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Re: [Chimera-users] [chimerax-users] Automate calculation and saving of residues' structural attributes
by Elaine Meng 04 Feb '22

04 Feb '22

Hi Christian, I guess this is a Chimera question now, so I set the "reply to" to chimera-users in case this generates further messages. The following pertains to Chimera. I believe it uses the MSMS code without modification to do the actual calculation, so it might be needless work to run all this benchmarking. Nevertheless I can understand why you want to figure out the cause of any differences. (a) I would expect differences in VDW radii to be a major factor. The Chimera default radii are described/listed in the User Guide, see this and links therein: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdwrad.html> You could try assigning the MSMS-provided radii within Chimera before performing the area calculation in Chimera. See the bottom section of the help page URL above for possible ways of assigning different VDW radius values. (b) secondarily, it depends how you use the command... if you just used Chimera command "surface" it would automatically just surface the macromolecules and try to omit waters, ligands, etc. However, you can use "surfcat" command to define whatever sets of atoms you like for subsequent "surface" calculations. Chimera surface command <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/surface.html> Chimera surfcat command <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/msms.html> (c) dealing with the code is beyond my skill set, so if you still need pointers to look therein, somebody else would have to advise. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 3, 2022, at 12:33 AM, Christian Tüting via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hi All, > > Andre and I continued this conversation in private, as this was not > Chimera related anymore. > > Somehow, we have a question regarding the calculation of the of the SES > and SAS. > > In principle, I looked into the calcsurf.py file in the chimera folder, > and figured out, that this calculation is done by msms with a probe > radius of 1.4 and a density of 2 and noh. So I copied the code into my > workflow and tested this with a xyzr file, generated by the pdb_to_xyzr > shell script from msms, and got the same results, as if I am running > directly msms from command line. So far not suprisingly. > > But when we take the same pdb file, the msms code itself gives slightly > different values than chimera. Often, it's not siginificant, but Andre > benchmarked this, and sometimes the difference is more than 1.2 fold. > > > > So this let us come to the conclusion, that chimera somehow calculates a > different xyzr file, compared to what the shell script is doing. I was > not able to find the code for caluclating the xyzr file. Another > explanation is, that chimera treats the results a bit differently. msms > results ses and sas per atom, we "just" summed them per residue to get > the per residue value. But I don't think, that this is done differently > here. > > > So our questions are: > (a) is the radius definition different in chimera from what is given > with the msms software ( https://ccsb.scripps.edu/msms/downloads/; there > is a shellscript and, more importantly a text file, which defines the > radius of each atom, with a lot of special cases ). > (b) is the structure somehow "filtered" prior to surface calculation. > E.g. are waters, ions, ligands considered part of the structure, of are > they excluded, as this might introduce also some differences > (c) or can you help us find the actual code for this in chimera, than I > will be able to anwser the question myself > > Thanks in advance. > > Christian > > > >>>> André <andre.jfmdm(a)gmail.com> 01/21/22 7:06 PM >>> > Hi Elaine, > > Thank you so much for your very helpful answer! > > Yeah, Tom told me before that it wouldn't be possible to directly > calculate > SESA and relSESA with ChimeraX. So, I'll probably have to stick with > Chimera. I've just discovered the "list" command (functional in > Chimera), > and I think that with it I'll be able to easily get all the attributes > by > using the --nogui startup. > I'll work on it in the following days, then I'll come back with updates. > > Once again, thank you very much! > > Best, > André. > > Em sex., 21 de jan. de 2022 às 13:55, Elaine Meng <meng(a)cgl.ucsf.edu> > escreveu: > >> Hi André, >> Although it displays an SES, ChimeraX does not calculate SES areas, > only >> SAS areas (command "measure sasa" which also assigns a residue > attribute). >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa> >> >> For Chimera, another group had provided SES reference areas for the >> exposed state represented by G-X-G tripeptides, but I don't know of a >> similar SAS reference area set for ChimeraX that could be used to > calculate >> relative exposure, sorry. In case others are interested, the Chimera >> relative exposure calculation giving relSESA is described here: >> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfnorm.html> >> >> So depending on the importance of SESA and relSESA, you may need to > use >> Chimera, or at least some method outside of ChimeraX. >> >> In both ChimeraX and Chimera, bfactor is read from the input PDB file, > and >> phi and psi are calculated automatically for peptide/protein > structures >> when they are read in. ChimeraX atom and residue attributes: >> <https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#atom> >> <https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#residue> >> >> kdHydrophobicity is not a calculation, but a simple lookup table by > amino >> acid type. You may not need either program to "calculate" it, but it > is >> automatically assigned in Chimera. It can be assigned in ChimeraX by >> running this comand script: >> < >> > https://rbvi.ucsf.edu/chimerax/docs/user/kyte-doolittle> values along with some alternative hydrophobicity scales (lookup > tables) >> are summarized here: >> > <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.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 Jan 21, 2022, at 7:28 AM, André via ChimeraX-users < >> chimerax-users(a)cgl.ucsf.edu> wrote: >>> >>> Hi Christian, >>> >>> Thank you so much for your solution! That indeed helps a lot, since > it >> shows me how to execute ChimeraX scripts independently and directly > from >> Python! >>> >>> Now, do you know which commands I should use to calculate the > following >> structural attributes for all residues: areaSAS, areaSES, relSESA, > bfactor, >> kdhydro, phi, psi? >>> >>> I do it manually in Chimera (haven't figured out how to do the same > in >> ChimeraX yet), by following the route: Tools -> Structure Analysis -> >> Render by Attribute -> File -> Save Attributes -> Attribute to Save, > which >> allows each attribute of residues to be saved as txt files, which > contain >> the residue number and respective attribute, for all residues in the >> protein. For example, the file for areaSAS looks like this: >>> >>> attribute: areaSAS >>> recipient: residues >>> :1.B 116.71626508235931 >>> :2.B 118.39353680610657 >>> ... >>> >>> Thus, that's what I wanted to do: figure out which commands I should > use >> to get the same result as the manual route above (although it is not >> really necessary that the txt file is generated directly -- if the > needed >> information appear in the stdout_as_str string, just like in the > example >> you showed, I'd be able to parse it to a file, and the problem would > be >> solved!). >>> >>> Once again, thank you for your help! >>> >>> Best, >>> André. >>> >>> >>> >>> Em sex., 21 de jan. de 2022 às 09:56, Christian Tüting < >> christian.tueting(a)biochemtech.uni-halle.de> escreveu: >>> Hi André, >>> >>> i am pretty sure, that my solution is very crude and that there are >>> better ways of doing it (like importing chimerax in the python code >>> directly). I guess, you'll get more anwsers soon. >>> >>> I quickly wrote a script, which performs a chimerax task > independently, >>> by just running python code. >>> >>> First: a chimerax script file with the desired commands: >>> >>> script.cxc: >>> open 7ott >>> surface #1 >>> mearuse area #1 >>> exit >>> >>> Note: the exit command is needed, otherwise the subprocress will > idle in >>> the chimerax cmd line. >>> >>> >>> Second: a python script, which execute this script in chimerax and >>> fetches the output: >>> >>> test.py: >>> >>> import subprocess >>> import os >>> >>> cwd = os.getcwd() >>> >>> chimerax = > "/Applications/ChimeraX_Daily.app/Contents/MacOS/ChimeraX" >>> scriptfile = f"{cwd}/script.cxc" >>> >>> cmd = [chimerax, "--nogui",scriptfile] >>> p = subprocess.run(" ".join(cmd),shell = True,capture_output=True) >>> >>> stdout_as_str = p.stdout.decode("utf-8") >>> print(stdout_as_str) >>> >>> This just runs a subprocess and fetches the output to a string, > which >>> you can than further analyse. >>> >>> >>> Best >>> Christian >>> >>> >>> >>> Dr. rer. nat. Christian Tüting >>> >>> Kastritis Laboratory for Biomolecular Research >>> Cryo-Electron Microscopy & Computational Structural Biology >>> ________________________________________________ >>> Martin-Luther-Universität Halle-Wittenberg >>> Biozentrum, Room A.2.19 >>> IWE ZIK HALOmem NWG III >>> "Kryo-Elektronenmikroskopie an Membranproteinkomplexen" >>> Weinbergweg 22, 06120 Halle >>> tel: +49 345 5524985 >>> web (Lab): https://blogs.urz.uni-halle.de/kastritislab/ >>> web (HALOmem): https://www.halomem.de/en/ >>>>>> André via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> 01/21/22 > 1:29 >>> PM >>> >>> Hello! >>> >>> I'm working on an automated pipeline (in Python) for the structural >>> analysis of proteins. In particular, I'm using Chimera to> > areaSES, relSESA, bfactor, kdhydro, phi, psi). These files are the >>> inputs >>> of the pipeline. >>> However, currently the files are exported manually, and, for the > purpose >>> of >>> building a fully automated pipeline, it would be great to also > automate >>> this step of calculating the attributes and exporting their > respective >>> files. >>> >>> I searched a lot, and tried some ways to achieve such an automation >>> (using >>> Chimera), but nothing worked. >>> And I also considered using ChimeraX. In particular, I went through >>> ChimeraX Programming Manual ( >>> https://www.cgl.ucsf.edu/chimerax/docs/devel/index.html#) but, if I >>> understood correctly, I'd only be able to import chimerax and use > its >>> functions in the Python interpreter within ChimeraX (Tools >> > General >> >>> Shell). >>> At first, I'd like to import chimerax as a module in a Python >>> interpreter >>> outside of ChimeraX, so that manually opening ChimeraX wouldn't be >>> necessary in order to save the files with the residues' attributes. > But, >>> from some other threads in the mailing list, I found that it > wouldn't be >>> possible (right?) >>> >>> But I also found out that I could write a .py script which > calculates >>> and >>> exports the files with the residues' properties, and then run it > with >>> ChimeraX application from the command-line, something like: > *chimerax >>> --nogui myscript.py* >>> If that works, I think that my automation problem would be solved! > The >>> only >>> problem is that I really couldn't figure out the Python code to >>> calculate >>> and export the aforementioned residues' properties (I took a look in >>> ChimeraX Recipes (https://rbvi.github.io/chimerax-recipes/) but I >>> couldn't >>> find what I need, nor more detailed documentation). >>> >>> Given that, I'd like to know if anyone has done something like this, >>> and/or >>> have any guidance on how I could proceed. >>> >>> I really appreciate any help you can provide! >>> (And thanks to Tom Goddard for suggesting moving the discussion here > to >>> the >>> ChimeraX mailing list). >>> >>> Thank you so much, >>> André. >>> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu >>> Manage subscription: >>> https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users >> >> > > _______________________________________________ > ChimeraX-users mailing list > ChimeraX-users(a)cgl.ucsf.edu > Manage subscription: > https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users >

