- Chimera-users - RBVI Mailing Lists

Question: How to do add charge and minimazation?
by Kenji MATSUI 10 Jan '23

10 Jan '23

Dear chimera I am sorry to interrupt your busy schedule. My name is Matsui, and I am a second-year master's student at a Japanese university. Thank you for taking time out of your busy schedule to respond to my question the other day. We are investigating interactions between protein and ligand. I want to optimize the attached file compound. I want to adjust the charge for this purpose. [image: image.png] Question However, when I press OK in the first photo section, a black screen appears as in the second photo.In you tube and other videos, I was moved to the save etc. screen. Is the charge optimization done correctly here? [image: image.png] --------------------------------------------------------------------------- Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology M2 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan Mail: s214903z(a)st.go.tuat.ac.jp

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Question concerning rotamer choosing
by Noe Robert 09 Jan '23

09 Jan '23

Hi, I'm currently trying to write a python script which automatizes mutageneses on Chimera 1.16, and calculates clashes inducted by the change of amino acid through a local minimization (which explains why I'm using Chimera instead of ChimeraX). I would like to choose which rotamer to use depending on their probability from the rotamer library Dunbrack (for instance, when probability is >0.1), which is visible on the "Rotamers graphical user interface". Is there a way to extract these probability values using a script, in order to run it on a certain number of rotamers ? That way it would be quite automated. On Jul 1, 2015, Eric Pettersen advised to modify the "Python script that uses the functions in the Rotamers module" (here<https://www.cgl.ucsf.edu/pipermail/chimera-users/2015-July/011193.html>), but I don't which one it is. Thank you, Noé Robert, Fifth-year student in bioengineering, minor in Bioinformatics and Modelling, at engineering school Polytech Nice Sophia, France Phone : +33 7 81 00 52 02 "let's limit the use of our resources and lighten our mails"

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Save cut open model for 3Dprinting
by Haselbach,David 03 Jan '23

03 Jan '23

Hi, I wanted to build a cut open model of a cryoEM map which I achieved through clipping in Chimera. But I am failing to apply the clipping in a way that I can save the cut open mesh as poligone file for 3D printing. Is this possible? All the best, David

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Is there an option to open pdbqt as PDB format smoothly?
by 夏前程 27 Dec '22

27 Dec '22

Hi Chimera team, I'm wondering if there is any chance that I can open a .pdbqt file smoothly (just like open a .pdb file ) through some strategies (for example, maybe modifying some source codes?). Since AutoDock (and vina) always gives a .pdbqt format file but not .pdb format, however the content of which is somewhat like pdb and we always want to open it in pdb format. This is not an important issue. But if so, the experience will be much better at least for me (Now, I have to choose the PDB format or rename the file suffix into .pdb). With Regards Qiancheng Xia 2022/12/23

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Chimera startup error: "Display misconfiguration" (Debian GNU/Linux)
by Powell, William A. 25 Dec '22

25 Dec '22

Hi, Chimera community. I have seen similar problems addressed, and the solution is always to update drivers and make sure there is only on OpenGL renderer. I am unable to resolve my problem this way. When Chimera is launched using my dedicated NVIDIA 3060 Mobile graphics card, there are mixed results. If launched from a terminal instance an by the NVIDIA card, it produces the error below. Display misconfiguration. Please increase the color quality (24 bit color or greater), update your display (graphics) driver, and/or upgrade your graphics card. Also see chimera installation instructions. Using primusrun, it succesfully launches on the dedicated card. Unfortunately, the nvidia-primus and bumblebee-nvidia packages seem to conflict with the NVIDIA drivers. The only way Chimera works reliably is by launching it through an instance of Steam ran on the NVIDIA card. The Steam client opens ~/.local/bin/chimera, the same file opened through the terminal. I am not sure what is so special about launching an application through Steam. Thanks! W. Andy Powell, B.S., A.S., Graduate Teaching Assistant The University of Oklahoma Singh Lab, INPART Department of Chemistry and Biochemistry Dodge Family College of Arts and Science w.a.powell(a)ou.edu

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Re: [Chimera-users] Is there an option to open pdbqt as PDB format smoothly?
by 夏前程 23 Dec '22

