- ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] Export pLDDT scores
by Tom Goddard 22 Nov '22

22 Nov '22

Hi Asmahan, The pLDDT scores for an AlphaFold prediction are in the bfactor column of the PDB atomic model file. Here is an example of lines from such a file where the value 85.53 is the pLDDT for residue 1. ATOM 1 N ASP B 1 -0.818 -36.026 -12.912 1.00 85.53 N ATOM 2 CA ASP B 1 0.545 -35.783 -13.373 1.00 85.53 C ATOM 3 C ASP B 1 0.706 -34.352 -13.882 1.00 85.53 C The bfactor is assigned to every atom. But pLDDT is only assigned for each residue and measures CA position so you might want to look at only the CA lines. $ grep CA ~/Downloads/ChimeraX/AlphaFold/prediction_14/af252_unrelaxed_rank_1_model_2.pdb ATOM 2 CA ASP B 1 0.545 -35.783 -13.373 1.00 85.53 C ATOM 10 CA CYS B 2 1.983 -32.130 -13.721 1.00 95.45 C ATOM 16 CA PRO B 3 3.029 -30.770 -17.151 1.00 93.20 C ATOM 23 CA SER B 4 6.629 -31.094 -18.066 1.00 93.36 C You can also write the values into a ChimeraX attribute file using ChimeraX commands select #1@CA save ~/Desktop/plddt.defattr attrName bfactor models #1 selectedOnly true and that file looks like the following attribute: bfactor recipient: atoms match mode: 1-to-1 /A:1@CA 56.150001525878906 /A:2@CA 53.33000183105469 /A:3@CA 53.59000015258789 /A:4@CA 59.380001068115234 documentation here https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html#attributes Tom > On Nov 22, 2022, at 7:08 AM, Asmahan Alghamdi <Asmahan.Alghamdi(a)nottingham.ac.uk> wrote: > > Dear Tom, > I hope you are well. I was wondering if there is away to export pLDDT scores of the best predicted model of a protein using ChimeraX e.g. 1.5 (which I am using in my investigations)? > > Thank you very much. > Asmahan

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Zoom over frames
by Krishnan Raman 21 Nov '22

21 Nov '22

Hi , Can I have the zoom command execute over several frames? Thanks Krish

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Re: [chimerax-users] [Chimera-users] Coloring the unit cell box
by Elaine Meng 21 Nov '22

21 Nov '22

(switching to chimerax-users address since this is all about ChimeraX, not Chimera) Sorry no, there is no linewidth setting on the unit cell outline box. However, you can "fake it" by selecting that model so that there are green outlines to show the selection, and then changing the selection-outline color and width: (1) select the outline box model, e.g. as described in the previous message by checking the selection box in the Model Panel (2) use "graphics selection" command to change the selection-outline color and thickness <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#selection> 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 18, 2022, at 9:12 AM, F.Xavier Gomis-Rüth via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Thanks a lot, Elaine, this worked indeed! > Just one final point: how can I make the linewidth larger? When I make a picture, the thin lines of the box disappear. > I understand ChimeraX interpretes these lines as a surface, I can change the colour when choosing surface in the colour blow up. > > On 18/11/22 17:49, Elaine Meng wrote: >> Hi Xavier, >> As far as I can tell, it is exactly the same in ChimeraX as in Chimera. First, make sure you aren't using a very old version of ChimeraX. I tried it in ChimeraX 1.5 release candidate (2022-11-08) just now: >> >> - open your structure that has unit cell information, e.g. 1fav >> >> - in Unit Cell tool (menu: Tools... Higher-Order Structure... Unit Cell) click Outline to show unit cell box >> >> - if you want to change box outline color, can use the same method as described below for Chimera. I wasn't able to select it by Ctrl-click, however, so instead use the selection (hand with green dot) checkbox in the Model Panel to select it, then use Actions... Color... [...]. Or, you can just click the color square in the Model Panel and use the system color chooser to change the color interactively. Screenshot: >> >> <Screen Shot 2022-11-18 at 8.48.02 AM.png> >> >> >> 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. for ChimeraX questions specifically, you may want to use the other mailing list, chimerax-users(a)cgl.ucsf.edu >> >>> On Nov 18, 2022, at 7:03 AM, F.Xavier Gomis-Rüth via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: >>> >>> Dear Elaine, >>> I am now trying to get this done in ChimeraX where there is indeed a similar option. Unfortunately, if I proceed as in the instructions >>> I do not get the cell box, in contrast with old Chimera. I also tried through the command line but unsuccessfully. >>> Am I missing something? >>> Thanks a lot in advance, >>> Xavier >>> >>> On 26/10/22 17:45, Elaine Meng wrote: >>>> Hi Xavier, >>>> You can select the box (Ctrl-click on it) and then use menu: Actions... Color... [choose color], then clear selection by Ctrl-click on blank area of window or menu Select... Clear Selection. >>>> 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 26, 2022, at 1:56 AM, F.Xavier Gomis-Rüth via Chimera-users <chimera-users(a)cgl.ucsf.edu> >>>>> wrote: >>>>> >>>>> Dear all, >>>>> is there a way in Chimera or ChimeraX to get the unit-cell box being drawn in another colour than white? >>>>> This forces the background to be dark.... >>>>> Thanks a lot in advance, >>>>> Xavier >>>>> >>> >> > > -- > <fxgr_signanew.jpg> > _______________________________________________ > 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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Re: [chimerax-users] [Chimera-users] Alphafold
by Tom Goddard 20 Nov '22

