- ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] [Chimera-users] Finding SASA for individual residues
by Elaine Meng 17 Nov '22

17 Nov '22

On Nov 17, 2022, at 8:01 AM, Prathvi Singh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi Elaine, > > The methods you suggested for calculating SASA for residues saved me so much time. Thank you once again for it. > But I have noticed an ambiguity. > When I calculate the SASA for the same residue using chimera and chimeraX, I am getting different values. > For ex: in the PDB file 1TY4, the SASA value for residue 174.a is 2.55 when calculated using chimera and it is 292.44 when calculated using chimeraX. The same is true for other amino acids in other PDB files as well. > Why is there such a difference? > On which of the two software should I rely on? > Also, what is the unit of SASA calculated by these two softwares? > > On Mon, Nov 14, 2022 at 9:42 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > [...] > In Chimera, they are automatically calculated when you show a molecular surface. It creates an attribute named areaSAS, as explained here: > <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfa…> > > See also this previous chimera-user post on using Chimera to get a list of residue SASA values > <http://www.cgl.ucsf.edu/pipermail/chimera-users/2018-June/014729.html> > > (If you use this page <https://www.rbvi.ucsf.edu/chimera/docs/feedback.html> to search chimera-users by "sasa", that was the top hit) > > In ChimeraX, you would use the command "measure sasa" > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa> > ... then save attribute "area" to file > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes> > Hi Prathvi, The atomic coordinates are in angstroms so the surface areas are in angstroms squared. Since this answer is mostly about ChimeraX, I'm also CCing the chimerax-users list. Regarding the differences in value: The programs are both right but based on different surfaces. By default, Chimera encloses all of the protein chains together into one surface (and chain A residue 174 is buried by some interactions with chain C, which you can probably see if you look at the structure). In ChimeraX, the default for display is to make each chain a separate surface, but for SASA calculation, it only depends on what you wrote in the "measure sasa" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa> As mentioned in my earlier answer, the important part of what you get from "measure sasa" is not (in your case) the total reported in the Log, but instead the "area" attribute value that you will get for each residue. If you just use this ChimeraX command: measure sasa /A:174 ... then it will make a surface that only encloses that one residue, with area 292 as you said. I'm pretty sure that is NOT what you want. Instead you want tthe surface of the whole protein (or maybe one chain) and then the area of the residue given that larger surface. If you wanted to enclose all the protein chains of a model in a single surface (like Chimera default), then measure sasa protein If you wanted to make a separate surface for chain A only, then something like measure sasa /A & protein (the & protein part is still needed so that it won't enclose ligands, water, etc. that also happen to have chain ID A) Using "measure sasa" gives the residue "area" attribute that you could save to file, show in labels, etc. as explained in the help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes> <https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html> For your example structure 1TY4, using these ChimeraX commands: measure sasa protein info residues attribute area ...gives 2.55 for residue 174 in chain A, the same as in Chimera. 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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Multiplying the model around the helical cryo-EM map
by Dmitry Semchonok 16 Nov '22

16 Nov '22

Dear colleagues, I am trying to multiply the model subunit into the helical density. I found some command for Chimera sym #1 group c2*h,4.328,23.27,120,1 center 191.99,191.99,191.99 coord #0. Probably I have to somehow find the centre - perhaps with this command, right? Measure center #1 But not for ChimeraX. So my question is, how to do that in ChimeraX? Could you please provide the usage - it would be most helpful. Thanks in advance! Kind regards, Dmitry

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Bond Rotation Questions
by FUNG Chun Po 15 Nov '22

15 Nov '22

Hello I have recently tried to use the bond rotation feature of Chimera X (Windows 10), and I have not been able to get it to work. I have tried the Bond rotation button on the toolbar, and the torsion command to no avail. The bond rotation button does not seem to do anything even when I click and drag with right click. The Torsion command states that my bond “is part of a ring/cycle and cannot be rotated” or “To set torsion, middle two atoms (/A ARG 543 N C) must be bonded;they aren't” I want to ask how do I use this function to rotate upon a simple amide bond. I am not sure am I just selecting the wrong atoms/bonds or is the function just locked for this PDB. The PDB file I am using is 7Y4P and I am trying to rotate about residues 543-544. I have also tried to do it in normal Chimera’s rotation command with no results. Thank you any advice would be welcome. Regards, Chun Po Fung

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create chain as a new model from exiting PDB model
by tim smith 15 Nov '22

15 Nov '22

Hi All, I would like to create chain A as a separate model from the existing model. Could you please help me. Thank you. Best regards Tim

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Question about pad parameter
by Thu Nguyen 14 Nov '22

14 Nov '22

Hello, I am using the volume cover command to crop the chain from the protein map. Here is what I did: > open 12554 from emdb > open 7ns0 > volume cover #1 atomBox #2/A1 pad 1.0 Suppose I want to add extra 17 voxels on each size of the chain, what value of pad should I add? Also, could you tell me the unit of pad in this command? Thank you very much. Best regards, Thu

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Re: [chimerax-users] Google colab sign in inquiry
by Tom Goddard 14 Nov '22