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Fwd: choose the rotation center
by Eric Pettersen 01 Feb '22

01 Feb '22

> Begin forwarded message: > > From: Yanhe Zhao <yanhezhao1990(a)gmail.com> > Subject: choose the rotation center > Date: February 1, 2022 at 1:02:12 PM PST > To: chimera-users-owner(a)cgl.ucsf.edu > > Hello there, > > I want to fixed the center for my rotation but have two questions here: > 1, how I easily read out the xyz coordinate of the point I want to use as center? > 2, as attached, what the xyz sequence here, xyz from top to bottom? > > Thanks and appreciate for your help! > Yanhe

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Location of executable local docking path
by Shreeramesh 01 Feb '22

01 Feb '22

Dear Sir, I am performing molecular docking using Autodock vina in Chimera. Could you please guide me how to operate an executable location locally? Which is the file to be loaded in the local path? I will be thankful to you for your kind help *Thanks & Regards* *Dr. Ramesh M* *B. Pharma., M.Pharma., Ph.D. (MedChem)* *Post-Doctoral Fellow (PDF) in Pharmaceutical Sciences* *Researcher ID:* https://orcid.org/0000-0003-0119-206X <https://www.portfoliobox.net/pb4/admin/#/drrameshm> *Website: *https://scholar.google.com/citations?user=VHOE1dgAAAAJ&hl=en Hyderabad, INDIA Email: shreeramesh(a)gmail.com Mob.: +91-9542200332

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Calculating correlation value between PDB and volume
by Long Gui 01 Feb '22

01 Feb '22

Dear Chimera-user group, I am using Chimera version 1.14. After I have manually place the PDB model in the volume file, I would like to calculate the correlation value between the current position of PDB file and the volume. I have used "Fit dialog" and "use simulated map" but the correlation value only displayed the optimized value after shift and rotation. I have also disabled "rotation" and "shift" but the results were the same. Because my volume contains more proteins than the PDB files, the "Fit in map" always place the PDB files into the densities corresponding to other proteins. I just want to have the correlation value between the manually placed PDB and the volume. How could I do this in Chimera? Thanks, Long Gui, Ph.D. Postdoc Researcher, Nicastro Lab University of Texas Southwestern Medical Center Long.Gui(a)utsouthwestern.edu Tel: (214)-645-1561 ________________________________ UT Southwestern Medical Center The future of medicine, today.

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"Cartoon" command unrecognized
by Dmitry Lyumkis 01 Feb '22

01 Feb '22

Dear Chimera support, I am trying to display a protein as tubes, using the “cartoon” command. I am following some of the instructions here: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style However, I get “unrecognized command” when I enter “cartoon” on the command line. Could this be a version issue? My Chimera version is 1.15 (build 42258) 2020-12-18. Best, Dmitry

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Selecting and listing all residues in a specific area
by Eunice Gwee 29 Jan '22

29 Jan '22

To whom this may concern, I have been using the Autodock Vina function on Chimera for my studies and I was wondering if it is possible to list the residues in the selected area of the protein used in docking. Thank you. With regards, Eunice

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Stereoscopic 3D with vr
by Danielson, Jacob 29 Jan '22

29 Jan '22

Hi, I have a valve index and I tried out the VR mode in chimerax. It was quite impressive, however it is less practical for in office/lab use due to space limitations. In the past we have used sequential stereoscopic viewing but this technology is getting harder to service due lack of support from manufacturers. Is there a way to view the model with a VR headset and use standard keyboard and mouse controls? I noticed there was a capability of separate left and right stereoviews in chimera but couldn't figure out how to clone the model with two cameras so that the views rotate together. Thanks, Jacob Danielson

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the problem how to show distance
by Kenji MATSUI 28 Jan '22

28 Jan '22

Dear Chimera X Thank you very much for your kind answers. I tried to find the distance between ligand(cluster14) and protein(TRP420) by referring to the tutorial, but I could not do it, so I contacted you. Detail Objective: To display the distance between cluster14 and TRP420(The area circled in yellow）. [image: image.png] I chose cluster 14 and TRP420 (shift+ctrl+click)→tool →structure Analysis →distance Refernece: Chimera tutorial *To measure distances*: ・Select two atoms – press Shift + Control + Left click on the atoms in the graphics window >> ・ Tools >> Structure Analysis >> Distances >> Create - Distance reported in graphics and new window But, error is shown. How to solve this problem? [image: image.png] [image: image.png] What else I tried. combine ligand and protein(OSBP)→But, I couldn't display. --------------------------------------------------------------------------- Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan Mail: s214903z(a)st.go.tuat.ac.jp

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the docking confidence score
by Yanhe Zhao 27 Jan '22

27 Jan '22

Greeting there, I'm doing the sequential fitting to fit 3 models to my map. The question is where I can find the docking confidence score? I did try molmap to simulate the map of one model and then use the "Fit in map" to have the correlation readout. But I'm not sure is the correlation good to describe confidence, and what I want is the score to describe overall confidence of sequential fitting not just one model. So any log file I can find to report the score of docking? Thanks and cheers, Yanhe

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Change atom size and color depending on atomic charge
by henriquecsj＠gmail.com 27 Jan '22

27 Jan '22

Hi! I was wondering if it is possible to iteratively change each atom's size and color relative to, let's say, the atomic charge computed by a quantum chemistry package. This is to help the reader understand changes happening between the ground and excited states of the molecules. Cheers!

