- Chimera-users - RBVI Mailing Lists

Measuring rotation
by JAVAD KARIMBAYLI 18 May '21

18 May '21

Greetings dear sir/madam I was trying to measure the rotation of my protein before vs after activation using the "measure rotation #0 #1" command, which worked smoothly. Then I wanted to check the rotation of specific residues. However, when I tried to specify residues, for example, residue 45 of model0 vs model1, the code didn't work. I have gone through Chimera documentation but didn't really find how to solve the issue. So, I kindly ask for your suggestions about how I may get residue-specific rotations. Thank you in advance Javad Karimbayli

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Covalent bond making and docking
by Zhang, Bixia 14 May '21

14 May '21

Good evening, I was trying to make a man made side chain, which is serine plus uracil. I used the command "bond sel" to connect the oxygen and nitrogen. Then I was trying to do docking to see if this mutation changed the binding affinity. However, after I ran dock prep, the uracil was got rid of because of "poor connection". I am wondering if this arbitrary bond is feasible in chimera and can I do docking with this artificial model? Thank you, Bixia

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Question about error: "the exit code was: -1073731819"
by Sergio Garay 13 May '21

13 May '21

Dear Chimera Users My name is Sergio Garay, I have installed chimera-1.15-win64.exe on Windows 10pro 64bit. But when the program starts to run, the system gives me the following error message and the program closes: chimera exited abnormally; the exit code was: -1073731819. use the -- debug command line option for the full error message I tried installing the two previous versions of the program, with the same result. My PC has a Radeon RX 580 series videocard, and the system uses a WDDM 2.7 video controller. Could you give me any advice on how to fix this problem? Sincerely -- *Prof. Dr. Sergio Garay* *Càtedra de Práctica Profesional de Bioquímica* *Cátedra de Bioinformática* *Facultad de Bioquimica y Cs. BiológicasUniversidad Nacional del LitoralSanta Fe - ArgentinaC.C. 242 - Ciudad Universitaria - C.P. S3000ZAAArgentinaPh. +54 (342) 4575-213Fax. +54 (342) 4575-221 *

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Enquiry regarding application
by Prem Rajak 13 May '21

13 May '21

Dear Sir/madam, I have a query regarding the use of UCSF Chimera for molecular docking studies. I am a faculty at an University and would like to analyse my molecular docking research studies using UCSF Chimera. Moreover, I would like to publish the images thus analysed in national/international standard journals. Publications may be multiauthored. Therefore, please let me know whether I can use the software free of cost or I have to purchase the licence. Looking forward to your reply. Thanks and regards, Dr. Prem Rajak Kazi Nazrul University West Bengal, India

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Help for Chimera launch fail
by 黄华 12 May '21

12 May '21

Dear Eric Pettersen, This is a Chimera User in South China Normal University(Guang zhou, China).  Now, I found I can not start the Chimera even after I reinstalled. Would you tell me how could I fix this problem? This is the message after I launch Chimera-debug: Cannot execute 'gzip': no automatic decompression of .Z files initializing general preferences loading Tix initializing graphics Return code: -1073741819 Press return or enter to to exit thanks for your help! hua ------------------ Hua Huang Principal Investigator School of Life Science South China Normal University Guangzhou, China 黄华华南师范大学M邮箱/未归类/生命科学学院/教职工/办公华南师范大学始建于1933年，是一所学科门类齐全的国家“211 工程”重点建设大学。 “艰苦奋斗、严谨治学、求实创新、为人师表 ”是华南师范大学校训。  

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BLAST fix
by Eric Pettersen 12 May '21

12 May '21

Hi all, The RCSB switching off http access and only allowing https (which had been announced) unfortunately broke the fetching of PDB info associated with BLAST results, basically breaking the BLAST tools in both Chimera and ChimeraX. Fixes have been applied and will be available in tomorrow's daily builds. For ChimeraX, also available in the 1.2.3 release candidate -- hopefully also out tomorrow. --Eric Eric Pettersen UCSF Computer Graphics Lab

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Re: [Chimera-users] S33C .mrc file
by Elaine Meng 11 May '21

11 May '21

Dear Neha, Now you tell me that you opened 1qwa as the pdb (atomic structure) file, so this mrc file is completely irrelevant. I believe you just used the wrong steps to save the pdb. You need to use menu: File... Save PDB, and in that dialog "Save models" area, choose the atomic structure model. (Hiding the map does not matter, centering the view does not matter, it is only what you choose in the dialog). Then as Tom already said, you also have to turn on the "Save relative to model" option and chose the map model as the one you want to save the PDB relative to. Here is the help for the Save PDB dialog: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb> I hope this helps, Elaine ---- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 10, 2021, at 9:15 PM, Neha Goel <nehagoel24march(a)gmail.com> wrote: > Dear Elaine, > Thank You. Here I .mrc is attached. I was using a reference pdb like 1qwa from pdb database. > Regards > Neha Goel

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Unable to save file in pdb
by Neha Goel 10 May '21

10 May '21

Dear Chimera, I have a .mrc file. I reopened the file in chimera and would like to save it in pdb. I am unable to save it. It needed the molecular model pdb. Kindly guide me the way to save it. Regards Neha Goel

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Rotate chains independently
by Roy Batty 10 May '21

10 May '21

I have a pdb with a homodimeric conformation for two alpha helix transmembrane domains. This structure features a cross-like conformation, interacting at given residues. I want to rotate each of the domains 15º along the z-axis. So for example, something like this would be fine: select :.A (select chain A) turn z -15 *@*ca,cb (rotate chain A 15º, from the residues given as an anchor point) Is there anything like this? Thx

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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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Re: [Chimera-users] Chimera-users Where does Chimera copy command save images?
by Susan 08 Apr '21

08 Apr '21

Hi there honey! I'm a 30 years old lonely housewife looking for an affair. I'm ready to try anything You can see my photos, you can see them right here <http://gallery.prince-ss.com?n=frfya&s=687474703a2f2f646174696e6773722e636f…> On Thu, Apr 8, 2021, at 5:41 PM, Chimera wrote: >Hi Martti, >I don't know the answer, but another thing you can do is use the Chimera cd command to change the working directory so that later in the same session, you no longer have to specify it in the filenames of files to open or save. (Alas, there is no Chimera pwd command to tell you what it thinks is the current working directory, however.) > > >I hope this helps, >Elaine >----- >Elaine C. Meng, Ph.D. >UCSF Chimera(X) team >Depa >

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rna model
by Divita Mathur, Contractor Code 6910, FN 06 Apr '21

06 Apr '21

Hello Chimera community I am trying to run the “rna model sequence #0” code but it is returning the following error: IndexError: list index out of range File “…path/RNALayout/rna_layout.py”, line 393, in place_residues rprev = rlist[0] See reply log for Python traceback. Anything elementary that I am missing? My fasta file is very simple and it is stored in the Documents folder. Regards, -- Divita Mathur, PhD Research Assistant Professor George Mason University & Center for Bio/Molecular Science and Engineering Naval Research Laboratory (202) 767-0687 (Office)

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ENQUIRY
by ogochukwu ngozi 05 Apr '21

05 Apr '21

Dear Concerned,I am a PHD student from University Putra Malaysia. This is my first time using Chimera, please I need your assistance. I want to use chimera to calculate RMSD values, could you direct me on steps to take please? Thanks as I await your kind reply.Ogochukwu Nwaefulu

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Re: [Chimera-users] ResProp Python code
by Elaine Meng 05 Apr '21

05 Apr '21

Dear Chittari Jaya Shree, I can't answer about python, but maybe you didn't know about the related feature that you can simply assign names to whatever you want. There is no need to use the ResProp tool if this is all going to be in a script anyway. For example, command: alias neutral :ile,val,leu,phe,cys,met,ala,gly,thr,ser,trp,tyr,pro,gln,asn ... will then let you use "neutral" in other commands, e.g. select neutral "alias" command <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.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 Apr 5, 2021, at 4:54 AM, Jayashree Chittari <jayashreechittari27(a)gmail.com> wrote: > > Respected sir/ma'am > > Greetings for the day! > I want to make a new category named as neutral in which I would assign some amino acids to this category. So, in GUI we know that it could be done through tools-->structural analysis--> ResProp. > > My question is how to do the similar process in python, like how to assign certain amino acids to a new category and then perform the selection("select neutral")? > > Here is the attached ss of Residue category definition. I want to use this process in python where the new category contains assigned amino acids. > > Kindly help me in this issue, it would be very grateful if you suggest the code. > thank you, > > Regards > Chittari Jaya Shree > > <Capture.PNG>

1 0

translation along x,y and z
by Ashok Nayak 01 Apr '21

01 Apr '21

HI Elaine, I want to know the rotation and translation components along x,y and z separately from the rotation matrix obtained from chimera reply log upon fitting a model into a map. Will it be possible to know? Matrix rotation and translation 1.00000000 -0.00000000 -0.00000000 1.83458738 -0.00000000 1.00000000 -0.00000000 1.15016978 -0.00000000 -0.00000000 1.00000000 -0.53835221 Axis 0.00000000 0.00000000 1.00000000 Axis point 0.00000000 0.00000000 0.00000000 Rotation angle (degrees) 0.00000000 Shift along axis -0.53835221 thanks, Ashok

2 2

identifying and counting selected residues
by Smit Patel 01 Apr '21

01 Apr '21

3 3

count the selected residues in linux terminal
by Jayashree Chittari 31 Mar '21

31 Mar '21

Respected sir/ma'am Greetings for the day! I want to use chimera commands in shell scripting or python. So, my problem is how to count the residues using Chimera? in gui we know that there is a magnifying icon at the lower right portion of the window, but while running in linux terminal I'm unable to generate the same results. Here is the attached ss of inspect selection, so if I want to print this in linux terminal what steps should I follow to get to this result? I'm trying my best to search in the tutorials but unable to create a command related to inspect selection. Kindly help me in this issue, it would be very grateful if you suggest the code. thank you, Regards Chittari Jaya Shree

1 0

Questions about probabilities in the Dunbrak library
by Moradkhan, Tiglath A 31 Mar '21

31 Mar '21

Hi I'm trying to understand the meaning of probabilities in the Dunbrak library. From what I've found, this parameter is a measure of how probable a particular rotamer is to be found within a given conformation. Is this what this is? Thanks Tiglath

2 1

in *.gro file, chimera takes CL atom as C (in compound) and gives it wrong color
by Lei Qian 31 Mar '21

31 Mar '21

Dear users, Could I ask a question on chimera? Thanks! I tried to open a gro file (small compound) using chimera. Like below: ... ... 1 LIG CL 18 x.xxx x.xxx x.xxx 1 LIG CL1 19 x.xxx x.xxx x.xxx ... ... Although chimera shows the CL name "CL" when the cursor is above the atom, but the CL atom color is incorrect: the same as Carbon. I tried to change the "CL" to "BR", and the chimera shows the correct color: dark red. It seems weird to me. Could you please give me any suggestions? Thanks! Best, Lei

3 11

No MMTK name for atom "HD2" in standard residue ASN
by Sina Analoui 31 Mar '21

31 Mar '21

Hi All, I am currently attempting to minimize a large molecule (ACE2 alongside the RBM of a spike protein). I Dock Prep both chains (A chain is ACE2) and then go on to attempt to minimize them. However, I keep returning this error "No MMTK name for atom "HD2" in standard residue ASN" I have attempted to remedy this by rewriting parts of the PDB file and importing it back in and have had no success. Is there any way to either remove NAG that is associated with these residues or change this hydrogen to something feasible? This seems to be an issue for only the ASNs on the A chain and not elsewhere on the molecule Thank you in advance for your help

2 3

Debug
by 안예림 29 Mar '21

29 Mar '21

Hi I have tried to make a movie of MD simulation by Chimera. I could be done one time, then for other MD’s it exits abnormally with the code -1073741819. Even I have decreased the size of .xtc file, it exits abnormally yet. Please check my capture picture. I have reinstalled chimera, but the problem did not resolve.What should I have to do ? I need your assistant. Thanksbe

2 1

Can't open a VTK file in chimera
by Diego Amaya 24 Mar '21

24 Mar '21

Hello, I exported a surface in VTK format with the chimera extension but I can't open this vtk file back with chimera. This behavior is expected ? Best regards -- Diego A. Amaya Ramírez -- *Aviso legal:* El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web www.unal.edu.co <http://www.unal.edu.co/>.* *Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.

3 2

how to generate different starting points to do md simulations
by Seera Suryanarayana 22 Mar '21

22 Mar '21

Dear chimera users, I have a small peptide of 20 residue length and I would like to do the simulations of this peptide at different starting points. How could one can generate the different starting points? Can I use the replica exchange MD simulations to generate the different starting points? I request you to please suggest me how to generate different starting points of peptide. Thanks in advance Surya Graduate student India.

2 1

Re: [Chimera-users] select only side chains to calculate contacts
by Elaine Meng 21 Mar '21

21 Mar '21

> On Mar 20, 2021, at 10:03 PM, Jacqueline Vitali <jackie.vitali(a)gmail.com> wrote: > > Hi Elaine, > > How do I calculate contacts among side chain atoms of a given category (aliphatic, hydrophobic, etc). Even when I select them, I cannot remove the main chain of them in the calculations. > > Thank you. > > Jackie Vitali Hi Jackie, Please send questions to chimera-users(a)cgl.ucsf.edu (CC'd here) rather than my individual address to clarify which program you're using and to ensure it gets answered. I'm assuming you are asking about Chimera. (If you're asking about ChimeraX, there is a different address: chimerax-users(a)cgl.ucsf.edu ...and the answer might be different.) You can use the "select" command and intersect your selection with sidechain only. It's explained in the command-line specification page: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#buil…> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#comb…> Examples: select hydrophobic & without CA/C1' select :phe,tyr & without CA/C1' (or "with" instead of "without" if you wanted to include the alpha-carbon) You can't see the difference if you are showing ribbons. You can only see the difference if displaying backbone atoms, e.g. menu: Presets... Interactive 2 (all atoms) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

Visualizing Amber Trajectory in MD Movie
by Jatin Kashyap 17 Mar '21

17 Mar '21

Dear UCSF Chimera Community, I am trying to visualize an Amber NetCDF(.nc) trajectory in UCSF Chimera using a tutorial.[1] I have two trajectory files of the same system: first, the solvated system, and second I stripped the water molecules in the CPPTRAJ utility of AMBER. I am using the same .top file for both visualizations; however first one showing me the system, although the water molecules are missing. But the second one is throwing me an error, and nothing appears in GUI window.[2] Please help me find out my mistake in the process as I am a beginner-level user of UCSF Chimera. Thank you very much. [1] http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html [2] Assigning chain ID A to 306 residues, e.g. SER fillCoordSet: coordinates [arg 2] must be same length as atoms TclError Exception in Tk callback Function: <bound method ComboBox._resizeArrow of <_Pmw.Pmw_1_3_3.lib.PmwComboBox.ComboBox instance at 0x7fc164add170>> (type: <type 'instancemethod'>) Module: <module '_Pmw.Pmw_1_3_3.lib.PmwComboBox' from '/Volumes/ChimeraInstaller/Chimera.app/Contents/Resources/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwComboBox.py'> (line: 350) Args: (<Tkinter.Event instance at 0x7fc164ae65a8>,) Event type: ConfigureNotify (type num: 22) Traceback (innermost last): File "/Volumes/ChimeraInstaller/Chimera.app/Contents/Resources/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/Volumes/ChimeraInstaller/Chimera.app/Contents/Resources/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwComboBox.py", line 351, in _resizeArrow bw = (string.atoi(self._arrowBtn['borderwidth']) + File "/Volumes/ChimeraInstaller/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 1336, in cget return self.tk.call(self._w, 'cget', '-' + key) TclError: invalid command name ".140468625963920.140468635650744.140468640420064.140468635457080.140468635625736.140468640714048.140468640714120.140468594528696.140468594529848" ================================================ Event contents: char: ?? delta: 0 height: 24 keycode: ?? keysym: ?? keysym_num: ?? num: ?? send_event: False serial: 79507 state: ?? time: ?? type: 22 widget: .140468625963920.140468635650744.140468640420064.140468635457080.140468635625736.140468640714048.140468640714120.140468594528696.140468594529344.140468594529488 width: 1194 x: 0 x_root: ?? y: 0 y_root: ?? TclError: invalid command name ".140468625963920.140468635650744.140468640420064.140468635457080.140468635625736.140468640714048.140468640714120.140468594528696.140468594529848" File "/Volumes/ChimeraInstaller/Chimera.app/Contents/Resources/lib/python2.7/lib-tk/Tkinter.py", line 1336, in cget return self.tk.call(self._w, 'cget', '-' + key) See reply log for Python traceback. —— Jatin Kashyap Ph.D. Student Dr. Dibakar Datta Group Department of Mechanical and Industrial Engineering New Jersey Institute of Technology (NJIT) University Heights Newark, NJ 07102-1982 Phone- (201)889-5783 Email- jk435(a)njit.edu