14 Nov '22

Hi Alejandro, On Windows the QtWebEngine Google Colab authentication info is in C:\Users\<username>\AppData\Roaming\ChimeraX\QtWebEngine\AlphaFold You can delete that directory and try using ChimeraX AlphaFold prediction again. Tom > On Nov 14, 2022, at 5:38 PM, Abraham, Alejandro <alejandro.abraham(a)icahn.mssm.edu> wrote: > > Hi Tom, > > Thank you for your email. I cannot see the login page anymore, and uninstalling ChimeraX to later reinstall it does not work. > Is there a folder where sign in is saved like in Macs ? I am using a Windows 10 PC. > Thanks again. > > Best, > > Alejandro > > > On Mon, Nov 14, 2022 at 12:59 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > Hi Alejandro, > > ChimeraX remembers your Google Colab sign-in. I don't understand why it would not let you sign in. A screenshot showing what you see would help understand the problem. > > If you signed in and ran AlphaFold previously but you want to change the account you sign in with, that should also be possible by clicking the image in the upper right corner of the AlphaFold Run panel which is just a web browser -- that button which shows the icon for your Google account will pull down a menu and let you sign out. And then you can also use it to sign in to another account. > > If somehow the ChimeraX remembered Google sign-in is causing problems you can delete that remembered sign-in info. On Mac you would delete the directory > > ~/Library/Caches?/UCSF ChimeraX/QtWebEngine/AlphaFold > > This is described further in this ChimeraX bug report > > https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7654#comment:2 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7654#comment:2> > > Tom > > >> On Nov 14, 2022, at 7:36 AM, Abraham, Alejandro via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> Dear ChimeraX Support Team, >> >> Before all, congratulations on such awesome software. >> On another note I wanted to contact you because I am not able to connect to Google sign in when trying to predict with alpha fold. Is there a way to reset login ? >> >> Thanks again. >> >> Best, >> >> Alejandro >> >> _______________________________________________ >> 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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stretching protein?
by Noriega, Heather 14 Nov '22

14 Nov '22

Hello, I hope this email finds everyone well. I was wondering if ChimeraX had a function specific to "stretching" the protein. I am going to attach a picture, for reference. Is it possible to stretch the monomer to build a larger capsid? Thanks in advance. Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883 [image: image.png]

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Export PAE plot
by Clara Jegousse (TSL) 14 Nov '22

14 Nov '22

Dear ChimeraX team, After watching the YouTube tutorial on “how to show AlphaFold error estimates with ChimeraX”, I was wondering how to export the plot as an image (pdf, png?). Kind regards, Clara

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Google colab sign in inquiry
by Abraham, Alejandro 14 Nov '22

14 Nov '22

Dear ChimeraX Support Team, Before all, congratulations on such awesome software. On another note I wanted to contact you because I am not able to connect to Google sign in when trying to predict with alpha fold. Is there a way to reset login ? Thanks again. Best, Alejandro

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ChimeraX 1.5rc running on Nvidia RTX Titan [ubuntu 22.04]
by HONG ZHAN 11 Nov '22

11 Nov '22

Dear, I recently installed a Nvidia RTX Titan GPU card, and ChimeraX 1.5rc, it is a bit wired. I can open the window using intergrated GPU but if I just clicked on Chimerax or try to open it in terminal, it failed to open the program... Is ChimeraX only working on integrated GPU? Also, I cannot install the chimerax using apt install as in the website description, but dpkg -i works... is this the right way to install? many thanks! Hong

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.pdb from Protein Data Bank has more chains than expected
by McClean, Phillip 10 Nov '22

10 Nov '22

Hi Everyone, I downloaded the 7FDL .pdb from the Protein Data Bank. I was expecting just two chains (it is a heteromeric complex), but I found 12 chains in the file (A-L). I was expecting two chains because the manuscript suggested they were just modeling protein fragments of the two protein. It appears that chains that A,C,E,G,I,K are multiple models of one fragment, while chains B,D,F,H,J,L are multiple models of the second fragment. Two questions. Why are multiple structures reported, and how to I visualize just two fragments at the same time, for example A and B. I have attached the .pdb file. Thanks for any advise. Phil McClean

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Density extraction
by Dmitry Semchonok 09 Nov '22

09 Nov '22

Dear colleagues, I have a 3D map of the helix. 1. Do you know how can I extract 1 subunit? 2. Also, if there is no x-ray structure available. Thanks in advance. Kind regards, Dmitry

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Fast Archive Search
by Kazan Ramy 09 Nov '22

09 Nov '22

Greetings to all, How can one search the archive with given keywords? Like for example, Ctrl + F search. I can only find the manual search by subject, thread ... and limited by month. Cheers, Ramy

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Problem with the addcharge command
by svle＠tiscali.it 09 Nov '22

09 Nov '22

Hi all, for Chimerax version 1.4 (2022-06-03) when in the command line I use addcharge or addcharge #1 I receive in the Log panel the following: Unknown command: addcharge or Unknown command: addcharge #1. Where I'm wrong? Thanks. Saverio VOUCHER CONNETTIVITÀ per P.IVA e PMI: internet a canone 0 per 48 mesi. ATTIVA ORA https://casa.tiscali.it/promo/?u=https://promozioni.tiscali.it/voucher_busi…..

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Re: [chimerax-users] [Chimera-users] MD simulation movie in chimeraX
by Elaine Meng 09 Nov '22

09 Nov '22

Hello! For ChimeraX questions you may want to use the other address, chimerax-users(a)cgl.ucsf.edu CC'd here. You can see what formats ChimeraX reads by using command "open formats," or view this User Guide page: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#formats> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#trajectory> ChimeraX can read .trr trajectory coordinates, but it cannot read .tpr trajectory topology. If your MD program can output a single PDB snapshot you can use that for the topology. First you would open the PDB file. Then to open the .trr file you would need to use the "open" command and also specify the already-open PDB file with the "structureModel" option. For example, if you open the PDB file as model #1, then something like: open myfile.trr structureModel #1 See details and more examples: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#traj-options> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#structureModel> When you open the trajectory in ChimeraX, I believe that a playback slider will automatically appear. However, if it does not you can use "coordset slider" to show it. The "coordset" command can also be used to play the trajectory frames directly (not using the interactive slider): <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.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 8, 2022, at 6:17 PM, Shivam Gupta via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello Support Team, > > I am a commercial license user of chimeraX. I have .trr and .tpr files from the Gromacs MD simulation. I am not getting any option to create an MD movie. I know how to do it in chimera but couldn't find a similar GUI/option in chimeraX. Literature/tutorial of chimeraX didn't help me much. > > Please help me out by guiding me to generate MD movies. > Please reply to this email inline. > > I am Looking forward to hearing from you. > Thanks > > -- > With Regards > Gupta　Shivam グプタ　シヴァム > E-mail: shivam-gupta(a)pharmafoods.co.jp > Biomedical Department > Pharma Foods International, Kyoto Japan > 株式会社ファーマフーズ > 〒615-8245　京都市西京区御陵大原1-49 > TEL:075-748-9811 > FAX:075-948-9818 > URL: http://www.pharmafoods.co.jp/