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Re: [Chimera-users] A specific request for visualizing a model in Chimera
by Elaine Meng 24 Jan '22

24 Jan '22

Hi Qian, I don't know of any way to "smooth" those junctions between coil and helix/strand, but I believe that many people 3D print the ribbons and they have not been a problem as long as you make the overall ribbon thick enough, e.g. with the "struts" command or Ribbon Style Editor. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/struts.html> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribb…> Although I've seen it in other programs, Chimera does not have an option to smoothly taper the ribbon between coil and helix/strand. In general we recommend sending questions to the mailing list CC'd here, but only if you are not including private data. In this case I don't think it matters what protein structure is involved, so it is a general question ... to which I don't have an answer but maybe others on the list will. I did not include your session in this public message. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jan 24, 2022, at 9:37 AM, Qian Zhang <qzhang30(a)gmail.com> wrote: > > Dear Dr. Meng, > I hope you are doing well. I emailed you guys about 4 years ago and got someone to help me write a script to do this but I can't find that script anymore. > > What I wanted to achieve is to 'smooth' out the connections between random coil vs. helixes or vs. sheets. Not like the one shown in this picture that the coil just inserts into the start of the sheet. > > > I've attached a session file (v.1.15) that can be used as a starting point. > > The purpose of this is to 3D-print this into a structure and I am afraid all those non-smooth connections are going to break off. > > Please let me know. > Qian >

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Fwd: Model protein with coenzyme
by Eric Pettersen 24 Jan '22

24 Jan '22

> Begin forwarded message: > > From: Xinxin <zhuxinxin17(a)mails.ucas.edu.cn> > Subject: Chimera bug report submission > Date: January 22, 2022 at 4:36:13 AM PST > To: chimera-bugs(a)cgl.ucsf.edu > > The following bug report has been submitted: > Platform: windows > Chimera Version: 2022 > Description > I want ask a question, could the Chimera model protein with coenzyme? And how to perform? > Thank you very much.

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Fwd: Making copies of an atomic structure and fit in the map
by Eric Pettersen 21 Jan '22

21 Jan '22

> Begin forwarded message: > > From: "Sen, Anindito" <andysen(a)tamu.edu <mailto:andysen@tamu.edu>> > Subject: Making copies of an atomic structure and fit in the map > Date: January 20, 2022 at 4:08:11 PM PST > To: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu <mailto:chimera-users-bounces@cgl.ucsf.edu>> > > > Dear All, > > What will be the correct complete command (sym) for making copies of an atomic structure and symmetrize them to dock in the relevant density map. > > 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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Automate calculation and saving of residues' structural attributes
by André 21 Jan '22

21 Jan '22

Hello! I'm working on an automated pipeline (in Python) for the structural analysis of proteins. In particular, I'm using Chimera to calculate and save to .txt files some structural properties of residues (namely: areaSAS, areaSES, relSESA, bfactor, kdhydro, phi, psi). These files are the inputs of the pipeline. However, currently these files are exported manually, and, for the purpose of building a fully automated pipeline, it would be great to also automate this step of generating the attributes and exporting their respective .txt files. I searched a lot, and tried some ways to achieve such an automation, but nothing worked (if you'd like to know about these (unsuccessful) ideas that I had, I can share them in next messages). Given that, I'd like to know if anyone has done something like this, and/or have any guidance on how I could proceed, if that's something possible at all to be done with Chimera (or even ChimeraX). I really appreciate any help you can provide! Thank you so much, André.

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Question: How ro show the H-bond
by Kenji MATSUI 17 Jan '22

17 Jan '22

Dear Chimera company Thank you for always answering my questions so carefully. Thank you for allowing me to use your software. I am Japanese, so I hope you will understand that there are some inappropriate expressions. I would like to ask you one question. I entered the data as per the manual. However, the hydrogen bond did not show up. What should I do? The figure of Parameters [image: image.png] The result of showing [image: osh4,ID 223-230 .png] Details on how to do it *Display interactions between ligand and protein.* 1.Favorites→Model Panel→group/ungroup( Go down at close.) [image: image.png] 2.Favorite→Command line: combine #0.1,0.2 →select combination at model Panel [image: image.png] 3.rename 4.Select →Residue→ LIG or command: select :LIG 5.Tool→Surface/Binding Analysis→ Find H Bond [image: image.png] Check three points 1."Only find H-bonds..." e.g. "with at least one end selected". 2. "If endpoint atom hidden, shown endpoint residue" or else it will not show all of the H-bonds it finds 3.Write information to reply log Apply→OK --------------------------------------------------------------------------- 松井健治東京農工大学大学院工学府産業技術専攻修士〒184-8588 東京都小金井市中町2-24-16 Mail: s214903z(a)st.go.tuat.ac.jp Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan Mail: s214903z(a)st.go.tuat.ac.jp

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zoom on the selection after orientation of the selected object
by Enrico Martinez 16 Jan '22

16 Jan '22

Dear Chimera users! I am using ChimeraX for the visualization of protein-ligand interactions comparing two different pdb structures A - ensemble for doclong; B- X-ray pose: open A.pdb open B.pdb' match #2 to #1.1 # close all docking poses with the exemption of the first pose: close #1.2-end view wait # hide the protein from X-ray pose keeping only ligand for visualisation: hide #2 & protein cartoon hide #2 & protein surface hide #2 & protein #orient view on the model 1.1 and zoom closer view #1.1 orient; turn z 90 zoom 1.5 wait The problem is that when I use zoom 1.5 after view #1.1 it hides completely the representation for the molecule on the current GUI. Otherwise, it works fine if I center view on the both A and B: view orient; turn z 90 zoom 1.5 How could I zoom the screen properly after orientation of the view on the first molecule? Many thanks in advance! Enrico

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Re: [Chimera-users] ChimeraX in no-gui mode: visualisation of protein-ligand interactions
by Enrico Martinez 15 Jan '22

