- Chimera-users - RBVI Mailing Lists

Depth-cued view
by Thirumurugan Prakasam 24 Feb '22

24 Feb '22

Hi, I need to make some stacked COF with stacked view with descending order transparency as shown below within the same molecule [image: image.png] from a stacked view [image: image.png] Please let me know how I can select each 2D layer and decrease the transparency while going down. Please help me to make some nice images. Looking forward to hearing from you, Many thanks, Thiru -- Thirumurugan Prakasam, Research Scientist, New York University Abu Dhabi, Experimental Research Building Building C1, Saadiyat Island Abu Dhabi, UAE Phone no: +971-561976358

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Saving segmented regions from EM map not working
by Shruthi Viswanath 22 Feb '22

22 Feb '22

Hello Chimera team, We have a problem with saving segmented regions from EMD 2329 using Segger. When we segment one of the 9 spokes from this EM map and try to do File -> save selected regions to .mrc from the Segger window it displays a box around the selected region (see screenshot) and the saved .mrc file just shows a small blob and does not look like the original selected region. Could it be because of the lower than usual density range of this particular map? Thanks very much Shruthi -- Shruthi Viswanath Reader F (Assistant Professor), National Center for Biological Sciences (NCBS) GKVK, Bellary Road, Bangalore, India 560065 Tel: +91 80 6717-6152 Email: shruthiv(a)ncbs.res.in Web: https://www.ncbs.res.in/faculty/shruthi

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Molecular dynamics simulation plugin
by Enrico Martinez 21 Feb '22

21 Feb '22

Dear Chimera Users, I have a question related to the molecular dynamics simulation plugin integrated into the Chimera. As I understand it correctly, Chimera uses Amber integrated into the GUI. Here are my questions: 1) What are the limitations of this version of MD engine compared to the Amber software, which we may use to run molecular dynamics in terminal? 2)May I increase the integration step to 2 fs (assuming that there are constraints on the hydrogen atoms) during the production phase? 3) how the ligands may be parametrized ? What is the difference between two methods that are used for charges ? 4) Is it really slower compared to Amber ? May I use multi-cpu stations for the run ? I've just made it on my iMAC with 6 available CPUs but would like to try on the 96 CPUs linux station. Yours with thanks Enrico

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Regarding command line
by Aradhya Tripathi 20 Feb '22

20 Feb '22

Hello Sir, I am Aradhya Tripathi, currently working as a Ph.D scholar. I have installed the Chimera 1.15 version but the command line is not working in my workstation. Please give suggestions to solve this issue. I look forward to your valuable suggestions. With regards! Aradhya Tripathi CSIR-CDRI India

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error code -1073741819
by Gregor Schmidberger 18 Feb '22

18 Feb '22

Dear chimera support, I cannot start chimera 1.16 anymore. I attached the error code as png. Do you know how to solve this problem? Thanks a lot! Best regards, Gregor Schmidberger

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how to solve the problem of topology
by Kenji MATSUI 17 Feb '22

17 Feb '22

Dear Chimera Thank you very much for your kind answers. Sorry, I have a question about the issue of ligand topology for the docking study. The topology did not match when I used this ligand for the docking study. Could you tell me how to solve this problem? The thing I tried 1. I tried to add hydrogen atoms on UCSF Chimera by following the URL below, but it did not work Reference: https://www.swissparam.ch/SwissParam_gromacs_tutorial.html 2. Compare with the contents of the Mol2 file for cholesterol that was correctly docked. 25-hydroxycho_only_0216 → original file 25-hydroxycho_only_0216_Chimera →after adding H using UCSF Chimera --------------------------------------------------------------------------- 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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(no subject)
by Cathy 15 Feb '22

15 Feb '22

I am supposed to pull up the picture of VIG which is one of the amino acides in the GABA T Complex. Can someone please tell me how to do this? Thank you. --

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Adding charges to insulin receptor
by Saousen Diaf 15 Feb '22

15 Feb '22

Hello Elaine, I want to energy minimize a model of insulin receptor using chimera, but it is asking me to specify the net charges of some residues, which most of them are glycans that I added using CHARMM GUI, would you please help me with that? Thank you in advance for your help. Best Saousen

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multiple small molecule overlay
by Tyler St Denis 15 Feb '22

15 Feb '22

Hello, I have had success overlaying two small molecules in chimera by using the following process and using the "match sel" command in the command line. Each molecule I want to compare has 3 similar nitrogens http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-August/010205.html Though this process works for overlaying two small molecules, it does not work for a third. The first error I received indicates "an odd number of atoms has been selected." Clearly the 'match sel' command works by comparing pairs of homologous atoms -- is there a way to expand this 'pair' to a larger set (e.g. triplets) to multiple small molecules? Thanks! Tyler _______________________ Tyler G. Saint-Denis, Ph.D. Postdoctoral Fellow T. Don Tilley, Ph.D. Laboratory College of Chemistry University of California, Berkeley tstdenis(a)berkeley.edu 914-462-1954 [05537c13-eec7-4b35-bc2c-f774f520f544]

