- Chimera-users - RBVI Mailing Lists

Transfer of docked substrate co-ordinates
by Jayashree Chittari 08 May '21

08 May '21

Respected sir/ma'am Greetings for the day!!! I have docked ligand into an enzyme which contains two active sites. My docked ligand is in one active site. I want to transfer the ligand conformation from one active site pocket to another using superimpose option in chimera. Find herewith the attached file of PDB in which i want to transfer propionaldehyde coordinates from one active site to another is there any way that we can transfer the docked confirmation coordinates into another chain. Kindly, help me to solve this issue. It will be helpful if you suggest the process. Thank you Regards Chittari Jaya Shree

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Measuring rmsd without having exact number of atoms
by Ahmad Khalifa 07 May '21

07 May '21

Hi, Is there a work around measuring rmsd between two structures of the same protein, with one of them missing some segments, without having to rebuild / model the missing parts?! I'm thinking of writing a quick script to check for the matching segments, calculate rmsd for those and take an average of these measurements, unless there's a quicker way to do it! Regards.

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Chimera - remote start up issue
by Filip Kadlec 07 May '21

07 May '21

Good afternoon! I haven't found a solution to this problem in one of your user threads, internet and I haven't succeeded resolving the issue. I have installed chimera 1.15 today and it runs well when working on the desktop. However, it would be very convenient if I could run chimera remotely. Chimera is installed on Centos 7, I am trying to remotely operate this PC with Windows 10 PC using MobaXterm. When I run chimera as chimera --debug: initializing general preferences loading Tix initializing graphics create application loading Pmw creating main window creating menus creating toolbar creating viewer initializing OpenGL X Error of failed request: GLXBadCurrentWindow Major opcode of failed request: 146 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 2711 Current serial number in output stream: 2711 With OpenGL on Centos-7 PC glxinfo | grep "OpenGL": OpenGL vendor string: Mesa Project OpenGL renderer string: Software Rasterizer OpenGL version string: 1.4 (2.1 Mesa 10.5.4) OpenGL extensions: Have you encountered such problem? Could the problem be with coliding OpenGLs, or graphical transfer through mobaxterm? It would be a major help if you could point me in the right direction. Thank you in advance and have a great day! Kind regards Filip Kadlec

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The app is not working
by Fatma Elzahra Alhuassein Elfourtia 07 May '21

07 May '21

HI I am trying to use the app for my gene but When I try to open the gene in the Chimera because it shows me an error. Please reply me as soon as possible Thank you IMPORTANT NOTICE OF DISCLAIMER The information in this e-mail and any attachments is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you are not an intended recipient, please delete the message and any attachments and notify the sender of misdelivery. Any views expressed by an individual within this e-mail do not necessarily reflect the view(s) of UCSI University wholly owned by UCSI Education Sdn. Bhd. and shall include but not limited to UCSI Group Holdings Sdn. Bhd. and all of its subsidiaries and associated companies.

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Adjust torsion angles
by Moradkhan, Tiglath A 07 May '21

07 May '21

Hi I'm using the adjust torsions tool in Chimera. I was wondering whether there is an easier way of selecting several amino acids at once and adjusting their torsion angles rather than selecting them individually. I'm working with dimers and trying to select individual amino acids would take a very long time. Thank you Tiglath

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job opening for ChimeraX developer
by Elaine Meng 06 May '21

06 May '21

Hello everybody, We're looking for somebody to join the ChimeraX development team! Please see this posting for details: <https://sjobs.brassring.com/TGnewUI/Search/Home/Home?partnerid=6495&siteid=…> On behalf of the team, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Contact in angstrom
by Arthur Pereira da Fonseca 06 May '21

06 May '21

Hello, I’m trying to measure contacts between a protein and a peptide using Chimera. I have to do this with different angstroms distances, 2, 3 and 4 Å. I'm using the command line: findclash :.A test :. B overlap -0.4 hbond 0.0 namingStyle simple save However I don’t know exactly how to modify the overlap to the desired distances. Which values can I use to measure contacts within 2, 3 and 4 Å. Thanks in advance, Arthur Pereira

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python code to loop over molecules
by Julian Tirado-Rives 04 May '21