2 1

Orienting mol maps in space?
by Cynthia Lee Page 16 Mar '21

16 Mar '21

HI, I am a newbie with Chimera. I have learned a lot in this process of making reference maps for use in Relion, thanks to the tutorials and rich information available on this list and in the documentation for Chimera. I have followed this tutorial cool tutorial (https://www.cgl.ucsf.edu/chimera/videodoc/MicrotubuleSym/index.html) for making 14 pf tubes (using EMDB 5194), 1JFF ( alpha/beta tubulin) plus the A chain of 3B6U (KIF3B) to represent the monomer of this motor protein. I made a 15 resolution mol map of the resulting model, then cropped off the ends to make the volume flush at the MT ends using the Subregion selection feature in the Volume Viewer. When I open this map in Chimera it does not open as other mrc files open. Specifically, instead of looking down the microtubule (considered Z axis, I believe) I am looking at the X-Y axis. “Centering" the map in Volume Viewer only centers it horizontally, “orienting” the file does nothing. Where as, if I orient any other reference files (including Relion generated 3D.mrc files) the map volume will orient so that the viewer is looking down the microtubule. Please see the attache image, the yellow volume centers/orients correctly, the pink volume is the one I made via the tutorial and doesn’t orient. I am guessing I am missing a coordinate system to align this volume in space but I haven’t been able to figure out how to add this information to my mrc file. I am also assuming that this orientation information is important to include in the mrc file formats. Any help or insight much appreciated! Thanks, Cynthia PS I did try to "vop resample onGrid” using pink onto the yellow models and learned that’s how you can create the same voxel size (!), but it did not change the orientation capabilities of the pink model. [cid:84AEE0E2-633C-4425-9B01-EA6207A3F276@colorado.edu]

2 1

Occupancy clusters
by Yasser Almeida 16 Mar '21

16 Mar '21

Hello, I want to do an occupancy analysis of a rigid ligand in a MD trajectory. I used the MD Movie > Analysis > Calculate occupancy tool, and obtained the volume maps of each heavy atom of the ligand. To check, I also used the gmx spatial tool from GROMACS and the VolMap from VMD, to obtain the grids for the whole ligand, which have basically the same shape. This grid has a characteristic shape showing that particular orientations are stable through the MD run. I want to extract representative structures of these orientations, something like an "occupancy clustering". Note that I say orientations and not conformations. Since the ligand is rigid, there is no point to calculate the RMSD. So, what I want is to calculate clusters of orientations of the ligand in the binding site. Is this possible with Chimera? Thanks in advance, -Yasser

3 2

Problem with nucleotide objects settings for 1d86
by svle＠tiscali.it 16 Mar '21

16 Mar '21

Hi, I have a visualization that seems not a correct one for 1d86 for DT 20.b when using Actions -> Atoms/Bonds -> nucleotide objects -> settings... . Settings: Show backbone as: Ribbon Show sides( .... ) as ladder Ladder Options: Ignore non-base H-bonds: false Shows stubs: false Rung radius: 0.45 Using existing H-bonds: true In the png file the problem. Where I'm wrong? Thanks Saverio Con Tiscali Mobile Smart 30 4G hai minuti illimitati, 100 SMS e 30 Giga in 4G a soli 8,99€ al mese. http://tisca.li/smart30

2 2

render by attribute displacement of a NMA
by Giorgio Giardina 15 Mar '21

15 Mar '21

Hy, I have a pdb file containing the models (only CA atoms) describing the lowest mode from a NMA. I can easily generate a movie using the morphing tool, but I would like to visualize the mode as an image, using the render by attribute tool and with the displacement of each CA as value of the worm radius. How can I generate this attribute? Thanks in advance for you rhelp! Giorgio -- ------------------------------- Giorgio Giardina, Ph.D. Dep. of Biochemical Sciences (CU027) - Room T2 SAPIENZA - University of Rome Tel. +39.06.49910713 | Lab: http://www.macinmec.it/giorgio-giardina/ | Art: http://www.giorgio-giardina.com/ Art. 33 della Costituzione: *L’arte e la scienza sono libere e libero ne è l’insegnamento* -- ________________________________________________________ Le informazioni contenute in questo messaggio di posta elettronica sono strettamente riservate e indirizzate esclusivamente al destinatario. Si prega di non leggere, fare copia, inoltrare a terzi o conservare tale messaggio se non si è il legittimo destinatario dello stesso. Qualora tale messaggio sia stato ricevuto per errore, si prega di restituirlo al mittente e di cancellarlo permanentemente dal proprio computer. The information contained in this e mail message is strictly confidential and intended for the use of the addressee only. If you are not the intended recipient, please do not read, copy, forward or store it on your computer. If you have received the message in error, please forward it back to the sender and delete it permanently from your computer system.

2 3

Failure Running ANTECHAMBER
by Mailyn Terrado 12 Mar '21

12 Mar '21

To whom it may concern: I am trying to use Chimera for protein Energy Minimization. I encountered a problem in running the program. Please find the attached screenshots of the error details. The problem seemed to be with the ligand BEF (beryllium trifluoride). Any help would be greatly appreciated. Many thanks, Mailyn

2 5

ORCA XYZ FILES
by Rade Jibawi Rivera 10 Mar '21

10 Mar '21

Hello, I am a student from Nova Southeastern University, and I am conducting research where I am interested in utilizing your software "Chimera" for visualization of molecular dynamics. My concern is if your software will be able to create a movie of bond interactions with multiple time frames using ORCA XYZ output files. I would greatly appreciate it if you can give in some input. I hope to hear from you. Thank you for your time and consideration. Best regards, Rade Jibawi Rivera

3 4

Regarding Chimera vina executable file
by Heshani Mudalige 10 Mar '21

10 Mar '21

Dear Elaine, Hi, hope you are doing well. I used Chimera for protein docking. But I got stuck in the last step when setting the local path. I downloaded the windows version and that installed to C drive program files and like this C:\Program Files(86)\The Scripps Research Institute But even after browse even it doesn't show any vina.exe file when setting the local path.Can you please tell me where I can find that? Or how to check whether that properly installed or not? Inside the Vina folder there are 3 files which two were applications files.But no exe file is visible I went many tutorials and heard after 2020 we need to install Auto dock vina to support Chimera. I did that as well.But still I can't properly debug this. Different you tube videos they mentioned inside Vina folder can fine vina.exe or inside bin can find vina.exe. Apperciate your help on this and your earliest reply.Thank you Kind regards Heshani

3 2

Sidechain selection in Python
by achatz 10 Mar '21

10 Mar '21

Hello, I want to select a sidechain without CA in Python. The working command line select #0:30 & without CA/C1' is recreated in Python like this: chimera.selection.OSLSelection("#0:30 & without CA/C1'") But the lexer complains about an "illegal symbol in identifier" which is the apostrophe after C1. How do I solve this issue? Thanks Stefan

2 1

Problem trying to download Chimera
by Elaine Meng 10 Mar '21

10 Mar '21

> From: Austine Gozie <austinegozieaustine(a)gmail.com> > Date: March 8, 2021 at 11:47:40 PM PST > > Good day sir/madam, > > I am trying to download the ucsf Chimera software for my ongoing project but its not responding. When i try to proceed to download icon, the next page displays "cant open page or refresh page, connection failed" I need your assistance in helping me with the download methodology or right website to enable me download the software. Thanks in anticipation for your kindest help. Hello Austine, I don't know what you mean by "proceed to download icon". In the download page, you would click on the link for the installer that you want: <https://www.rbvi.ucsf.edu/chimera/download.html> Then it shows the license, and if you agree, then click the "Accept" button at the bottom of the page to start the download. Occasionally the website is down, but as far as I can tell it is fine right now. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

3 3

Scene transition is delayed in chimera animation
by Shanti Pal Gangwar 10 Mar '21

10 Mar '21

Hi All, I am trying to make scene based animation in chimera where every scene is rotated 360 by using action Roll 360. What I observe is that the scene transitions from 1 scene to another is extremely slow and not continuous also. For some scenes it is fast as well. How can I keep this transition minimum and fixed to all scenes to make a continuous animation. Thank you very much Shanti Pal

2 1

Fwd: error code -1073741819
by Tom Goddard 09 Mar '21

09 Mar '21

Beni's problem with Chimera not starting was a graphics problem related to supersampling / super-resolution / multisampling. Not clear whether the fix was to change a graphics driver setting or the Chimera multisampling setting. Beni's email below. Tom > Begin forwarded message: > > From: Beni Sued <benisued(a)gmail.com> > Subject: Re: [Chimera-users] error code -1073741819 > Date: March 9, 2021 at 1:50:10 PM PST > To: Tom Goddard <goddard(a)sonic.net> > > > That's impressive knowledge! I was indeed using supersampling and superresolution (not sure if They are the same as multisampling but it worked) > Thanks so much! > solved > > On Tue, 9 Mar 2021 at 20:54, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > Hi Beni, > > The gzip message is just misleading. It is not an error and is explained here > > https://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-July/011199.html <https://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-July/011199.html> > > The real problem is almost surely that your graphics driver is broken since it gets to "Initializing graphics" and then dies. Updating the graphics driver was the right thing to try. > > One other remote possibility is that some Chimera preference setting is causing startup to fail -- like maybe you enabled multisampling in the past and the new graphics driver wipes out whenever you try to use it. The location of preferences is > > C:\Users\username\AppData\Roaming\.chimera\ > > (from documentation here https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html>). You might rename that .chimera folder so Chimera starts with factory default preferences and try to start. > > Tom > >> On Mar 7, 2021, at 1:18 PM, Beni Sued <benisued(a)gmail.com <mailto:benisued@gmail.com>> wrote: >> >> Hey there >> I've been using UCSF chimera for some time with no problems but it is having trouble starting up, this is the error message: >> >> Cannot execute 'gzip': no automatic decompression of .Z files >> >> initializing general preferences >> loading Tix >> initializing graphics >> Return code: -1073741819 >> Press return or enter to to exit >> >> precisely like this gentleman: >> https://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-April/015675.html <https://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-April/015675.html> >> and this >> https://www.cgl.ucsf.edu/pipermail/chimera-users/2011-December/007021.html <https://www.cgl.ucsf.edu/pipermail/chimera-users/2011-December/007021.html> >> >> my dxdiag info is attached, nothing wrong jumps to me. >> >> What I've tried: >> - uninstalling and reinstalling Chimera >> - manually installing GZIP for windows ( https://sourceforge.net/projects/gzip-for-windows/ <https://sourceforge.net/projects/gzip-for-windows/> ) >> - updating drivers (graphics drivers and chipset drivers) >> - getting the alpha version of the program >> - going to and fro compute mode in the the graphical settings >> >> I'm using Chimera 1.15 and this is my hardware >> chipset b550m >> ryzen 5600x >> RX 590 >> >> in trying to fix it I learned about ChimeraX, I'm learning to use it, but I would still like to keep chimera until i can properly stop and change my workflow >> >> thanks so much, let me know if I missed any info >> <DxDiag.txt>_______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >

1 0

error code -1073741819
by Beni Sued 09 Mar '21

09 Mar '21

Hey there I've been using UCSF chimera for some time with no problems but it is having trouble starting up, this is the error message: *Cannot execute 'gzip': no automatic decompression of .Z filesinitializing general preferencesloading Tixinitializing graphicsReturn code: -1073741819Press return or enter to to exit* precisely like this gentleman: https://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-April/015675.html and this https://www.cgl.ucsf.edu/pipermail/chimera-users/2011-December/007021.html my dxdiag info is attached, nothing wrong jumps to me. What I've tried: - uninstalling and reinstalling Chimera - manually installing GZIP for windows ( https://sourceforge.net/projects/gzip-for-windows/ ) - updating drivers (graphics drivers and chipset drivers) - getting the alpha version of the program - going to and fro compute mode in the the graphical settings I'm using Chimera 1.15 and this is my hardware chipset b550m ryzen 5600x RX 590 in trying to fix it I learned about ChimeraX, I'm learning to use it, but I would still like to keep chimera until i can properly stop and change my workflow thanks so much, let me know if I missed any info

2 1

renseignements
by Camelia Hamadouche 09 Mar '21

09 Mar '21

je n'arrive pas a télecharger votre logiciel meme si je clique sur accepter on me dirige vers une fenetre disant quelle partie vous ne voulez pas accepter? alors que j'ai bien cliqué sur accepter

2 1

each rotation of the molecule in chimera will unexpectedly add an extra "c" at command line
by xiaoyu liu 03 Mar '21

03 Mar '21

Hello, I'm Xiaoyu Liu, a chimera user. Thank you for developing and sharing this powerful software. I have a problem now and bothered me for a while when using chimera. I'm wondering if you know how to solve it. I downloaded chimera-1.15-mac64.dmg <https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=mac64/c…> from "https://www.cgl.ucsf.edu/chimera/download.html" for my Mac OS Catalina(10.15.5). When I rotate the molecule with left mouse button, an extra character "c" will be automatically added in command line. Each rotation will result in adding one "c". Here I have some screen shot to show more clearly. [image: image.png] [image: image.png] [image: image.png] I tried to restart my computer. It is helpful within the first 10 minutes after the restart, but later it has the problem again. Please let me know if you know how to solve it. Many thanks! Best, Xiaoyu

2 1

problem with pdb file saved from chimera-autodock vina analysis
by Amol Ghodke 03 Mar '21

03 Mar '21

Hi, First of all thank you so much for making such a wonderful tool and sharing it freely with scientific community. I have been using chimera for sometime now and performed docking analysis using autodock vina. I recently come across a problem. After exporting pdb file with desired docking pose, I tried to run protein ligand interaction analysis on PLIP<https://plip-tool.biotec.tu-dresden.de/plip-web/plip/index> server. But ligand in my file does not get recognised for analysis. I opened pdb file in a text editor and upon looking care fully I see chimera saves receptor and ligand as separate model like this ATOM 7453 HD2 PRO A 462 15.986 11.983 20.450 1.00 0.00 H ATOM 7454 HD3 PRO A 462 16.532 10.334 20.885 1.00 0.00 H ENDMDL MODEL 2 HETATM 1 S1 CGT A 1 9.051 5.106 43.099 1.00 0.00 S HETATM 2 C6 CGT A 1 8.150 3.680 42.370 1.00 0.00 C After comparing it with the pdb file from pbd database I removed “ENDMDL” and “MODEL 2” and re-ran the PLIP analysis. This time it works but PLIP also mentions that – [cid:image001.png@01D7103D.5D0AB030] Analysis went well but the .pse file that I get from PLIP server does not allow me to show ligand in stick format in Pymol software. I suspect this is due to the original pdb file format. I also noticed that pdb file when opened in pymol shows ligand and receptor as different states which is not correct (if I am right). I have attached both original pdb file that I saved from Chimera-autodock vina and pse file from PLIP analysis. May I request to help me resolve this issue? Please let me know if you need any further information or clarification. Thanks for your time and support Amol --------------------------------------------------------------------------------------------------------------------------------------------------------- Dr Amol Bharat Ghodke | Post-Doctoral Research Fellow Queensland Alliance for Agriculture and Food Innovation Level 3, Queensland Bioscience Precinct [#80] Room 3.318, 306 Carmody Rd, St Lucia The University of Queensland St Lucia, Brisbane Qld 4072, AU E. a.ghodke(a)uq.edu.au<mailto:a.ghodke@uq.edu.au>

2 1

active/non active
by Ana Andreea ARTENI 03 Mar '21

03 Mar '21

Dear all, I want to fit a pdb structure into a cryoem map. Accordingly to the youtube tutorials I open both, place the correct pixel size, centre, and then I want to zoom only on the pdb file, but inactivating the cryoem map doesn't work: both maps zoom together. What am I doing wrong? Best regards, -- Ana Andreea ARTENI, PhD ******************************** UMR 9198 Institut de Biologie Intégrative de la Cellule Platforme de cryo-microscopie électronique Bâtiment 14B (RDC. pièce 111) 1 avenue de la Terrasse 91198 Gif-sur-Yvette Cedex, FRANCE Phone: + 33 (0)1 69 82 38 56 Fax: +33 (0)1 69 82 43 08 E-mail : ana-andreea.arteni(a)i2bc.paris-saclay.fr Site web: http://www.i2bc.paris-saclay.fr/spip.php?article277