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side view window : lines are too thin
by Valerie Biou 08 Nov '22

08 Nov '22

Hello, I am a Chimera user slowly adapting to ChimeraX. I find that the moving lines in the Side view window are very thin, almost invisible when a cryoem map is displayed. is there a way to make them thicker ? thanks, kind regards, Valérie

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RMSD Problem
by Timothy JM Clayson 08 Nov '22

08 Nov '22

Hiya, I am currently having a problem when trying to use RMSD on 2 sequences. *I am using the command: * *rmsd #1:149,264 to #2:469,553* (where a.a. on chain 1 are 149-264 and on chain 2 they're 469-553) *It is coming up with the error:* *'Number of atoms from first atom spec (21) differs from number in second (10)'* I was wondering if there is a fix to this problem? Thanks, Tim

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Re: [chimerax-users] Applying symmetry operations to generate an oligomeric model
by Tom Goddard 07 Nov '22

07 Nov '22

Hi Rob, Hopefully you are using ChimeraX, not Chimera -- we have only done maintenance on Chimera for the past 6 years. The ChimeraX commands all work in physical coordinates (Angstroms), not grid index units (pixels), and usually they use scene coordinates, not local model coordinates which makes a difference if you have moved individual models relative to one another in the scene. Your Dn symmetry problems are because the two-fold symmetry that flips one Cn ring to the other stacked Cn ring needs to be aligned on the x-axis. In your map apparently it is not aligned with the x-axis. In general it is helpful to have your map aligned in a standard way if you will be applying symmetry. For dihedral symmetry the z-axis is the cyclic symmetry axis, the origin should be on that cyclic symmetry axis mid-way between the two rings, and the x-axis should be a two-fold symmetry axis. If you don't use standard map orientations for symmetric maps it is going to be very painful to make symmetric copies of atomic models in those maps. Tom > On Nov 6, 2022, at 12:58 PM, Robert Harkness <r.harkness(a)utoronto.ca> wrote: > > Hi Tom, > > Thank you for your detailed response! > > I think I am using an older version of chimera. When I use the center <map> command, I just get one line of output that corresponds to the center of the map in grid coordinates. I have been converting these into angstrom coordinates using the pixel size and applying those in sym. > > Sometimes when I open a model and a map, I have to rotate and translate the model into a reasonable position inside the map and then do a “fit in map” to get the initial placement for sym, so this means that the model’s coordinates will now be different relative to the scene and the map. If I save the fitted model to a new PDB and then re-open it, will it now have the same coordinates of the scene (and map if I haven’t moved the map at all)? I think that way I can use scene coordinates for all maps and models. > > I am finding for other cages I am working on that have Dn symmetry, in some cases they work beautifully if I just fit the model into the portion of the map that corresponds to one unit of the cage, then save that model as a PDB relative to the map, then open it and use sym <model> group <Dn> center <map center in angstrom units> coordinateSystem <map>. In other cases doing this same procedure, the first half of the cage units are made perfectly as sym goes from the initial model around the Cn axis placing copies in the density, but when it flips over the 2-fold axis to do the other half, the model units are out of alignment with the density. So I have been adding the axis option to get it closer but find it requires a little tweaking. I guess the axis command doesn’t always give the perfect axis of rotation because the map is not perfect. Will this also be alleviated by just using everything in scene coordinates? > > Best, > > Rob > >> On Nov 5, 2022, at 7:55 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> You don't often get email from goddard(a)sonic.net <mailto:goddard@sonic.net>. Learn why this is important <https://aka.ms/LearnAboutSenderIdentification> >> Hi Rob, >> >> It sounds like you did everything right. Using "measure center #1" where model #1 is the map should give the right center of the tetrahedron. When you use that command it reports the center in map grid index units and also in scene coordinates, for example, >> >> measure center #1 <cxcmd:measure center #1>Center of mass grid index for emdb 15560 = (279.52, 279.92, 253.25) >> Center of mass xyz coordinates for emdb 15560 = (289.20, 235.85, 185.32) >> >> >> In the sym command were you use that center to copy your atomic model with tetrahedral symmetry you should use the scene coordinates (the second line of output) not the grid index coordinates. The "sym" command expects scene coordinates for the "center" option and you should not use the "sym" command coordinateSystem option. The coordinateSystem option is used only if the center coordinates are given in the coordinate system of a specific model rather than the whole scene. The models start out with the same coordinate system as the whole scene, but if you move a model in the scene (e.g. when you fit an atomic model into the map) then that model has different local coordinates than the scene. >> >> I see another potential problem in your sym command. The "axis" option is supposed to be a 3-fold symmetry axis of the tetrahedron. You are giving it the symmetry axis of the asymmetric unit trimer which may or may not be a symmetry axis of the tetrahedron. To determine the symmetry axis of the tetrahedron open two copies of the map and rotate one copy by hand using the "Move Model" mouse mode (which moves only the selected model) to roughly align two different trimeric subunits then optimize the alignment with "fitmap #2 in #1", then use measure rotation #2 to #1 and it will report a symmetry axis of the tetrahedron. Another way to go about this is if you density map already has a standard orientation, such as tetrahedron 2-fold symmetry axes along x,y,z then you don't need to specify the axis in the sym command, just use "t,222" in the sym command. Or if it has a symmetry axis along z use "t,z3" with no axis specification. You can probably see if it has a standard symmetry using "measure symmetry #1". >> >> Sorry for the delayed answer. I was at a workshop all last week and did not have time for email. >> >> Tom >> >>> On Nov 3, 2022, at 4:35 AM, Robert Harkness via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Hello, >>> >>> I am trying to generate a model of an oligomeric protein cage that consists of 4 trimers and has tetrahedral symmetry. I am using the asymmetric unit model consisting of one monomer (#0) and a density map (#1) as a starting point. My strategy has been to take the asymmetric unit and fit it into a portion of the map corresponding to one of the monomers within one of the trimer faces of the tetrahedron. Then I generate a copy of that asymmetric unit (#2) and fit it into the map for an adjacent protomer within the same trimer face. This results in the two asymmetric unit models being rotated 120 degrees relative to one another and part of the same trimer. Then I use the measure rotation command to measure the rotation of the second asymmetric unit relative to the first, giving me a rotation matrix and axis parameters. I then do >>> >>> sym #0 (first asymmetric unit) group t,z3 axis <axis from measure rotation> center <axis points from measure rotation> coordinateSystem #1 (the density map) >>> >>> And this generates the right looking trimers, so the 3-fold axis appears to be correct, but the center is off such that only one of the four trimers matches the density map and is placed at the top of the tetrahedron, while the other 3 trimers are off into the void of the scene but placed at the other 3 vertices. I am not sure how to appropriately define the center. My feeling is that it should be the center of the map, taken from the measure center #1 command, but implementing those numbers in sym doesn’t work either. Any thoughts on how these center coordinates are defined/should be measured, or if there is a better approach for doing this would be awesome! >>> >>> Best, >>> >>> Rob >>> >>> _______________________________________________ >>> 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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error saving session in v 1.5
by Yoda Muppet 07 Nov '22

