChimeraX didn't receive my update to the bundle. I tried reinstalling ChimeraX, the selector bundle still works without a separate installation and it doesn't register any updates I have made. I am using macOS and have experimented with both daily build and 1.2.5. Is there a way of completely removing the old version of my bundle? What is the best way to do bundle reloading and testing in ChimeraX? I also want to use the print command for debugging, but printing doesn't seem to work with the ChimeraX log, is there a separate log for this situation? Thank you for your help. Regards, Katie

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Re: [chimerax-users] Measuring volume inside virus capsid
by Tom Goddard 05 Nov '21

05 Nov '21

Hi Heather, Your "No symmetry for #1" error when you use command "sym #2 symmetry #1 copies true" is likely because you opened the 1LP3 (#1) PDB file in mmCIF format instead of using the command I suggested "open 1lp3 format pdb" which opens it in PDB format. The ChimeraX sym command currently only uses the "biological assembly" information from PDB format, not mmCIF format as described in the sym command documentation https://www.cgl.ucsf.edu/chimerax/docs/user/commands/sym.html#symmetry <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/sym.html#symmetry> In the future please copy and paste commands and the error message into your email. That gives us enough info to help you and is better than a screenshot. Tom > On Nov 5, 2021, at 6:46 PM, Noriega, Heather <heather.noriega(a)bison.howard.edu> wrote: > > Hi, > > Yes, so I have read your manual about the symmetry and have been trying to do what you suggested, before you suggested it (the symmetry portion). That is why I reverted to the one-by-one. It keeps giving me this error. I have also tried using the chain /A for the symmetry and it does create the complete icosahedral, but once I try to complete the molmap it only does the single monomer. I don't know what to do. > > Thank you, > > Heather Noriega > PhD-Pharmaceutical Science student > Howard University > heather.noriega(a)bison.howard.edu <mailto:heather.noriega@bison.howard.edu> > 520-203-1883 > > > On Fri, Nov 5, 2021 at 6:26 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > Hi Heather, > > I looked at the ChimeraX session and see you opened 60 copies of your alphafold model, then ran matchmaker 60 times to align those to the 1LP3 virus capsid, then ran molmap 60 times. That is a lot of tedious work and does not get quite what you want. So here are some commands to try go get the enclosed volume. > > open 1lp3 format pdb > open ~/Downloads/ChimeraX/AlphaFold/prediction_23/best_model.pdb > matchmaker #2 to #1 > sym #2 symmetry #1 copies true > molmap #3 12 > volume #4 level 0.07 > # Choose "blob" mouse mode under the "Right Mouse" toolbar tab and right click (option key on Mac) the volume surface to color it. > surface splitbycolor #4.1 > view position #5 sameAs #4 > hide #4,5.1 model > measure volume #5.2 > -> 2.5 million cubic Angstroms > > Here I aligned a single copy of the AlphaFold model (#2) to the 1lp3 capsid monomer (#1) with matchmaker, then applied the symmetry of 1lp3 to the AlphaFold model to produce all 60 copies (#3), then made a density map from those 60 copies (#4), then set a low enough density map threshold so that their are no holes connecting the inside and outside of the capid, then colored the outside surface different from the inside with the blobs mouse mode, then split that two color surface into two pieces (outside #5.1, inside #5.2), then realigned the split surface to the density map (it was a bug that it did not preserve the alignment), then measured the volume of the inside surface. > > If you have questions about any of these commands the ChimeraX user manual has thorough documentation on all of them, so read about them. > > I described a slightly simpler case of finding the interior volume of 1lp3 on the ChimeraX Recipes web page. > > https://rbvi.github.io/chimerax-recipes/virus_volume/virusvol.html <https://rbvi.github.io/chimerax-recipes/virus_volume/virusvol.html> > > Tom > > >> Begin forwarded message: >> >> From: "Noriega, Heather" >> Subject: measuring volume >> Date: November 5, 2021 at 2:25:42 PM PDT >> To: Tom Goddard >> >> Hello Tom, >> >> I hope this email finds you well. I am very grateful for your email a couple days ago with chimeraX and trying to compute the interior volume in a virus capsid shell. I am very new to all this molecular modeling software, but am trying very hard to learn and understand. I have been working on a few different capsids particularly through alpha fold predictions on ChimeraX. I have created this one below through one-by-one aligning the predictions to create T=1 (1LP3 as biological assembly reference). Now, I one-by-one again used the molmap application for each copy and changed to volume level 0.676 and colored dark blue. My issue is when I go to measure volume it says the surface selected is wrong. I am unsure how to fix it or if I can fix it. Also, I do not know if this has anything to do with it, but I am using a Windows computer, I have noticed most of your videos are done through apple. Would this make a huge difference? I await your response and again thank you very much for your help. >> >> Thank you, >> >> Heather Noriega > > > > >> On Nov 3, 2021, at 11:49 AM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Hi Heather, >> >> Here is a tricky way to compute the interior volume in a virus capsid shell in ChimeraX. >> >> open 1LP3 >> sym #1 assembly 1 copies true >> molmap #2 12 >> volume #3 level 0.676 >> # Choose "blob" mouse mode under the "Right Mouse" toolbar tab and right click (option key on Mac) the volume surface to color it. >> surface splitbycolor #3.1 >> hide #4.1 model >> measure volume #4.2 >> -> 2.6 million cubic Angstroms. >> >> The idea is to make a low resolution (12 Angstrom) density map from the atomic model, low resolution so there are not holes in the capsid, set the map threshold so there are no holes connecting the inside and outside, then color the outside layer with the "pick blob" mouse mode, then split the surface by color (producing inside and outside surfaces), then measure the volume enclosed by the inside surface. >> >> Tom >> >> Here's a cut in half view showing the interior surface produced by the above example >> >> >>> On Nov 3, 2021, at 11:21 AM, Elaine Meng via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> I don't know if it would work on your specific case, but there is a "3V" server that makes maps that fill cavities and tunnels that you could try. Namely, I don't know if it works for fully enclosed cavities. >>> >>> <http://3vee.molmovdb.org/ <http://3vee.molmovdb.org/>> >>> >>> If it gave a suitable output (a map blob that fits inside your capsid) then you can use "measure volume" after opening it in ChimeraX and showing its isosurface. >>> >>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#volume <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#volume>> >>> >>> I'm sure there are other creative ways if you think about it... like trying to make a sphere that fits inside and calculating the volume of the sphere from the standard geometric formula. >>> >>> I was trying to think of a way involving a low-resolution surface (e.g. from using "molmap" on the capsid atoms) and "volume onesmask" but couldn't come up with anything. The problem with just using a molecular surface or low-res surface from molmap is that it is hollow, and the volume calculation will just include the shell with the atoms, not the big empty part inside. >>> >>> As you can see, none of these are like a one-step thing that is already figured out for you. Part of being a PhD student is trying to solve problems that haven't been worked out for your specific situation! >>> >>> Elaine >>> >>>> On Nov 3, 2021, at 10:38 AM, Noriega, Heather via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>> >>>> What other ways can you measure the inter space of the icosahedral? >>>> >>>> Thank you, >>>> >>>> Heather Noriega >>>> PhD-Pharmaceutical Science student >>>> College of Pharmacy >>>> Howard University >>>> heather.noriega(a)bison.howard.edu <mailto:heather.noriega@bison.howard.edu> >>>> 520-203-1883 >>>> >>>> On Wed, Nov 3, 2021, 12:09 PM Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: >>>> Hi Heather, >>>> I guess my first question is "why would you want to do that?" If the goal is to measure the cavity volume, there may be other ways. I'm not aware of any ChimeraX capability to fill it with waters (you may have to write your own code if that's what you really want to do). >>>> >>>> In general you can count the waters (or any other residue type) in some structure using a similar method to what I described recently on the chimera-users list, except that to show the Selection Inspector you click the green magnifying glass on the top bar icons of ChimeraX instead of the lower-right corner of the Chimera window. >>>> <https://plato.cgl.ucsf.edu/pipermail/chimera-users/2021-November/018182.html <https://plato.cgl.ucsf.edu/pipermail/chimera-users/2021-November/018182.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 Nov 3, 2021, at 6:20 AM, Noriega, Heather via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>>> >>>>> Good morning, >>>>> I am working on trying to find a measurement inside my alphafold prediction icosahedral. My advisor mentioned using the water molecules to fill the inside and then use a counter of some sort. I have no idea how to start this, I have been reading the volume commands but am still having a hard time. Can you direct me to 1) fill only the inside of my icosahedral? and 2) how to count the water molecules inside? >>>>> Thank you, >>>> >>>> _______________________________________________ >>>> 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> >>> >>> >>> _______________________________________________ >>> 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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A couple questions
by Noriega, Heather 05 Nov '21