15 Jan '22

Thank you Elaine! I played with it today and it looks great! Some additional questions (sorry for it at the first time the thing seems abit tricky): 1)may I automatically place the 2D label on the top left corner of the screen instead of manually defining its X-Y using xpos ypos? 2dlab create title text \"name_of_the_complex" color red font gothic xpos .04 ypos .99 size 40 2) assuming that I open 2 molecules in the same session open A.pdb open B.pdb then I remove all the models with the exemption of the first close #1.2-end How could I superimpose A to B (align the structures) and then hide cartoon from B.pdb (keeping only ligand) ? 3) Is there any possibility to put your signature on the screen-shot? like "Observed by Enrico Martinez" ? :-) Many thanks in advance!! Enrico сб, 15 янв. 2022 г. в 00:11, Elaine Meng <meng(a)cgl.ucsf.edu>: > > See the "color" command for coloring the ligand, and "set" or "graphics" for coloring the background, and "label" (or "2dlabels" but that usually requires you to position them interactively) for labeling. All of these are included in the "making images" page I mentioned near the end of my previous message. > Best, > Elaine > > > > > On Jan 14, 2022, at 3:03 PM, Enrico Martinez <jmsstarlight(a)gmail.com> wrote: > > > > Thank you very much, Elaine! > > I really like ChimeraX and it looks so great for me with all of those > > presents :-) I will look for the details regarding the options. Just a > > few addtional questions regarding customizing representation of > > protein-ligand interactions using ghost preset: > > In particular: I would like to color ligand (in orange??) > > To add labels (like Try-193) on the displayed side-chains around the ligands > > To change background from black to indigo! > > :-) > > Many thanks in advance! > > Cheers > > Enrico > > > > пт, 14 янв. 2022 г. в 23:48, Elaine Meng <meng(a)cgl.ucsf.edu>: > >> > >> Hello, > >> It isn't my area of expertise, but I don't think you can save images in nogui mode except with Linux OSMesa. > >> > >> As for your other questions, which commands do certain things... > >>> may you suggest some commands that I may introduce into my batch file to > >>> 1) delete all models from the multi-model pdb file with the exemption > >>> of the first model. > >>> 2) switch from cartoon to surface representation of the protein > >>> 3) visualize protein-ligand non-covalent interactions in the current model > >> > >> > >> (1) close submodels except for first one. Maybe something like command: > >> > >> close #1.2-end > >> > >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/close.html> > >> > >> (2) switch from ribbon to molecular surface of protein. Well, you probably want to do some coloring and other stuff besides just hiding ribbon and showing surface, which could be something like commands: > >> > >> ~ribbon > >> surface protein > >> > >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html> > >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html> > >> > >> Or you could try a surface-showing preset, e.g. > >> > >> preset ghost > >> > >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/preset.html> > >> > >> (3) depends what you mean by showing interactions (lines? selection? coloring?). You should take a look at commands "contacts" and/or "hbonds" and choose the options that give what you want. > >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html> > >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/hbonds.html> > >> > >> You will need to spend some time trying the commands since there are an infinite number of possibilities for combinations of coloring and display styles and lighting and graphics effects. See also commands "lighting" and "graphics" and "set" > >> > >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html> > >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html> > >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/set.html> > >> > >> ... and the "making images" page with several relevant commands > >> <https://rbvi.ucsf.edu/chimerax/docs/user/images.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 Jan 14, 2022, at 2:17 PM, Enrico Martinez via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > >>> > >>> Dear Chimera's users! > >>> First I wish Happy New Year to everyone! > >>> I am just switching from Chimera to ChimeraX that I am going to use in > >>> no-gui (batch) mode to prepare screen shots of protein-ligand > >>> interactions based on the protein-ligand docking poses. Basically I am > >>> loading a pdb file of the complex (consisted of protein and ligand in > >>> multi-model format) from the terminal of my macOSX. I have a template > >>> for a batch file created in the bash script on the fly, that I used 2 > >>> years ago with an early version of ChimeraX. > >>> > >>> # a batch file for chimeraX > >>> printf "open ${pdb} > >>> view; zoom 1.0; turn x 90; turn z -80; > >>> wait > >>> # options for appearance > >>> preset 'overall look' publication > >>> # set bg powder blue > >>> set silhouettes t; set silhouetteColor indigo; set silhouetteDepthJump 0.02 > >>> > >>> # make info of the screen > >>> 2dlab create title text \"${pdb_name}\" color red font gothic xpos .04 > >>> ypos .92 size 35 > >>> > >>> # options for light > >>> light depthcuestart .4 depthcueend .8; lighting full intensity 1.4 > >>> shadows true qualityOfShadows finer > >>> > >>> save image ${structure}/${pdb_name}.png format png width 800 height > >>> 600 supersample 4 transparentBackground false > >>> wait > >>> exit" > chimeraX.${pdb_name}.cxc" > >>> > >>> then I use it directly in terminal as > >>> chimerax-daily chimeraX.${pdb_name}.cxc" > >>> > >>> may you suggest some commands that I may introduce into my batch file to > >>> 1) delete all models from the multi-model pdb file with the exemption > >>> of the first model. > >>> 2) switch from cartoon to surface representation of the protein > >>> 3) visualize protein-ligand non-covalent interactions in the current model > >>> > >>> Yours with thanks > >>> Enrico > >> > > >

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ChimeraX in no-gui mode: visualisation of protein-ligand interactions
by Enrico Martinez 15 Jan '22

15 Jan '22

Dear Chimera's users! First I wish Happy New Year to everyone! I am just switching from Chimera to ChimeraX that I am going to use in no-gui (batch) mode to prepare screen shots of protein-ligand interactions based on the protein-ligand docking poses. Basically I am loading a pdb file of the complex (consisted of protein and ligand in multi-model format) from the terminal of my macOSX. I have a template for a batch file created in the bash script on the fly, that I used 2 years ago with an early version of ChimeraX. # a batch file for chimeraX printf "open ${pdb} view; zoom 1.0; turn x 90; turn z -80; wait # options for appearance preset 'overall look' publication # set bg powder blue set silhouettes t; set silhouetteColor indigo; set silhouetteDepthJump 0.02 # make info of the screen 2dlab create title text \"${pdb_name}\" color red font gothic xpos .04 ypos .92 size 35 # options for light light depthcuestart .4 depthcueend .8; lighting full intensity 1.4 shadows true qualityOfShadows finer save image ${structure}/${pdb_name}.png format png width 800 height 600 supersample 4 transparentBackground false wait exit" > chimeraX.${pdb_name}.cxc" then I use it directly in terminal as chimerax-daily chimeraX.${pdb_name}.cxc" may you suggest some commands that I may introduce into my batch file to 1) delete all models from the multi-model pdb file with the exemption of the first model. 2) switch from cartoon to surface representation of the protein 3) visualize protein-ligand non-covalent interactions in the current model Yours with thanks Enrico

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Re: [Chimera-users] Question on pdb to mrc
by Elaine Meng 14 Jan '22

14 Jan '22

> On Jan 13, 2022, at 6:54 PM, Guan, Lan <Lan.Guan(a)ttuhsc.edu> wrote: > > Dear Elaine, > > I try to generate a reference model from crystal structure pdb file for cryo-EM particle alignment. > > I can get the map by “molmap #1 6”; #1 = my pdb file id; 6 = resolution I want to get in the output model. > > After imported into cryosparc, I can not use it. Error “ Cubic volumes only”. My question is how to change this Molmap output into a cubic volumes in Chimera? > I would appreciate for your input. > > Lan Hi Lan, (CC'ing chimera-users(a)cgl.ucsf.edu which is the address recommended for asking questions since others may have better answers) I don't know what cryosparc means by "cubic volumes only". My only guess is that maybe you did not save the molmap map correctly. The molmap command should make a new model which is the map, and then you can save the map with the Volume Viewer tool's File menu, or with the "volume" command. Saving data: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html> Volume Viewer menu (File... Save map as...) <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/vol…> volume command saving options <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output> Or, maybe cryosparc does not read any of the map formats that Chimera can write (listed in the link above). 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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Re: [Chimera-users] Protonating Histidine Residues using Chimera
by Elaine Meng 13 Jan '22