07 Nov '22

Greetings. We're having an issue savings session with ChimeraX 1.5. Trying to save a session file results in the following error: [save] (help: user/commands/save.html) /data/processed/staggers/cryofib- tryps/process/YTAT9-1 lamella4 0206 def -5 110e tilt-7/full seg session.cxs [save /data/processed/staggers/cryofib- tryps/process/YTAT9 - 1 lamella4 0206 def -5 110e tilt-7/full seg session.cxs] (cxcmd: save /data/processed/staggers/cryofib- tryps/process/YTAT9 - 1 lamella4 0206 def -5 110e tilt-7/full seg session.cxs) Traceback (most recent call last) : File "/opt/cryoem/chimerax-2022.10.28/lib/python3.9/site- packages/chimerax/core/session.py", line 285, in process data = sm. take snapshot (obj session, self.-state flags) File "/opt/cryoem/chimerax-2022.10.28/lib/python3.9/site- packages/chimerax/log/tool.py", line 542, in take snapshot "contents': self.page source, AttributeError: *Log' object has no attribute 'page source' The above exception was the direct cause of the following exception: Traceback (most recent call last) : File "/opt/cryoem/chimerax-2022.10.28/lib/python3.9/site- packages/chimerax/core/session.py", line 262, in discovery self.processed[key] = self.process (obj, parents) File "/opt/cryoem/chimerax-2022.10.28/lib/python3.9/site- packages/chimerax/core/session.py", line 290, in process raise RuntimeError (msg) from e RuntimeError: Error while saving session data for "tools' -> ‹chimerax.core. tools. Tools object at 0x7f90efeb0310> => <chimerax.log. tool. Log object at 0x7f90ee2b3c10> During handling of the above exception, another exception occurred: Traceback (most recent call last) : File "/opt/cryoem/chimerax-2022.10.28/lib/python3.9/site- packages/chimerax/core/session.py", line 896, in save session. save (output, version=version, include maps=include maps) File "/opt/cryoem/chimerax-2022.10.28/lib/python3.9/site- packages/chimerax/core/session.py" line 625, in save mgr.discovery(self. state containers) File "/opt/cryoem/chimerax-2022.10.28/lib/python3.9/site- packages/chimerax/core/session.py", line 266, in discovery raise ValueError ("error processing: %S: %S" % ( obj stack(parents, obj), e)) ValueError: error processing: "tools' <chimerax.core. tools. Tools object at 0x7 f90efeb0310> <chimerax.log. tool.Log object at 0x7f90ee2b3c10>: Error while saving session data for 'tools' -> <chimerax.core. tools. Tools object at 0x7f90efeb0310> <chimerax.log. tool. Log object at 0x7f90ee2b3c10> BUG: ValueError: error processing: 'tools' for "tools => -> ->: Error while saving session data File "/opt/cryoem/chimerax-2022.10.28/lib/python3.9/site- packages/chimerax/core/session.py" line 266, in discovery raise ValueError ("error processing: %S: %5" % (obj stack(parents, obj), e)) See log for complete Python traceback.

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Change luminance in color palette
by Scott, Brandon L. 07 Nov '22

07 Nov '22

I am coloring surfaces using palettes (purples or a custom green-white-magenta). These both have a single luminance value, is it possible to generate a color palette that also has changing luminance. The ideal palette would be green -> white -> magenta along the color axis, and 0 - > 255 scaling the luminance of the rgb. We would effectively have a color bar matrix that goes from dark green to black to dark magenta if the values are low and bright green to white to bright magenta if the values are high. Thanks for your insights! -Brandon Brandon Scott, PhD CZI Imaging Scientist, Assistant Professor Nanoscience & Biomedical Engineering South Dakota Mines EEP 229 501 E. Saint Joseph St., Rapid City, SD 57701 724.510.1253 | Brandon.Scott(a)sdsmt.edu<mailto:Brandon.Scott@sdsmt.edu> [South Dakota Mines]<https://www.sdsmt.edu/>

