- Chimera-users - RBVI Mailing Lists

calculating orientation parameters between two asymmetric units
by Sen, Anindito 04 Feb '22

04 Feb '22

Dear All, How can I compute the parameters (angle , shift) of orientation between 2 asymmetric units w.r.t the central axis in a density map (and the map is not helical). 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: [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 28 Jan '22

28 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 16 Jan '22

16 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 11 Jan '22

11 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

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Convenient way to move 2D labels around
by Prathvi Singh 09 Jan '22

09 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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