23 Dec '22

Hi Sette and again Chimera team,I know what you said. But what I really want to ask is that if there is any way to open .pdbqt smoothly just like .pdb (without the format-choosing step). Just imagine the suituation of mine: I have to open like 10 .pdbqt file in a chimera session. If I didn't rename the suffix from .pdbqt to .pdb, I have to choose format for 10 times. That should be a bit annoying for me. So I ask the question here to find some smart solutions...With regardsQiancheng Xia2022/12/24> Hi Qiancheng, > > as far I know the File-Open allows to open a .pdbqt file. > simply > choose pdb in the list of possible formats. > > Best > > Marco > > Il 23/12/2022 14:20, ??? via Chimera-users ha scritto: > > > > Hi Chimera team, > > > > I'm wondering if there is any chance that I can open a .> pdbqt file > > smoothly (just like open a .pdb file ) through some > strategies (for > > example, maybe modifying some source codes?). > > > > Since AutoDock (and vina) always gives a .pdbqt format file > but not > > .pdb format, however the content of which?is somewhat like > pdb and > > we always want?to open it in pdb format. > > > > This is not an?important issue. But if so, the experience > will be > > much better at least for me (Now, I have to choose the PDB > format or > > rename the file suffix into .pdb). > > > > > > With Regards > > > > Qiancheng Xia > > > > 2022/12/23 > > > > > > > > > > _______________________________________________ > > Chimera-users mailing list:Chimera-users@cgl.ucsf.edu > > Manage subscription:https://www.rbvi.ucsf.edu/mailman/> listinfo/chimera-users -- > Dr Marco Sette, PhD. > Department of Chemical Sciences and Technology > University of Rome, "Tor Vergata" > via della Ricerca Scientifica, 00133, Rome, Italy > e-mail:sette@uniroma2.it > Tel.: +39-0672594424

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Re: [Chimera-users] Is there an option to open pdbqt as PDB format smoothly?
by sette＠uniroma2.it 23 Dec '22

23 Dec '22

Hi Qiancheng, as far I know the File-Open allows to open a .pdbqt file. simply choose pdb in the list of possible formats. Best Marco Il 23/12/2022 14:20, 夏前程 via Chimera-users ha scritto: > > Hi Chimera team, > > I'm wondering if there is any chance that I can open a .pdbqt file > smoothly (just like open a .pdb file ) through some strategies (for > example, maybe modifying some source codes?). > > Since AutoDock (and vina) always gives a .pdbqt format file but not > .pdb format, however the content of which is somewhat like pdb and > we always want to open it in pdb format. > > This is not an important issue. But if so, the experience will be > much better at least for me (Now, I have to choose the PDB format or > rename the file suffix into .pdb). > > > With Regards > > Qiancheng Xia > > 2022/12/23 > > > > > _______________________________________________ > Chimera-users mailing list:Chimera-users@cgl.ucsf.edu > Manage subscription:https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users -- Dr Marco Sette, PhD. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail:sette@uniroma2.it Tel.: +39-0672594424

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Question about Labeling Beta Sheet
by Yifan Wang 22 Dec '22

22 Dec '22

Hi Chimera team, I have a question for labeling beta sheet. After I get secondary structure, when I look at the 3D structure, It is very clear to see coli, helix and beta-strands. But how can I label and tell the beta strands are in same sheet or not? Does chimera contain the information for beta sheet? Thank you so much! Yifan

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AttributeError of "Model Panel" when using nogui mode to save session
by 夏前程 20 Dec '22

20 Dec '22

Hi, I've tried to use chimera nogui mode to save chimera sessions for a large number of tasks (one session for each task). However, an error message was returned and without the wanted output.py being written. The command I used is chimera --nogui --silent run.cmd. ( followed this https://www.cgl.ucsf.edu/pipermail/chimera-users/2011-October/006863.html) The content of run.cmd ------------------------------------- background solid white set silhouette open rec.crg.pdb xtal-lig.pdb sel #1-2 zone sel 5 ~sel #1-2 sel up ~rib ~ sel color white sel color byhet sel rlabel sel color black ,lr dis sel ~dis HC open rec.crg.pdb save output.py stop ------------------------------------- The error message returned ------------------------------------- Starting extension 'Model Panel' failed Error processing trigger "save session": AttributeError: 'ModelPanel' object has no attribute '_updateHandler' File "/home/xiaqc/.local/UCSF-Chimera64-1.16/share/ModelPanel/base.py", line 1301, in _saveGroups if _mp._updateHandler: See reply log for Python traceback. Error while processing run.cmd: AttributeError: 'ModelPanel' object has no attribute '_updateHandler' File "/home/xiaqc/.local/UCSF-Chimera64-1.16/share/ModelPanel/base.py", line 1301, in _saveGroups if _mp._updateHandler: See reply log for Python traceback. -------------------------------------- I've tested 1.16 (build 42360) and 1.15 (build 42233). Both of them failed.