05 Nov '21

Good morning, I am working on trying to find a measurement inside my alphafold prediction icosahedral. My advisor mentioned using the water molecules to fill the inside and then use a counter of some sort. I have no idea how to start this, I have been reading the volume commands but am still having a hard time. Can you direct me to 1) fill only the inside of my icosahedral? and 2) how to count the water molecules inside? Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883

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alpha-fold error
by Moustafa, Ibrahim M. 05 Nov '21

05 Nov '21

Dear all, I am trying to use alpha fold in ChimeraX but I get the following error during computing multiple sequence alignmenet step: -------------------------------------------------------- TypeError ________________________________ 2 frames ________________________________ <ipython-input-1-a242dc837c9a><https://localhost:8080/#> in multiple_seq_align(dbs) 247 for i, result in enumerate(db_results): 248 from alphafold.data import parsers --> 249 msa, deletion_matrix, target_names = parsers.parse_stockholm(result['sto']) 250 e_values_dict = parsers.parse_e_values_from_tblout(result['tbl']) 251 e_values = [e_values_dict[t.split('/')[0]] for t in target_names] TypeError: cannot unpack non-iterable Msa object --------------------------------------------------------- I followed the instructions of ChimeraX tutorial. I was able to use it successfully before, but not sure why I keep getting this error. Any idea what could be wrong? I use ChimeraX version 1.3 (09-08-2021) Thanks for help Ibrahim

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Residue priority for Matchmaker alignment?
by Steven Truong 04 Nov '21

04 Nov '21

Dear ChimeraX Admins, I have a question about the Matchmaker (mmaker) command. If I wanted to specify which residues to prioritize in the alignment, how would I specify that in the command line? Is there a way to do this without changing the alignment algorithm/scoring matrix? I have tried tinkering with the matrix but wasn’t able to get it to work. I see that you can specify which chains to align, but I can’t seem to find the equivalent for residue ID numbers. Thank you for your help, Steven Truong Vendruscolo Lab Cambridge University [cid:280F6707-7208-4DBD-9A6C-ED9A0DF8E3BF]

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How to open .py file downloaded from MOLEonline in ChimeraX?
by Kate Kim 01 Nov '21