04 May '21

Dear Chimera (and ChimeraX) team: I need to find some python example or code snippet capable of looping over all the molecules in a particular model and do some actions separately in each one. In our research we use several different docking programs and other ways of generating poses of protein-ligand complexes, and using several different programs to analyze them gets quite complicated. Instead, we've found that the easiest way is to generate from each code, or using conversion utilities such as babel, a pdb file of the host and a sdf or mol2 file containing all the ligand poses and read them into chimera. An excellent program, by the way. We use it all the time. I would love to automate the process even further by doing all the coloring, rendering, Hydrogen Bond and contact analysis, etc. in Python rather than manually. I have been trying to do this, but have not found a way to do the following: If we have, for instance, the host in model #0, and the ligand poses in model #1 (#1.1, #1.2, ..., #1.N): - Get from chimera the number of molecules in model #1 (e.g what is N) - loop from the first #1.1 to the last #1.N molecule - do some cations there (e.g select, color, find HB's, etc) I think this should be a problem other people have encountered and solved before, but I have not been able to find an example in your depository, the mailing lists, or even the book ... I would appreciate your input. Thanks for your help, and for an excellent program! - Julian - -- ----------------------------------------------------------------- | Julian Tirado-Rives | | | Department of Chemistry | Phone: (203)432-3356 | | Yale University | Fax: (203)432-6144 | | P. O. Box 208107 | email: Julian.Tirado-Rives(a)yale.edu | | New Haven, CT 06520-8107 | | -----------------------------------------------------------------

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Rotate model
by C.J. 03 May '21

03 May '21

Hi all, I tried "turn y 180 #1" ( https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html) but it doesn't work. It said "turn frame arguement must be an integer". While I tried "turn y 180 0 #1" or "turn y 180 1 #1", it said "wait_frames arguement not implemented". Even "turn y 180 0 0 #1" doesn't work. Did I miss something? Thank you! Jianhao

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Combine focuse refined maps in Chimera
by Zheng, Fengwei 03 May '21

03 May '21

Dear Chimera developers: Thank you so much for developing this powerful and elegant software for our community! I am a newbie in cryoEM, and recently I got a consensus map, and split it into two parts to do the further focused refinement, after that I want to combine them together, and then to build my model. I learned that the command "vop maximum #0 #1" can achieve this, what I did is that, firstly, I used this command to merge my consensus map with one focused map, and then merged the resulted map with my second focused map, but it seems that the order of those two maps in my executable command (e.g. #0 #1 or #1 #0) will lead to slightly different resulting map~ I just wondering if this is the correct way to combine my focused maps, or there are other commands can achieve this better? Appreciate! Best, Fengwei

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Fwd: Hydrogen bond
by Eric Pettersen 03 May '21

03 May '21

> Begin forwarded message: > > From: shakira shukoor <shakirashukoor1993(a)gmail.com> > Subject: Hydrogen bond > Date: May 2, 2021 at 3:09:46 PM PDT > To: chimera-bugs(a)cgl.ucsf.edu > > Dear sir > Does chimera software have any option to set the distance and angle criteria to view the hydrogen bond. I was not able to see any hydrogen bond in my system although hydrogen bonds do exist which I have confirmed from vmd. Why is it not visible in chimera then? > > -- > Best Regards > > Shakkira E > PhD student INSPIRE Scholar > Department of Chemistry > sdmdlab <http://sdmdlab.xyz/>-iitp.com <http://iitp.com/> > IIT Patna > Bihta > Patna 801106 >

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Problem downloading Chimera
by Mahmoud Soliman 02 May '21

02 May '21

Hello there, We are trying to download Chimera, however, the link below never works, not sure if the server is down, but we have been trying for a few days with no luck. Can you please guide us on how to download chimera perhaps you send us a working link. <%0b%0dhttps:/www.cgl.ucsf.edu%20›%20chimera%0d> https://www.cgl.ucsf.edu › chimera<%0b%0dhttps:/www.cgl.ucsf.edu%20›%20chimera%0d> Thanks & Best Regards -------------------------------------------------------- Prof. M Soliman Professor of Pharmaceutical Chemistry M.Pharm, B.Pharm, MPhil/PhD (Bath, UK) Discipline of Pharmaceutical Sciences School of Health Sciences University of Kwazulu-Natal Westville Campus, Durban 4000 Email: soliman(a)ukzn.ac.za<mailto:soliman@ukzn.ac.za> Webpage: http://soliman.ukzn.ac.za/ ---------------------------------------------------------

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2D panorama view of a 3D model
by Kandolf,Susanne 30 Apr '21

30 Apr '21

Hello, I was wondering if it is possible to display a 3D model as a 2D panorama view? I would like to show all sides of a holoenzyme and instead of taking several pictures of each view, I thought it would be more convenient to have one picture displayed as panorama showing all sides at the same time. Thank you for your help, Susanne …………………………………………………………………….. Susanne Kandolf Research Technician at Haselbach Lab Mobile: +43 699 17250493 susanne.kandolf(a)imp.ac.at<mailto:susanne.kandolf@imp.ac.at> www.imp.ac.at<http://www.imp.ac.at> IMP Research Institute of Molecular Pathology Campus-Vienna-BioCenter 1 1030 Vienna, Austria Part of Vienna BioCenter www.viennabiocenter.org<http://www.viennabiocenter.org>

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Problem Saava9ng merged PDB Files
by Stephen P. Molnar 30 Apr '21