13 Jan '22

> On Jan 13, 2022, at 10:54 AM, Joshi, Keya <keyajoshi1996(a)ku.edu> wrote: > > Hello Prof. Meng, > Hope you are doing well and staying safe. My name is Keya Joshi. I am a second year PhD student in the department of Computational Biology at the University of Kansas. I am trying to use Chimera to protonate Histidine residue 816 in chain B. But I have no idea about how to do this using Chimera. > Can you please help me with this? > > With Regards > Keya Joshi Hi Keya, I hope you are well, too! (CC-ing the chimera-users(a)cgl.ucsf.edu address which is recommended for asking Chimera questions unless you are sending data that needs to remain private) In the structure that you sent, histidine 816 in chain B is already protonated (already has hydrogens). However, it is protonated to the neutral state. Maybe you meant you wanted one more hydrogen to make it the positively charged state. Two ideas: (1) You can just use the AddH tool (menu: Tools... Structure Editing... AddH) or "addh" command to add hydrogens to the whole protein. See help for information about the options: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addh/addh.html> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/addh.html> On the PDB file that you sent, the default options of AddH (= simply using command "addh" without any other options) do add a hydrogen to 816 in chain B to put it in the positively charged state, but it also adds lots of other hydrogens including on carbons and on all of the other residues. I don't know if that is a problem for you, or whether it is an improvement on the original structure. Of course you can delete some hydrogens afterward, but it depends what you want. (2) To just add one hydrogen to that sidechain nitrogen, instead use Build Structure (menu: Tools... Structure Editing... Build Structure), and in that tool change from "Start Structure" to "Modify Structure". Select (Ctrl-click on) the nitrogen of His 816 that needs the hydrogen. Selection is shown with a green outline on that atom. Then in the tool, you want that selected atom to be N (stay the same element) but with 3 bonds and trigonal geometry as shown in the screenshot. Also as shown in the screenshot, choose the option to leave the residue name unchanged. Then click Apply to add that one hydrogen. ... after I click Apply it looks like this: about selection: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> Build Structure tool: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.…> You can find Chimera features using Chimera menu: Help... Search Documentation, e.g. to search for "hydrogens" or "building" Our newer program ChimeraX also has an "addh" command. 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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Autodock Vina plugin
by Enrico Martinez 12 Jan '22

12 Jan '22

Dear Chimera Users, First Happy New Year to you and your families! I am trying to perform protein-ligand docking using UCSF Chimera 1.16v installed on my iMAC Big Sur. Using the pdb of the receptor and mol2 of the ligand (that I have already tested with VINA 1.2.3!) I got the following error: Model 1 (receptor.pdb) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. No SEQRES records for receptor.pdb (#1) chain A; guessing terminii instead Chain-initial residues that are actual N terminii: #1 SER 1.A Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: Chain-final residues that are not actual C terminii: #1 THR 304.A 278 hydrogen bonds Removing spurious proton from 'C' of #1 THR 304.A Hydrogens added Wrote test.receptor.pdb into /Users/gleb/Desktop/docking_tuto adding gasteiger charges to peptide Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/vina/ws.py", line 395, in prepareReceptor execfile(scriptPath, d) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/AutoDockTools/Utilities24/prepare_receptor4.py", line 172, in <module> delete_single_nonstd_residues=delete_single_nonstd_residues) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/AutoDockTools/MoleculePreparation.py", line 533, in __init__ version=version, delete_single_nonstd_residues=delete_single_nonstd_residues) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/AutoDockTools/MoleculePreparation.py", line 140, in __init__ self.addCharges(mol, charges_to_add) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/AutoDockTools/MoleculePreparation.py", line 226, in addCharges chargeCalculator.addCharges(mol.allAtoms) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/MolKit/chargeCalculator.py", line 80, in addCharges babel.assignHybridization(atoms) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/PyBabel/atomTypes.py", line 127, in assignHybridization a.babel_atomic_number = self.get_atomic_number(a.babel_type) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/PyBabel/atomTypes.py", line 103, in get_atomic_number (name,_name) ) ValueError: Could not find atomic number for Hn Hn Receptor preparation for AutoDock Vina failed; please look in Reply Log to see error messages.cannot prepare receptor for AutoDock Vina; please look in Reply Log and/or run Chimera with --debug flag to see errors. So here are my questions: 1) May this error be related to the version of OSX installed on my imac (I can not run MGL tools on the Big Sur for instance) ?? 2) Alternatively may I use the ADT scripts integrated in the Chimera like prepare_receptor4.py for my scripting purposes (outside of the UCSF Chimera) on the same iMAC machine ? Many thanks in advance! Cheers Enrico

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Error on installation on a student's computer
by Kenward Vaughan 12 Jan '22

12 Jan '22

Hello all, As usual I have my students installing Chimera as part of their continuing adventure in organic chemistry, but have one of them reporting an error on attempted startup after installation. So far I have little information (we haven't started classes yet--next week--but she has sent the error message obtained. It is apparently on Windows. I suggested that she try starting from the command line to do the debug run, but this is from a distance at this time and I don't know how savvy she is with such stuff. Is there enough information in just the number noted by this message for someone to know what might be happening with her setup? Many thanks, and cheers! Kenward -- In a completely rational society, the best of us would aspire to be _teachers_ and the rest of us would have to settle for something less, because passing civilization along from one generation to the next ought to be the highest honor and the highest responsibility anyone could have. - Lee Iacocca Any fool can know. The point is to understand. - Albert Einstein

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Problem with the app
by Nicola De Trino 11 Jan '22

11 Jan '22

I have download the chimera-1.16-win64.exe <https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=win64/c…> for Windows 64 bit. I have installed but when i try to launch the program, it appears an error message : *chimera exited abnormally; the exit code was: -1073731819. * I try to install again the program but same result. I don't know how to fix the problem. <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> Mail priva di virus. www.avg.com <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> -- ------------------------ Indirizzo istituzionale di posta elettronica degli studenti e dei laureati dell'Università degli Studi di TorinoOfficial University of Turin email address for students and graduates

2 2

Convenient way to move 2D labels around
by Prathvi Singh 10 Jan '22

10 Jan '22

Hi Elaine, Is there a convenient way (a keyboard or mouse shortcut) to move 2D labels around once the 2D labels window has been closed? Thanks -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Model placement side by side
by George Tzotzos 07 Jan '22

07 Jan '22

Hi, Having superimposed 4 structures using MatchMaker, is there a way to view the aligned structures in a window grid? Moving them manually after superimposition is not optimal. Thanks in advance for any suggestions and best wishes for 2022

2 1

Introduce a-helices into protein structure ab initio
by Chara Spanou 06 Jan '22

06 Jan '22

Hello chimera-users, I would like to introduce a-helices into my protein structure ab initio. Is it possible to do this with chimera? Another option that I have is to take a-helical pieces of sequence from a different model and introduce these into the desired model. Would that be more feasible? There is a chance I also need to introduce loops and turns ab initio to best localize the introduced a-helices within my protein structure. Can you please indicate how can a chimera user build all this ab initio? Thank you in advance for your time and help, Chara SpanouPhD studentUniversity of Cologne

2 2

report rotate and shift value in MatchMaker
by Yanhe Zhao 06 Jan '22

06 Jan '22

Greeting there, Happy New Year! How can find the rotate and shift value after I done the 'MatchMaker' in Chimera? Thanks and regards, Yanhe

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Question: PDB file creation
by Kenji MATSUI 06 Jan '22