01 Nov '21

Hello, I've been using Chimera in the past for opening downloaded .py files from MOLEonline to visualize tunnels in my structure. When I try to do the same in ChimeraX, I get the following error: Traceback (most recent call last): File "/Users/katekim/Downloads/mole_channels_6Qzq10eGEqLciv3DpeS8Q_1_chimera.py", line 1, in <module> import chimera, _surface, numpy ModuleNotFoundError: No module named 'chimera' Error opening python file /Users/katekim/Downloads/mole_channels_6Qzq10eGEqLciv3DpeS8Q_1_chimera.py toolshed show Any suggestions on the best approach to visualize MOLE channels using ChimeraX? Thank you, Kate

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Making multiple icosahedral pentamers (assembly 3)
by Noriega, Heather 01 Nov '21

01 Nov '21

Hello, I am trying to make different monomer amounts of the icosahedral for my alphafold prediction. Now, I am able to use 1LP3 as my reference to create a icoshedral pentamer, but that is only 5. I would like to be able to do 10-mer, 15-mer, 20-mer, etc. I however can not seem to connect the pentamers to create the portions of virus capsid. Can you direct me? Thank you, Heather Noriega PhD-Pharmaceutical Science student College of Pharmacy Howard University heather.noriega(a)bison.howard.edu <mailto:heather.noriega@bison.howard.edu> 520-203-1883

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mmcif assemblies for alphafold prediction
by Noriega, Heather 30 Oct '21

30 Oct '21

Hello, I am trying to create an asymmetrical assembly similar to 4 and 6 with an alphafold prediction. There are no mmCIF assemblies connected with this prediction, is there a way to add the assemblies, if so how? Or is there another way to create this figure without the assembly? Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883

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Distances in the 3D map - visualisation analysis
by Dmitry Semchonok 29 Oct '21

29 Oct '21

Dear colleagues, I would like to measure the distances of within my 3D map - so I want to draw the arrows from the center of the map to the periphery in different directions and probably depth. (I want to have arrows and an length) Do you have any tips how to do that? Thank you Sincerely, Dmitry

2 1

Unit cell box
by Diego Sebastian Ferrero 27 Oct '21

27 Oct '21

Dear all, I am trying to make a figure using ChimeraX to show the contents of the unit cell in one protein structure. I would like to show the cell box with the asymmetric unit (similar to that box obtained in chimera using “Tools>Higher Order Structure>Crystal Contacts” ) but ChimeraX apparently doesn’t recognize the command returning the following message in the log window: unitcell outline Unknown command: unitcell What I’m doing wrong? Is it the right command to show the box? Thanks in advance, Diego

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ChimeraX bug report submission
by Samuel Haysom 27 Oct '21

27 Oct '21

i want to show just the CA atoms of a selection of residues (starting with the rest of the model shown as a cartoon). To do this I am trying to use a command like this: show #3/A:436,464,465,495,498,500,550,697,755,764,795,798,799@CA target a But this doesn't do anything. If I take off the @CA bit I can show all the atoms in the residue. Full .cxc is as follows: open 5ljo open 5d0o hide #1,2 atoms show #1,2/A cartoons color #1,2/A rgb(0.252,0.680,1.000) color #1,2/B rgb(0.000,0.831,0.321) color #1,2/C rgb(1.000,0.861,0.137) color #1,2/D rgb(1.000,0.400,0.100) color #1,2/E rgb(0.780,0.000,0.400) ### Align barrels ### # mmaker #2/A:435-810 to #1/A:435-810 view matrix model #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.82647,-0.51941,0.21716,224.85,-0.53861,0.61724,-0.57351,177.83,0.16385,-0.59096,-0.78989,191.81,#2.1,1,0,0,0,0,1,0,0,0,0,1,0 ### Color EPR regions ### color #1,2/A:424-447 green color #1,2/A:454-518 red color #1,2/A:348-423 dark orange ### Create Morph ### morph #1,2 frames 40 ### Show single mutant CA ### ### New positions ### show #3/A:436,464,465,495,498,500,550,697,755,764,795,798,799@CA target a color #3/A:436,464,465,495,498,500,550,697,755,764,795,798,799 magenta ### Existing Positions ### show #3/A:435,499,501,535,564,751,793 target a color#3/A:435,499,501,535,564,751,793 purple Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.3.dev202110261153 (2021-10-26) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 5ljo Summary of feedback from opening 5ljo fetched from pdb --- warnings | Atom H is not in the residue template for LEU /B:22 Atom H is not in the residue template for CYS /C:25 Atom H is not in the residue template for GLU /D:26 Atom H is not in the residue template for GLU /E:24 Atom H is not in the residue template for PHE /A:24 5ljo title: E. coli BAM complex (BamABCDE) by cryoEM [more info...] Chain information for 5ljo #1 --- Chain | Description | UniProt A | Outer membrane protein assembly factor BamA | BAMA_ECO45 B | Outer membrane protein assembly factor BamB | BAMB_ECOLI C | Outer membrane protein assembly factor BamC | BAMC_ECOLI D | Outer membrane protein assembly factor BamD | BAMD_ECO57 E | Outer membrane protein assembly factor BamE | BAME_ECOL6 > open 5d0o 5d0o title: BamABCDE complex, outer membrane β barrel assembly machinery entire complex [more info...] Chain information for 5d0o #2 --- Chain | Description | UniProt A | Outer membrane protein assembly factor BamA | BAMA_ECOLI B | Outer membrane protein assembly factor BamB | BAMB_ECOLI C | Outer membrane protein assembly factor BamC | BAMC_ECOLI D | Outer membrane protein assembly factor BamD | BAMD_ECOLI E | Outer membrane protein assembly factor BamE | BAME_ECOLI > hide #1,2 atoms > show #1,2/A cartoons > color #1,2/A rgb(0.252,0.680,1.000) > color #1,2/B rgb(0.000,0.831,0.321) > color #1,2/C rgb(1.000,0.861,0.137) > color #1,2/D rgb(1.000,0.400,0.100) > color #1,2/E rgb(0.780,0.000,0.400) > view matrix models > #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.82647,-0.51941,0.21716,224.85,-0.53861,0.61724,-0.57351,177.83,0.16385,-0.59096,-0.78989,191.81,#2.1,1,0,0,0,0,1,0,0,0,0,1,0 > color #1,2/A:424-447 green > color #1,2/A:454-518 red > color #1,2/A:348-423 dark orange > show #3/A:436,464,465,495,498,500,550,697,755,764,795,798,799@CA target a

