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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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