2 2

editing session file
by Olivier Bignucolo 02 Mar '21

02 Mar '21

Dear Chimera-users, I am new to Chimera. I saved a session.py file that manages the appearance of, say, folder1/proteinA.pdb. I would like to apply exactly the same formats, colors, etc... to proteinB.pdb located in folder2. I edited session.py but was unable to find out how to do it. It seems that the python script does not contain any line like: "open("filename","r") or anything similar. How can I reuse session.py for a new pdb file? Thanks Olivier

2 3

Hydrophobicity extensions
by Sam Hopgood 26 Feb '21

26 Feb '21

Hello, I'm currently studying at Imperial to complete my final year project for my MSci in Chemistry, but due to remote working I have to take on more of a computational project rather than something lab based and I'm not too experienced in the area and neither is my group. I have been told to use chimera to model the hydrophobic surface of proteins and determine a value for the surface hydrophobicity that can be later linked to data collected from HIC studies. I've been told to use chimera to model this but even basic visualisation of the hydrophobic surface does not work for proteins as large as rubisco. I know this is a big ask and an open ended question but are you aware of any extensions available to use to mitigate this issue? Or are you aware of any techniques I could use utilising the software to calculate an actual value for the surface hydrophobicity? I hope you are all keeping safe and well, and thank you for any insight! Best, Sam

2 1

Re: [Chimera-users] Chimera-users Digest, Vol 214, Issue 8
by Khurram Shahzad 26 Feb '21

26 Feb '21

My username and password incorrect plese help me On Thu, Feb 25, 2021, 7:11 PM <chimera-users-request(a)cgl.ucsf.edu> wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://plato.cgl.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..." > > > Today's Topics: > > 1. Re: (no subject) (Thomas Cheatham) > 2. MD analysis of ion position (Elaine Meng) > 3. Re: Chimera Visualization Tool (Ela Ka) > 4. Chimera help submission (David Leeming) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 24 Feb 2021 21:06:55 +0000 > From: Thomas Cheatham <tec3(a)utah.edu> > To: K Jan <10dunajkr(a)gmail.com>, "chimera-users(a)cgl.ucsf.edu" > <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] (no subject) > Message-ID: <6bbb12c3268847adbbf93577d9f4313a(a)utah.edu> > Content-Type: text/plain; charset="us-ascii" > > > The program CPPTRAJ can bin ion densities on a grid which can be > visualized with chimera... > > See: > https://www.livecomsjournal.org/article/9974-lessons-learned-in-atomistic-s… > > CPPTRAJ is available in AmberTools or via GitHub - > https://github.com/Amber-MD/ > > Also AmberHub may have a tutorial related - > https://amberhub.chpc.utah.edu/making-a-3d-histogram/ > > --tec3 > > ________________________________________ > From: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of K > Jan <10dunajkr(a)gmail.com> > Sent: Wednesday, February 24, 2021 1:53:36 PM > To: chimera-users(a)cgl.ucsf.edu > Subject: [Chimera-users] (no subject) > > Hello, > > I`ve just finished a simulation on DNA with K+ ions and I would like to > get images of the average ion location at different points in the > simulation. > > I was wondering how I could find the average location of K+ ions ( because > right now they`re scattered around the DNA) at different points of the > simulation.? > > Thanks > > > > ------------------------------ > > Message: 2 > Date: Wed, 24 Feb 2021 13:22:02 -0800 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > To: K Jan <10dunajkr(a)gmail.com> > Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Subject: [Chimera-users] MD analysis of ion position > Message-ID: <870D7C13-E4ED-49DB-8AA0-5E503A94DCA9(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=us-ascii > > Thanks, I agree that CPPTRAJ is a great solution for analyzing > trajectories. Looks like it can read several formats: > <https://amberhub.chpc.utah.edu/cpptraj/trajectory-file-commands/> > > Alternatively: > In Chimera, if you can view your trajectory in the MD Movie tool, you can > also use that tool to calculate and display an occupancy map. I think > that's essentially the same thing that Tom mentioned, a density map on a > grid that can be viewed as isosurfaces. > > MD Movie help, click "Occupancy Analysis" in the left hand links: > < > https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie… > > > > Occupancy analysis is also covered in the last section of this Chimera > tutorial: > < > https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.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 Feb 24, 2021, at 1:06 PM, Thomas Cheatham <tec3(a)utah.edu> wrote: > > > > > > The program CPPTRAJ can bin ion densities on a grid which can be > visualized with chimera... > > > > See: > https://www.livecomsjournal.org/article/9974-lessons-learned-in-atomistic-s… > > > > CPPTRAJ is available in AmberTools or via GitHub - > https://github.com/Amber-MD/ > > > > Also AmberHub may have a tutorial related - > https://amberhub.chpc.utah.edu/making-a-3d-histogram/ > > > > --tec3 > > > > ________________________________________ > > From: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of K > Jan <10dunajkr(a)gmail.com> > > Sent: Wednesday, February 24, 2021 1:53:36 PM > > To: chimera-users(a)cgl.ucsf.edu > > Subject: [Chimera-users] (no subject) > > > > Hello, > > > > I`ve just finished a simulation on DNA with K+ ions and I would like to > get images of the average ion location at different points in the > simulation. > > > > I was wondering how I could find the average location of K+ ions ( > because right now they`re scattered around the DNA) at different points of > the simulation.? > > > > Thanks > > > > > > > ------------------------------ > > Message: 3 > Date: Wed, 24 Feb 2021 22:18:45 +0330 > From: Ela Ka <e.kashani.a(a)gmail.com> > To: Chimera User Help <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Chimera Visualization Tool > Message-ID: > < > CAFiNxG3Ca3WthCUCR3Oad2bt+i6mmMSTsCAkOTvG3oez7s1dzQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear Elaine, > > Thank you very much. I appreciate your consideration. Sure, we'll take care > of the credit and other considerations. > > Best Regards > Elaheh Kashani-Amin > > On Wed, Feb 24, 2021, 10:13 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > > Dear Elaheh Kashani-Amin, > > Thanks for asking. Yes, it would be acceptable to use Chimera (free > > version) to create images for your slides, providing that Chimera is > > credited for the images in these materials. > > > > However, if you were going to use Chimera interactively as part of the > > paid educational sessions, your group would need to license the software > as > > described here: > > <https://www.rbvi.ucsf.edu/chimera/commercial_license.html> > > > > Best regards, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > > On Feb 24, 2021, at 2:40 AM, Ela Ka <e.kashani.a(a)gmail.com> wrote: > > > > > > Dear Madam/Sir, > > > > > > We are a group of researchers who try to prepare educational contents > in > > different aspects of protein molecular modeling for the students. Access > to > > these educational content is not free. We need to prepare some pictures > of > > proteins, ligand-receptor interaction, etc. for the slides. Can we use > the > > Chimera software (free version) to prepare some pictures for the slides? > > Though, we won't use the tool, itself, for those educational sessions. > > > > > > Thank you for your consideration > > > > > > Best Regards > > > Elaheh Kashani-Amin > > > PhD, Bioscience > > > > >

2 2

Chimera help submission
by David Leeming 25 Feb '21

25 Feb '21

Dear Chimera users, I'm attempting to write a chimera script to automate the process of calculating the relative exposure of residues as per this tutorial: https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfnorm.html The script I have is as follows: rc('surface') # defines areaSES of residues rc('defattr C:/Users/Admin/Downloads/areaSESgxg.txt log 0') # define attribute using areaSESgxg.txt for m in chimera.openModels.list(modelTypes=[chimera.Molecule]): for r in m.residues: r.relSESA = r.areaSES/ r.areaSESgxg However, when I run this script, I am receiving this error: [cid:39cc50d4-a627-494c-b0f5-411a7785a9a2] When I run the process using the UI I can successfully calculate relSESA By using the command: "surface" Then using the assign attribute function to assign areaSESgxg.txt Followed by using the calculate attribute function to calculate per residue: residue.areaSES/ residue.areaSESgxg Could you advise on any methods I could use to fix this script to produce the output I am receiving from the UI. Kind regards, David

3 2

(no subject)
by K Jan 24 Feb '21

24 Feb '21

Hello, I`ve just finished a simulation on DNA with K+ ions and I would like to get images of the average ion location at different points in the simulation. I was wondering how I could find the average location of K+ ions ( because right now they`re scattered around the DNA) at different points of the simulation.? Thanks

3 2

Chimera Visualization Tool
by Ela Ka 24 Feb '21

24 Feb '21

Dear Madam/Sir, We are a group of researchers who try to prepare educational contents in different aspects of protein molecular modeling for the students. Access to these educational content is not free. We need to prepare some pictures of proteins, ligand-receptor interaction, etc. for the slides. Can we use the Chimera software (free version) to prepare some pictures for the slides? Though, we won't use the tool, itself, for those educational sessions. Thank you for your consideration Best Regards Elaheh Kashani-Amin PhD, Bioscience

2 2

No mmcif module in ChimeraX 1.0?
by Yangqi Gu 23 Feb '21

23 Feb '21

Dear Chimera Developer, I am trying to use an external python script to run some calculations. I am using ChimeraX 1.0 and the script requires the import of mmcif module but apparently it is not installed in ChimeraX 1.0? How should I install this module? I also downloaded a newer version 1.1, but it is a precompiled version. Do I need to remove ChimeraX 1.0? Because the older version was installed in /usr/bin with an executable file, but for the newer version, I assume I need to add the path for the executables? I also need to run some ISODLE refinement with my gpu, will ChimeraX configure gpu automatically? Best, Yangqi -- Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus

2 1

volume position/placement question
by Chen Mu 23 Feb '21

23 Feb '21

Hi Dear List, I am new to Chimera and I have a question using the volume viewer: I have three volumes (reconstructions from different tomographic reconstruction algorithms) to compare. They are in the same size and structure as saved in the .mrc files. I will rotate one volume and adjust the volume viewer and view it. And I then will create an animation video by adding 'roll' in timeline. But the question is, how can I make sure that when I open the other volumes, all of them are in the same starting position/placement, in order to compare and each frame in the animation video to make it possible to compare, because they should start at exactly the same volume position/placement. How can I set up this placement of the volumes to be the same? Thanks very much in advance! Best, Chen

2 1

On pdb structure match or align
by Smith Lee 23 Feb '21

23 Feb '21

Dear All, With chimera I open A.pdb abd B.pdb. A.pdb contains domain a and doain b, B.pdb contains domain b and domain c, which is to say, the 2 structures share a common domain b. Will you please tell me the chimera specific command to align or match the 2 structures based fully on the common domain b in each structure, without consideration of the domain a and domain c for calculation of the alignment? Best wishes, Smith

2 1

on chimera mask
by Smith Lee 22 Feb '21

22 Feb '21

Dear All, When I use command "mask ones #0" to get the mask for #0 image and use the mask.mrc for further processing by other program, it says the mask.mrc got was not in the "cube volume" format. Will you please explain what is the "cube volume" format mrc, and is any way to convert the above mentioned 'non-cube volume" format mask.mrc to "cube volume" format mask.mrc? Best wishes, Smith

4 3

Green bars in side view on new install
by Rochelin Dalangin 21 Feb '21

21 Feb '21

Hello, I installed Chimera 1.15 on a Windows 10 Pro laptop running i5-10300H and Intel UHD 630. When I try to open side view to clip the protein, I end up with green bars on the side view window (as shown). I've tried reinstalling to see if that fixes the issue, but it didn't work. Would you have any idea what's causing this? Thanks, Rochelin [image: image.png] -- ------------- Rochelin Dalangin Department of Chemistry 4-135 Centennial Centre for Interdisciplinary Science University of Alberta Edmonton, AB T6G 2G2

2 1

saving several pdb files in one
by Dieter Blaas 18 Feb '21

18 Feb '21

Dear Elaine and all, I have a large number of aligned pdb files and want to mask a volume including density near all these atoms. Is there an easy way of doing so? Usually I would load map and pdb, position the pdb model accordingly, activate all atoms and use 'zone' to mask everything further away from all atoms than a given distance. But this seams to be difficult with more than 100 coordinate files, each containing about 1000 coorinates! I also tried to combine all coordinates in a single file omitting everything else but chimera tries desperately to find secondary structure elements, which is difficult with this mess.... Is there an easy way of doing so? Thanks, best, 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@meduniwien.ac.at ------------------------------------------------------------------------

4 7

Installing chimerax linux
by Francesco Pietra 18 Feb '21

18 Feb '21

Hello I would like to change to chimerax, installing it on Debian (10 Buster) Regrettably, it has become practice to refer to ubuntu when .deb packages are concerned. I would appreciate being informed which u. version, if any, is suitable for Debian 10 thanks francesco pietra

2 1

Hide (pseudo-)bond between neighboring residues
by Konstantin Richter 18 Feb '21

18 Feb '21

Dear Chimera Community, I currently experience some trouble hiding certain bonds that Chimera automatically displays. But first things first: I want to design a figure of the active site of two very similar protein structures (models #0 and #1; let's assume they are mutants of the same molecule differing in only a few amino acid residues). I therefore display the ribbon as well as certain residues of model #0. Additionally, I align #1 on #0 and display the same residues in #1, but without the ribbon. So, the side chains of #1 should end in the ribbon of #0 (which is basically identical to ribbon #1). Since Chimera automatically displays all atoms of the residues when the respective ribbon is hidden, I also hide C,O,N of #1 residues. Now this looks fine expect for one thing. Chimera creates long (pseudo?)bonds between the CA atoms of residues that follow one another in sequence, e.g. res 64 and 65. This very long 'bond' messes up my figure, and I haven't yet figured out how to delete or hide it. I already tried the ~bond #1:64-65@CA command, but this one hides ALL bonds in residue 64 (but not the one between 64-Ca and 65-Ca) and other variations of the atom specifier. Is something wrong with my atom specification, or is this command not suitable for what I want to do? I also tried the bonddisplay command without succes, since it deletes all bonds in one residue. In the end, I want the residues of #1 to contain all atoms except for C,N,O including bonds between all atoms, but not the elongated connection between Ca atoms. best regards Konstantin Richter -- P. Konstantin Richter - M.Sc. Biochemistry Department of Structure Analysis of Biopolymers - Institute of Bioanalytical Chemistry Center for Biotechnology and Biomedicine (BBZ) - Leipzig University Deutscher Platz 5 D-04103 Leipzig Tel.: +49 341 9731316

2 2

Writing each rotamers to individual PDB file
by Chemmama, Ilan 17 Feb '21

17 Feb '21

Dear Developers, I am trying to write a PDB for each rotamer in Chimera. I run the command: `swapaa RES :RESNUM lib Dunbrack criteria manual` I get the enumeration for each rotamers from SCRWL library. I was wondering if there was a way to write each of those rotamers into separate PDB file using a script. Some residues have large number of possible rotamers and manually selecting the rotamer and saving the PDB file is not tractable. Thank you very much ! Ilan

2 3

fill solvent accessible channels
by Dieter Blaas 16 Feb '21

16 Feb '21

Hi, I am wondering whether chimera can fill/colour channels accessible from outside of a cryo-EM density map at a given level! If so, how? I'd like to check for size selectivity. Thanks, best, 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 ------------------------------------------------------------------------

2 1

Homology modelling with Chimera/Modeller
by StaidsonBio 16 Feb '21

16 Feb '21

Hi: I am trying to do homology modelling with Chimera/Modeler for a Fc fusion protein, which contains three domains, one is Fc, one is receptor and the 3rd is ligand. Fc has many PBD structures in PDB database and the receptor has couple of 3D structures with the ligand as well. I used the fusion protein sequence to do blast in Chimera and it gave matched sequence files to Fc domain only, no sequence files for the receptor-ligand complex, even it already has couple of solved 3D crystal structure files in PDB database. Is there any suggestion about this issue? Can I do separately, use Fc domain alone as search sequence for its template and use receptor-ligand sequences as search sequence for its template? If it is ok, there are two template files. How to make them into one template file for modelling late? Thanks very much for your suggestion. Sincerely TW Sent from Mail for Windows 10

3 4

Cutoff for clustering
by Yasser Almeida 15 Feb '21

15 Feb '21

Hello, I have a question regarding the clustering in the MD Movie tool (MD Movie/Analysis/Cluster). What's the RMSD cutoff value to make the clustering? I don't see any mention of this in the documentation. Thanks in advance, -Yasser