2 1

clashes after mutagenesis
by tiger wang 26 Oct '21

26 Oct '21

Dear I am quite new to Chimera. I am using ChimeraX to do some mutagenesis in the protein with its 3D structure. After mutagenesis, the clashes were found. I tried to use tool torsion to adjust the atoms' angles and found when one clash was solved the other clashes came up. It seems it is a endless process. The question is how to correct the clashes due to mutagenesis, only manually adjust one by one using tool torsion or there is other ways to do in the same time simutaneously, such as using modeller inbeded in ChimeraX? Thanks very much for your help Sincerely Tiger Wang

2 2

Refine predicted structure by pulling
by Roden Deng Luo 26 Oct '21

26 Oct '21

Dear ChimeraX Users, There is this AlphaFold prediction: https://alphafold.ebi.ac.uk/entry/P02549. And we know this protein should be more or less in a rod-like shape rather than a globular shape: https://en.wikipedia.org/wiki/Spectrin and related literature such as https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218374/. I wonder is there a way that we can pull the two ends of the predicted structure while maintaining the secondary structures, mostly alpha-helices in this case, inside ChimeraX? I am quite new to ChimeraX. I understand this is more fitted to an MD simulation. But I got to know there are options to fit a PDB to a density map. So I wondered if this can be achieved in ChimeraX. Best, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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Re: [chimerax-users] Test files for bug report [ChimeraX] #5467: AmiraMesh
by Tom Goddard 26 Oct '21

26 Oct '21

Hi Roden, These 3 Amira files are vertex/edge/point data, not 3D lattices. The ChimeraX reader only handles 3D lattices Amira files. It does not look like our ChimeraX documentation explains this. I'll try to get this on our docs (3d lattice volume data, float, unsigned 16-bit, uncompressed only). Tom > On Oct 25, 2021, at 12:20 PM, Roden Deng Luo <deng.luo(a)kaust.edu.sa> wrote: > > Dear Tom and Andrea, > > Thanks for the quick responses. Upon the kind approval from Andrea, I attached the .am file I received from Andrea (in the format of 2.0), as well as the other two that are exported from this file (in the format of 3.0, one is in ascii as revealed by the name). > > Best regards, > Roden

2 3

Open AmiraMesh 3.0 in ChimeraX
by Roden Deng Luo 25 Oct '21

25 Oct '21

Dear ChimeraX Users, I have an AmiraMesh .am file exported from Amira 3D 2021.1 (Build date: 2021-06-21 13:21:22, SHA id: 213bd1......13c73e). When I load it into ChimeraX 1.2.5 or ChimeraX 1.3.dev202110231141, ChimeraX tells me the following error. First line of AmiraMesh file must start with "# AmiraMesh BINARY-LITTLE-ENDIAN 2.1", instead got "b'# AmiraMesh BINARY-LITTLE-ENDIAN 3.0\n'" Googling "AmiraMesh site:https://www.rbvi.ucsf.edu/pipermail/chimerax-users" shows no result. Can anyone kindly help here? Many thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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problem with displaying secondary structures
by Elżbieta Wątor 24 Oct '21

24 Oct '21

Hi, I am trying to prepare figures for my publications and I have a problem with ss assignment. When I open structure in pymol, everything is assigned correctly. However, when I open the same structure in ChimeraX (1.2.5) I have gaps in helices and also not all of B strands are assigned correctly. I tried "dssp" command, but I probably type something wrong, because everytime I got "expected keyword" reply. Also I tried to do that manually using such commands setattr /B:5-7 res ss_type 1 and for some regions it works and for some not e.g I can change the whole helices with gaps to loop but in other way around it again gives me back helices with gaps. I've just started learning ChimeraX so probably there is some easy explanation, but I would be really grateful for your help. Best regards, Ela Wator

2 1

red-cyan 3D view in chimera X?
by Maya Shmulevitz 22 Oct '21

22 Oct '21

Hi everyone, Does anyone know how to switch to red-cyan for the structures so that my class can see them with 3D red/cyan glasses? I used to do it on the old chimera with the camera feature but cannot find the option in chimera X. Thank you!! -- Maya Shmulevitz Canada Research Chair in Molecular Virology and Oncotherapy Associate Professor University of Alberta Medical Microbiology and Immunology Li Ka Shing Institute for Virology 6-21 HMRC Edmonton, Alberta, T6G 2E1 CANADA

