- ChimeraX-users - RBVI Mailing Lists

ChimeraX import multiple positions of the same .pdb structure
by Frey, Lukas 23 Nov '21

23 Nov '21

Dear Elaine, I have an external file with a transformation matrix (orientation and translation) for a .pdb structure and I would like to apply the transformation in ChimeraX to a .pdb file. I’m aware that ChimeraX needs a matrix like [[1,1,1],[2,2,2],[3,3,3],[x,y,z]], where the first 3 columns are the orientation the last column the x,y,z translation positions. One can load a new orientation/translation into chimeraX with the „open“ command: https://rbvi.ucsf.edu/chimerax/docs/user/formats/positions.html in the command line of chimeraX I had to type in: open path-to-file/test.positions models #1 childModels true matchNames true my test.positions file is a .txt file containing the name of the .pdb structure and transformation matrix and I already loaded the .pdb structure before I applied the transformation matrix. Below you can find the input of the transformation matrix file, called text.positions: 6y2l.pdb,-0.6515591636522021,-0.6041757901381976,-0.45873987277293393,0.09148867345316551,-0.662890582358989,0.7431055769199559,-0.7530607405054541,0.44220774578318395,0.48718767500700594,30.0,20.0,30.0 If I apply the open command in chimera somehow it leads to a distortion of the .pdb protein structure. If I check the transformation position of the model with „view matrix“, then I have the following output: view matrix camera position: 0.94464,-0.25925,-0.20113,-578.87,-0.29451,-0.94014,-0.17144,1242.4,-0.14464,0.22118,-0.96445,-8143.8 model positions: #1,-0.65156,-0.60418,-0.45874,0.091489,-0.66289,0.74311,-0.75306,0.44221,0.48719,30,20,30,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0 Somehow the transformation matrix is only applied to #1 but not to #1.1 and #1.2, do you have an idea what I have to change? If I save the transformation matrix of the distorted .pdb structure via the save command: save path-to-file/test_2.positions models #1 childModels true I have the following output: 6y2l.pdb,-0.651559163652,-0.604175790138,-0.458739872773,0.0914886734532,-0.662890582359,0.74310557692,-0.753060740505,0.442207745783,0.487187675007,30,20,30 metal coordination bonds,1,0,0,0,0,1,0,0,0,0,1,0 missing structure,1,0,0,0,0,1,0,0,0,0,1,0 The goal in the future is to load several positions (1 … 100) of the same .pdb structures. Best, Lukas Lukas Frey Visiting Postdoctoral Associate UMASS Medical School Worcester Grigorieff Laboratory

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Re: [chimerax-users] meshmol in chimeraX
by Tom Goddard 23 Nov '21

23 Nov '21

Hi Vijay, The meshmol command from Chimera which converts a surface mesh from wire edges to cylinder edges (making a fake molecule) is not yet in ChimeraX. But I can add it pretty easily, maybe tomorrow if time permits. Tom Icosahedral cage shown with wires and with meshmol cylinders > On Nov 18, 2021, at 2:38 PM, Vijay Reddy <reddyv(a)scripps.edu> wrote: > > Hi Tom, > > Greetings! Hope are staying safe and healthy. > > I am finally transitioning to chimeraX. > > Could you please tell me what is the equivalent of > > the chimera command “meshmol #26 6” in chimeraX > > Many thanks, > Vijay >

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Toolshed
by Moustafa, Ibrahim M. 23 Nov '21

23 Nov '21

Dear ChimeraX, Trying to install iSolde but toolshed page seems to be down! Is there another link to https://cxtoolshed.rbvi.ucsf.edu ? ChimeraX Toolshed<https://cxtoolshed.rbvi.ucsf.edu/> Resource for Biocomputing, Visualization amd Informatics (RBVI), and its precursor, the Computer Graphics Laboratory (CGL), develops cutting-edge interactive software tools and advanced web-based computational resources that provide integrated visualizations and analyses of molecular structures and related non-structural biological information. cxtoolshed.rbvi.ucsf.edu Thanks, Ibrahim Ibrahim M.Moustafa, Ph.D. Pennsylvania State University Biochemistry & Molecular Biology Dept. Millennium Science Complex University Park State College, PA16802 Phone: (814) 863 5940 Fax: (814) 865 7927

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Question about Chimerax
by JANE LEE 22 Nov '21

22 Nov '21

Hi, I was wondering how/if I could open saved session files from Chimera in Chimerax? Also, when I tried to open a protein in Chimera, it opened. But when I tried to open the same protein in Chimerax, it only showed up as atoms and I received the message "start residue of secondary structure not found." I was wondering if you have any suggestions for troubleshooting? Thank you! Regards, Jane

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ChimeraX AlphaFold2
by Ichcharisma 20 Nov '21

20 Nov '21

Hi ChimeraX Dev I wondering if I can run oligomer prediction on ChimeraX AlphaFold features. As we can do it with others colabfold version out there. Thank you

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Feature request: windowsize to be stored with session
by mailman-bounces＠cgl.ucsf.edu 18 Nov '21

18 Nov '21

From: Vorländer,Matthias Kopano <matthias.vorlaender(a)imp.ac.at <mailto:matthias.vorlaender@imp.ac.at>> Date: November 18, 2021 at 8:47:33 AM PST Dear all, I would like to suggest that the current windowsize is associated with a ChimeraX session. This is particularly useful when making figures in a reproducible manner (if I am not mistaken, when opening a .cxs file it will open it with the same windowsize that has been used for the last chimera session, rather than the one that was used when the session was created). I am aware that the windowsize can be specified in a script file. Thanks a lot for your consideration : ) Best, Matthias

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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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