30 Apr '21

I am using Chimera v-1.14 (build 42094) on my Debian Buster Linux computer and have run into a problem saving a pdb file containing two pdb files. The files are attached to this email.This is a portion of the combined flies: The structure of the D21.pdb file isthe ball image. I followed the instructions in the Building Structures, Modifying and Saving Data in the Help pages. However, when I open DD21Mod1 in LigPlot to identify the docked ligand I get: Clearly, this is not the ligand docked int the active site. I have used LigPlot on a number of pdb files with good results and am forced to conclude that there is a problem with D21Mod1.pdb. I would appreciate help in solving this problem. Thanks in advance. -- Stephen P. Molnar, Ph.D. www.molecular-modeling.net 614.312.7528 (c) Skype: smolnar1

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problem (exit code -1073741819)
by Ichrak Benamri 23 Apr '21

23 Apr '21

Hello, I hope you are doing well. I have problem launching the chimera tool (error code: -1073741819), I don't know exactly where the problem is. Please, can you help me? Thank you [image: image.png] -- *Ichrak BENAMRI* PhD Student in Bioinfomatics *+212648548583* ichrakbenamri(a)gmail.com Systems and Data Engineering Team, National School of Applied Sciences, Abdelmalek Essaâdi University, BP1818 Route Ziaten, 90 000, Tangier, Morocco Chlamydiae and Mycoplasma Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco

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Four letter residue names
by Francesco Pietra 21 Apr '21

21 Apr '21

Hi all A pdb file deriving from a mmCIF file (with chimerax) and comprising both nucleotides and proteins, shows the protein residue names with four characters (i.e., using also column 21), such as ALAM in one subunit, or GLNm in another subunit. I read on passing somewhere (and I am unable to trace that back) that chimera accepts such four character names but was unable to find a description from chimera help. I also got lost in deciphering the intricacies of mmCIF files. What is the scope of the column 21 character? Could that simply be ignored, or deleted, for use with the CHARMM FF? Thanks for advice francesco pietra

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Chimera Errors
by Henry Shook 18 Apr '21

18 Apr '21

Chimera Team, I have been using Chimera to test several Sialic Acid isomers on the Sars-CoV-2 spike protein over the past couple of months and a couple of days ago, I have been getting this error telling me that there was an "application stderr" and "application stdout". Previously to a couple of days ago, anytime I tried to run it during the day, this message would show up, however, I was able to run the docks from 9-12 pm at night without any problem, so I just worked on the docking during that time. Now, no matter what time I run the docks at, this message shows up. I have not changed any procedures from when I started until now. Is there a way I can fix this problem? I attached a screen recording of my procedures and how I arrived at the problem. Here is a link <https://drive.google.com/file/d/1QkQakaG7QnY_pjJsbdlK0HWNEuupnJqJ/view?usp=…> if the video does not load. Thanks! Henry Shook Screen Recording 2021-04-18 at 11.19.06 AM.mov <https://drive.google.com/file/d/1QkQakaG7QnY_pjJsbdlK0HWNEuupnJqJ/view?usp=…>

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ADP EM Chimera plugin
by Eric Pettersen 15 Apr '21

15 Apr '21

Hi Vilde, Since ADP EM is a third-party plugin, I don't know that I know that much more than you about how it works. Hopefully the plugin developers will get back to you. Nonetheless, I can offer some generic advice about seeing/finding the fitted structure. First, check the Model Panel (Favorites→Model Panel) to ensure that the structure model is shown (the "Shown" column for the structure model is checked). Second, type the 'window' command (Favorites→Command Line) to ensure the view is large enough to show the position of the structure. Third, click on the color well in the Volume Viewer panel (the square next to "Color") and adjust the 'A' component of the color (A = alpha, or opacity) so the the contour surface is semi-transparent, in case the structure is completely within a contour. --Eric Eric Pettersen UCSF Computer Graphics Lab > Hello, > > I’m trying to use the ADP EM molecular fitting tool (Chimera Plugin) to fit my PDB-models into a low resolution map. The plugin works as it should, but I’m having trouble visualizing the solutions. Once the fitting is finished (the table with all the coordinates is produced) and I chose for example solution 1, the PDB structure disappears in the Chimera Window. The EM map is still showing. If I click on the “Back to initial”-button, the PDB structure comes back, but in the initial position, of course. I have tried to save the solutions, but they are still not showing (the solutions are selected as “show” as a cartoon in the model panel). According to the description of the plugin developers, the solutions/fits should be visualized just by selecting one, no extra steps needed. > I’m doing something wrong in Chimera or is there a bug? > I have tried with the two latest versions of Chimera for Windows (1.14 and 1.15), with the same result. > > Any help or advice would be much appreciated! I have also tried to contact the developers of the plugin, but no response so far. > > Best regards, > Vilde Leipart > PhD-student, > > Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences > Høgskoleveien 12, 1430 Ås, Norway > > Honey Bee Research Lab, Arizona Sate University > 427 East Tyler Mall, Tempe, AZ 85287