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Visualizing gaussian output files in UCSF chimera
by Prathvi Singh 15 Feb '22

15 Feb '22

Hello again Elaine, I have one more question. Is there a way to open & visualize a gaussian output file (it has extension of *.log*) in UCSF chimera? I found that if you convert the *.log *file to *.mol *file using gaussian's software GAUSSVIEW, you can visualize the *.mol *file in chimera. However, the identity of the residues is lost; all the residues are shown as UNK. Is there a better way to do this? Thanks again & always -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Regarding ramachandran plot
by Prathvi Singh 15 Feb '22

15 Feb '22

Hi Elaine, Is there a way to see the phi and psi values of two different proteins on the same ramachandran plot? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Re: [Chimera-users] Chimera-users Digest, Vol 226, Issue 6
by Martti Tolvanen 12 Feb '22

12 Feb '22

Hi Kaina and Elaine, If the goal is just to demonstrate the similarities of the two domains in your proteins, you could also consider breaking the model in two and superimposing each domain separately. Another feasible but tedious approach for rotating bonds (which I do not recommend because it means altering the structure from what was observed) would be to measure torsion angles in the protein backbone of the "linker" region of one model and then set the torsion angles into the same values in the other model, using the command line or a script. Best, -Martti -- Martti Tolvanen Lecturer in bioinformatics U of Turku, Finland -----Original Message----- From: chimera-users-request(a)cgl.ucsf.edu [mailto:chimera-users-request@cgl.ucsf.edu] Sent: 11. helmikuutata 2022 23:31 To: chimera-users(a)cgl.ucsf.edu Subject: Chimera-users Digest, Vol 226, Issue 6 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..."

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superimposing structures with Chimera
by Elaine Meng 11 Feb '22

11 Feb '22

> On Feb 10, 2022, at 1:42 PM, Kaina Quintero Chavez <kaina.quintero(a)uabc.edu.mx> wrote: > > Hi, My name is Kaina. I am a current college student in UABC. I am currently doing my thesis in biology and came upon using UCSF chimera and am in a stuck position on how to use the superimpose feature. I was hoping you can guide me or reference me to a workshop/ course? anything really to get the job done. > Thanks, hope to here from you. > -- > Kaina Hi Kaina, We usually recommend the chimera-users(a)cgl.ucsf.edu address for asking questions -- I CC'd it here, hope that's OK. Also it would be helpful to include more information when you send a question, like what you are trying to superimpose, what you tried already, what problem(s) caused you to be stuck, etc... but I will try to answer below. There are lots of different ways to superimpose structures in Chimera and it depends on your situation as to which one you would use. There is a discussion of the different ways here: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> If you have atomic structures of proteins or nucleic acid chains, probably the easiest approach is to try using the Matchmaker tool, menu: Tools... Structure Comparison... Matchmaker. You would choose one structure as the reference and the other one as the one to match, and then just click "Apply" to see if the default settings work. Here is the help for Matchmaker <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/match…> ...and this tutorial includes examples of using it <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html> There is also a "matchmaker" command that does the same thing, and the help includes some example commands: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html> However, maybe your situation is different and you would need to use one of the other methods discussed in the first 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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Animation utility question
by Zhang, Bixia 11 Feb '22

11 Feb '22

Dear developers, I have a question about using the animation tool in chimera. I made a pdb files with three chains, they are different protein domains. I am trying to make animation showing chain B moves (rotate and translate) in relative to A and C. For all the desired positions of B, I added to the scenes and dragged to the timeline. But when I hit play, I noticed that the relative position of B was maintained same as the last scene. Does that mean I failed to save the position of previously scenes? I also noticed that if I don’t move the chain, and I just rotate the whole thing and the animation works. Is there a special command to save the relative position? I tried savepos but it doesn’t seem to help. I would appreciate it if you could help me with this issue. Thank you! Best, Bixia

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Chimera
by Kaina Quintero Chavez 10 Feb '22

10 Feb '22

Hello, I was wondering if the university or program had a course of using the superimpose feature, I would like to conduct an experiment and would need assistance in the usage and also permission of the images -- Kaina

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Measuring distances
by Eric Pettersen 09 Feb '22

09 Feb '22

> > From: "Sen, Anindito" <andysen(a)tamu.edu <mailto:andysen@tamu.edu>> > Subject: Measuring distances > Date: February 9, 2022 at 11:51:15 AM PST > To: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu <mailto:chimera-users-bounces@cgl.ucsf.edu>> > > > Dear All, > > How do I measure distances between 2 helices > > 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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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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