3 3

Running ChimeraX and a REPL
by Tom Mulvaney 21 Oct '21

21 Oct '21

Hi all, I'm wondering if anyone has any experience running ChimeraX with either a standard REPL or IPython REPL? ChimeraX already has a 'shell' tool that allows interacting with ChimeraX through a Python REPL which I've found invaluable for testing out ideas and poking around in ChimeraX in general. It would be really nice though if I could send Python code directly from my IDE to be evaluated. In order to make this work, it would be great if ChimeraX could be run from a terminal and provide a Python (or preferably IPython) REPL. As it stands, I've managed to nearly make this work with the following script: import IPython.terminal.embed IPython.terminal.embed.embed() I then run: ChimeraX --script repl.py After typing, `%gui qt5`, the ChimeraX GUI appears. I can then interact with the REPL directly from the comfort of Emacs and evaluate things - but! - the main 3D view does not end up being displayed. Does anyone know how to get the REPL and 3D stuff to work side-by-side? Kind regards, Tom

3 3

ChimeraX issue
by Amaya Cuesta, Joan 20 Oct '21

20 Oct '21

Dear ChimeraX Team, I'm trying to use ChimeraX on my VM (Ubuntu 20.04.01), but I'm having the error on the screenshot attached below. I tried to update OpenGL to 3.3, and on the terminal it seems that it installed everything but then when I try to open again I'm getting the same issue. I tried to update OpenGL following this: https://www.reddit.com/r/Ubuntu/comments/8tpq05/how_can_update_my_display_d… But always when I do the command: glxinfo | grep "OpenGL version" , it shows: "OpenGL version string: 3.1 Mesa 21.0.3". Not sure why it is not updating to 3.3 while all the other packages are upgraded. Could you please advice? Kind regards Joan Cuesta (BSc) Viral Zoonoses Research Scientist Rabies and Viral Zoonoses Group Animal & Plant Health Agency (APHA) Internal extension: 71528 External: 02087201528 | Email: Joan.Cuesta(a)apha.gov.uk<mailto:Joan.Cuesta@apha.gov.uk> Website: www.gov.uk/apha<http://www.gov.uk/apha> | Twitter: @APHAgovuk<http://www.twitter.com/aphagovuk> | Facebook: aphagov<http://www.facebook.com/aphagov> Address: APHA Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK Working hours - Monday - Friday, 9 - 5:30 pm Department for Environment, Food and Rural Affairs (Defra) This email and any attachments is intended for the named recipient only. If you have received it in error you have no authority to use, disclose, store or copy any of its contents and you should destroy it and inform the sender. Whilst this email and associated attachments will have been checked for known viruses whilst within Defra systems we can accept no responsibility once it has left our systems. Communications on Defra's computer systems may be monitored and/or recorded to secure the effective operation of the system and for other lawful purposes.

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I Have a Problem Installing ChimeraX on Debian Buster
by Stephen P. Molnar 20 Oct '21

20 Oct '21

I am attempting the installation of ChimeraC-1.2.5(chimerax-1.2.5-rc-2021.05.24) on my up to date Debian v-1064 bit platform. I open the tar.gz package without any difficulties, but when I attempt to execute ChmieraX i get the following: comp@AbNormal:~/Apps/chimerax-1.2.5-rc-2021.05.24/bin$ ./ChimeraX qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found. This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, xcb. Fatal Python error: Aborted Current thread 0x00007fcb3dafd740 (most recent call first): File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/chimerax/ui/gui.py", line 157 in __init__ File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/ChimeraX_main.py", line 577 in init File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/ChimeraX_main.py", line 1015 in <module> File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/runpy.py", line 87 in _run_code File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/runpy.py", line 194 in _run_module_as_main Aborted comp@AbNormal:~/Apps/chimerax-1.2.5-rc-2021.05.24/bin$ xcb is installed, but the Debian v-10 default version of python is 3.7. Is this the problem? Is there a solution? Reinstalling did not fix the problem. Thanks in advance. -- Stephen P. Molnar, Ph.D. www.molecular-modeling.net 614.312.7528 (c) Skype: smolnar1

2 1

Remote Desktop usage
by Dmitry Semchonok 20 Oct '21

20 Oct '21

Dear colleagues, What could be the solution for the remote desktop of Chimera X user? One of the solution can be VNC but is there any other? Thank you Sincerely, Dmitry

2 1

coil thickness
by Lisandro Otero 18 Oct '21

18 Oct '21

Dear Chimera developer; How can I change the coil thickness in a specific loop in ChimeraX? I have tried with the Hierarchical Specifiers but I was unsuccessful? Could you please give me a command line as example? I'm using “cartoon style coil thickness XX” Thanks in advance. Best. Dr. Lisandro H. Otero PhD. Leloir Institute Foundation Av. Patricias Argentinas 435 C1405BWE Buenos Aires, Argentina Phone: +054-11-5238-7500 ext. 2552 Fax: +054-11-5238-7501

2 1

Feature suggestion - Models panel
by William Hofsøy 18 Oct '21

18 Oct '21

Hi, I would like to suggest/request that the "Models" panel should be able to rename models and change their ids from the list of models directly either through double click, like changing file names on windows, or through the right click context menu. Best regards, William

2 1

Re: [chimerax-users] labelling hbond atoms
by Rangarajan, Amith 14 Oct '21

14 Oct '21

Dear Group, I have a possibly rookie level question. When i use name flag with hbonds command to define two groups of hbonds like this hbonds (#1.1 & protein) restrict (#1.2.* ) distslop .2 reveal t rad .2 color gold name HBONDS-1 hbonds(#1.1 & ~protein) restrict(#1.2.*) distslop .2 reveal t rad .2 color magenta name HBONDS-2 then when i try to label the hbond atoms , la hbondatoms residues font "Rockwell Extra Bold" height .6 bg 20,20,20 I am not getting the labels. I am not getting any errors so i figured that it got to do with hbonds being given a name , however i am not able to fix this. welcome to hear your suggestions. thanks again., amith