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Create command for subunit model
by tim smith 06 Nov '22

06 Nov '22

Hi All, I would like to create a separate subunit model in chimeraX like create command in Pymol. In my PDB model, 3 subunits are present, I want to make each subunit as a model for representation. Thank you and best regards Tim

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Applying symmetry operations to generate an oligomeric model
by Robert Harkness 05 Nov '22

05 Nov '22

Hello, I am trying to generate a model of an oligomeric protein cage that consists of 4 trimers and has tetrahedral symmetry. I am using the asymmetric unit model consisting of one monomer (#0) and a density map (#1) as a starting point. My strategy has been to take the asymmetric unit and fit it into a portion of the map corresponding to one of the monomers within one of the trimer faces of the tetrahedron. Then I generate a copy of that asymmetric unit (#2) and fit it into the map for an adjacent protomer within the same trimer face. This results in the two asymmetric unit models being rotated 120 degrees relative to one another and part of the same trimer. Then I use the measure rotation command to measure the rotation of the second asymmetric unit relative to the first, giving me a rotation matrix and axis parameters. I then do sym #0 (first asymmetric unit) group t,z3 axis <axis from measure rotation> center <axis points from measure rotation> coordinateSystem #1 (the density map) And this generates the right looking trimers, so the 3-fold axis appears to be correct, but the center is off such that only one of the four trimers matches the density map and is placed at the top of the tetrahedron, while the other 3 trimers are off into the void of the scene but placed at the other 3 vertices. I am not sure how to appropriately define the center. My feeling is that it should be the center of the map, taken from the measure center #1 command, but implementing those numbers in sym doesn’t work either. Any thoughts on how these center coordinates are defined/should be measured, or if there is a better approach for doing this would be awesome! Best, Rob

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Create subunit model
by tim smith 05 Nov '22

05 Nov '22

Hi All, I would like to create a separate subunit model in chimeraX like create command in Pymol. In my PDB model, 3 subunits are present, I want to make each subunit as a model for representation. Thank you and best regards Tim

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Re: [chimerax-users] [Chimera-users] Jagged edges in chimera X
by Elaine Meng 03 Nov '22

03 Nov '22

Hi Prathvi, For ChimeraX questions, you may want to use the other mailing list, chimerax-users(a)cgl.ucsf.edu CC'd here. As per this recent post, ChimeraX does not have multisampling, but if you are saving an image you can use supersampling: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-September/004310.ht…> ChimeraX also has a "graphics quality" command to increase the number of facets used to draw atoms, bonds, and cartoons (ribbons), although I don't know if that is going to help your issue very much: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#quality> 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, 2022, at 4:59 AM, Prathvi Singh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello Elaine, > > Is there a way to smoothen the jagged edges seen around ribbons and sheets in ChimeraX? > The jagged edges can be removed in UCSF chimera by setting the subdivision value to 20 and enabling multisampling but I do not see these features in chimeraX. > > -- > Prathvi Singh, > Research Fellow, > Department of Biological Sciences & Bioengineering, > Indian Institute of Technology, Kanpur-208016 > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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How to discover hydrophobic between two chains
by McClean, Phillip 02 Nov '22

02 Nov '22

Hi Everyone, I ran AF2 multimer and have a two-chain complex. I ran the mlp command on the two chains separately and together. The two chains seem to interact via hydrophobic residues where chain B fits into a pocket on chain C. Here are the chain residues: /b:72-124 /c:1-190 Is there any way to determine which residues (hydrophobic) in each of these two regions are interacting via hydrophobic interactions. Thanks for any help you can provide. Phil McClean

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Copy attribute value from one attribute to another
by Sean Connell 02 Nov '22

02 Nov '22

Hello, I have a question with a probably obvious answer but I cannot figure it out. Is there a command to copy an attribute value from one attribute to another, for example, seq_conservation to bfactor? The idea would be to save a pdb file with the conservation stored in bfactor (for sharing). In this case I guess there is the issue that one is an atom attribute and the other is residue attribute but one could assign all atoms of the residue the same value. Sorry in advance if I miss something obvious.

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Get atom from selection string in script
by Thibault TUBIANA 02 Nov '22

02 Nov '22

Hi! I would like to create a function to copy the torsion angle from a model to another one. The function would take in argument the model ID of the reference and target model (<int>) and the residue id (<int>). I looked a bit at the scripts available in [ https://rbvi.github.io/chimerax-recipes/ | https://rbvi.github.io/chimerax-recipes/ ] to have an idea of how to add function in ChimeraX, but I'm currently stuck at "how to get the list of atoms from a selection string ?". Here's my current script from chimerax.core.commands import run def copy_torsion(session, model1, model2, residue): selection = f"torsion #{model2}:{residue}@n,ca,c:{residue+1}@n" from chimerax.atomic import AtomsArg atoms = AtomsArg(selection) from chimerax.geometry import dihedral cur_torsion = dihedral([*a.scene_coord for a in atoms]) torsion=run(session, f"torsion #{model1}:{residue}@n,ca,c:{residue+1}@n {cur_torsion}") def register_command(logger): from chimerax.core.commands import CmdDesc, register, FloatArg, IntArg, BoolArg, Color8Arg, StringArg from chimerax.atomic import AtomsArg desc = CmdDesc(required = [ ('model1', IntArg), ('model2', IntArg), ('residue', IntArg), ], synopsis='Copy torsion angle') register('copyTorsion', desc, copy_torsion, logger=logger) register_command(session) Thank you for your help :) Best regards, Thibault. -- Thibault Tubiana, PhD Postdoctoral Fellow @ [ https://www.i2bc.paris-saclay.fr/equipe-interactions-and-assembly-mechanism… | IMAPP ] Institute for integrative biology of the cell ( [ https://www.i2bc.paris-saclay.fr/ | I2BC ] ) - CNRS UMR 9198 CEA Saclay, 91191 Gif sur Yvette - Bât 532 pce 34 Web Site: [ http://www.tubiana.me/ | http://www.tubiana.me/ ]