06 Jan '22

Dear Chimera company Thank you for allowing me to use your software. I am Japanese, so I hope you will understand that there are some inappropriate expressions. I would like to ask you one question. I would like to know how to overlay the docked protein (osh4)-ligand (cholesterol) complex (the gray one in the figure) and the complex on the PDB. [image: image.png] Aim I would like to know how well the docked data matches the data in the PDB. Methods I have tried I did it based on the following link from Chimera. https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matcha… Thank you for your cooperation. --------------------------------------------------------------------------- 松井健治東京農工大学大学院工学府産業技術専攻修士〒184-8588 東京都小金井市中町2-24-16 Mail: s214903z(a)st.go.tuat.ac.jp Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan Mail: s214903z(a)st.go.tuat.ac.jp

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report rotate and shift in MatchMaker
by Yanhe Zhao 05 Jan '22

05 Jan '22

Greeting there, How can find the rotate and shift value after I done the 'MatchMaker' in Chimera? Thanks and regards, Yanhe

1 0

Opening .py files
by Henry Shook 04 Jan '22

04 Jan '22

Chimera User Support, I'm working on dockprepping the sars-2 main protease and whenever I try and save it as a .py file, I can't open it from sources other than the saved session I wrote. Whenever I try and open it from a dropbox or my finder, I get the message: Error while processing /Users/8642165/Desktop/Research/DC AP Research /[7l0d]DOCKPREPPEDFINAL.py: File "[7l0d]DOCKPREPPEDFINAL.py", line 1 @<TRIPOS>MOLECULE ^ SyntaxError: invalid syntax File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 1325, in _openPython loadFunc(sandboxName, fileName, f) See reply log for Python traceback. Is there any way that I can fix this problem? Thanks, Henry Shook

2 1

Helix Display Artefact
by Sebastian Guettler 28 Dec '21

28 Dec '21

Dear Chimera users, I have a problem with what I think is some sort of a helix display artefact is UCSF Chimera (including the latest release, 1.16). I attach an image. In cartoon display, the helix appears turned inside out for the last turn. It is displayed normally in ChimeraX and PyMol, and the display problem is independent of the secondary structure assignment algorithm (dssp, ksdssp, Stride). Any suggestions on how to solve this issue are welcome. Thank you, Sebastian --------------------------------------------- Sebastian Guettler, PhD Team Leader The Institute of Cancer Research (ICR) Divisions of Structural Biology and Cancer Biology London, UK --------------------------------------------- [cid:image001.jpg@01D7FC0A.1ED3ABA0] The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

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Blank screen after MD simulations
by Sri Oruganty 28 Dec '21

28 Dec '21

Hello, I am a senior in high school, and I was interested in learning about proteins and mutations. I download Chimera to run MD simulations on a specific protein, but not all the frames are loading. After the frame number gets to a certain point (i.e. 14) every subsequent frame is completely blank. Why is this happening? Best regards, Srigouri Oruganty Pronouns: She, her, hers sri.oruganty(a)gmail.com (610)-207-6325

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Problem related to the "Near" atom in the "Adjust Torsions" tool of UCSF chimera
by Prathvi Singh 27 Dec '21

27 Dec '21

Hi Elaine, I have one more query. I have a residue (its ID is #0:140.a) in a protein model. I want to change the torsion angle between its backbone N, backbone C-alpha, sidechain C-beta & sidechain C-gamma. In order to do that, I execute the following command: rotation 1 :140.a@CA,140.a@CB The execution activates the torsion & lists it in the "Adjust Torsions" tool. However, I have noticed that the "near" atom in the "Adjust Torsions" tool is sometimes assigned to backbone N & other times is assigned to backbone C. This is messing up my calculations. Is there a way to fix the "near" atom to backbone N so that it does not change to backbone C? Thanks again -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Move models around independent of each other in Chimera X
by Prathvi Singh 24 Dec '21

24 Dec '21

Hi, First of all, thank a million to the chimera X development team for incorporating the drag & drop feature in chimera X. I really missed it in chimera. However, after opening two models in the same window, I am unable to find a way to move/rotate model-1 in such a way that it does not move/rotate model-2. I could do this in chimera by unchecking the box for model-2 but when I do the same in chimera-X, it doesn't seem to work. Also, I am unable to find a way to disable depth cueing in chimera X. Please help. Thank you -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Fwd: Chimera bug report submission
by Eric Pettersen 22 Dec '21

22 Dec '21

> Begin forwarded message: > > From: Kenji Matsui <s214903z(a)st.go.tuat.ac.jp> > Subject: Chimera bug report submission > Date: December 19, 2021 at 11:33:41 PM PST > To: chimera-bugs(a)cgl.ucsf.edu > > The following bug report has been submitted: > Platform: windows_x86_64 > Chimera Version: 1.16 > Description > I would like to see the interaction between the ligand and the protein, but I was not able to display it in the way described in the tutorial. How can I do that? > > Method > select →ligand > > Tool Structure analysis Find H-bond Line length 3.0 Å > > check Relax H-bond ~, Only find, Include intera-molecular, Include intra-residue > > apply →OK > File attachment: osh4,OSW-1220.py

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1.16 release
by Eric Pettersen 20 Dec '21

20 Dec '21

Chimera production release 1.16 is now available <https://www.cgl.ucsf.edu/chimera/download.html>. This will be the last release to support Windows 7. See the release notes <https://www.cgl.ucsf.edu/chimera/docs/relnotes/1.16.html> for what's new. --Eric Eric Pettersen UCSF Computer Graphics Lab

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Re: [Chimera-users] .dae export for ChimeraX
by Tom Goddard 19 Dec '21