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Pixel size/box size and map display
by Cynthia Lee Page 14 Apr '21

14 Apr '21

Hi, I have three maps to be used in Relion for reference models. All of these maps are different in pixel size and box size, however they display as the same size in Chimera, with the same size outline box. The voxel size in volume viewer is correct according to the pixel size I designated in Relion_image_handler. I assumed that these maps would be different in size since they have different pixel sizes and box sizes. Can someone set me straight on this? Many thanks, Cynthia

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Need help- Why there is network connection
by Siddhartha Pradhan (Contractor) 14 Apr '21

14 Apr '21

Hi, Before we install any software in our system within Gilead organization, we do the software security assessment. During our assessment for " UCSF ChimeraX v1.1", we found below external network connection is being made. 1. Connection to 13.107.4.52 on tcp/80 (www.msftconnecttest.com) * Why the network connection is being made and what is the reason behind it? * Is there any sorts of data transfer is being happened from the user system, if yes then what kind of data are being transferred? * Is there any settings in the application to disable the network connections? * If users can use the software to export/import data. Is there any cloud service associated with this? It would be of great help if you can kindly give a clarity for the above network connection ASAP. Regards, Siddhartha

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Need help- Why there is network connection
by Siddhartha Pradhan (Contractor) 13 Apr '21

13 Apr '21

Hi, Before we install any software in our system within Gilead organization, we do the software security assessment. During our assessment for " UCSF Chimera v1.15", we found below external network connection is being made. 1. Connection to 169.230.27.29 on tcp/80 (www.cgl.ucsf.edu) * Why the network connection is being made and what is the reason behind it? * Is there any sorts of data transfer is being happened from the user system? * Is there any settings in the application to disable the network connections? * If users can use the software to export/import data. Is there any cloud service associated with this? It would be of great help if you can kindly give a clarity for the above network connection ASAP. Regards, Siddhartha

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combine models
by Francesco Pietra 11 Apr '21

11 Apr '21

Hi (1) I am faced by the coordinates for a nucleics/protein assembly being given in several bundle.pdb, while I need a sequential, continuous pdb file that comprises all nucleotides and proteins, not made of models (2) If I load all the bundles to chimera, I see all expected ligands around the small molecule. (3) With all models selected, copy/combine (adopting default first model as reference and allowing renaming chains) generates a new model. The new model laks some proteins that should lie near the ligand, as described at (2). I feel that I am missing something. Thanks for advice francesco pietra

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greeting and acknowledgement
by kajihara 09 Apr '21

09 Apr '21

Dear Prof. Ferrin, Dear stuff of Chimera, I am prof Yasuhiro Kajihara, Department of chemistry, Osaka University. Last April, Corona pandemic suddenly attack us, and our university closed in-person style classes. I needed to do online class of biochemistry. I recommended students to download UCSF Chimera for understanding protein structure and behavior. The Chimera soft wear was great help for us under the terrible Corona Pandemic and all students enjoy to deal with Chimera. They got unbelievable knowledge through the Chimera. I could not find a suitable word to express my thank. I thank you again for your great support and kindness to deliver it as free. Within a week 80 students will start download chimera. So, I need to send greeting e-mail to give my thanks. Sincerely Yasuhiro Kajihara, Ph. D. Department of Chemistry Osaka University Machikaneyama, 1-1, Toyonaka, 560-0043 Japan kajihara(a)chem.sci.osaka-u.ac.jp

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Where does Chimera copy command save images?
by Martti Tolvanen 09 Apr '21

09 Apr '21

I have tried to use the command copy on command line to save images, with a goal to do that in a script. The messages of rendering a high-res image and image saved come up, but the file is nowhere to be found. My guess is that the default save location is in the Chimera program folder, which would not be permitted, but Chimera just doesn't see it as a failed attempt. I do have a workaround of including the full path in a filename, but I'm just curious where the file would be going by default, and whether there is some command to change the working folder by a command. FYI it's Chimera 1.15 in Windows 10. Martti Tolvanen University Lecturer in Bioinformatics U of Turku, Finland

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Query about adding charge to ligand
by Nirban Dey 19MSM0098 08 Apr '21

08 Apr '21

Hello, I am a Masters student of VIT University India. I am using chimera to prepare my ligand. In the add charge option I noticed that if my ligand has negative or positive charge and I try to add AM1-BCC it gives error but I can add Gasteiger charge. Even if I set charge to +0 for the ligands that have charge like -1 or +1 and try to add AM1-BCC it gives error. I want to know what is the reason that Gasteiger charge can be added but AM1-BCC cannot be added..Kindly help me in this regard. Thanking You Nirban

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