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Chimera
by Добромир Калчевски 19 Dec '22

19 Dec '22

Hello, I would like to suggest an improvement in the GUI: when a data set of multiple files is opened (for example multiple .cube files) the Volume Viewer displays options (including hide / show) for only 3 of them. There is no scroll up or down. Resizing the window does not change the number of loaded files to manipulate for visualization. Let's say I want to browse a set of 12 molecular orbitals - I have to manually click on each one in the "Data set list", then click the hide (eye) icon in the detailed options list below and do this for all molecular orbitals / .cube files, otherwise Chimera visualized all of them at the same time. It is simply not convinient to hide and show them if I want to view more than 3 files in the Volume Viewer. In ChimeraX that issue does not exist, yet it lacks working linux binaries (too many dependencies to cover outside of distros like debian ot red hat, especially if the dependencies are not explicitly mentioned and the distro does not provide them with a package manager). Best Regards, Dobromir

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Chromophore missing
by Marco Sette 16 Dec '22

16 Dec '22

Dear all, When I fetch a protein with a chromophore (PDB code 2h5q), the chromophore, not a standard one, is missing, and not present in the Select-Residue menu. Is there any way to obtain it? Thanks, Marco -- Questa email è stata esaminata alla ricerca di virus dal software antivirus Avast. www.avast.com

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Question about Model Loops Option in Chimera
by Ecem Güngör 14 Dec '22

14 Dec '22

Hello, I have a protein crystal structure where some regions are not resolved in the crystal. Therefore, I want to predict and fill these regions, without touching the rest, by using the Model Loops/Refine Structure option of Modeller in Chimera. When I select the non-terminal missing structure as a model and standard as a loop modeling protocol, some atoms in the rest of the structure are shifted from the original positions. However, I want to keep them as they are. Here I would like to ask what standard loop modeling protocol corresponds to. Does it also refine or optimize the structure as a whole? What does it actually correspond to? Any help would be appreciated. Thanks. Ece

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Issues with software in complex building
by Kumar Pratyush 07 Dec '22

07 Dec '22

Hello Sir/Mam, I am not able to save complex of docked output.pdbqt and protein.pdbqt as save button is not getting active. I used to do the same protocol earlier with ease but now not able to execute. I tried by uninstalling and re-installing but still things are not working smoothly. Please help. Thanks & Regards Kumar Pratyush (Dr.) Assistant Professor, Department of Pharmaceutical Chemistry, Contact :- +91-7709714926 Email-<mailto:Email-aherkiran22@gmail.com> kumar.pratyush(a)svkm.ac.in Shri Vile Parle Kelavani Mandal's Institute of Pharmacy, Survey No. 499, Plot No- 03, Behind Gurudwara, Mumbai – Agra National Hwy, Dhule, Maharashtra 424001 Phone : 02562-297802 https://svkm-iop.ac.in/ Vision of Institute: To pursue excellence in pharmaceutical education and research to develop competent professionals

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Question: How to find the area of hydrophobic interaction?
by Kenji MATSUI 06 Dec '22

06 Dec '22

Dear Chimera I am sorry to interrupt your busy schedule. My name is Matsui, and I am a second-year master's student at a Japanese university. Thank you for taking time out of your busy schedule to respond to my question the other day. We are investigating hydrophobic interactions between protein and ligand. ,but how can I display the following? distance between faces:show how many Å2 are within Å of each other. I found a hydrophobic contact, but does it work well in my case? https://www.cgl.ucsf.edu/pipermail/chimera-users/2012-February/007236.html Please confirm. --------------------------------------------------------------------------- Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology M2 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan Mail: s214903z(a)st.go.tuat.ac.jp

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Missing bonds
by Naima syed 06 Dec '22

06 Dec '22

Hello, I have one question that when i checked the hydrogen bonds of my original and docked (control) file, 2 bonds are missing. When I checked the distance between them, it is less than 3.40 angstroms. Can you please tell me the reason why these bonds are not showing in the Chimera. Thank you.