19 Dec '21

Hi Byrne, Thanks for the info about exporting models for iOS. Glad you found a way to export a virus model from ChimeraX suitable for use in iOS apps made with Xcode. The STL format is just a list of triangles, each with 3 vertex (x,y,z) coordinates, used mostly for 3D printing. It does not have vertex normal vectors which are used to give smoother lighting. In the future maybe ChimeraX will directly export Collada (*.dae) files and you will be able to export a usable model without running it through Blender. As I mentioned before we support GLTF but not Collada currently. Our ChimeraX efforts are mostly to help researchers analyze molecular structures so adding this does not have highest priority. Unfortunately there are hundreds of feature requests we do not have time to implement with our limited funding. Tom > On Dec 18, 2021, at 9:34 AM, Byrne Pedit <bpedit(a)comcast.net> wrote: > > Hello again Tom, > > A follow-up follow-up. After extensive testing I have found a useable workflow from ChimeraX to iOS. Of course iOS apps may utilize PDB viewers, this is for folks who may want to incorporate models, in customized ways, into SceneKit for manipulation. > > ChimeraX ––> STL ––(graphics editor)––> DAE ––Xcode––> SCN > > • In Chimera > – reduce polys as much as possible* > – export individual elements, e.g. chains, if you want individual control (materials, etc) > • In a graphics editor: > – eliminate polygonal faceting of STL files > - Blender, check Auto Smooth in addition to toggling on Smooth Shading > - Cinema 4D, add a phong tag > – recenter if desired, add additional elements > > *You might want to add surfaces to your reducing file-size tutorial. In the model below, the spike's resolution was set to 7, gridSpacing 3. You also need to click Hide for Atoms and Cartoons; otherwise they will severely bloat the file even though not seen. The entire file size of this SARS-CoV-2 model, as used by iOS, is 1.2 Mb (all but one of the spikes are all clones). > > Thanks again for the help, > > Byrne > > > > > > >> On Dec 3, 2021, at 11:00 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Hi Byrne, >> >> Thanks! So Blender can convert GLTF to Collada. The ChimeraX GLTF is binary and Collada is all text, so no surprise that the file size is much larger. If we add Collada support it would be produced directly from the ChimeraX scene, not converting from GLTF. But we have hundreds of new feature requests so I don't think Collada output is likely to be added soon, unless a funded project needs it. >> >> Tom >> >>> On Dec 3, 2021, at 9:48 AM, Byrne Pedit <bpedit(a)comcast.net <mailto:bpedit@comcast.net>> wrote: >>> >>> Hi Tom, >>> >>> A follow-up for future reference. Blender, the one recommendation I found on StackOverflow, is indeed capable of converting GLTF to DAE. But the conversion bloats the files by as much as 10x! In addition, the hierarchy is only partially preserved. I tried an on-line converter with even less satisfactory results. So I think this pathway is a bust. This might serve as a fair warning for ChimeraX developers to avoid an internal conversion from GLTF if introducing a DAE export option. >>> >>> >>> Byrne >>> >>> >>> >>> >>>> On Dec 2, 2021, at 2:22 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >>>> >>>> Hi Byrne, >>>> >>>> I agree, OBJ and STL are very limited compared to Collada and GLTF. OBJ is supported by almost every 3D model program and STL is commonly used for 3D printing (single color) which is why they are in ChimeraX. GLTF is definitely the best option in ChimeraX for your case. >>>> >>>> There appear to be lots of programs that convert GLTF to Collada and the other direction too. But I have not tried any of them so don't have any recommendation. Let us know if you find one that works well -- other ChimeraX users may have the same need. >>>> >>>> A major stumbling block exporting 3D models from ChimeraX (or Chimera) is that they use vertex colors, while most of the non-biology 3D model world uses texture colors, and will simply ignore vertex colors losing all your color information. That example I linked to in the last email describes a relatively new ChimeraX feature to export texture colors (for limited cases, e.g. discrete colors only). >>>> >>>> Another common problem exporting molecular models for use in other software is that the file size and number of triangles is too large for the application that you want to use them in, often tens of millions of triangles or hundreds of Mbytes to Gbytes in size. The example also shows how to tell ChimeraX to limit the number of triangles. >>>> >>>> https://www.rbvi.ucsf.edu/chimerax/data/texture-may2021/export_3d.html <https://www.rbvi.ucsf.edu/chimerax/data/texture-may2021/export_3d.html> >>>> >>>> Tom >>>> >>>> Model from gltf export from linked ChimeraX example >>>> >>>> <spike.png> >>>> >>>> >>>>> On Dec 2, 2021, at 2:04 PM, Byrne Pedit <bpedit(a)comcast.net <mailto:bpedit@comcast.net>> wrote: >>>>> >>>>> Hello Tom, >>>>> >>>>> Thanks for the response. I tried the GLTF export, not recognizable by Xcode (the development platform for iOS and Mac OS). The only ChimeraX file options I’ve found to be openable are OBJ and STL. These are, however, problematic and unusable. >>>>> >>>>> But your hint of using GLTF as an intermediary offers an avenue for exploration, it’s not a format I’ve used. I see it supports scene graph hierarchy, absent with OBJ and STL( exported from ChimeraX anyway) so this is promising. Now to find a converter. >>>>> >>>>> The GLTF export link is informative, it may help further refine my approach. Interestingly, the molecule you’ve chosen for demo purposes appears to be the one, or a variant thereof, I’ve been testing with! >>>>> >>>>> Thanks again, >>>>> >>>>> Byrne >>>>> >>>>> >>>>>> On Dec 2, 2021, at 12:30 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >>>>>> >>>>>> Hi Byrne, >>>>>> >>>>>> We have long been interested in adding Collada format export of scenes from ChimeraX. Here is the feature request for that >>>>>> >>>>>> https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/485 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/485> >>>>>> >>>>>> But our scene export in ChimeraX has focused on GLTF format, as that has been the most requested. Here is an example showing GLTF export from ChimeraX (including texture colors). >>>>>> >>>>>> https://www.rbvi.ucsf.edu/chimerax/data/texture-may2021/export_3d.html <https://www.rbvi.ucsf.edu/chimerax/data/texture-may2021/export_3d.html> >>>>>> >>>>>> ChimeraX also exports OBJ, STL, X3D, VTK as shown in the save command docs >>>>>> >>>>>> https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#formats <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#formats> >>>>>> >>>>>> Can you make use of GLTF files? If not, a quick solution might be to convert ChimeraX GLTF files to Collada with third-party software. >>>>>> >>>>>> Tom >>>>>> >>>>>>> On Dec 2, 2021, at 10:41 AM, Byrne Pedit via Chimera-users <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote: >>>>>>> >>>>>>> ChimeraX is awesome and definitely superior to the original but for the inability to export as .dae (Collada). Is that possibly on the to-do list? This is important for those of us (just me?) writing interactive molecular apps for devices. It is the only satisfactory path I’ve found between a PDB file and SCNNodes/Scenes in iOS. (See the iOS app ‘BioMole’, free, if interested in an application.) >>>>>>> _______________________________________________ >>>>>>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>>>>>> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >>>>>>> >>>>>> >>>>> >>>> >>> >> >

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Selection command for atoms in different models
by Woodbrey Anne 14 Dec '21

14 Dec '21

Hi, Is there a way to select residues from 2 different models using a single line of command? For example, I want to select residues 230 and 260 of Model 0 and residues 232 and 262 of Model 1. I then want to display the side chains, color magenta, then color by heteroatom. This is what my current (annoying) workflow is: select #0:230,260 Actions --> Color --> Magenta Actions --> Color --> By heteroatom select #1:232,262 Actions --> Color --> Magenta Actions --> Color --> By heteroatom I know I can do the following instead: disp #0:230,260 color magenta #0:230,260 color byhet #0:230,260 Repeat for #1:232,262 ...but it doesn't really save any time. I want to select all 4 residues at once without having to ctrl + shift + click on them all. Please tell me there's a way! Thank you, Annie

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calculating radius of gyration
by Elaine Meng 14 Dec '21

14 Dec '21

> On Dec 14, 2021, at 11:10 AM, Simon.Chapman <simon.chapman(a)open.ac.uk> wrote: > > Hello again Elaine. All going very well with Chimera, and I've introduced the software to some more of mt students. > > But, is there a way to plot radius of gyration from the simualtion data? I would have thought somehow the RMSD over time should allow that? > > Best wishes Hi Simon, Thanks for introducing others to Chimera! I'm not the expert on this topic, so I had to consult with others to answer this question. Just as a reminder, it's recommended to send questions to chimera-users(a)cgl.ucsf.edu (CC'd here) unless what you are sending needs to remain private. I don't know everything (surprise!) or I might not understand your question as well as somebody else does. RMSD compares different sets of coordinates, so I don't think that gets you anything like the radius of gyration of a single set of coordinates. There are some scripts to calculate radius of gyration on the Chimera Python Scripts page: <https://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts> 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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Translate onto the X-axis
by Yasser Almeida 14 Dec '21

14 Dec '21

Hello, I have a complex of two proteins that I want to align to the X-axis. Specifically, I want to define a vector between the COMs of each protein, and then translate the whole system so that the vector is on the X-axis, where the COM of one protein is on the cartesian origin [0, 0, 0] and the other COM is in [+X, 0, 0]. How can I achieve this with Chimera? Thanks in advance, Yasser

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Save multiple fitted maps in Chimera
by Huabin Zhou 13 Dec '21