2 1

fitting open conformation (map)
by Neha Gandhi 13 Feb '21

13 Feb '21

Hi Elaine, There is a cryo-EM structure of the spike trimer in closed conformation. I have downloaded pdb file and map files for the locked conformation. I am interested in aligning or mapping map of the open conformation (fitting pdb from closed conformation pdb on the map). Could you please advise how this can be achieved? Many thanks, Neha -- Regards, Dr. Neha S. Gandhi, Vice Chancellor's Research Fellow, Queensland University of Technology, 2 George Street, Brisbane, QLD 4000 Australia LinkedIn Research Gate <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> Virus-free. www.avg.com <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

2 1

on chimera vop threshold
by Smith Lee 13 Feb '21

13 Feb '21

Dear All, I have a map (A.mrc). When I open it in chimera (the map should be #0), the Volume Viewer shows the Range is -0.618 to 1.63, the default Level is 0.175. With command "vop threshold #0 minimum 0.18 set 0" I got another map (let us call it B.mrc, should be #1), the Volume Viewer shows the Range is 0 to 1.63 (understandable, the maximum value is still 1.63 as in A.mrc, the minimum value is 0 as for all values not higher than 0.18 has been set to 0), the default Level is still 0.175. Immediately I run the command "vop threshold #1 maximum 0.17 set 1". Before I running the command, I guess all the density value should be either "0" or "1", because all the value lower than 0.18 has been set to "0", and all value higher than 0.17 has been set to "1". However after I run the command "vop threshold #1 maximum 0.17 set 1", I got another map (let us call it C.mrc, should be #2),the Volume Viewer shows the Range is 0 to 0.17 rather than 0 to 1, and wen I change the Level, the image of #2 changes correspondingly with the Level from 0 to 0.17. Here I would ask, why the command "vop threshold #1 maximum 0.17 set 1" did not lead to a map with all values greater than 0,17 as 1? How to get a map based on A.mrc so that all values less than 0.18 as 0 and all values greater than 0.17 as 1 (please tell me the specific method)? Is any significance for the obtained C.mrc with range from 0 to 0.17? I am looking forward to getting your reply. Smith

3 7

Apple M1 chip
by 163 11 Feb '21

11 Feb '21

Hi There, Is there a version that is suitable for Apple M1 Mac? I found the old version is quite on M1 Mac. Thanks! ML

3 5

Re: [Chimera-users] Creating new models from existing crystal structures
by Elaine Meng 08 Feb '21

08 Feb '21

You're welcome, I'm glad you figured it out! Elaine > On Feb 8, 2021, at 2:40 PM, Moradkhan, Tiglath A <tmoradkhan(a)csus.edu> wrote: > > Hi Elaine > Nevermind, I found my error. I tested the Join Model tool with 1AV1 which has four chains and I was able to correctly pick the correct C and N atoms to join residue segments from each chain. The select command that I had written originally wasn't right so it was picking the correct atoms to join. > Thanks for your help. > Best > Tiglath > > > On Feb 8, 2021, at 2:27 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > > > If the residue is already in a peptide bond, you can't add another peptide bond. You would have to delete the rest of the chain after 130 in one copy of the model and the rest of the chain before 131 in the other copy for it to make sense. > > > > Also, make sure that your "select" command is selecting exactly two atoms, 1 from each model. > > > > Elaine > > > >> On Feb 8, 2021, at 1:53 PM, Moradkhan, Tiglath A <tmoradkhan(a)csus.edu> wrote: > >> > >> Hi Elaine > >> > >> I've been using the biological assembly of 3R2P and I'm thinking that the reason why it's not working is because both chains are labeled A. I'm just following a paper where they're building a monomeric structure using the residue fragments but in their case the biological assembly of 3R2P is labeled as chain A and chain B. > >> From: Elaine Meng <meng(a)cgl.ucsf.edu> > >> Sent: Monday, February 8, 2021 1:01 PM > >> To: Moradkhan, Tiglath A <tmoradkhan(a)csus.edu> > >> Cc: chimera-users(a)cgl.ucsf.edu <chimera-users(a)cgl.ucsf.edu> > >> Subject: Re: [Chimera-users] Creating new models from existing crystal structures > >> > >> Hi Tiglath, > >> If you just opened 3r2p one time, you only have one model. Join works on bonding two separate models. Also it contains only chain A (there is no chain B in this structure) and residue 130 in chain A is already bonded to residue 131 in chain A. So I do not understand what you already did to modify the structure(s) before joining, or what you are trying to do now, sorry. > >> > >> You could send a session file if you want. > >> Elaine > >> ----- > >> Elaine C. Meng, Ph.D. > >> UCSF Chimera(X) team > >> Department of Pharmaceutical Chemistry > >> University of California, San Francisco > >> > >>> On Feb 8, 2021, at 12:35 PM, Moradkhan, Tiglath A <tmoradkhan(a)csus.edu> wrote: > >>> > >>> Hi > >>> > >>> I'm trying to join two models together using the Build Structure tool but I'm having problems. Here is my process. > >>> > >>> • Using the 3R2P crystal structure I select residues 3-130 from chain A and 131-182 from chain B > >>> • Then using the following command in Chimera I select the N atom of residue 130 that will form a bond with the C atom of residue 131: sel #0:130@N#1:131@C (#0 is the name of the 3-130 segment and #1 is the name of the 131-182 segment) > >>> • Then using the Build Structure tool I select Form C-N peptide bond, but the Apply button doesn't activate. > >>> I don't understand what the issue is. Is the command that I've written wrong? > >>> > >>> I would be very glad for your help. I can provide the pdb files of the residue segments if necessary. > >>> Thanks > >>> > >>> Tiglath > > > > > > _______________________________________________ > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

1 0

Creating new models from existing crystal structures
by Moradkhan, Tiglath A 08 Feb '21

08 Feb '21

Hi I'm trying to join two models together using the Build Structure tool but I'm having problems. Here is my process. 1. Using the 3R2P crystal structure I select residues 3-130 from chain A and 131-182 from chain B 2. Then using the following command in Chimera I select the N atom of residue 130 that will form a bond with the C atom of residue 131: sel #0:130@N#1:131@C (#0 is the name of the 3-130 segment and #1 is the name of the 131-182 segment) 3. Then using the Build Structure tool I select Form C-N peptide bond, but the Apply button doesn't activate. I don't understand what the issue is. Is the command that I've written wrong? I would be very glad for your help. I can provide the pdb files of the residue segments if necessary. Thanks Tiglath

2 3

Re: [Chimera-users] Video tutorials
by Tom Goddard 04 Feb '21

04 Feb '21

Hi Cynthia, Ok, I converted all the Chimera video tutorials (about 40 of them) to use standard web browser video playback. https://www.rbvi.ucsf.edu/chimera/videodoc/videodoc.html <https://www.rbvi.ucsf.edu/chimera/videodoc/videodoc.html> Thanks for pointing out that they were using the obsolete Flash plugin for movie playback. Tom > On Feb 4, 2021, at 10:29 AM, Cynthia Page wrote: > > Hi Tom, > Do you all have any plans of porting the tutorial flash videos to another player? I see there are some YouTube videos available for Chimera but I am thinking of the tutorials that are available on the website. > Maybe there is another source of video tutorial I am unaware of? > > Thanks very much, > Cynthia Page > CU Boulder > > Sent from my iPhone >

1 0

MD simulation in Chimera : 10 ns simulation is equivalent to 1 million of production steps 10 fs each?
by Giovanni Roviello 29 Jan '21

29 Jan '21

Dear Sirs, I would like to perform a MD simulation by UCSF Chimera. Should I wish to perform a 10 ns simulation (for example) how could I set the parameters related to time? For example in production a number of phase steps of 1000000 and a time step of 10 fs is OK? Does the relaxation time Nosé thermostat has effect on the overall simulation time? In simpler words if I set 1000000 steps, 10 fs time step, and I leave selected Nosè thermostat with 0.2 ps (but leave unselected the barostat option) will it correspond to a 10 ns MD simulation? Of course if I will publish using Chimera I will cite the program and the reference as indicated in https://www.cgl.ucsf.edu/chimera/docs/credits.html Thank you in advance for your kind help. Kind regards, Giovanni _______________________________________________________ Dr. Giovanni N. Roviello, Ph.D. Researcher at Istituto di Biostrutture e Bioimmagini IBB - CNR; Via Mezzocannone 16; I-80134 Naples; Italy giroviel(a)unina.it giovanni.roviello(a)cnr.it http://www.ibb.cnr.it/?command=viewu&id=387&lang=en https://orcid.org/0000-0001-6065-2367

2 7

less color depth possible?
by Cheng, Tat 27 Jan '21

27 Jan '21

Hi all, We are trying to set up cryoEM data processing in the university HPC. We use X2go for remote accessing the HPC, but it doesn't have enough color depth, so Chimera (24-bit) doesn't start. One workaround is to download the volume from HPC to local machine, but it is less convenient. But I wonder is there a way to use Chimera in less color? Thanks a lot. Best, Tat

3 3

how to color an model by an attribute in chimerax
by sunyeping 27 Jan '21

27 Jan '21

Dear all, I wish to color an model by an attribute in chimerax. The attribute is the entropy which is calculted by an external software. I wrote the entropy values of each residue in a text file (attr.txt) like the following: attribute: entropy match mode: 1-to-1 recipient: residues :1 0.0 :2 0.0014948 :3 0.0090952 :4 0.0004805 :5 0.1102497 :6 0.0095258 :7 0.0008226 :8 0.0042205 :9 0.0037255 :10 0.0006678 :11 0.0027988 :12 0.0193925 :13 0.0153925 :14 0.0052115 :15 0.0020136 .......... However, when I input the command "color byattr attr.txt", I get the following error information: "No known/Registered attribute attr.txt" Could anyone tell me what is the correct way to do this? With many thanks. Best regards

2 3

coloring the volume series
by Arto Pulk 26 Jan '21

26 Jan '21

Dear all, I would like to make a movie using volume series. I have 10 maps (from Relion) that I upload to volume series. Now I would like to color the moving parts of the map. One can use zone coloring, but it does not do the precise job to color specific volumes of the map as it is radius specific. Then there is "surface coloring" by "volume data value". I can make a mask and color the mask region, but it makes the color gradient and I do not have control of the region outside of the mask at it will be mixture of colors. The best way to color is to use "segment map" and then go to "Regions" and "color density map". It does good job to color specific map volumes but the colors are not permanent. If you Play the Volme Series then colors vanish. So, is there any good way to color Volume Series? Regards, Arto Institute of Technology University of Tartu Nooruse 1 50411, Tartu Estonia Dr. Arto Pulk email: arto.pulk(a)ut.ee phone: 58244846

2 2

Chimera RMSD
by Elaine Meng 25 Jan '21

25 Jan '21

> From: "Sharyn Endow, Ph.D." <sharyn.endow(a)duke.edu> > Subject: Chimera RMSD > Date: January 23, 2021 at 11:27:17 AM PST > > Thank you for your work in developing Chimera. We are trying to use Chimera RMSD to quantitate twisting of a beta-sheet and would like to know what the syntax is to list rmsd values for specified residues corresponding to a beta-strand, not just for single residues. Is it possible to list these values using RMSD? If so, we would greatly appreciate knowing how to get started. > > Sincerely, > Sharyn Hi Sharyn, You can specify any sets of atoms/residues that you like in the RMSD command, as long as there are equal numbers of atoms in the two sets that you specify (from two different models). They will be paired in the order specified. We have a command-line "atom specification" syntax for that kind of thing. There is a longish page with lots of examples here: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> In your case, you may need to specify residue numbers, chain ID, and possibly atom names if you just want to use alpha-carbons or backbone as opposed to all atoms of the residues. E.g. something like rmsd #0:12.A,57-63.A #1:14.A,59-65.A ... for all atoms of model 0 residues 12 and 57-63 in chain A vs. all atoms of model 1 residues 14 and 59-65 in chain A. Or to use CA-only or backbone only: rmsd #0:12.A,57-63.A@ca #1:14.A,59-65.A@ca rmsd #0:12.A,57-63.A@n,ca,c,o #1:14.A,59-65.A@n,ca,c,o Of course the numbers could be the same in the two models, I just was trying to give a more general example. 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. the chimera-users(a)cgl.ucsf.edu address CC'd here is recommended for general Chimera how-to or is-it-possible types of questions

1 0

adding chimera-trimmings alias
by Dmitry A. Semchonok 25 Jan '21

25 Jan '21

2 3

command line > vol all surface level 0.1 colour gradient
by Dieter Blaas 20 Jan '21

20 Jan '21

Dear Elaine, please forgive me for asking again, I cannot find your previous mail and my notes: How can I, in command line, do the following, i.e. what is the correct syntax? vol all style surface level 0.1 colour by gradient colours 5 palette rainbow set I have a number of volumes loaded and want to colour their surfaces, at level 0.1 by 'volume data gradient norm' with 5 rainbow colours setting them to the full range Thanks a lot, best 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 ------------------------------------------------------------------------

2 1

Coloring peptide bonds in Chimera
by Tynan A. Becker 19 Jan '21

19 Jan '21

Good afternoon, I have been trying to figure out how to color just a single peptide bond between 2 residues in a protein. What I have figured out so far is to show chain trace under actions|atoms/bonds. Then invert the selection (whole protein). This shows the bonds. I can select a residue and color the bond on both sides. But I want to color the bond between 2 residues. If I pick the bond by manual selection, the action|color|choice doesn't work. The manual tantalizingly suggests using the "halfbond" setting or "bondcolor" for the command line. The problem that I encounter is that I can't figure out how to tell the program which bond I want. I've read the "atom specifications" page of the manual and tried every logical combination I can figure to tell the program which bond I want to color. But each time, I get the "mangled atom specifier" error. I was told today that there is a way to do this, but I'm stuck. Any input is welcome. Thank you, Tynan

2 6

Problem with electron density
by Elaine Meng 14 Jan '21

14 Jan '21

Dear Francesco, Probably you just need to use "vop cover" as described in these previous posts: <https://www.cgl.ucsf.edu/pipermail/chimera-users/2013-September/009142.html <https://www.cgl.ucsf.edu/pipermail/chimera-users/2013-September/009142.html>> <https://www.cgl.ucsf.edu/pipermail/chimera-users/2020-July/017021.html <https://www.cgl.ucsf.edu/pipermail/chimera-users/2020-July/017021.html>> Details on the "vop cover" command: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover>> For future: the recommended address for questions is chimera-users(a)cgl.ucsf.edu (CC'd on this message) ... since I'm not the expert in everything (or might be sick or away from work), it's helpful if more people see the question! I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > From: Francesco Papi <Francesco.Papi(a)iit.it> > Subject: Chimera: Problem with electron density > Date: January 14, 2021 at 3:03:55 AM PST > To: "meng(a)cgl.ucsf.edu" <meng(a)cgl.ucsf.edu> > > Dear Elaine, > I am using Chimera to get a picture of a small molecule (cif file) in an electron density map (xplor file). My issue deals with the position of some atoms of the molecule in an adjacent unit cell (see attached image) which prevents me to see some atoms within the map. I thought to simply expand the map beyond the cell boundaries and eventually crop the map, but it didn’t work. I have checked different tutorials and the chimera mailing list for troubleshooting but I haven’t found a solution to this problem. Is there something you can think of? > Thank you. > Regards, > Francesco Papi > > Francesco Papi, PhD > PostDoc > Center for Nanotechnology Innovation@NEST > Istituto Italiano di Tecnologia > Piazza San Silvestro, 12 > 56127 Pisa, Italy > Phone: +39 050 509 495 > E-mail: francesco.papi(a)iit.it <mailto:francesco.papi@iit.it> > Skype: francesco.papi.89 >

2 1

Can't open large .bild files
by Hannah Bridges 13 Jan '21

13 Jan '21

Hi all, I would like to visualize in Chimera the orientations from some angdist.bild files output from relion. I am able to open some .bild files (up to ~5.6MB in size) but I get "not responding" from Chimera when I try to open .bild files ~10-70MB (lots of particles and high angular sampling). I tried on a machine with more RAM but it was the same. Any hints about how to open these or is it just not possible? Best wishes Hannah -- Dr Hannah Bridges Investigator Scientist MRC Mitochondrial Biology Unit The Keith Peters Building University of Cambridge Cambridge Biomedical Campus Hills Road Cambridge CB2 0XY United Kingdom Telephone : 01223 252812

4 5

APBS
by mailman-bounces＠cgl.ucsf.edu 12 Jan '21

12 Jan '21

From: benjamintam <benjamintam(a)um.edu.mo <mailto:benjamintam@um.edu.mo>> Subject: APBS Date: January 11, 2021 at 7:28:44 PM PST To: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu <mailto:chimera-users-bounces@cgl.ucsf.edu>> Dear All, I can see that we have to run the APBS locally, however, which default execute file that I need to select in the Chimera in order to run APBS? Best, Ben