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Issue while importing Chimera's runCommand module
by Noe Robert 06 Dec '22

06 Dec '22

Good morning, I'm trying to use a python script for ChimeraX version 1.5, to automate mutageneses on a specific protein. As a first try, it looks like this : from chimera import runCommand as rc rc("open " + "hERGts_compiled.pdb") rc("color red") rc("surf"); So it refers to the chimera module for the runCommand. I tried to install it on Python through the command pip but it failed : ################################# Example of my shell while trying to install chimera module ####################### PS C:> python3 -m pip install chimera Collecting chimera Using cached chimera-0.4.7.tar.gz (355 kB) Preparing metadata (setup.py) ... error error: subprocess-exited-with-error �� python setup.py egg_info did not run successfully. �� exit code: 1 �t��> [9 lines of output] Traceback (most recent call last): File "<string>", line 2, in <module> File "<pip-setuptools-caller>", line 34, in <module> File "C:\Users\CE PC\AppData\Local\Temp\pip-install-cfq97mii\chimera_bd7187074876462a9782eded8cb3a816\setup.py", line 1, in <module> import ez_setup File "C:\Users\CE PC\AppData\Local\Temp\pip-install-cfq97mii\chimera_bd7187074876462a9782eded8cb3a816\ez_setup.py", line 170 print "Setuptools version",version,"or greater has been installed." ^ [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed �� Encountered error while generating package metadata. �t��> See above for output. note: This is an issue with the package mentioned above, not pip. hint: See above for details. ###################################################################################################### So it looks like the temporary file generated has an error that doesn't allow the installation of the module, and so I cannot use any command from my script as runCommand is not recognized. There seem to be no mention of this issue in the mail archive but one colleague encountered the same problem, which I find strange. Do you have an idea on how to solve this issue ? Thank you and have a great day, No�� Robert, Fifth-year student in bioengineering, minor in Bioinformatics and Modelling, at engineering school Polytech Nice Sophia, France Phone : +33 7 81 00 52 02 "let's limit the use of our resources and lighten our mails"

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Robbon colouring
by F.Xavier Gomis-Rüth 30 Nov '22

30 Nov '22

Hi Elaine, when coloring a helix differently from the attached coils, is there a means to prevent the first short segment of the coil to get the color of the helix? It seems to me there was some kind of "halfbond"-mode one... Best, Xavier --

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Writesel command in chimeraX
by Prathvi Singh 27 Nov '22

27 Nov '22

Hi Elaine, Is the writesel command available in chimeraX because I could not find it in the Actions menu? If not, then is any equivalent available apart from the command which saves selection as a new PDB file? Thanks once again in advance -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Visualizing negative volume as in CastP
by Neelen, Christopher 24 Nov '22

24 Nov '22

Hello everyone, I am trying to visualize cavities from a protein I am currently working on. Therefore I calculated the cavities volume using CastP. I then import the obtained files into chimera. Unfortunately CastP visualizes the cavities as a negative volume of the solvent accessible area. Chimera on the other hand only shows the surface. So is there a way to also visualize the negative volume in Chimara just like in CastP ? Thanks in advance! All the best, Chris

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Query regarding depth cueing
by Prathvi Singh 22 Nov '22

22 Nov '22

Hi Elaine, Is there a way to change the depth cueing gradually using command line in either chimera or chimeraX? If possible, then it would be a great way to emphasize on a specific part of the protein while making a chimera movie. -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Alphafold
by Kornelius Zeth 20 Nov '22

20 Nov '22

Dear all - I'm using Alphafold in Chimera and I have a problem to run this properly on Colab. The people from Colab say that the error messages I get since recently are related to Alphafold developers having installed a new version. Could you please let me know what I could do to get the program running again? Thanks and have a nice day Kornelius

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Using Chimera and Autodock Vina on Catalina OS
by Rao, Mallika 18 Nov '22

18 Nov '22

Hello, I was wondering if anyone had been able to find a workaround in order to use the autodock vina add-on in Chimera for a mac that is running Catalina OS. Thanks in advance, Mallika

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Saving omega angles to file
by Prathvi Singh 18 Nov '22

18 Nov '22

Hello Elaine, Is there a way to save the omega angle of residues to a file using either chimera or chimeraX? I am able to save the phi, psi, chi angles using the *Render by attribute *tool in chimera but I could not find a way to save the omega angle. -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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How to insert a nucleotide to a pdb
by Magdalena Riad 18 Nov '22

18 Nov '22

Hi, I have a pdb-file of the ribosome and would like to insert two nucleotides to one of the rRNA-chains. How do I do that? I’ve found the addaa command for amino acids, is there a similar one for nucleotides? Best regards, Magdalena När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>.