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ProblemI am attempting he installation of ChmimeraX Installing ChimeraX on Debian mv-10
by Stephen P. Molnar 14 Oct '21

14 Oct '21

I am attempting the installation of ChimeraC-1.2.5(chimerax-1.2.5-rc-2021.05.24) on my up to date Debian v-1064 bit platform. I open the tar.gz package without any difficulties, but when I attempt to execute ChmieraX i get the following: comp@AbNormal:~/Apps/chimerax-1.2.5-rc-2021.05.24/bin$ ./ChimeraX qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found. This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, xcb. Fatal Python error: Aborted Current thread 0x00007fcb3dafd740 (most recent call first): File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/chimerax/ui/gui.py", line 157 in __init__ File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/ChimeraX_main.py", line 577 in init File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-packages/ChimeraX_main.py", line 1015 in <module> File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/runpy.py", line 87 in _run_code File "/home/comp/Apps/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/runpy.py", line 194 in _run_module_as_main Aborted comp@AbNormal:~/Apps/chimerax-1.2.5-rc-2021.05.24/bin$ xcb is installed, but the Debian v-10 default version of python is 3.7. Is this the problem? Is there a solution? Reinstalling did not fix the problem. Thanks in advance. -- Stephen P. Molnar, Ph.D. www.molecular-modeling.net 614.312.7528 (c) Skype: smolnar1

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Question about pruned set in rmsd
by Chang Jang 14 Oct '21

14 Oct '21

Hi Chimera Users, I want to understand a result from "match" command. There are two results for 1) pruned set and 2) across all. What exactly is the pruned set in this calculation? Thanks, Chang Woon Jang

2 1

Use values printed from Log inside a script (e.g. RMSD)
by Steven Truong 12 Oct '21

12 Oct '21

Dear ChimeraX Admins, I was hoping to use the “rmsd” command in ChimeraX to measure distances between models within a .py script. Is there a way to use the output of “rmsd” (or generally any other output in Log) within the script? For example, if rmsd > 2 Angstroms, then do X. Ultimately, I am attempting to align chains between models. Because my protein is asymmetric, chain A on Model #1 might actually be chain B on Model #2. I was hoping to use “rmsd” to map one chain to the other. Is it a better idea to do this in another program and re-write chain IDs in the .PDB file? If so, what other program would be better at making RMSD calculations between .PDB chains? Thank you, Steven Truong Cambridge University

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Electrostatic color key problem
by Luca Pellegrini 12 Oct '21

12 Oct '21

Hi, Coloring a surface with ‘electrostatic’ in the ‘Molecule display’ works fine. However, when I try to modify the red-blue boundary values from the default -10, 10 in the color key box, the surface color doesn’t seem to change. Can you please advise? Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK

2 3

fold
by Ruggero Gabbrielli 11 Oct '21

11 Oct '21

Maybe it’s a little too early for that, but can’t you just add a button for folding a sequence?

2 1

"fly" interrupting "turn"
by Anderson, Jacob 11 Oct '21

11 Oct '21

Dear ChimeraX Users, Making a movie with a CXC script/command file, I find that the "fly" command interrupts the "turn" command. For example if I run these two lines: turn y 0.25 1440 fly Frame_01 400 Frame_02 400 Frame_03 400 Frame_04 400 Frame_05 Before the turn completes, the view goes to Frame_01. Is this the expected behavior? If not, would love any tips on how to complete a turn of the molecular model before flying to Frame_01 (or p1 in the ChimeraX fly user help documentation). Jacob

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Re: [chimerax-users] Measuring Colocalisation using ChimeraX
by Tom Goddard 08 Oct '21