13 Dec '21

Dear Chimera team and users, I am trying fit hundreds of protein density maps into a tomogram by manually adjusting their positions. After the placement, I found I can't save all the maps together in a single mrc file. Is there anyway to do so? Or is there a way to extract the relative orientations of the individual models? Thank you! Best, Huabin ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Help please: extracting distances from each frame of a short MD
by Anne-Frances Miller 11 Dec '21

11 Dec '21

Dear Chimera support, I want to extract a set of distances and one angle from each snapshot of an MD trajectory (there are 11 of them). My plan was to have all my distances appear in one of the MD-movie analysis>plot distances windows and use ‘Dump Values’ to get my numbers out in a way I could use for other plots. I realize angles cannot appear in the same plot, but hope I can measure an angle in the same script. I have a ‘per-frame’ script that runs fine on the first frame, however it returns ‘Problem in per-frame script: Distance monitor already exists’ when I step forward to a second frame. Nothing appears in a 'MD plots' window (such a window does not open on its own either). Reply Log shows the correct distances for the first frame but then only repeats the error after that. Problem in per-frame script: Distance monitor already exists My work-flow: Open MD/movie, load my trajectory open analysis, Per-Frame copy my script into the window (chimera commands) click ‘apply' in the script window, click ‘play’ or step forward one frame in the MD GUI (looping disabled) My script: ~disp ~ribbon disp :718,720,721,722,730,740,741,1058 distance :1058@O2 :741@ND1 distance :730@OH :741@NE2 distance :721@OG1 :1058@N5 distance :718@O :1058@N3 distance :721@N :1058@O4 distance :722@N :1058@O4 distance :720@N :1058@O4 distance :740@O :720@N angle :1058@C2 :1058@O2 :741@HD1 :741@ND1 Reply Log output: Distance between FDM 1058 O2 and HID 741 ND1: 2.8 Distance between TYR 730 OH and HID 741 NE2: 2.8 Distance between THR 721 OG1 and FDM 1058 N5: 3.4 Distance between ILE 718 O and FDM 1058 N3: 3.2 Distance between THR 721 N and FDM 1058 O4: 2.9 Distance between GLY 722 N and FDM 1058 O4: 3.2 Distance between GLN 720 N and FDM 1058 O4: 3.2 Distance between GLN 740 O and GLN 720 N: 3.0 Dihedral #0:1058@C2 #0:1058@O2 #0:741@HD1 #0:741@ND1: -51.0515 Problem in per-frame script: Distance monitor already exists Thank you for any assistance, Anne-Frances - • - • - • - • - • - • - • - • - A.-F. Miller, Ph. D. (she/elle/sie) University Research Professor Professor of Chemistry University of Kentucky https://www.uky.edu/~afm/ Visiting Fellow, Einstein Foundation of Berlin

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Questions about Matchmaker and GDT
by Ralph Loring 11 Dec '21

11 Dec '21

Hi, I don't know if there's a special user group for Matchmaker but this also involves other aspects of Chimera. 1) I'm looking at AlphaFold structures of RIC-3, a chaperone for nicotinic receptors that is also an intrinsically disordered protein. There are pdbs for six species in the AlphaFold database: Human, mouse rat, fish, fly and worm. These differ tremendously in terms of sequence, size and predicted secondary structures but they all have a putative signal sequence and a transmembrane domain. I used Matchmaker to align the human pdb to each of the others. The results of combining all 6 looks like a bowl of spaghetti until the parts before the putative signal sequence and the C-terminal tails are deleted. Then I can see that the putative signal sequences and the transmembrane domains are in the same plane as if they are in a membrane. I just want to confirm that this is merely a lucky coincidence and that Matchmaker has no preference for aligning hydrophobic alpha helices into a planar space corresponding to a membrane. The coincidence, if it is one, is striking and I just want to make sure. Note that I have a similar question for AlphaFold, the source of the pdbs. 2) Does Chimera do Global Distance Testing (GDT)? For that matter, does ChimeraX (I've been thinking about switching and if it does, this may be what it takes to get over the activation energy barrier)? I can't find GDT in any of the directions. When Matchmaker runs, for instance comparing human and fly RIC-3, the sequence alignment score is only 270 but the RMSD is 1.6 angstroms (but only for 7 pruned atom pairs and when all 233 atom pairs are considered, the RMSD is 55 angstroms, so clearly not much overlap). I've heard that GDT corrects somewhat better than RMSD for not having precise superimposition. However, I don't know that it would make a lot of difference in this case but I'd like to find out. The mystery is that drosophila RIC-3 works almost as well as human RIC-3 in helping assemble human pentameric nicotinic receptors even though the structures are so different. Thanks for your help, Ralph Loring

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re-sampled map (volume resample #X onGrid #Y) difference with general mrc map
by Dmitry Semchonok 10 Dec '21

10 Dec '21

Dear colleagues, I have an issue with the output map re-sampled from the resampling step protocol. Could you please explain how different the re-sampled map is compared to the general mrc map (without rotation manipulations)? Because it seems that some important information is missing or/changed in the re-sampled.mrc Kind regards, Dmitry

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Questions about IMOD files in Chimera software.
by 박시훈 10 Dec '21

10 Dec '21

Dear chimera-users community, I have questions about opening IMOD files in Chimera software. Can I open the IMOD files (*.mod) in Chimera? Or, Can I make a hand-drawn mask file in Chimera? I could apply several filters and masks in my iso-surface map, however, I don't know how to apply these options in Chimera. Moreover, the reconstructed tomograms were shown to the inverted iso-surface map unlike IMOD.. Can I re-invert the iso-surface map in Chimera? Best regards Si Hoon Park

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Selecting residues from one chain
by Joao M.C. Teixeira 09 Dec '21

09 Dec '21

Hi, I am a bit confused on how to select residues from a chain. This is the command I am trying:

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Chimera error at start-up
by Hernando J Sosa 09 Dec '21

09 Dec '21

Dear Chimera, I cannot open Chimer anymore in a computer (Windos10 64) where it was running until yesterday. I tried with no success reinstalling the program and installing the latestChimera daily release. The error that I get at startup says: [cid:cfb0a3aa-9306-42f0-bfd0-328d433ceb1e] If I start in debug mode I get the following error in a command window: Cannot execute 'gzip': no automatic decompression of .Z files initializing general preferences loading Tix initializing graphics Return code: -1073741819 How can I resolve this issue? Thanks Hernando ___________________________________

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Mismatch between display and saved image
by Visvaldas K. 09 Dec '21

09 Dec '21

Dear all, I get a very odd mismatch between what is displayed and what is saved as a png image. I am attaching two figures, and you can probably guess what I want. Of course I will try this in ChimeraX if I am not able to fix the figure, but the image took quite some work, so I'd hate redoing it... Or I could use screenshot I guess... But certainly this is some sort of bug. I'm using Chimera 1.15 on MacOS 12.0.1. Thank you, Vis

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Chimera on RDS Servers farm
by ROTH Stephane (DNUM) 09 Dec '21

09 Dec '21

Hi, We want to use Chimera on RDS Windows Server (Windows Server 2012). Its possible to use it on this environment ? What is the system recommendation to windows platform ? Best Regards, -- Cordialement, Stephane Roth 03 68 85 11 94 Chef de Projet / Ingénieur Systèmes Direction du Numérique Université de Strasbourg

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aPNG
by Frank Irby 07 Dec '21

07 Dec '21

I produce high quality Animated PNG files and it takes a lot of juggling different computers to accomplish.Is there a way to simply chose APNG from the movie recorder output pulldown menue?Would there be a plug in for that? My animations can be found at:https://www.deviantart.com/mandelscape/gallery/24158715/molecular Thank you Sent from Yahoo Mail on Android

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