20 Nov '22

AlphaFold prediction is running fine in ChimeraX, just tested a monomer and heterodimer prediction in the ChimeraX release candidate. AlphaFold prediction is not available in the old Chimera software. You would have to give details such as the exact pasted error, the input you were running on, the ChimeraX version, and best to do that with ChimeraX menu Help / Report a Bug.... Tom > On Nov 19, 2022, at 11:38 PM, Kornelius Zeth via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear all – > > I’m using Alphafold in Chimera and I have a problem to run this properly on Colab. The people from Colab say that the error messages I get since recently are related to Alphafold developers having installed a new version. Could you please let me know what I could do to get the program running again? > > Thanks and have a nice day > > Kornelius > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users>

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Chimerax Error
by Natalie Loui 20 Nov '22

20 Nov '22

Hi all, I’m trying to visualize a capsid by using the sym command but I keep getting this error ”Assembly "1" not found, have" If you have any advice, please let me know. Natalie Loui PhD Student | Skaggs Graduate School of Chemical and Biological Sciences Email: nloui(a)scripps.edu | Phone #: (808)221-8270 Scripps Research Institute | 130 Scripps Way, Jupiter, FL 33458 | https://education.scripps.edu

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ChimeraX Render by Attribute tool
by Elaine Meng 18 Nov '22

18 Nov '22

Hi Prathvi, There is a different address for ChimeraX questions, chimerax-users(a)cgl.ucsf.edu CC'd here. You can see the currently available tools listed in the ChimeraX User Guide, and links to their pages: <https://rbvi.ucsf.edu/chimerax/docs/user/index.html> <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/render.html> ... and the dates that they were added in the ChimeraX Change Log <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> ... so yes, we just started adding Render by Attribute to ChimeraX, but you have to get a recent daily build of version 1.6, and it does not have many options yet. Only ChimeraX (not Chimera) has a command to save attributes to a file. In Chimera you have to use the GUI. In ChimeraX we are specifically trying to make commands for all or nearly all actions you can perform with the GUI. 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 18, 2022, at 4:23 AM, Prathvi Singh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Thanks once again Eric. > I have two more questions. > Is the "Render by Attribute" tool available in chimeraX because I get nothing when I run the command: ui tool show "Render by Attribute". If it isn't available, can I expect it to be added to chimeraX in the future? > Is there a command to save attributes of a residue in chimera (not chimeraX; that you covered in the previous reply) >

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cif writer broken in ChimeraX
by Pranav Shah 18 Nov '22

18 Nov '22

Hi Team, I am trying to save my coords in mmcif format to keep up with the times and I am running into the following error - ///////////////////////////////////////////////////////////////////////////////////////////////////////// AttributeError: 'SaveOptionsWidget' object has no attribute 'compute_sheets' File "/Users/ps/software/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/mmcif/gui.py", line 130, in options_string if self.compute_sheets.isChecked(): See log for complete Python traceback ////////////////////////////////////////////////////////////////////////////////////////////////////////// Admittedly I am on a nightly build of the program details of which are - version 1.6.dev202211090831 (2022-11-09) Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

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Distance between two atoms
by McClean, Phillip 17 Nov '22

17 Nov '22

Hi Everyone, I have a two chain model. I would like to determine the distance between the CD1 atom of residue 77 in chain B and the CD1 atom of residue Leu 150 in chain C. What would be the proper distance command. Thanks for the help again. Phil McClean

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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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