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Query regarding the Zone tool in UCSF chimera
by Prathvi Singh 18 Nov '22

18 Nov '22

Elaine, In UCSF Chimera, when I try to find all the atoms within 4A of a selected residue using the *Zone* tool, it selects several atoms around that residue. However, I am not able to understand which atom of the selected residue was taken as the reference point for calculating the distances. Please help. -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Information regarding double bonds
by Naima syed 18 Nov '22

18 Nov '22

Hello, I have one concern, before docking there is a double bond which i can check in pymol but after docking that double bond was lost. Can you please tell me how to fix this problem. Thank you

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No MMTK name for atom "H" in standard residue "GLY"
by Marco Sette 15 Nov '22

15 Nov '22

Dear all, i'm trying to minimize a peptide (Tools, Structure editing, Minimize Structure) but I obtain this error message: No MMTK name for atom "H" in standard residue "GLY". I have a Gly in position 1, does this depends on the NH protonation? Also, I fixed most of the residues, including Gly 1, trying to minimize a small region (Fixed Atoms: selected, in minimize panel) but still have the same errors. How can I solve it? Thanks for your help, Best Marco -- Dr Marco Sette, PhD. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it Tel.: +39-0672594424 -- Questa email è stata esaminata alla ricerca di virus dal software antivirus Avast. www.avast.com

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combining two models into single model with two chains
by Elaine Meng 13 Nov '22

13 Nov '22

Hi Ali, I don't know what you mean by "sub-branches of that chain" -- if they are listed as two separate things in the Model Panel (e.g. #0.1 and #0.2), then it means they are two separate models. You can show Model Panel from the Favorites menu. If so, then you want to put them together into one model with two different chains. For that, see the "copy/combine" function in the Model Panel (in the menu under Favorites) or the "combine" command. Details in the User Guide: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#combine> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> If they are really only one model with one chain, then you can only change the ID of part of the chain if the two parts are really disconnected. See Tools... Structure Editing... Change Chain IDs: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/changech…> If they are NOT disconnected, you would have to manually edit the PDB file in some text editor first to add a TER between the parts. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.h…> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. for general questions the better address is chimera-users(a)cgl.ucsf.edu CC'd here. The chimera-dev address is for programming questions. > On Nov 12, 2022, at 5:56 AM, Ali Doostmohammadi via Chimera-dev <chimera-dev(a)cgl.ucsf.edu> wrote: > > Hi! > I gave my protein to ClusPro for docking and it gave me the PDB file. For the next step, I need to upload to Prodigy, which requires me to separate the ligand chain and receptor chain to perform the analysis. But in the PDB file that I open in Chimera, there is only one chain, and ligand and receptor are divided as sub-branches of that chain, and Prodigy algorithm does not accept it. > I wanted to know how to divide the protein and its receptor into two different chains? > > Best regards!

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NHR Atomistic Simulation Center Online Symposium 2022, Nov 28-29
by Harald Lanig 11 Nov '22

11 Nov '22

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MD simulation movie in chimeraX
by Shivam Gupta 09 Nov '22

09 Nov '22

Hello Support Team, I am a commercial license user of chimeraX. I have .trr and .tpr files from the Gromacs MD simulation. I am not getting any option to create an MD movie. I know how to do it in chimera but couldn't find a similar GUI/option in chimeraX. Literature/tutorial of chimeraX didn't help me much. Please help me out by guiding me to generate MD movies. Please reply to this email inline. I am Looking forward to hearing from you. Thanks -- With Regards Gupta Shivam グプタシヴァム E-mail: *shivam-gupta(a)pharmafoods.co.jp <a-higashiyama(a)pharmafoods.co.jp>* Biomedical Department Pharma Foods International, Kyoto Japan 株式会社ファーマフーズ〒615-8245 京都市西京区御陵大原1-49 TEL:075-748-9811 FAX:075-948-9818 URL: http://www.pharmafoods.co.jp/

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EULA modification request
by Smith, Lua J. 08 Nov '22