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Re: [chimerax-users] [Chimera-users] xyz axis indicator
by Elaine Meng 01 Nov '22

01 Nov '22

Hi Xiang, I am guessing you are using ISOLDE with ChimeraX (not Chimera) so I am cross-posting this question to the chimerax-users(a)cgl.ucsf.edu list. I am not expert with ISOLDE so I am not sure about the answer. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Oct 30, 2022, at 10:58 PM, Xiang Zhang via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi all, > > I was wondering how I could hide the xyz indicator in the center of window when I was viewing the X-ray density from mtz file? It only appears in crystal unit view mode but disappears in EM projection side view. > > Best, > Xiang > <1667192316818.png>_______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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Co-centering maps and pub models
by mailman-bounces＠cgl.ucsf.edu 31 Oct '22

31 Oct '22

Dear ChimeraX users I have a density map and a pdb model opened in ChimeraX. How to move one of them to have a common axis (for both) , without disturbing the other. Stay safe & Regards Anindito Sen. Ph.D Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257 Office: ILSB Room 1133 <http://microscopy.tamu.edu/>Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu <http://microscopy.tamu.edu/>

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Re: [chimerax-users] AlphaFold Prediction
by Tom Goddard 31 Oct '22

31 Oct '22

Hi Raihan, The maximum sequence length that can be predicted by AlphaFold is limited by GPU memory. The following table says that paid Google Colab services only offer at most 16 Gbytes of GPU memory (from https://blog.paperspace.com/alternative-to-google-colab-pro/ <https://blog.paperspace.com/alternative-to-google-colab-pro/>). Not sure if it is correct since the table is from a Google competitor. You can run sequence length 1000, sometimes 1200, with 16 GB of GPU memory as shown here https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html Various cloud compute services offer modern GPUs like Nvidia A40, A100, A6000 with 48 GB, or 40 or 80 GB of GPU memory usually charging about $2-3 per hour. But ChimeraX can only currently use Google Colab for AlphaFold predictions. Tom > On Oct 31, 2022, at 2:45 PM, S.M. RAIHAN RAHMAN <smrrbtgeiu(a)gmail.com> wrote: > > Thank you. I saw the run times. Is it possible to run sequences of around 1200 in Google Colab pro plus paid service through ChimeraX? In the website link you shared, I only saw about Google Colab pro paid service. Please let me know. > > Regards, > Raihan > > On Mon, 31 Oct 2022 at 14:33, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > ChimeraX only runs AlphaFold on Google Colab. Because Google Colab provides 5 year old GPUs with little memory (16 GB) it can only run sequences of length about 1000 or less. With better equipment and your own AlphaFold installation you can run sequences up to length 3000 or 4000 although that can take 30 hours. Here are example run times > > https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html <https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html> > > Tom > > >> On Oct 31, 2022, at 2:28 PM, S.M. RAIHAN RAHMAN <smrrbtgeiu(a)gmail.com <mailto:smrrbtgeiu@gmail.com>> wrote: >> >> Thank you so much. Is there any alternative to Google Colab for running AlphaFold through ChimeraX? Please let me know. >> >> Regards, >> Raihan >> >> On Mon, 31 Oct 2022 at 14:22, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> Hi Raihan, >> >> The ChimeraX AlphaFold prediction produces 5 models but it only automatically opens the best model. All 5 models are in the ~/Downloads/ChimeraX/AlphaFold/prediction directory after the job completes. There is no option to run fewer models. Running AlphaFold not through ChimeraX also produces 5 models. This is because AlphaFold works by running 5 slightly differently trained neural networks and the best is chosen. If you install your own AlphaFold (a somewhat difficult task, needs Linux and an Nvidia GPU and a few Tbytes of disk for databases) then you can modify the AlphaFold Python code to predict only one or a few models by choosing which of the 5 networks it should run. >> >> Tom >> >> > On Oct 31, 2022, at 1:39 PM, S.M. RAIHAN RAHMAN via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> > >> > Hi! >> > Good Afternoon. I hope that you are doing well. I am facing a problem in running structure prediction of large protein sequence in AlphaFold prediction. Is there any way of predicting only 2 models of a given sequence in lieu of 5 models before providing the final model in AlphaFold prediction? Please let me know. Thank you. >> > >> > Regards, >> > Raihan >> > _______________________________________________ >> > 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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AlphaFold Prediction
by S.M. RAIHAN RAHMAN 31 Oct '22

31 Oct '22

Hi! Good Afternoon. I hope that you are doing well. I am facing a problem in running structure prediction of large protein sequence in AlphaFold prediction. Is there any way of predicting only 2 models of a given sequence in lieu of 5 models before providing the final model in AlphaFold prediction? Please let me know. Thank you. Regards, Raihan

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Copy a part of a model ?
by mailman-bounces＠cgl.ucsf.edu 31 Oct '22

31 Oct '22

Hi :) I wanted to duplicate only one part of a model and I haven't found a copy function (I found this old thread tho https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-January/000783.html <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-January/000783.html>) For now my strategy is to duplicate the model with "combine #1 close false" and then delete what I don't want on the new model like for example (to delete helices) "delete ~helix & #2" I know you are always super busy with ChimeraX dev, but I thought this could be a good "quick way" to create a "copy" function of example (if there are no alternative that I missed of course). Have a great day! Best regards, Thibault. -- Thibault Tubiana, PhD Postdoctoral Fellow @IMAPP <https://www.i2bc.paris-saclay.fr/equipe-interactions-and-assembly-mechanism…> Institute for integrative biology of the cell (I2BC <https://www.i2bc.paris-saclay.fr/>) - CNRS UMR 9198 CEA Saclay, 91191 Gif sur Yvette - Bât 532 pce 34 Web Site: http://www.tubiana.me/gallery <http://www.tubiana.me/>