08 Oct '21

Hi Dominic, Ok, here is a way to do what you described that does not need any Python. First you place a marker at the enter of the green blob using ChimeraX Markers toolbar using the Center mode (mark center of connected surface). Once you select that mouse mode, right click on the green blob to place the marker. Then make a sphere centered at that marker with the shape command, e.g. "shape sphere center #3 radius 100". Then mask the red map to get just the part inside that sphere, e.g. "volume mask #1 surface #4". Then measure the volume enclosed in that masked map surface, e.g. "measure volume #5". You might also be interested in exactly how much red blob is inside the green blob and you could mask the red using the surface of the green to do that. Tom > On Oct 8, 2021, at 2:33 AM, BINGHAM Dominic <dominic.BINGHAM(a)univ-amu.fr> wrote: > > The custom python code sounds more applicable to what I am doing. I will give that a try but also would greatly appreciate some tips > > > To give context, I have several maps like shown above, with 2-channels showing the staining of one protein each. Each map is a synapse, and these are taken from 3D-STORM images contains several synapses. I have 3 different conditions, and I would like to compare what I measure and how it changes between these conditions. So for instance, ideally, what I would like to do is to measure from the centre of the large green structure which is colocalised to the large red structure (Circle on image above). I would then like a value to represent the relative amount of the ‘red’ protein within a set volume around the ‘green’ structure. I would then compare this value between each condition. > > So any tips on the code for python would be great here! > > Thanks so much for the help! > > Dominic > >> Le 6 oct. 2021 à 20:08, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> a écrit : >> >> Hi Dominic, >> >> The ChimeraX Distances tools measures distances between atoms in an atomic structure. You have image data, not an atomic structure so that is why it will not report any distances. >> >> One way to proceed would be to place a marker on every connected surface piece in each of the two images, then measure distances between these centroid markers. There is code to place the markers using ChimeraX here >> >> https://rbvi.github.io/chimerax-recipes/mark_blobs/mark_blobs.html <https://rbvi.github.io/chimerax-recipes/mark_blobs/mark_blobs.html> >> >> Markers are treated just like atoms in ChimeraX so the Distance tool would work. But you want all nearby distances so you might try the Contacts tool >> >> https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html> >> >> That may not give you what you want. Very likely you would need to write some custom Python code to get exactly what you want. Probably you also want the volume enclosed in each blob. If you need tips on how to write that Python code I can advise if you give specifics of what you want. >> >> Tom >> >> >> >> >> >> >>> On Oct 6, 2021, at 4:11 AM, BINGHAM Dominic via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Hello, >>> >>> I have a problem with which I’m trying to use chimeraX to solve. I have some images of synapses with which I have super-resolved two proteins in 3D (so two images/channels). I want to quantify the colocalisation of a structure of one protein to the blobs of the other protein within a certain distance. Shown below is the non-segmented map of the 2 images of proteins. So for example I would want to quantify the colocalisation of the red blobs within a certain distance of specific larger green blobs. I want to then compare these between different conditions. >>> <Capture d’écran 2021-10-06 à 12.58.42.png> >>> >>> I have segmented the images already using "segmentat map ». I have been trying to start with the « distance » tool to measure how far one blob of protein is from the structure (Image shown below of two selected structures in just the map of one protein to practice). >>> >>> <Capture d’écran 2021-10-06 à 12.57.28.png> >>> >>> However, this doesn’t seem to work functionally as no distance is shown when I try to perform the function. Also, this function may possibly be too basic for what Im trying to do. That said, any help on how to use this function would still be greatly appreciated. >>> >>> >>> Ultimately, I think the best thing for what I would like is to be able to select a specific structure and have a measurement of all the blobs of the other protein within a defined 3D radius of this structure, and then compare this value between different conditions. I have been looking through the user manual and I can’t seem to find anything that will do something like this… I (and my PhD) would be monumentally grateful if you could possibly help me with this problem? Either by pointing me to the correct function, or even a thread that has discussed a similar problem that I may have missed? >>> >>> >>> Thanks and have a wonderful day, >>> >>> Dominic Bingham >>> PhD student at Aix-Marseille University >>> >>> _______________________________________________ >>> 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> >> >

1 0

hbonds display problem
by Maciej Basczok 08 Oct '21

08 Oct '21

Dear Expert, at the beginning would like to thank you for developing such a wonderful tool as ChimeraX is! I have one problem, namely, when hbonds calculation is run on an RNA molecule with an option to display as pseudobonds, there are many hbonds detected, but displayed are only two of them. Do I keep doing something wrong? I would be very grateful for your help. Kind regards, Maciek

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polishing video
by Ruchika Bajaj 07 Oct '21

07 Oct '21

Hi Elaine Hope you're doing well !! I need to polish my videos. I am mainly using the following commands. I am just wondering if you have any more suggestions to improve the quality of the movie. Please let me know. I would appreciate your help in this regard. Thanks !! Regards Ruchika set bgColor white; lighting simple; graphics silhouettes true; lighting soft movie record supersample 3; movie encode quality higher

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Re: [chimerax-users] Error on installing isolde
by benhaijing＠sina.com 07 Oct '21

