- ChimeraX-users - RBVI Mailing Lists

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

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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

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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

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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

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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

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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

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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

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