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Re: [chimerax-users] [Chimera-users] Question regarding protein-protein interactions in ChimeraX
by Elaine Meng 31 Oct '22

31 Oct '22

Hi Camille, ChimeraX does not move the proteins to predict how they might bind each other, although you could move one relative to the other "manually" (with the mouse) yourself, or use some other program to do protein-protein docking. ChimeraX is just showing the coordinates in the Protein DataBank data files that you opened, i.e. whatever the authors deposited. If you are using ChimeraX, for future questions you may want to use ChimeraX mailing list chimerax-users(a)cgl.ucsf.edu CC'd here instead of the Chimera one. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Oct 30, 2022, at 3:26 PM, Lake, Camille (NIH/NIAID) [C] via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello, > > My name is Camille Lake and I have used ChimeraX to model proteins. I was wondering - if I load two completely separate proteins from PDB, what is the nature of their interaction as shown by ChimeraX? The two proteins I'm interested in, TIM-3 (5f71) and CEACAM1 (5dzl), are predicted to interact in the literature, but if I load them separately into ChimeraX, is this predicted interaction what displays automatically? It seems that they are, but I can't find anywhere on the web whether this is automatically done in ChimeraX. Other proteins I randomly add in generally keep far away from each other in space. > > Thank you, > > Camille

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can not download
by keqing yin 29 Oct '22

29 Oct '22

Hello, There is no reaction after I clicked the save as the CSV when I want to download the clipper from tools/more tools . I would be very appreciate if you could solve this problem. [cid:image003.png@01D8EAFB.ECAB74A0] 从 Windows 版邮件<https://go.microsoft.com/fwlink/?LinkId=550986>发送

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How do I visualize an amber nc file in ChimeraX?
by Yasmene Wang Elhady 28 Oct '22

28 Oct '22

Hello, I'm new to molecular modeling, and new to Chimera. I'm trying to visualize an AMBER .nc output file from an AMBER tutorial ( http://ambermd.org/tutorials/basic/tutorial0/) and I have a topology file that in VMD is the type AMBER7 Parm. How can I visualize this in ChimeraX? I saw another thread suggesting to use the MD movie tool, but I don't see that option in ChimeraX. Is this something I need to add? If so, where can I get it from, and how do I add it? Thanks in advance, Yasmene

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Selection by segid
by CUNIASSE Philippe 28 Oct '22

28 Oct '22

Dear all, Is there a way in ChimeraX to make a selection by segid (column 73-76 in pdb format from CHARMM of XPLOR)? Thanks in advance. Philippe Cuniasse. ----------------------------------------------- Philippe Cuniasse, PhD/HDR. Institut de Biologie Integrative de la cellule. UMR 9198 CNRS-CEA-Univ Paris Sud Bat 144 CE-Saclay 91191 Gif-sur-Yvette Cedex France Tel: (33) 1 69 08 56 35 Fax: (33) 1 69 08 47 12 Email: philippe.cuniasse(a)cea.fr<mailto:philippe.cuniasse@cea.fr> Web: http://biodev.cea.fr/rasmot3d/ [signature_700846419][signature_2907812893][signature_966493179] -----------------------------------------------

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Re: [chimerax-users] ChimeraX sequence alignment score?
by Elaine Meng 27 Oct '22

27 Oct '22

> On Oct 27, 2022, at 4:46 PM, Budayr, Omar Mahdi <obudayr(a)vols.utk.edu> wrote: > > Dear Dr. Meng, > > I looked through the documentation for ChimeraX and I still cannot figure out what the value for sequence alignment score indicates. I aligned two b-adrenergic receptors from PDB (2RH1 and 3NH8) and it gives a value of 2423.9. What does this value actually represent? The documentation refers to it but never gives specifics besides the parameters in the table that matchmaker generates > > Sincerely, > Omar Budayr Dear Omar Budayr, The value itself is not at all important. The reason to have a score is that the alignment process tries to maximize it for the pair of sequences that it is given. By changing parameters for scoring you can change the relative importance of the different parts of the score, and thus what is most important for the alignment method to align. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. we recommend sending questions to the chimerax-users(a)cgl.ucsf.edu address (CC'd here) so that others can benefit from the answers and/or help to answer the questions - thanks!

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Selecting residues in two chains
by McClean, Phillip 27 Oct '22

27 Oct '22

Hi Everyone, I have a .pdb file created using AF2 Multimer. It consists of two chains, B and C. Chain B is a protein with 315 residues, while Chain C is a protein with 662 residues. Each chain is modeled with structured and unstructured regions. I would like to only show residues 19-24 of Chain B and residues 1-190 of Chain C in the display window. I have tried using the information provided on the "Command-Line Target Specification" page, but I have not had any success with just displaying those ranges of residues in the display window. My goal is to highlight specific features of those ranges of residues to display their interaction. Thanks for any information you can provide. Phil McClean

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segmented tomogram density in chimeraX
by Jesse HANSEN 25 Oct '22

25 Oct '22

hi all, I have segmented a tomogram in Amira and exported to chimera for visualization. I first opened the .rec file in chimera and re-saved as .mrc. Okay, the segmentation output gives a fully filled volume cube except for the regions of segmentation. Obviously things are inverted. Also, the volume viewer shows clear sharp peaks (delta functions) rather than continuous density, as volume slider moves to the right new segmentation features appear. So I used volume filter with "scale" to -1, and I turned off "displayed subregions only". This fixed the inversion problem and now as I slide toward the right I see more segmented densities. However the threshold values are all negative (-250 on the far left to -240 on the far right). This, combined with the densities being sharp peaks, makes it impossible to use this volume like a regular volume for surface coloring, filtering, segger, etc. Any suggestion on how to go from this step to a usable density would be appreciated. thanks! Jesse ================================= Dr. Jesse Hansen Schur Group Institute of Science and Technology Austria Am Campus 1 3400 Klosterneuburg Austria