2 1

view along a crystal axis
by Michael Elbaum 11 Jan '21

11 Jan '21

Hi. I would like to view a lattice of molecules generated by "Unit Cell" along a given axis. Is there a way to set the view accordingly, say along a, b, or c axis? Other than showing the I'm showing the outline box and eye-balling, but probably there's a more precise way to do this. thanks for your help, Michael

3 6

Identifying type of interaction
by nitya yerabandi 09 Jan '21

09 Jan '21

Hi, I'm using UCSF Chimera right now to analyze the contact residues between two proteins, Hsp70 and BAG3. I have created a distance monitor table on chimera that shows residues, atoms, and the distances between them. I am now trying to identify the type of interaction between each pair of atoms, like polar, nonpolar, hydrogen,etc. However, I am having difficulty doing this. I was wondering if you could assist me with this. Thank you, Nitya Yerabandi

2 2

command line "vol all style surface plane z,60,8
by Dieter Blaas 08 Jan '21

08 Jan '21

Hi, I am trying to display a volume (128 px box) sliced through the middle as seen down the z axis but 8 slices thick instead of just one. I can render a single slice with "vol #0 style surface plane z,64" but I could not find out how to make it e.g. 8 slices thick. In VolumeViewer there is the parameter 'Depth' but it is not accepted as parameter in the command line! Rater, adding one more number at the end of the command starts playing a movie of one slice after the other.... Thanks a lot for hints, bw 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 ------------------------------------------------------------------------

3 3

Make a new pdb model from a part of pdb file
by C.J. 07 Jan '21

07 Jan '21

Hi, I have a pdb with a A chain of 1000 amino acids. How can I make a new model with a part of A chain (i.e. 500 amino acids) using command line? Thank you! Best, Jianhao

2 2

(no subject)
by Hemapriya Kumar 07 Jan '21

07 Jan '21

While clicking on the fetch, its getting like certificate no verified as command -- With Regards Hemapriya Kumar

2 1

RMSD after superimposition
by Subhabrata Majumder, PhD 07 Jan '21

07 Jan '21

Dear Support, I have recently started using chimera_ucsf. I was trying to look at Calpha RMSD list after superimposition two conformation of a particular protein. Do you know where should I get the list after superimposition? Thanks, Subhabrata -- Subhabrata Majumder, PhD Assistant Professor Biophysics & Structural Genomics Saha Institute of Nuclear Physics HBNI Sector 1, Block AF Saltlake Kolkata -700064 India Email subhabrata.majumder(a)saha.ac.in ; subhabrata.sinp(a)gmail.com

2 2

Deleting lipid molecules
by Moradkhan, Tiglath A 04 Jan '21

04 Jan '21

Hi I've built a lipid particle containing 252 molecules and I'm trying to randomly delete 20 lipid molecules. Does the delete command allow this? I've tried using it but it doesn't seem to work for this case. Thanks Tiglath

2 1

Re: [Chimera-users] betacavity web and chimera
by Elaine Meng 03 Jan '21

03 Jan '21

On Jan 2, 2021, at 10:42 PM, Jacqueline Vitali <jackie.vitali(a)gmail.com> wrote: > > Hi Elaine, > is there a way to incorporate in chimera the option to read cavities from betacavity web (Nucleic Acids Res 2015 vol 43 W413-W418) ? Right now you do it for CASTP. > Please let me know. > THank you. > Jackie Vitali > Cleveland State University Hi Jackie, Unfortunately we don't have resources to provide visualization capability for the many useful web servers that exist. A related server with Chimera visualization capability is MOLEonline: <https://mole.upol.cz/> I hadn't heard of betacavity before. In general it would be useful to say or give examples of what outputs they do provide, to give some idea of whether it might be possible... I had to run it myself to figure that out. Looks like they just give Jmol visualization in the web browser and a script for Pymol. Maybe you could ask the authors of betacavity if they would also provide a Chimera script too, but it's probably unlikely. I also see they give lists of atoms on the right side of the results page, but not in PDB format. You could try manually showing surface for those atoms in Chimera (with a Chimera command) but it would be (1) tedious, and (2) just the molecular surface of those atoms, so there may be jagged edges and bits sticking out, not a nice enclosed blob as in their Jmol visualization. Our Castp visualization has this same issue. E.g. for 2gbp I get in the betacavity results: VOID 3 VOID-VOLUME 8.468 A^3 VOID-BNDRY-AREA 41.050 A^2 VOID-DEFINING-ATOMS 27 ATOM 131 CE1 PHE A 16 0.064 A^2 ATOM 689 CA ASN A 91 0.978 A^2 ATOM 691 O ASN A 91 3.921 A^2 ATOM 695 ND2 ASN A 91 1.857 A^2 ATOM 705 N GLU A 93 0.796 A^2 ATOM 709 CB GLU A 93 1.116 A^2 ATOM 713 OE2 GLU A 93 1.118 A^2 ATOM 829 CE2 TYR A 107 0.001 A^2 ATOM 831 OH TYR A 107 5.812 A^2 ATOM 840 CA GLY A 109 0.897 A^2 ATOM 843 N THR A 110 0.696 A^2 ATOM 846 O THR A 110 1.145 A^2 ATOM 848 OG1 THR A 110 2.830 A^2 ATOM 849 CG2 THR A 110 2.985 A^2 ATOM 863 OG SER A 112 2.918 A^2 ATOM 1174 CE1 HIS A 152 0.504 A^2 ATOM 1180 CB PRO A 153 2.424 A^2 ATOM 1182 CD PRO A 153 0.061 A^2 ATOM 1183 N ASP A 154 0.007 A^2 ATOM 1188 CG ASP A 154 1.146 A^2 ATOM 1189 OD1 ASP A 154 3.493 A^2 ATOM 1190 OD2 ASP A 154 1.781 A^2 ATOM 1944 OD1 ASN A 256 0.193 A^2 ATOM 1945 ND2 ASN A 256 0.811 A^2 ATOM 1982 OE1 GLN A 261 2.372 A^2 ATOM 2240 OH TYR A 295 0.069 A^2 ATOM 2356 O1 BGC A 310 1.045 A^2 ...and then in Chimera I could open 2gbp surf :16@ce1:91@o,nd2:93@n,cb,oe2:107@c32,oh:109@ca:110@n,o,og1,cg2:112@og:152@ce1:153@cb,cd:154@n,cg,od1,od2:256@od1,nd2:261@oe1:195@oh:310@o1 ...where the surf command is all one line although the mail program may break it up. (Or you could have multiple surf commands for subsets of those atoms.) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

2 1

Accession number
by Yasmeen Nasr 31 Dec '20

31 Dec '20

Hello there, This doesn’t seem very much chimera related but I hope someone could help me out. I’m trying to use phD-SNP server and SNP&GO server and they require a Swiss prot code and a uni-prot accession number respectively. Does anyone know where I retrieve such numbers for SNPs? Thank you in advance. Yasmeen Abdulhadi Sent from my iPhone

1 0

Clustering saving PDB
by Lorena Roldán 28 Dec '20

28 Dec '20

Good afternoon, I contact you as I would really appreciate your help. I have a MD trajectory which I have processed into Clusters with the Analysis ... Cluster tool. I have saved the resulting file with the members and the representative frame, but now I would like to save those representative frames in separate PDB files. This process is extremely tedious if manually done, so I have tried to perform a script: with open("/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/clusters_frame.txt", "r") as f: lines=f.readlines() cluster_number = 1 for i in range(len(lines)): frame = i if mdInfo["frame number"] == frame: name = "/HDD/lroldan/Master/Metals_bA/Template/2LFM/MD/GaMD/Clusters/_" + str(cluster_number) runCommand('write format pdb 0 $name) which would be run in the "Per-frame Commands", in order to 1) encounter the frames of the cluster and 2) save each frame in a PDB file, correctly numbered. However, this script is not working, and I would greatly thank any help you could provide me with. Lorena. -- <http://www.uab.cat> Lorena Roldán Martín *PhD Student in Bioinformatics* Departament de Química Unitat de Química Física Campus de la UAB · 08193 Bellaterra (Cerdanyola del Vallès) · Barcelona · Spain +34 690799431 www.uab.cat <http://www.uab.cat> <https://orcid.org/0000-0002-6902-8285><https://www.linkedin.com/in/lorena-roldan-biomedica/>

3 4

Density map tranformation
by Ahmad Khalifa 22 Dec '20

22 Dec '20

Hello, When I fit two maps into each other, I get the transformation matrix in the reply log, but what if the moving map doesn't converge by fitmap and require some initial manual alignment, how can I calculate the transformation matrix for that? Best regards.

2 3

Movies and Symetries
by Stéphane DUQUERROY 21 Dec '20

21 Dec '20

Hi, I generated a set of coordinates in a single PDB file for a movie (coord flanked by MODEL / ENDMDL tags) I can read it and play it with MD movie menu The PDB File has also BIOMT matrices set for displaying the biological assembly My question is how can I play the movie with multiscale model? How Can use automatically the color zone tool to color various protomer instances for all intermediate conformations? (The only way I know for doing that is to generate and select all sym instances but they moved with each of the models!) S Duquerroy -- -------------------------------------------- Duquerroy Stéphane, PhD, Assistant Professor, Univ Paris Saclay Structural Virology Unit, Institut Pasteur 28 rue du Dr Roux, 75015 Paris - France 33 - (0) 140 613 575 --------------------------------------------

2 1

Holiday greetings from the ChimeraX team!
by Elaine Meng 18 Dec '20

18 Dec '20

The Chimera(X) team at the UCSF RBVI wishes you a safe and happy holiday season! Our holiday card is virtual this year: =-=-=-=-=-= Atoms of Apoferritin At a miraculous 1.22 Å resolution, the electron microscopy map of mouse apoferritin (right, EMDB 11638) can be mistaken for an atomic model (left, PDB 7a4m), with each atom standing out. The map from Nakane et al. (2020 Nature 587:152-156) shows glimpses of the lightest atoms, hydrogen, directly revealing the hydrogen-bonding network. Ferritin stores iron, as many as 4500 ions (Fe3+), as crystallites within its shell of 24 proteins. Apoferritin, ferritin without its iron cargo, has rock-like stability, making it ideal for divining the limits of electron microscope resolution. The images were made with UCSF ChimeraX, using ambient-occlusion lighting, coloring to delineate trimeric subunits within the dodecahedral shell, and curved helix tubes. Best wishes for a happy and healthy 2021! Conrad, Greg, Elaine, Tristan, Tom, Scooter, Eric and Tom =-=-=-=-=-= Full-resolution image: <https://www.rbvi.ucsf.edu/Outreach/card-gallery/2020-apoferritin/2020a.png <https://www.rbvi.ucsf.edu/Outreach/card-gallery/2020-apoferritin/2020a.png>> Gallery of previous cards back to 1985: <https://www.rbvi.ucsf.edu/Outreach/card-gallery/index.html <https://www.rbvi.ucsf.edu/Outreach/card-gallery/index.html>>

1 0

Create an atom object
by Yasser Almeida 15 Dec '20

15 Dec '20

Hello, How can I create an atom object, with a given xyz coordinates, via command or python? Thanks in advance, Yasser

3 2

Volume information from segmentation data
by Juleen Dickson 14 Dec '20

14 Dec '20

Good Morning Everyone, I fear the answer to my question is probably 'no' but I wanted to ask the experts first. I have segmentation of vesicles that I did from a cryo-EM tomogram that I did in EMAN2. I can open the segmentations and view them in chimera, however, I wanted to find a way to extract volume and surface area data on the segmentations so I can do statistics on them. If I use the Volume--> Measure and color blobs, the individual blob information will show up in the log. I am not sure if this information is accurate. Is there away to do this for all of the vesicles and download the data, maybe with the volume--> Segment map? If so, how do I do it? Thanks for your help. Cheers, Juleen "Never interrupt someone doing what you said couldn't be done." *--Amelia Earhart, American aviator* "Friends... they cherish one another's hopes. They are kind to one another's dreams." *-- Henry David Thoreau* *“Life isn’t about waiting for the storm to pass. It’s about learning how to dance in the rain…” -Vivian Greene*

2 1

Can't open IMOD .mod file
by Luiza Mendonça 12 Dec '20

12 Dec '20

Good morning, Is it possible to open IMOD .mod file in chimera? I am trying to do so, and I select the IMOD .mod file in the pop-up window asking about the file type, but nothing is showing up (blue initial chimera window unchanged), even though the log states 'finished opening file'. My .mod file is just XYZ scattered points. Do I need to do any conversion before being able to open it? I appreciate any help. Best, Luiza Mendonca Zhang Lab University of Oxford

3 3

scaling models
by Rani Wiswedel 12 Dec '20

12 Dec '20

Good day, Is there any way to ensure that the scale you are looking at is kept constant when taking images of different models? I would like to include photos of pores from my structure, but each pore is saved in a different file, so I have to re-open Chimera and adjust the view each time. I have the scale bar open and the projection set to orthographic, but I am struggling to manually adjust the view so that the scale bar looks the same length in each picture (attached below is my manual attempt (pic1)). Is there any way to set the scale each time chimera is opened so that I don't end up with pictures that have scale bars that appear to be different sizes?(example of what I would like to achieve is in the second image(pic2)) Thank you! Regards, Rani Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://www.uct.ac.za/main/email-disclaimer or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://csirt.uct.ac.za/page/report-an-incident.php.

2 1

Using UCSF Chimera inside python environment
by Jeff Saxon 10 Dec '20

10 Dec '20

Dear Chimera Users, I would like to use chimera to do some calculations on PDB filles (mainly I am interesting to cluster conformations in multi-model PDB using Ensemble cluster) Could you explain to me how I could install chimera (I am using python3 with conda) in order that I could use some of Chimera's functions directly inside of my python scripts? I have already tried install package pychimers but did not succeed conda install -c insilichem pychimera nsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment: Specifications: - pychimera -> python[version='2.7.*|>=2.7,<2.8.0a0'] - pychimera -> python[version='3.4.*|3.5.*'] Your python: python=3.8 May I use chimera with my python using alternative ways of installations? Thank you in advance! J.

3 3

Chimera and All-in-One system tune up tools
by Nagy Milan 09 Dec '20

09 Dec '20

Hello, how to solve following problem: after using all-in-one system tune up tools (Wise Care 365 Pro or Ashampoo Win Optimizer) Chimera stopped to work. Greetings Milan

2 4

Failure Running ANTECHAMER
by Eric Choi 04 Dec '20

04 Dec '20

To whom it may concern, My name is Eric Choi and I am currently a student at Ithaca College doing research about virtual ligand screening where I utilize programs like Chimera and Dock6. In my workflow, I use Chimera to prepare ligands (downloaded from the ZINC database) by adding hydrogens (using the "steric only" method and "unspecified") and adding charges (AM1-BCC). Then, I run the Dock6 program, which predicts potential binding geometries and interactions of a molecule to a target protein. When I add hydrogens and charges to individual ligands (downloaded from the ZINC database), it works fine. However, when I downloaded different subsets of molecules (containing 100 ligands to 2000 ligands), an error message popped up saying that ANTECHAMBER failed to run (please see screenshots below). What does this mean? Is there any way that I can fix this issue? If a certain ligand is causing this problem, is there a way to see which one it is? Thank you very much for your time and help. Sincerely, Eric Choi

3 2

downtime on Monday, December 7, 2020
by Elaine Meng 03 Dec '20

03 Dec '20

Dear Chimera and ChimeraX users, We will be doing some system maintenance on Monday, December 7. During this downtime, which we expect to last one day, the Chimera and ChimeraX websites, downloads, e-mailing lists, and several web services accessed by the programs will not be available. Apologies for any inconviences this may cause, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

pythonw.exe always run new windows
by gb1995＠zju.edu.cn 03 Dec '20

03 Dec '20

After installing and opening the UCSF chimera software, pythonw.exe keeps popping up new windows, causing it to fail to work normally.I have tried to download various versions of UCSF chimera software, and found that it cannot be used when installed on the D drive and can only be installed on the C drive. But after the installation is complete, double-click to open it, and various interfaces will pop up continuously. At the same time, Microsoft Edge will pop up web pages continuously, causing the software and computer to fail to work normally.