08 Nov '22

Hello UCSF Chimera creators, Our Chemistry department of Missouri University of Science and Technology would like to use your software. Our attorney reviewed the non-commercial software license agreement, and is requesting the legal jurisdiction be struck from the license agreement as well as other modifications. Due to the University being an instrumentality of the state of Missouri and having sovereign immunity under Missouri and federal law, we are not authorized to waive our legal jurisdiction (See Fowler v. Board of Regents, 637 S.W.2d 352 (Mo.App. 1982)). Would you please review the attached requested license agreement modifications, and initial if acceptable? Thank you! Lua Lua Smith Software Support, Information Technology 800 University Drive ljhqn8(a)mst.edu<mailto:ljhqn8@mst.edu> | 573-341-7990<tel:573-341-7990> | it.mst.edu<https://it.mst.edu> [Missouri S&T - 150 Years]<https://www.mst.edu/>

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Finding disulphide bonds
by Prathvi Singh 08 Nov '22

08 Nov '22

Hi Elaine, I have found out a way to select the disulphide bonded CYS residues in UCSF chimera using the command: *select disulphide*. However, is there a way to count the number of disulphide bridges in a protein and save in a variable? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Question regarding 2dlabels in Chimera
by leonard.maurer＠uni-bonn.de 07 Nov '22

07 Nov '22

Hi, I am using Chimera for several years now and I really enjoy it, but there is one issue I could not solve until now: Is it possible to have subscript/superscript for the 2D labels? For example something like "subunit A\_{1}" and "subunit A\^{1}" that I can type either in the 2d labels GUI text part or with the 2dlabels command, which gives me the raised and lowered versions of the "1"? I am confident that this feature might be already implemented given Chimera's impressive amount of tools, but I was not able to find it in the documentation so far. Thanks in advance! Best regards, Leonard

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Running the Modify Structure tool using command line in UCSF Chimera
by Prathvi Singh 03 Nov '22

03 Nov '22

Hi Elaine, Is there a way to run the *Modify Structure *tool in UCSF Chimera using command line? I want to substitute a S-atom with O-atom in more than 100 structures and doing it for each structure using the GUI looks very time consuming. Please help. -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Jagged edges in chimera X
by Prathvi Singh 03 Nov '22

03 Nov '22

Hello Elaine, Is there a way to smoothen the jagged edges seen around ribbons and sheets in ChimeraX? The jagged edges can be removed in UCSF chimera by setting the *subdivision *value to 20 and enabling multisampling but I do not see these features in chimeraX. -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Doubt regarding Copyright for the use of UCSF Chimera free software in research paper
by aiswarya tressa chacko 03 Nov '22

03 Nov '22

Sir/Madam, I am a post graduate student who is working on a research article which involves molecular docking and analysis. I am using the free software of UCSF Chimera (version 1.16) for obtaining results and analysing them. I am wondering whether using these results and images that I acquired from Chimera in my research study, will subject me to Copyright Issues. Kindly address my doubt as soon as possible.

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xyz axis indicator
by Xiang Zhang 01 Nov '22

01 Nov '22

Hi all, I was wondering how I could hide the xyz indicator in the center of window when I was viewing the X-ray density from mtz file? It only appears in crystal unit view mode but disappears in EM projection side view. Best, Xiang

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AlphaFold Modeling
by S.M. RAIHAN RAHMAN 31 Oct '22

31 Oct '22

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

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How to invert a map values in UCSF Chimera
by Junha Song BA 31 Oct '22

31 Oct '22

Dear RBVI, I am currently looking into the ways to invert a map in UCSF Chimera so that I can flip the histogram of a map, but I cannot find a volume operation command that does the job. What command in UCSF Chimera allows creating a map with inverted map values? I thought it was vop but I cannot find a parameter that allows assigning negative value operation that would invert the map in UCSF Chimera command line documentation. Best, Junha Song.

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Question regarding protein-protein interactions in ChimeraX
by Lake, Camille (NIH/NIAID) [C] 31 Oct '22

31 Oct '22

Hello, My name is Camille Lake and I have used ChimeraX to model proteins. I was wondering - if I load two completely separate proteins from PDB, what is the nature of their interaction as shown by ChimeraX? The two proteins I'm interested in, TIM-3 (5f71) and CEACAM1 (5dzl), are predicted to interact in the literature, but if I load them separately into ChimeraX, is this predicted interaction what displays automatically? It seems that they are, but I can't find anywhere on the web whether this is automatically done in ChimeraX. Other proteins I randomly add in generally keep far away from each other in space. Thank you, Camille Camille Lake, PhD Emerging Leaders in Data Science (ORISE) Fellow National Institute of Allergy and Infectious Diseases (NIAID) - Office of Data Science and Emerging Technologies (ODSET) National Institutes of Health (NIH) 5601 Fishers Lane, 6C5 Rockville, MD 20871 camille.lake(a)nih.gov 301-761-7976 ---------------------------------------------- The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. The National Institute of Allergy and Infectious Diseases (NIAID) shall not accept liability for any statement made that are the sender’s own and not expressly made on behalf of the NIAID by one of its representatives.