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Useful tools ideas/requests
by Shayne Quinn 21 Oct '22

21 Oct '22

Hello, I have been using ChimeraX for a few years now for multidimensional cell bio-imaging and cannot thank the team and developers enough for such an amazing program. I am not sure where to ask for other useful tools so I am starting here. These may already exist but I was unsuccessful in finding them in the user guide so my apologies if I missed them. 1) Is there an option to color the different axis for the 'showOutlineBox' feature for volumes? For example box lines in x-blue, y-green and z-red to help keep orientation (I have included a mock version in the attachment) 2) I work specifically with Lattice Light Sheet Data which requires our 3D cells to be placed on glass coverslip that do not show up in the captured data but are useful for referencing orientation. Is there a feature in place already that would allow me to create a mock coverslip. So far I resorted to importing a throwaway volume (Volume 4 in attachment) and made the threshold for a surface ~0, set it to grey, and made it fill the bottom 5 pixels or so, shown in the attachment. 3) Is there a time stamp feature similar to the scale bar function that has already been implemented? Thank you so much for all the time and effort that has been put in and for creating such an amazing visualization tool! Cheers, Shayne Quinn

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Installing ChimeraX on Ubuntu 16.04 or openSuse Leap 15.2
by Miguel 19 Oct '22

19 Oct '22

Hello, I am trying to install ChimeraX on Ubuntu 16.04 or openSUSE Leap 15.2 without success. Is it possible? If so, what would be the procedure? Thanks, Miguel

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Center of the erase sphere
by Tianming Qu 19 Oct '22

19 Oct '22

Hi ChimeraX developers, Is there any way I can know the center of the erase sphere in CHimeraX? Best, Tianming

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Generate surface from a model using user defined color
by HONG ZHAN 17 Oct '22

17 Oct '22

Dear all, I would like to generate surface using my model but I want to keep the color as I defined. My protein contains only one chain so that when I ran Surface command, it generated surface with one color... Is there a way to generate surface to keep my defined color? Super thanks! Hong

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chimeraX clipper install
by Gutierrez, Dominique 17 Oct '22

17 Oct '22

Hello, I tried to install clipper with the popup window but it takes forever. I downloaded it directly from the website. Where do I put it .whl file? Best Regards, Dominique Gutierrez

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Re: [chimerax-users] [chimera-dev] ChimeraX pyhton script
by Elaine Meng 17 Oct '22

17 Oct '22

> On Oct 17, 2022, at 7:26 AM, Jan Hofmann via Chimera-dev <chimera-dev(a)cgl.ucsf.edu> wrote: > > To whom it may concern, > I want to write a python script to open a pdb file, then load a .xplor file in as well. After one rotation which I also want to do via the script I want to export the output file as a .png file. > Could you provide any advice to me on how to write such a script? I am having troubles loading any python script into ChimeraX. Eventually I want to use this script to batch wise output structures including guest adsorption where the guest species is introduced via the .xplor from previous analysis and the structure is provided by a .pdb file. I really would need some advice/tutorial at this stage so I would be more than happy to hear back from you. > Many thanks and kind regards, > Jan Hofmann, M.Sc. > PhD Student, Department of Chemistry > Chapman Group > Stony Brook University > jan.hofmann(a)stonybrook.edu > Office: Room 563, Chemistry Hi Jan, This is the Chimera list, maybe you wanted to send to chimerax-users(a)cgl.ucsf.edu instead? (Cc'd) Maybe it can be done at least partly with ChimeraX command script instead of a python script. If you do these steps interactively in ChimeraX, it should show the corresponding commands in the Log . A ChimeraX command script is just the same commands you would enter in the Command Line, except in a plain text file named something.cxc as explained here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc…> There is also a "forEachFile" option of the "open" command to read a ChimeraX command file and apply it to a series of input files, e.g. all the .pdb files in some folder. If you name the .xplor files to match the corresponding .pdb files, maybe you can use the $ mechanism described for that option, see: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#forEachFile> 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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How to hide a chain and overly the shown chain with another model
by McClean, Phillip 13 Oct '22

13 Oct '22

I have a .pdb file obtained from ColabFold. The model was developed with AlphaFold2 Multimer. It has two chains. How can I 1) hide only one chain and then 2) add a second model. The second model will be the visualized chain developed only on its own. I am looking for regions that might be different between the model with a second protein and by itself. I tried hide /c but that didn't work. Phil McClean

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Loading density files
by Tianming Qu 12 Oct '22

12 Oct '22

Dear Chimerax developers: I have a lot of density files, is there anyway I can load them at the same time and view then like a protein traj? Best, Tianming

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Problem reading ccp4 maps
by Luca Pellegrini 11 Oct '22

11 Oct '22

When I try to read ccp4 maps from Phenix Resolve_cryoEM into ChimeraX, I’ve started getting the following message: "MRC file is truncated. Failed reading 1 values, type int32” It’s ChimeraX version 1.5.dev202210110346 (2022-10-11)/ macOS Monterey/MacBook Pro 2021, M1 Pro. Best wishes, Luca

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Can you do convex hull on ChimeraX?
by Tianming Qu 10 Oct '22

10 Oct '22

Hi dear ChimeraX-Users and developers, Is ChimeraX available for drawing the convex hull of protein structures? Best, Tianming

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Fit in map, save new coords of map
by Nebojsa Bogdanovic 10 Oct '22

10 Oct '22

Hello, I open two maps and I fit #2 into #1. I need to save map #2 at it's new position, but there is no option "relative to model or map". By doing "volume resample #1 onGrid #1, I match the box sizes but the new position is not maintained after saving that new map. Is there any command/function I could do that with? Thank You and regards, Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University

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