2 3

label position
by Ruchika 02 Dec '20

02 Dec '20

Hi Elaine I selected alpha carbon of some specific residues and labeled them using label option (one letter specifier + number) in actions menu. After labeling these residues and setting these fonts, some of the labels are overlapping onto one another. I used following command (setattr m residueLabelPos 2) to place them on the alpha carbon. However, they are still overlapping. I am just wondering if there is any other way to separate the label and not overlap on each other. Please let me know. Thanks !! Regards Ruchika

2 1

(no subject)
by Prabuddha Bhattacharya 26 Nov '20

26 Nov '20

Dear Sir Can you help me with a step by step tutorial to find out the electrostatic potential map of a molecule on chimera? Thank you Best regards *Dr. Prabuddha Bhattacharya *

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Error message
by Kaitlyn Merrill 22 Nov '20

22 Nov '20

Hi there, I have been using Chimera and Autodock Vina through Chimera and started getting this error message whenever I attempt to use the Autodock Vina to dock a ligand. Can you please tell me how to fix this? Thanks, Kaitlyn

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Re: [Chimera-users] [chimera-dev] Problem with Matchmaker tool
by Elaine Meng 20 Nov '20

20 Nov '20

Hi Tiglath, (1) 1av1 is not a dimer. It is a tetramer, 4 copies of the same peptide, chains A,B,C,D. See: <https://www.rcsb.org/structure/1AV1> (2) Matchmaker is working correctly, but you have to choose "Specific chain of reference structure" (not "Best-aligning") and then specify exactly which chain of 1av1 you want as the Reference. You have to use it twice, so that you can match #0 to one reference chain and #1 to a DIFFERENT reference chain. Otherwise they will both go to exactly the same place because they will match the same chain, which I guess is what happened to you before. Actually, maybe you need to use it four times with four copies of your model if you expect to get something that looks similar to 1av1. The chimera-users(a)cgl.ucsf.edu address is recommended for "how to use" questions, so I'm CC-ing it here. The chimera-dev list is more for programming questions. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Nov 20, 2020, at 5:17 PM, Moradkhan, Tiglath A <tmoradkhan(a)csus.edu> wrote: > > Hi > For some reason I'm not able to use the matchmaker tool to build a dimer model of the protein I'm studying. Here are the steps that I use: > > • I open twice the monomer model > • Then I open the dimer template, then click on the Matchmaker tool. > <image.png> > 3. In the Reference structure panel I click on the dimer template (1AV1) > 4. In the Structure(s) to match panel I click on monomer#0 (Human Monomeric Apo A-I, the protein I'm studying) then click OK > 5. Then I click on monomer #1 followed by OK > > But when I close the dimer template I get back the monomer not the dimer model of the protein. I'm not sure what I'm doing right. > Thanks > Tiglath

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Question on aligning one molecule to two other molecules
by Doc Deldou 18 Nov '20

18 Nov '20

Dear Chimera team, I am trying to perform a "manual" docking of a DNA molecule in a protein structure using homology with proteins structures resolved with DNA. I know that the first part of my protein (the recognition domain) is similar to one structure and the other part (the cleavage domain) is similar to another one. So I built a dsDNA with the recognition sequence of my target protein and I first aligned it with the DNA of the similar recognition structure using the phoshore groups, then I matched aligned my protein structure to the protein part of the similar recognition structure. After that I matched aligned my protein to the similar protein cleavage domain bringing the DNA molecule with it. And now ideally I would like to align the DNA part with the DNA of the similar cleavage domain but keep the first recognition part of my DNA more or less at the same position. So I tried to align another copy of my DNA to both DNA molecules but I don't think it is possible. Do you have a trick or a command I could use to reach my goal? I'm using Chimera X. Below is what I obtained, in green my target protein, in purple the DNA I first aligned relatively to the DNA of my similar recognition structure, in "pink" the DNA strand of the similar cleavage structure with the bond to be cleaved in yellow, and the dsDNA with all the colored nucleotides is the one I am trying to position in between the two site with also the bond to be cleaved in yellow. I tried to rotate it and translate it manually to have something in between but some DNA parts are clashing with the protein part and I would like to have something the more accurate possible. [image: manualdocking.jpg] Best regards, -- Adèle Dramé-Maigné @Docdeldou Docteur en Biochimie et Instagrammeuse Blog: http://bit.ly/2zkiPWI LinkedIn: http://bit.ly/2afmtEq

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Saving representives from ensemble cluster
by James Lloyd 18 Nov '20

18 Nov '20

Hi, I have a few Gromacs trajectories (just protein in solvent) which I have clustered using the ensemble cluster tool. I want to save each representive model from each cluster. However I am unsure whether these representive models need to be saved relative to another model (this option was ready ticked). Since I want to use each file separately with VinaDock, would unticking this option be wise? Thanks This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please contact the sender and delete the email and attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. Email communications with the University of Nottingham may be monitored where permitted by law.

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Re: [Chimera-users] Saving Image of row stereo
by Tom Goddard 17 Nov '20

17 Nov '20

Hi Divita, I see. If you want to depict that a molecule can be in various positions a better approach is to actually open 2 to 4 copies of it positioned slightly differently, maybe showing the copies as transparent. Another approach is to save 5 copies of the image where you move the variable molecule a bit for each, then blend the images in Photoshop or Gimp. Tom > On Nov 17, 2020, at 10:14 AM, Divita Mathur <dmathur4(a)gmu.edu> wrote: > > Thanks for your response, Tom. I guess I should tell you what I am trying to achieve. > > The row stereo image is interesting to me as it can be interpreted as a “vibrating” or “shaky” molecule (check attached). I want to represent that the green dye (and perhaps the underlying pink scaffold) is shaking and it is not constrained enough. Is there a camera setting that you can recommend? > > The screenshot has these horizontal lines which I suspect have something to do with the quality of my computer screen. > > Best, > > -- > Divita Mathur, PhD > Research Assistant Professor > George Mason University & > Center for Bio/Molecular Science and Engineering > Naval Research Laboratory > (202) 767-0687 (Office) > From: Tom Goddard <goddard(a)sonic.net> > Date: Tuesday, November 17, 2020 at 12:58 PM > To: Divita Mathur <dmathur4(a)gmu.edu> > Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Saving Image of row stereo > > Hi Divita, <> > > I don't think Chimera can save the row interleaved image. Such an image is not very useful since it would have to be positioned on a row interleaved stereo display (e.g. Zalman) with no scaling to appear 3d since even rows give one eye image and odd rows the other eye image. Your best bet would be to try a screen capture program. > > Tom > > > >> On Nov 16, 2020, at 6:23 PM, Divita Mathur <dmathur4(a)gmu.edu <mailto:dmathur4@gmu.edu>> wrote: >> >> Hi all, >> >> I am trying to save a rendering created using the Camera setting – row stereo. The rendering appears dark and without the row stereo settings when the image is saved (tried many formats). How can I save the actual rendering as an image? >> >> Regards, >> Divita Mathur >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://secure-web.cisco.com/1xK9pP0Vy3veE9y4SgXHuL5DpartYSf6j9ncrP3zwdNXWs…> > > <Screen Shot 2020-11-16 at 9.30.16 PM.png>

2 1

POV-Ray surface color
by Greg Williams 17 Nov '20

17 Nov '20

I am rendering a two-submit protein, split, with different colored mesh surfaces on the subunits. If I render to an image with Chimera, the surfaces appear in the colors assigned. If I render with POV-Ray, both mesh surfaces render as black. I assigned the colors using MSMS surface attributes with color sources as "atoms", using the color well in the Component Atom Attributes panel. Where in the literature should I read to sort this out? Thanks!

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Color marker and bonds
by karine.gouriet 17 Nov '20

17 Nov '20

Dear all we want to correspond the marker color with the bond color. here the bond color is the angle of the scalar product of the bond line and another vector. It is possible to change the marker color by the bond color and not the inverse ? Thanks a lot for your help. PS: I joint the file.py corresponding to the modification of rgba function we want. -- -------------------------------------- Karine GOURIET Maître de Conférences tel : 03.20.43.43.98. Unité Matériaux et Transformation CNRS UMR 8207 - Université de Lille 1 Bat C6, Bureau 213 59655 Villeneuve D'ascq http://umet.univ-lille1.fr/ --------------------------------------

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Saving Image of row stereo
by Divita Mathur 17 Nov '20

17 Nov '20

Hi all, I am trying to save a rendering created using the Camera setting – row stereo. The rendering appears dark and without the row stereo settings when the image is saved (tried many formats). How can I save the actual rendering as an image? Regards, Divita Mathur

2 1

icosahedral annulus
by Pranav Shah 17 Nov '20

17 Nov '20

Hi Elaine, i was wondering if there was an "easy" way to create an icosahedral ring-mask using chimera's shape and mask commands. At the moment, I am creating two icosahedral shapes of big and small radii and them subtracting the small one from the big one, but this results in inconsistent results i.e the mask does not enclose the volume I wish to cover. Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

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Chimera morph map multiple volumes
by Ahmad Khalifa 15 Nov '20

15 Nov '20

Is there a way to morph multiple volumes into a single movie? I tried morphing two maps first with the hope that I can do another morph between the resulting morph and a third map, but it didn't work. Any suggestions or easy alternatives to join the morphs together? Thanks.

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solvent exposed surface area
by Jordan Alexis Gewing-Mullins 15 Nov '20

15 Nov '20

Hi there! I hope you're doing well. I am trying to calculate the solvent exposed surface area for each amino acid in a protein, and from the tutorial it says that once I create a surface it should automatically generate a text file with the areaSAS information, but I have no clue where to find that file. Where does it get saved? Thanks, Jordan

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zone & segname
by Francesco Pietra 15 Nov '20

15 Nov '20

Hello Working with charmm36, therefore with the great aid of segname for my homotrimer, when commanding sel :27.M z<3 I get also a water molecule, with O-atom Tip3 3687.W OH2 Is there any way to extend the above command in order to have the segname associated with this water residue? This is because there are eight 3687.W residues with different segnames. I tried to solve indirectly the problem with sel :3687.W@/pdbSegment=WT# where # ranges from 1 to 8 (i.e., the same residue name for segname WT1 to WT8). Contrary to my expectations, it does not work The same with sel :3687@/pdbSegment=WT# Thanks for advice francesco pietra

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help
by Rayna L. DeChance 13 Nov '20

13 Nov '20

Hi, I was wondering if you knew how to cut out (clip) a part of the protein and save the remaining part as a PDB file. I attached the file I was working with that has the two proteins that are aligned together and we want only a certain part of this alignment to be clip. Thank you

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distance with homotrimer
by Francesco Pietra 12 Nov '20

12 Nov '20

Hello I am trying to measure (from command line) the distance between atom NH1 in residue 27, chain M atom OG1 in residue 215, chain A command distance :27@NH1 :215@OG1 error: 6 atoms were selected. The error message is correct because the system is a homotrimer. My question: any way to specify the chains? Any of my attempts failed. Thanks for advice (getting distances from the command line would be quicker that graphically as I have a large number of disnces to measure)

2 2

I tasser models
by Sitbon, Yoel 10 Nov '20

10 Nov '20

Hello, I hope you are doing well. I obtained prediction models from I tasser and would like to visualize them on chimera. I was able to open them but i cannot open the sequence of amino acids. Do you perhaps know how to look at them? Thank you Yoel Get Outlook for Android<https://aka.ms/ghei36>

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Fw: Chimera can't open files
by Cain, Cheryl A 09 Nov '20

09 Nov '20

Please see the question below. Thanks, Cheryl Cheryl Cain cheryl.cain(a)ucsf.edu Operations Coordinator, Department of Pharmaceutical Chemistry Accreditation Project Coordinator, School of Pharmacy UCSF ________________________________ From: Jie Yang <jieyang(a)scripps.edu> Sent: Monday, November 9, 2020 4:12 PM To: chimera(a)cgl.ucsf.edu <chimera(a)cgl.ucsf.edu> Subject: Chimera can't open files Hi there, I have a problem that my Chimera can’t open/fetch .PDB files in my Mac(see attached). I believe the problem was because I accidentally denied access of Chimera to the Users/jieyang/Downloads. Could you let me know how should I reverse this? Thank you very much! Best Jie Yang [cid:8ef2ed16-18af-4541-aeab-3a4697900cb5]

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reset all models to the same center of rotation
by C.J. 06 Nov '20

06 Nov '20

Hi Chimera community, I have several models, both maps and pdbs, aligned. But the common center for rotation is far away from the model when I use "Volume Eraser". How can I reset the center for all models in command-line way? Thank you! Jianhao

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Re: [Chimera-users] PDB fetch broken
by Tom Goddard 05 Nov '20

05 Nov '20

Hi John, Try using the "Ignore any cached data" in the Chimera menu File / Fetch... panel. I suspect Chimera cached a bad file when the fetch was broken. If you use this ignore cached data option it will fetch a new copy of the file. Unfortunately when RCSB disabled their legacy web fetch the last couple days they made it so when you tried to fetch it returned an html page saying "PDB has discontinued this fetch" with an http "success" code (200). Since Chimera got the success code it assumed that html text was actually the PDB file and it cached it in ~/Downloads/Chimera/PDB Then when you try to open that same PDB file it is getting that cached html page instead of the cached PDB file. I asked RCSB to return an error code (404) on fetch so that does not happen, but they did even better and temporarily have reenabled the old fetch URLs to help Chimera users. They will still turn off the old fetch in a month or so. Tom > On Nov 5, 2020, at 6:26 AM, John Rose <rose(a)bcl4.bmb.uga.edu> wrote: > > Hi, > > Downloaded the Chimera 1.15 build but the problem still persists. > > Thanks, > > John Rose > > > John Rose Ph.D. > Associate Professor > SER-CAT Associate Director for Program > Rm. B204B > Department of Biochemistry and Molecular Biology > Davison Life Sciences Complex > 120 Green Street > University of Georgia > Athens, GA 30602-7229 > =============================== > Phone: 706-542-1750 > Fax: 706-542-3077 > > > > >> On Nov 4, 2020, at 1:28 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Chimera PDB fetch is broken starting November 3 and a command like "open 1a0m" produces an empty model with no error. >> >> We will be putting a new version (release candidate) of Chimera on the download page today or tomorrow that fixes this. >> >> What happened is that the RCSB has shutdown the URL Chimera uses to fetch PDB files (e.g. https://www.rcsb.org/pdb/files/1a0m.pdb <https://www.rcsb.org/pdb/files/1a0m.pdb>). Although RCSB announced this long ago the Chimera development team missed that this URL was going away. >> >> Tom >> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >

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PDB fetch broken
by Tom Goddard 04 Nov '20

04 Nov '20

Chimera PDB fetch is broken starting November 3 and a command like "open 1a0m" produces an empty model with no error. We will be putting a new version (release candidate) of Chimera on the download page today or tomorrow that fixes this. What happened is that the RCSB has shutdown the URL Chimera uses to fetch PDB files (e.g. https://www.rcsb.org/pdb/files/1a0m.pdb <https://www.rcsb.org/pdb/files/1a0m.pdb>). Although RCSB announced this long ago the Chimera development team missed that this URL was going away. Tom

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Fwd: How to setup Nvidia 3D Vision on Ubuntu
by Tom Goddard 03 Nov '20

03 Nov '20

Here's a picture from Kenneth of the DIN and USB cables needed to use the 3D Vision emitter on Linux. > Begin forwarded message: > > From: Kenneth Satyshur <kenneth.satyshur(a)wisc.edu> > Subject: Re: [Chimera-users] How to setup Nvidia 3D Vision on Ubuntu > Date: November 3, 2020 at 11:17:18 AM PST > To: Tom Goddard <goddard(a)sonic.net> > > Actually, the pic does not have the cable in it, only the extra on-board cable that connects to the GPU and serves up the 3pin female. Here is a pic of both the din and usb cable connected to the emitter. The DIN is a must for linux. the special cable is on the left and the usb is on the right. > > kas > > > Kenneth A. Satyshur, M.S., Ph.D. > Senior Scientist, > College of Ag and Life Sciences: Department of Bacteriology; > School of Medicine and Public Health: > Departments of Biomolecular Chemistry, > Neuroscience, Oncology, and Carbone Cancer Center > (Small Molecule Screening Facility) > University of Wisconsin-Madison > Madison, Wisconsin, 53706 > 608-215-5207 >

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How to setup Nvidia 3D Vision on Ubuntu
by Tom Goddard 03 Nov '20

03 Nov '20

Hi Wei, I'd suggest using Ubuntu 20.04, the latest Ubuntu, the current Chimera 1.14 or daily build will work fine on that. I am not certain that Quadro FX 4800 graphics drivers will be available for Ubuntu 20, probably they will be, but you might want to look for that online before proceeding. That graphics cards is very old, from 2008. The other thing to know is that Nvidia discontinued support for Nvidia 3D Vision stereo glasses in 2019 https://nvidia.custhelp.com/app/answers/detail/a_id/4845 meaning those glasses and emitter will no longer work using just the current Nvidia graphics driver. But they claim that there is a separate driver for the USB emitter that allows it to work. https://www.nvidia.com/en-us/drivers/nv3dvisionusb/390_41/nv3dvisionusb-dri… <https://www.nvidia.com/en-us/drivers/nv3dvisionusb/390_41/nv3dvisionusb-dri…> I have not tried it. If you get it to work I'd be interested in hearing about it since we have an old Nvidia 3D Vision system. Tom > On Oct 29, 2020, at 6:41 PM, Wei Zhang <zhangwei(a)umn.edu> wrote: > > Hi Tom, > > Hope everything is well. > > One university's computer lab recently retired some workstations that were used for 3D visualization before. I managed to get a couple workstations with the 3D glasses and emitters. But I need to reinstall the operating system on those machines. > > The graphic card of the workstation is Nvidia Quadro FX4800. > The emitter is NVIDIA P854. > The glasses are NVIDIA-P854 and ViewSonic-PGD250. > > I plan to install Ubuntu. I am wondering which version of Ubuntu is suitable for using UCSF Chimera. Do we need to install cuda to make it work? Do we need to install an older version of Chimera? > > Sorry I just sent the message to you to follow the previous chain of conversation. Shall I email the chimera-user in the future with such questions? > > Thank you, > > Wei >

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Capping in VRML
by Greg Williams 02 Nov '20

02 Nov '20

When I export a vrml file to process in my Cinema 4D application, the ends of the helices, coils and sheets are capped at the ends with a material that is different then the material I use to color the secondary structure features. In Cinema 4D, I have to change every capped end individually. Where do I change the vrml export settings so that the individual objects are capped with the right material? Thanks!