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Need guidance
by Naima syed 30 Oct '22

30 Oct '22

Hello I am trying to find the RMSD between docked ligand and original ligand but I am not able to do it. When i tried the command "match" it showed the error atom spec missing. Can you please tell me how to fix this problem? Thank you

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Question about use of Chimera to view data from SALIGN program
by Edmund Marinelli 26 Oct '22

26 Oct '22

Helllo: I used SALIGN to obtain alignment / superposition of peptides. On the SALIGN webpage there is a link for Launch Chimera. When I click this I get a download of a file named "show.chimerax". Then nothing happens. The file contents appear to be directing ChimeraX to the data on the web and are as follows: <?xml version="1.0"?> <ChimeraPuppet type="std_webdata"> <web_files> <file name="alignment.pir" format="text" loc=" https://modbase.compbio.ucsf.edu/salign/results.cgi/job_225330/str-str_out.…" /> <file name="model1_fit.pdb" format="text" loc=" https://modbase.compbio.ucsf.edu/salign/results.cgi/job_225330/model1_fit.p…" /> <file name="model2_fit.pdb" format="text" loc=" https://modbase.compbio.ucsf.edu/salign/results.cgi/job_225330/model2_fit.p…" /> <file name="model3_fit.pdb" format="text" loc=" https://modbase.compbio.ucsf.edu/salign/results.cgi/job_225330/model3_fit.p…" /> <file name="model4_fit.pdb" format="text" loc=" https://modbase.compbio.ucsf.edu/salign/results.cgi/job_225330/model4_fit.p…" /> </web_files> <commands> <py_cmd>chimera.processNewMolecules(chimera.openModels.list(modelTypes=[chimera.Molecule]))</py_cmd> <py_cmd>import MultAlignViewer</py_cmd> <py_cmd>mols = chimera.openModels.list()</py_cmd> <py_cmd> m=chimera.extension.manager for i in m.instances: if isinstance(i, MultAlignViewer.MAViewer.MAViewer): mav = i </py_cmd> <py_cmd> for m in mols: if not m in mav.associations.keys(): mav.associate([m]) mav.match(mols[0], mols[1:], iterate=True)</py_cmd> </commands> </ChimeraPuppet> What am I supposed to do with this file. ChimeraX does not have a file extension .ChimeraX hence I do not know how to proceed next. Can anyone help? Thanks in advance.

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Set a reference coordinate for a viral structure?
by Feng, Y. 20 Oct '22

20 Oct '22

Hi there, I am a fresh new user of Chimera and have literally no experience in it. So I was wondering how to perform the process as mentioned in the Figure S4 of the following article: DOI: 10.1021/acs.jpcb.6b10131. My questions would be: In Chimera, 1. How to make an appointed atom in a viral structure with coordinates of (0,0,1)? 2. How to rotate the target point to the coordinates (0,0,1) and read out the original coordinates of the target point? What I want to do in Chimera is exactly the same as mentioned in the above article. But I don't have much experience with Chimera. So if you could explain how to do that step by step, that would be very much helpful. Sincerely appreciate! With best regards, Yuzhen Feng

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Set a reference coordinate and rotate target point to the reference coordinate?
by Feng, Y. 18 Oct '22

18 Oct '22

Hi there, I am a fresh new user of Chimera and have literally no experience in it. So I was wondering how to perform the process as mentioned in the *Figure S4* of the following article: DOI: 10.1021/acs.jpcb.6b10131. My questions would be: In Chimera, 1. How to make an appointed atom in a viral structure with coordinates of (0,0,1)? 2. How to rotate the target point to the coordinates (0,0,1) and read out the original coordinates of the target point? What I want to do in Chimera is exactly the same as mentioned in the above article. But I don't have much experience with Chimera. So if you could explain how to do that step by step, that would be very much helpful. Sincerely appreciate! With best regards, Yuzhen Feng