07 Oct '21

Hi Greg!Thanks very much! After I deleted the two directories: (1) site-packages\ChimeraX_UI-1.2.1.dist-info and (2) site-packages\chimerax\ui in my computer, I have successfully reinstalled chimerax and isolde! It works now!Best regards, Haijing Ben ----- 原始邮件 ----- 发件人：Greg Couch <gregc(a)cgl.ucsf.edu> 收件人：benhaijing(a)sina.com, chimerax-users <chimerax-users(a)cgl.ucsf.edu> 主题：Re: [chimerax-users] Error on installing isolde 日期：2021年09月28日 06点24分 Actually, it worse than I thought. Uninstalling the user-installed version of the UI bundle is not doable from within ChimeraX. And uninstalling ChimeraX and reinstalling it doesn't help, because that only takes care of system files, not any of the user's customization. To get rid of the user installed bundle, the first step is to find where on the filesystem the files are. So start the Shell tool from the Tools / General menu. And then type in it: import chimerax chimerax.app_dirs.user_data_dir That will show where to go. For example, for me on Windows, it prints: 'C:\\Users\\gregc\\AppData\\Local\\UCSF\\ChimeraX\\1.2' So using the Windows file brower, I would navigate to C:\Users\gregc\AppData\Local\UCSF\ChimeraX\1.2. You may need to check "Hidden Items" in the View menu to navigate into AppData directory. macOS and Linux users should have an easier time going to the correct directory. And they would use forward slash, /, instead of backslash, \. The next step is to remove two directories: (1) site-packages\ChimeraX_UI-1.2.1.dist-info, and (2) site-packages\chimerax\ui. And then, when you restart ChimeraX, you'll be back to the version that came with ChimeraX. HTH, Greg On 9/27/2021 2:22 PM, Greg Couch via ChimeraX-users wrote: Hi Haijing, The output you pasted says that ISOLDE is already installed, so you don't need to install it again. It should be reinstallable, so that is a bug. If you use the graphical toolshed interface (click on More Tools... in the Tools menu), you would have seen that the install button for ISOLDE said Installed, meaning it is already installed. In this particular case, it looks you made things worse by deliberately installing an older version of the UI bundle from the toolshed than the version that came with ChimeraX. Using the graphical toolshed interface, you would have seen that it was a downgrade, which means do not install it unless necessary. Or maybe you used the Updates tool to do that? If so, you should have seen that installed version was 1.7.6 and the version on the toolshed is 1.2.1, so much older. Regardless of how you did it, to fix it, give the command: toolshed uninstall ui And that should revert back to version of the UI bundle that came with ChimeraX. The fact that you could install an older, incompatible, version of the UI bundle is a bug that is difficult to fix in the general case. Best regards, Greg On 9/26/2021 5:55 PM, benhaijing--- via ChimeraX-users wrote: Hi all！ I can’t install the plugin isolde using command 'toolshed install isolde'. Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Requirement already satisfied: ChimeraX-ISOLDE==1.2.2 in c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages (1.2.2) Requirement already satisfied: ChimeraX-AtomicLibrary~=3.1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (3.1.3) Requirement already satisfied: ChimeraX-Core~=1.2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (1.2.5) Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (1.0) Requirement already satisfied: ChimeraX-Clipper~=0.16.0 in c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages (from ChimeraX-ISOLDE==1.2.2) (0.16.0) Requirement already satisfied: ChimeraX-Atomic~=1.13.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.2.2) (1.13.2) Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0.1) Requirement already satisfied: ChimeraX-mmCIF~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.3) Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0) Requirement already satisfied: ChimeraX-Geometry~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.1) Requirement already satisfied: ChimeraX-Graphics~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0) Requirement already satisfied: ChimeraX-PDB~=2.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.4.1) Requirement already satisfied: ChimeraX-AtomSearchLibrary~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ConnectStructure~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0) Requirement already satisfied: ChimeraX-DataFormats~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.1) Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.5) Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0.1) Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.4) Requirement already satisfied: ChimeraX-IO~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-DataFormats~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0.1) Requirement already satisfied: ChimeraX-Surface~=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0) Requirement already satisfied: ChimeraX-UI~=1.0 in c:\users\dell\appdata\local\ucsf\chimerax\1.2\site-packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.2.1) INFO: pip is looking at multiple versions of chimerax-pdblibrary to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-pdb to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-opencommand to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-nucleotides to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-io to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-dataformats to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-mmcif to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-graphics to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-geometry to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-core to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-atomsearchlibrary to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-connectstructure to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-clipper to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-atomiclibrary to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-atomic to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-arrays to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of chimerax-isolde to determine which version is compatible with other requirements. This could take a while. The conflict is caused by: chimerax-nucleotides 2.0.1 depends on ChimeraX-UI~=1.0 chimerax-opencommand 1.5 depends on ChimeraX-UI~=1.0 chimerax-savecommand 1.4 depends on ChimeraX-UI~=1.4 To fix this you could try to: 1. loosen the range of package versions you've specified 2. remove package versions to allow pip attempt to solve the dependency conflict ERROR: Cannot install chimerax-nucleotides==2.0.1, chimerax-opencommand==1.5 and chimerax-savecommand==1.4 because these package versions have conflicting dependencies. ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/user_guide/#fixing-conflicting-dependencies WARNING: You are using pip version 21.0.1; however, version 21.2.4 is available. You should consider upgrading via the 'C:\Program Files\ChimeraX\bin\ChimeraX.exe -m pip install --upgrade pip' command. Thanks, Haijing Ben _______________________________________________ ChimeraX-users mailing list ChimeraX-users(a)cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users _______________________________________________ ChimeraX-users mailing list ChimeraX-users(a)cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users

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Mol2 file conversion
by Marcus Agyin 06 Oct '21

06 Oct '21

Hello, I am emailing to get clarification on how I would convert a chimera file into a Mol2 file. If I’m understanding correctly, I would need to click on “File” and in the pop-up menu there would be a “save as Mol2” option, however, all that it is showing the generic “Save” option. Thanks in advance, Marcus Agyin

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Measuring Colocalisation using ChimeraX
by BINGHAM Dominic 06 Oct '21

06 Oct '21

Hello, I have a problem with which I’m trying to use chimeraX to solve. I have some images of synapses with which I have super-resolved two proteins in 3D (so two images/channels). I want to quantify the colocalisation of a structure of one protein to the blobs of the other protein within a certain distance. Shown below is the non-segmented map of the 2 images of proteins. So for example I would want to quantify the colocalisation of the red blobs within a certain distance of specific larger green blobs. I want to then compare these between different conditions. [cid:5E6B5354-093F-44B8-BCD8-9C01AFDEAF72] I have segmented the images already using "segmentat map ». I have been trying to start with the « distance » tool to measure how far one blob of protein is from the structure (Image shown below of two selected structures in just the map of one protein to practice). [cid:ED6171EE-E03F-47C8-A3AE-81A7E5FC9177] However, this doesn’t seem to work functionally as no distance is shown when I try to perform the function. Also, this function may possibly be too basic for what Im trying to do. That said, any help on how to use this function would still be greatly appreciated. Ultimately, I think the best thing for what I would like is to be able to select a specific structure and have a measurement of all the blobs of the other protein within a defined 3D radius of this structure, and then compare this value between different conditions. I have been looking through the user manual and I can’t seem to find anything that will do something like this… I (and my PhD) would be monumentally grateful if you could possibly help me with this problem? Either by pointing me to the correct function, or even a thread that has discussed a similar problem that I may have missed? Thanks and have a wonderful day, Dominic Bingham PhD student at Aix-Marseille University

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