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Accessible surface area calculation
by Martino Benvenuti 02 Nov '20

02 Nov '20

Good morning, I would like to know if it is possible to calculate with Chimera the accessible surface area for a selected amminoacid of a protein. May you help me to figure it out? Thank you for having developed such a great program! Have a nice day, Martino Benvenuti. -- Martino BENVENUTI Ph.D. in chemistry. <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virus-free. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Screenshots for publication?
by Gustaf Olsson 02 Nov '20

02 Nov '20

Would it be acceptable to include screenshots of the Chimera GUI in publications as long as chimera is being cited as suggested? Best regards // Gustaf

2 1

Select multiple files and open in the same instance
by Ahmad Khalifa 30 Oct '20

30 Oct '20

I used to have Chimera configured to select multiple files, click open, and have them all open in the same instance. After I reinstalled it, now it opens an instance for every file, how can I change it back? Regards.

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Chimera: Per-model clipping and contour level
by Selenschik, Philipp 30 Oct '20

30 Oct '20

Hello, I really enjoy working with Chimera (version 1.14), however I encounter two problems: I fitted the X-ray based crystal structure of apoferritin to my cryo-EM density map, determined the symmetry and based on that the algorithm fits 24 subunits to the map. Really nice. Now I would like to show a "sliced" image of both map and structure. I tried doing so by "Side view", enabling "clip". That works, but I would like to rotate the clipped object. Then I tried per-model-clipping. Here I can clip the map and structures separately. However, I have to choose all fitted (e.g. 12 out of 24) substructures and the clipping works only partially. What am I doing wrong? Also, I tried to figure out the best contour level setting. It seems there is no guide as to which is ideal? Based on a tutorial, I assumed 1 A³/Da for a globular protein, which turns out to be around 620*10³ A³ for my protein. The problem here is: If I slide beyond approx.. 550*10³ A³ all that remains is a square. What's wrong? I hope you can help me out :) Kind regards Philipp

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Help with something really simple
by M. Elizabeth Stroupe 29 Oct '20

29 Oct '20

Hi ChimeraX team, I need to measure a simple angle between three atoms, two within one model and the third in another model to describe a domain motion. In Chimera I could do this from the Structure Analysis tab but now it seems you can only measure distances. I tried the following command(s) and they both gave me an error. I also tried including commas between the angles. What am I doing wrong? angle #1/A:602@C7m,:222@CB,#17/A:602@C7M measure angle #1/A:602@C7m #1/A:222@CB #17/A:602@C7M Thank you! Beth

2 1

MD Simulation on Chimera
by Samiha I Amer 27 Oct '20

27 Oct '20

Please may I know the ideal system specification to run a successful molecular Dynamics simulation on Chimera? Thank you Sent from Yahoo Mail on Android

2 1

REGARDING CHIMERA SESSION FILE
by ASIF JAHAN SHUVRO 26 Oct '20

26 Oct '20

Dear concern, this is Asif from BRAC University, Biotechnology program. I hope you're in good health. I need a little help from you. Recently, I have joined two peptide fragments by forming a peptide bond between them using your standalone UCSF Chimera software. The file has been saved as a Chimera session fle. However, I'm not finding any clue on how to convert it into an entire pdb file. I'm not being able to do any other modification to it since a pdb file is required for this purpose. Could you please help me out on this regard? kindly let me know how can I generate a pdb file from that session file format. I wish to hear your reply. Thanks in advance! Regards, Asif Jahan Shuvro Biotechnology Program Department of Mathematics & Natural Sciences BRAC University

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Morphing PDB
by Reza Khayat 26 Oct '20

26 Oct '20

Hi, Is it possible to morph multiple chains serially? I have a trimer in two different conformations, I would like to morph Chain A in conformation 1 to Chain A in conformation 2. Then, I'd like to do this with chain B and finally chain C. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

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Running Chimera on X server
by Ahmad Khalifa 26 Oct '20

26 Oct '20

The refresh rate of Chimera running on a linux server is very slow. I'm connected to the server with an ssh client with X server. I wonder if it's because Chimera is not configured properly or possibly the X server. I also tried to make some movies but they are always blank (black screen). Any suggestions?

2 1

Query on selecting one water molecule
by Izzati Mokthar 26 Oct '20

26 Oct '20

Hi, I am Izzati. I would like to ask how to select only one water molecule in chimera? Thank you

2 2

(no subject)
by Yasser Almeida 22 Oct '20

22 Oct '20

Dear Anabel, As others pointed out, you can just represent the beads as balls, points, or wire, and remove all the pseudbonds. On the other hand, how did you obtained your pdb? If you used GNOM in the ATSAS package (GUI version), it writes pdbs with a bigger bead size, which Chimera fails to represent by default. But if you use GNOM in the command line, it writes pdbs with a smaller bead size, which are more compact, smoother, and better for representation in Chimera, and others. Best, Yasser Dear Chimera team, > I am a user from your software and I would like to have a > superimposition of some crystallographic structures in a recent saxs > pdb model I obtained. However, I cannot visualize the saxs pdb file > with Chimera. Would you have any tips or inputs how can I do this? > Thank you very much in advance for all your help, > Kind regards, > Anabel

1 0

Broken links, system requirements
by Calvin Dodge 21 Oct '20

21 Oct '20

Hello, I have been trying to find out what the hardware requirements are for Chimera. For example, how can it be run in a cluster environment with CUDA cards, but no Nvidia graphics cards? My search for information has been hampered by an apparent failure or reorganization of the main site -https://www.cgl.ucsf.edu/chimera/ Every internal link from that page (like to Downloads) is broken. Will the broken links be fixed? Is another page the preferred one for Chimera? Do I need the OSMesa version to run without graphics cards? Thanks, Calvin Dodge Calvin Dodge Systems Analyst Office: 832-271-7148 Email : cdodge(a)x-iss.com<mailto:ellorente@x-iss.com> http://www.x-iss.com<https://mail.x-iss.com/owa/redir.aspx?C=32dc65a1e7df4e4289ad76e23a15fcf0&UR…> [cid:image001.png@01D5DB72.2E9C2F40]<http://www.x-iss.com/> Smart Management and Analytics for Clusters

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Re: [Chimera-users] Broken links, system requirements
by Greg Couch 21 Oct '20

21 Oct '20

Your university might want the regular version of Chimera to remotely display data. In that case, you should set up VirtualGL as well. And a RDP solution, like x2go. It doesn't perform as well as Chimera running locally on the desktop, but it might be sufficient. -- Greg On 10/21/2020 11:21 AM, Calvin Dodge wrote: > > Greg, > > Thanks for your reply _/I/_ don’t want to run Chimera in a cluster > environment, but the university I’m doing the install for does. I’ll > install the headless version. > > Sincerely, > > Calvin Dodge > > */Calvin Dodge/*/ > Systems Analyst/ > > /Office: 832-271-7148/ > > / > /Email : cdodge(a)x-iss.com <mailto:ellorente@x-iss.com> > > http://www.x-iss.com > <https://mail.x-iss.com/owa/redir.aspx?C=32dc65a1e7df4e4289ad76e23a15fcf0&UR…> > > <http://www.x-iss.com/> > > Smart Management and Analytics for Clusters > > *From: *Greg Couch <mailto:gregc@cgl.ucsf.edu> > *Sent: *Wednesday, October 21, 2020 12:24 PM > *To: *Calvin Dodge <mailto:cdodge@x-iss.com>; > chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> > *Subject: *Re: [Chimera-users] Broken links, system requirements > > (We're working on the web site issues.) > > So the real question is why do you want to run Chimera in a cluster > environment? > > Chimera is not designed to run in a cluster environment, it is > designed to run a user's desktop computer using 3D graphics. Chimera > does not use CUDA. That said, there is a headless version for Linux > that uses a software implementation of OpenGL to create images that > you could use in a cluster, so no graphics card is needed. > > ChimeraX, our successor to Chimera, can take advantage of CUDA in some > circumstances, but it is not required. ChimeraX also only works > headless on Linux, with a software implementation of OpenGL. The > headless operation is included in every Linux version. So no graphics > card is needed there either. We are investigating ways to take > advantage of the graphic card's performance when running headless, but > we're not there yet. > > HTH, > > Greg > > On 10/21/2020 9:24 AM, Calvin Dodge wrote: > > Hello, > > I have been trying to find out what the hardware requirements are > for Chimera. For example, how can it be run in a cluster > environment with CUDA cards, but no Nvidia graphics cards? > > My search for information has been hampered by an apparent failure > or reorganization of the main site -https://www.cgl.ucsf.edu/chimera/ > > Every internal link from that page (like to Downloads) is broken. > > Will the broken links be fixed? Is another page the preferred one > for Chimera? Do I need the OSMesa version to run without graphics > cards? > > Thanks, > > Calvin Dodge > > */Calvin Dodge/*/ > Systems Analyst/ > > /Office: 832-271-7148/ > > / > /Email : cdodge(a)x-iss.com <mailto:ellorente@x-iss.com> > > http://www.x-iss.com > <https://mail.x-iss.com/owa/redir.aspx?C=32dc65a1e7df4e4289ad76e23a15fcf0&UR…> > > <http://www.x-iss.com/> > > Smart Management and Analytics for Clusters > > > > _______________________________________________ > > Chimera-users mailing list:Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > > Manage subscription:https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >

1 0

issues with visualization of saxs models in chimera
by Anabel Pacios Michelena 20 Oct '20

20 Oct '20

Dear Chimera team, I am a user from your software and I would like to have a superimposition of some crystallographic structures in a recent saxs pdb model I obtained. However, I cannot visualize the saxs pdb file with Chimera. Would you have any tips or inputs how can I do this? Thank you very much in advance for all your help, Kind regards, Anabel

3 2

Writing residues coordinates and COMs
by Yasser Almeida 20 Oct '20

20 Oct '20

Hello, I am writing a python script to iterate through all the residues of my model and write the residue coordinates and its correspondent center of mass. I tried with 'runCommand' with the command 'write' but it only accepts a model to be written, not a specific residue. Any thoughts? Thanks in advance. Yasser

2 2

Query about energy minimisation
by Izzati Mokthar 19 Oct '20

19 Oct '20

Hi, I am Izzati. I have a few queries on UCSF Chimera. I need your guide to use the tools. I have two questions. Below are the questions: 1.I would like to do energy minimisation for protein structure with PDB ID: 2J9F. I click Structure editing > Minimize Structure. To be honest, I don't know how to set the settings. I used the default setting and a warning pops up as the attached picture. Do you have any suggestion of reference that I can refer to, to do the energy minimisation? [image: 5.png] 2. I need to also do molecular dynamics for my research. May I know whether I can use chimera to run molecular dynamics as well. If yes, where can I refer to the tutorials? Thank you in advance for your response. Regards, Izzati.

2 4

atom ID
by Francesco Pietra 18 Oct '20

18 Oct '20

Dear all Which is the quickest way to identify the atom ID? As visualized in the context of a multimer, where three identical subunits, distinct by chain name, bind the same peptide, also distinct by chain name. Atom IDs are needed to build a QM-MM simulation. thanks francesco pietra

2 2

PyChimera addCharge
by Matas Tiskus 16 Oct '20

16 Oct '20

Hello, I was looking for ways to add charges to protein structures in a python script and write a .mol2 file. I believe it is possible to do with importing pychimera into the script, but i can't seem to make it work. How would the code for this purpose look like? Matas

2 3

Re: [Chimera-users] [chimera-dev] Building a dimeric protein model
by Elaine Meng 15 Oct '20

15 Oct '20

On Oct 15, 2020, at 1:41 PM, Moradkhan, Tiglath A <tmoradkhan(a)csus.edu> wrote: > Hi > I've built a monomeric model using Chimera's MODELLER interface. I was wondering whether it's possible to use this model in Chimera to create a dimer. The dimer of the protein that I'm studying is composed of two antiparallel symmetric monomers. > Thank you > Tiglath > Hi Tiglath, Sure, but you would need to know the proper positioning of the two monomers in the dimer. There is nothing in Chimera to figure that out automatically. If there is a known dimer structure of a related protein and you think your modeled protein forms a similar dimer, you can simply (1) save your new monomer model as a PDB file (2) start a new Chimera, open that new PDB file two times so that you have two copies open (3) open the known dimer structure of the related protein, let's say it has chains A and B (4) superimpose one copy of your monomer model onto chain A of the known dimer structure, and superimpose the other copy of your monomer model onto chain B of the known dimer structure. Different methods of superimposing structures are discussed in the link below. Probably the easiest is to use the Matchmaker tool. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> (4) close the known dimer structure, and what you have left is the approximate dimer with two copies of your model, which can be saved as a session, or combined into a single model (see "combine" command) and then saved as a PDB file. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> Alternatively if you have a dimeric template structure you can use Modeller to make a dimeric comparative model directly, but to do that you would have to use the Modeller interface in our newer program ChimeraX. The one in Chimera only allows modeling monomers. Modeller interface in ChimeraX: <http://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html> This chimera-dev e-mail address is mostly for programming questions. For general user questions like this (for future reference) a better address to use is chimera-users(a)cgl.ucsf.edu CC'd here, and there is also a similar address for ChimeraX: chimerax-users(a)cgl.ucsf.edu I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

kill graphics windows after crash
by Dieter Blaas 15 Oct '20

15 Oct '20

Hi, please forgive me when this question is not directly related to Chimera: Sometimes Chimera becomes unresponsive because of a slow network connection. When I then try exiting it or killing it with <ctrl> c from the terminal I used to start it or killing the chimera-related process as shown with ps -ealf|grep UCSF or grep chimera the chimera windows remain and I cannot remove them. Any way of doing so? Thanks for hints, best, Dieter ----------------------------------------------------------------------- Dieter Blaas, Max Perutz Labortories 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 get specific view
by Shuo 15 Oct '20

15 Oct '20

Dear sir or madam, I wonder how to get specific view parameter in Chimera, just like command get_view in Pymol. So that next time I can easily adjust the view in Chimera. Best Shuo

2 1

Modelling missing residues in a protein
by Edmund Marinelli 14 Oct '20

14 Oct '20

Hello: I see that Chimera uses Modeller for modeling missing residues . Does Chimera have access to any other web based services that would perform similar function? Thanks, Edmund R Marinelli, PhD

