December 2022 - Chimera-users - RBVI Mailing Lists

Chimera interface to Modeller
by Vonderviszt Ferenc 03 Sep '24

03 Sep '24

Hello, I have been using the Chimera interface to Modeller via a web service. This service has been down for a few days. It always stops with the following error message: Service 'opal:Modeller9v8Service' is unavailable What should I do? Please help me. Thanks, Feri

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Finding SASA for individual residues
by Prathvi Singh 29 Aug '24

29 Aug '24

Hi Elaine, Can I use chimera or chimeraX to know the solvent accessible surface area (SASA) for selected residues? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Question about save images
by Chang, Jufang 29 Apr '24

29 Apr '24

Hi, there, I used Chimera for a very short period of time. When I just started using Chimera I was able to save image by going to "file" and "save image" to save the image on the display window. For some reason, this stopped working. Now, after I did the same thing, the image I saved has complete blackness (attached). I wonder whether I might get be able to get help from you. I also tried using command line to save image. The result is the same. The exact procedure I used are: Go to "Presets", choose "publication 1" , then go to "File" and "save image" I used window system. Thank you J ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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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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