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Question: Why hydrogen bonds are not displayed?
by Kenji MATSUI 16 Oct '22

16 Oct '22

Dear Chimera I am sorry to interrupt your busy schedule. My name is Matsui, and I am a second-year master's student at a Japanese university. Thank you for taking time out of your busy schedule to respond to my question the other day. I am now looking at protein-ligand interactions. We found in the paper that His 421 interacted with another ligand. Therefore, the interaction between His-421 and the ligand. Problem :However, no hydrogen bonds were displayed.(first figure) I would like you to ask why this is caused. ---------------------------------------------------------- <detail> This is because the distance between the His-421 and OH oxygen atoms was 3.7 Å. A ligand with a structure similar to this one in the paper formed a hydrogen bond with His-421 at 3.8 Å. The thing I tried The Relax H-bond constraints section was adjusted from 3.0 to 5.0. [image: image.png] you can show this figure when you open the attached file Wheat: Ligand the other color:protein [image: image.png] H-bond parameter [image: image.png] --------------------------------------------------------------------------- Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology M2 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan Mail: s214903z(a)st.go.tuat.ac.jp

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UCSF Chimera Non-Commercial License Agreement
by Sarah Haar 14 Oct '22

14 Oct '22

Hi, Bowling Green State University would like to use UCSF Chimera Non-Commercial License Agreement. As part of our University review process, all legal Terms need to be examined to assure that we stay in compliance with Ohio law. Please provide all Terms (i.e. Terms and Conditions, Master Service Agreement, EULA, SAAS, etc.) that we need to accept in order to use your product. Because we are a State-owned University there are some Terms that we cannot accept. For example, we cannot indemnify or agree to arbitration. Would you consider Amendment to your Terms if needed? Best regards, Sarah Haar Procurement Specialist Bowling Green State University 1851 N. Research Dr. Bowling Green, OH 43403 Office: 419-372-7926 [cid:image001.jpg@01D8DFDF.BAD37170]

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fit into map global
by Dieter Blaas 12 Oct '22

12 Oct '22

Hi, I am struggling to fit a model of a single protomer into a viral cryo-EM map. I usually succeed after a very long process of manually positioning the model approximately and then running 'fit into map' that arranges it in the best way. I filtered the map to low resolution and used the option to generate a density map of the pdb file which makes it easier but it is still complicated. However, I believe that there is a routine to globally fit that does not require the very cumbersome first manual fitting. Can anybody please give me a hint? Thanks a lot, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

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how to find size of a molecule using Chimera
by Aditi Laddha 10 Oct '22

10 Oct '22

Hi Elaine, I wanted to find the size of a molecule which acts as a substrate (consisting of multiple elements) for my protein, I want to know the diameter of the molecule. But I am unable to find a way to do it. Can you please guide me through the process of determining the size of a molecule? -- Regards, Aditi Laddha PhD Scholar Indian Institute of Technology, Kanpur, Uttar Pradesh 208016

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Enquiry about the ligand library generation by scripts in Chimera
by Zhenjiao Du 07 Oct '22

07 Oct '22

Good morning, Dear Professor, My name is Zhenjiao Du, from Kansas State University. I am employing molecular docking for peptide screening and need to build peptide ligands for docking screening. I used to generate ligand by VMD and then energy minimized by molecular dynamics simulation, but the final conformation is not that matchable to the crystallography results. Chimera generated ligands perform a better job. I find Chimera provides amazing ligand energy minimization protocols, but there is no any resource for the scripts based ligand generation and minimization since I might need to generate thousands of peptide ligands for virtual screening. I find Chimera also supports python programming. Could you please provide me some information for the ligand generation by Chimera based on python scripts? I really appreciate it. I am looking forward to your reply. Sincerely, Zhenjiao Du Vice president of CAFS Student Committee Ph.D. student, Cereal Chemistry Grain Science & Industry, Kansas State University 150A Waters Hall, Manhattan, KS 66502 Pronouns: He/His

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Unit cell for dcd
by Huang, Caleb 05 Oct '22

05 Oct '22

Hello, I'm trying to make a psf+dcd movie with periodic boundaries on. The feature I'm looking for I believe is "Unit Cell", but it seems to only work for pdb files. Is there a way to create repeating cells using psf+dcd files? Thanks for any help! -Caleb

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