4 4

MOLE 2.5 plugin
by Reza Khayat 13 Oct '20

13 Oct '20

Hi, I'm receiving the following error when launching the MOLE 2.5 plugin from Chimera. The plugin was installed as suggested by the developers: Favorites -> Preferences -> Add -> Select directory The plugin's icon appears in my tool bar. However, launching it generates the following error in the Reply Log. Traceback (most recent call last): File "C:\Program Files\Chimera 1.13.1rc\share\chimera\toolbar.py", line 26, in _guard func() File "C:\Mole2_ui\MOLE2_5\MainWindow.py", line 954, in <lambda> icon, lambda d=chimera.dialogs.display, n=MainWindow.name: d(n), 'MOLE 2.5', None) File "C:\Program Files\Chimera 1.13.1rc\share\chimera\dialogs.py", line 76, in display dialog = find(name, create=1) File "C:\Program Files\Chimera 1.13.1rc\share\chimera\dialogs.py", line 61, in find return d() File "C:\Mole2_ui\MOLE2_5\MainWindow.py", line 353, in __init__ with open(CONFIGFILE, 'w') as f: IOError: [Errno 13] Permission denied: '.MOLE_PluginSettings.txt' Error in toolbar callback: IOError: [Errno 13] Permission denied: '.MOLE_PluginSettings.txt' File "C:\Mole2_ui\MOLE2_5\MainWindow.py", line 353, in __init__ with open(CONFIGFILE, 'w') as f: See reply log for Python traceback.? Any help is appreciated. Best wishes, Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

2 2

Help on using Modeller interface
by Moradkhan, Tiglath A 09 Oct '20

09 Oct '20

Hi I'm currently trying to use the Modeller interface but I'm having difficulties. I am trying to model a monomeric protein but one of the templates is a homotetramer containing chains A, B, C and D. I only need to use chain A to model the protein but I'm not sure how to do it. Whenever I use the Modeller interface, it uses all of the chains which is not what I want. Unfortunately, this is the only template that I can use since the others are either structures that have since been refuted or don't really correspond to the protein I'm studying. I would be very grateful for your help. Thanks Tiglath

2 3

Help for Chimera please
by EMILIE MONTELLIER 09 Oct '20

09 Oct '20

Hello, I have just downloaded your Chimera software. It looks great! I would like to map a list a specific amino acid on p53 protein and I struggle to find a way to do it. I have downloaded the PDB file of 1TUP TUMOR SUPPRESSOR P53 COMPLEXED WITH DNA (at [ https://www.rcsb.org/ | https://www.rcsb.org ] ). For exemple what would be the command to hightlight amino acid 175 + 248 + 273 + 282 on p53 protein? Thanks by advance for your help, Regards, Emilie Emilie Montellier, PhD Postdoctoral Researcher Institute for Advanced Biosciences Team Tumor Molecular Pathology & Biomarkers Tel: +33 (0)4 76 54 95 76 Email: emilie.montellier(a)univ-grenoble-alpes.fr

2 1

Latest nightly broken on Mac (10.15.7)
by Oliver Clarke 09 Oct '20

09 Oct '20

Hi, In the notes for the latest nightly Chimera build, it states "Many user-interface problems on Mac fixed by upgrading the Tk windowing toolkit to version 8.6.10" - this sounds great, but it seems to have broken basic functionality, at least on my system. See screen recording here: https://www.dropbox.com/s/rme49vjwsu8zz89/chimera_gui_issues.mov?dl=0 <https://www.dropbox.com/s/rme49vjwsu8zz89/chimera_gui_issues.mov?dl=0> Many UI elements are not responsive any more (including the "Report a Bug" dialog, hence why I am reporting here). This is using Mac OS X 10.15.7 on a macbook pro 16", using the trackpad. Cheers Oli

3 4

AutoDOCK plugin for UCSF Chimera
by James Starlight 08 Oct '20

08 Oct '20

Dear Chimera users! Having already used AUTODOCK plugin of UCSF Chimera (for simple docking of 1 receptor with the ligand and structural examination of binding pocket) I wonder to know whether there is some tool built-in CHIMERA (or ChimeraX) suitable for the manipulating with DLG filles produced by Autodock? Particularly I would be interested to combine several DLG filles with their further reclasterization (in the same manner like it could be found in Autodock-Tools) and examination of particular clusters. I would be helpful for any suggestions! Kind regards Gleb

3 2

matchmaker and MSA
by arrafzaher＠campus.technion.ac.il 06 Oct '20

06 Oct '20

Hi, Suppose I have 3 structures #0 #1 and #2. If I impose structure alignment of both #1 and #2 to #0. I receive two MSA alignment. Is there a way to view one MSA of the 3 structures and not 2 MSA of them. Thanks, Zaher

2 14

Volume eraser accelerator not working properly
by Ahmad Khalifa 01 Oct '20

01 Oct '20

As I keep clicking "es", the shadows / lighting keep changing, but after clicking 10 times or so, it finally erases. Is this something I'm doing? How can I change to a more easier accelerator?

2 1

bound ligand's are exposed to solvent. Current calculations do not protect surface of ligand embedded in protein
by Anne-Frances Miller 01 Oct '20

01 Oct '20

Dear Chimera, I see on-line advice on calculating areaSAS and areaSES, however Chimera is calculating these for my bound flavin as if the protein were not there. I would like to assess the area exposed outside the protein, not total area (on an atom-by-atom basis). Indeed, the show surface command produces two surfaces, one for the FAD and a different one for the protein, even though both are chain A. Can I edit the pdb file to cause Chimera to create a single surface for both chains including both bound FADs, so that SASA calculated will represent the extent to which the FAD protrudes from the protein? (My protein is a heterodimer with two bound FADs, my Chimera version is 1.13.1 running on Mac OS 10.15.6) Thank you, Anne-Frances Novel Meritorious Research (and teaching) —————————————— A.-F. Miller, Ph. D. Professor of Chemistry University of Kentucky https://www.uky.edu/~afm/ Visiting Fellow, Einstein Foundation of Berlin Chair, Div. of Biological Chemistry, American Chemical Society

2 2

Undo for volume eraser
by Ahmad Khalifa 30 Sep '20

30 Sep '20

Is there a way to undo a recent erasing that I did? Also, are there ways to use custom shapes, or other surfaces to erase density?

2 1

scipy
by Hernando J Sosa 29 Sep '20

29 Sep '20

Is scipy installed with Chimera? If not how can it be installed? Thanks Hernando >From Chimera idle: >>> import chimera >>> import scipy Traceback (most recent call last): File "<pyshell#1>", line 2, in <module> ImportError: No module named scipy ___________________________________

2 1

Re: [Chimera-users] Troubleshooting request for help
by Cain, Cheryl A 29 Sep '20

29 Sep '20

Hi Tanuja, I've added chimera-users(a)cgl.ucsf.edu to this email as they should be able to help you there. Thanks, Cheryl Cheryl Cain cheryl.cain(a)ucsf.edu Operations Coordinator, Department of Pharmaceutical Chemistry Accreditation Project Coordinator, School of Pharmacy UCSF ________________________________ From: Saswat, Tanuja (NIH/NCI) [F] <tanuja.saswat(a)nih.gov> Sent: Friday, September 25, 2020 9:56 AM To: chimera(a)cgl.ucsf.edu <chimera(a)cgl.ucsf.edu> Cc: Goins, Jerquan (NIH/NCI) [C] <jerquan.goins(a)nih.gov> Subject: Troubleshooting request for help Hi, I am a researcher at the NIH who uses this software to complete analysis. But as of recently some of the features that I usually use have not been able to access them. Can you guys assist me in finding a resolution. I’ve CC’s my IT support in case there was something above my cresds level. Regards -- Tanuja Saswat, Ph.D. Postdoctoral Research Fellow Laboratory of Dr. Laurie T. Krug HIV and AIDS Malignancy Branch (HAMB) Center for Cancer Research National Cancer Institute tanuja.saswat(a)nih.gov<mailto:tanuja.saswat@nih.gov> Building 10, Room 4A08 Ph:240-858-3201 NCI Website<https://urldefense.proofpoint.com/v2/url?u=https-3A__ccr.cancer.gov_HIV-2Da…>

4 6

vop subtract removing too much of my map
by Ahmad Khalifa 29 Sep '20

29 Sep '20

I'm trying to subtract two overlapping molmaps: map1-map2, but the subtraction ends up removing too much of map1 where map2 doesn't overlap with map1! how can I get precise subtraction?

3 7

clustering models of a single pdb
by Subhrangshu Das 29 Sep '20

29 Sep '20

Dear sir, I have 100 pdb files. named as output.1.pdb to output.100.pdb what i do manually for clustering is as follows 1. select 100 pdbs -> open in chimera -> golto *File *-> *save PDB.. *-> *Save Multiple Models as PDB File *(renamed as all.pdb) 2. open chimera -> goto *Tools *->* MD/Ensemble Analysis *->* MD Movie* 3. in *Get Ensemble Info *dialogue box set -> *Trajectory format :* *PDB* *PDB frames contained in:* *single file* * Browse *to select File <all.pdb> *Use frames **first **through * *last* 4. on click *OK,* a dialogue box pops out, *MD Movie: PDB trajectory from all.pdb*, in which, goto *Analysis -> Cluster...*5.. on click* Cluster,* a dialogue box pops out,* Get Clustering Parameters,* in which I set *Cluster trajectory *as: *Starting frame: * *1* *step size: **1* *Ending frame:* * 100* *Cluster based on current selection, if any: * *true* *Ignore solvent and non metal ions: true* *Ignore hydrogens: * *true* *Ignore metal ions: * *alkali* 6. on click *OK, *after some RMSD calculation, i get the *Clustering* result, which I save to a text file <cluster> Now, as I need to do this for multiple times, I want to automate these steps by a python script. Can you please help with a scipt or some command help for the aforesaid tasks. Any help will be helpful in these regard. -- Thanks & Regards, Subhrangshu Das Junior Research Fellow, CSIR-IICB Department of Structural Biology & Bioinformatics Contact - IICB TRUE Campus, CN-6, Salt lake, Sector V, Kolkata-700091 *+919804938813*

3 3

tile from command line
by Dieter Blaas 28 Sep '20

28 Sep '20

Hi, I am trying to use the command line command TILE as given here: Usage <https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/usageconvent…>: *tile* /models/ [ columns /N/ ] [ spacingFactor /f/ ] [ independentRotation true|false ] [ viewAll true|false ] [ label true|false ] I tried (following the syntax of e.g. "vol all level 0.02": "tile vol all columns 3" or "tile all columns 3" or "tile models all columns 3" or "tile #0, #1, #2, #4, #5, #6 columns 3" but none works can you please give me an example! Thanks, best, 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 ------------------------------------------------------------------------

2 1

Is RTX support planned?
by Gokhan Tolun 25 Sep '20

25 Sep '20

Hi Tom, Are there any plans to implement RTX (real-time ray tracing) support to ChimeraX (and even better, allow the use of physically modelled materials and textures)? Thanks, Gökhan Gökhan Tolun<https://scholars.uow.edu.au/display/gokhan_tolun>, M.S., Ph.D. Senior Lecturer School of Chemistry and Molecular Bioscience<https://www.uow.edu.au/science-medicine-health/schools-entities/school-of-c…> | Faculty of Science, Medicine and Health (SMAH)<https://smah.uow.edu.au/index.html> | Room 125 / Building 18 Molecular Horizons Research Institute<https://www.uow.edu.au/molecular-horizons/index.html> Illawarra Health and Medical Research Institute<https://www.ihmri.org.au/researchers/gokhan-tolun/> University of Wollongong NSW 2522 Australia T +61 2 4221 3365 uow.edu.au<http://uow.edu.au/> | Facebook<https://www.facebook.com/UOW> | Twitter<https://twitter.com/uow> | Instagram<https://www.instagram.com/uow/> | LinkedIn<http://www.linkedin.com/edu/school?id=10255> NOTICE: This email is intended for the addressee name and may contain confidential information. If you are not the intended recipient, please delete it and notify the sender. Please consider the environment before printing this email.

2 1

X-PLOR format, finding a maximum
by Gustaf Olsson 25 Sep '20

25 Sep '20

Hello Chimera users This might be a somewhat “of-topic” question though I thought that this would be a good place to start. When loading density maps (particularly the X-PLOR format density maps) into Chimera the 'volume viewer’ window provides a maximum number of gridpoints for the map. My question has to do with the format of the XPLOR files. The documentation regarding this format is rather sparse and my I have not been keeping my knowledge regarding matrices up to date. Is there a way to identify this maximum value by just inspecting the content of these files? I have a lot of these files and as I en up presenting results only for ligands with grids visible above a specific cut-off, I though it would save me a lot of time and headache if I could just load the density maps with maximum densities above the cutoff. My though was to just parse the files through AWK or similar to find files with a x > a and then only load these. Sadly, I keep looking at the content of these files and I am not able to make much sense of what I am looking at. Any solutions, suggestions or suggested reading to be able to find a way to create a solution would be greatly appreciated. Best regards // Gustaf

2 1

Error reading multiple models
by Francesco Pietra 25 Sep '20

25 Sep '20

In my hands CHIMERA can't read multiple models as in .trj.xyz provided by ORCA software in QM calculations Error reading 5-sulf-min_trj.xyz: Coordinate line of XYZ file '/home/francesco/work_AGAs/VITTORIO/5-sulf-min_PBE0_OPT_FREQ_SMD/ 5-sulf-min_trj.xyz' is not element,x,y,z: '36' That is no problem for Jmol, however I would be interested in opening the models with also CHIMERA (which can open these models as a single-model-file. thanks for advice francesco pietra

2 1

Open .mrcs stack in chimera
by Ahmad Khalifa 24 Sep '20

24 Sep '20

Can I open a .mrcs stack in chimera? What file type should I pass to Chimera in order to do that?

2 1

Re: [Chimera-users] Stereo Red Cyan
by Greg Couch 24 Sep '20

24 Sep '20

Yes, the red and gray is normal, but you're seeing the combined channels. You need the glasses to separate the channels. Try viewing the image with the glasses that come with a 3D comic book. -- Greg On 9/21/2020 11:43 PM, Michael Elbaum wrote: > Red-cyan, sorry. No, I didn't look for stereo at all, just to > reproduce the condition posted that one channel appears in red and the > other in gray. Is that normal? > Michael > ------------------------------------------------------------------------ > *From:* Greg Couch <gregc(a)cgl.ucsf.edu> > *Sent:* Tuesday, September 22, 2020 4:57:50 AM > *To:* Michael Elbaum <michael.elbaum(a)weizmann.ac.il> > *Subject:* Re: [Chimera-users] Stereo Red Cyan > > Are you wearing red-cyan glasses to see the stereo? It doesn't work > without them. > > > -- Greg > > > On 9/21/2020 1:08 PM, Michael Elbaum wrote: >> >> I'm confirming the problem with a different dataset (optical >> deconvolution in tif format). Red-green shows red and gray, >> green-magenta shows green and gray. This is with version 1.14 on linux. >> >> regards, >> Michael >> >> >> >> ------------------------------------------------------------------------ >> *From:* Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu> on behalf >> of Angus McDonald <amcdonald(a)boisestate.edu> >> *Sent:* Monday, September 21, 2020 9:46:24 PM >> *To:* chimera-users(a)cgl.ucsf.edu BB >> *Subject:* [Chimera-users] Stereo Red Cyan >> I am looking at some cryo em data. When I try to view a a 3D stack of >> em dat with the Red-Cyan stereo setting I seem to only get Red and >> grayscale. The data is in 32-bit floating point and is in MRC2014 >> header format. I cannot figure out what I am doing wrong. Is anything >> obvious? >> >> Thanks for your time. >> >> >> >> -- >> Angus McDonald >> amcdonald(a)boisestate.edu <mailto:amcdonald@boisestate.edu> >> >> _______________________________________________ >> Chimera-users mailing list:Chimera-users@cgl.ucsf.edu >> Manage subscription:https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

4 4

electrostatic interactions
by Ruchika 23 Sep '20

23 Sep '20

Hi Elaine I do see "Find out clashes and contacts" feature in Chimera. I am wondering if there is any feature which can check on electrostatic interactions as well. Please let me know. Thanks !! Regards Ruchika

2 5

Fitting structure in rescaled map
by Ahmad Khalifa 23 Sep '20

23 Sep '20

Hello, How to fit an atomic model after downscaling my map (map shrinks)? Are atomic models built to scale?! Regards.

2 3

Writing a SINGLE pose (with ligand and protein) to a PDB file
by Edmund Marinelli 22 Sep '20

22 Sep '20

Hello: I used ViewDock to open a pdbqt file generated by use of AutoDock Vina. The ligand was shown in the graphics window. Then I opened the protein pdb file that was used in the docking experiment. The ViewDock dialog lists the poses obtained and I can select each and view the resulting pose in the graphics window fine. I opened the Model Pane. I selected from the list of models the first pose (#0.1) and the protein (#1) in the list. I assumed that saving these two into a file would give a file that contained only the protein and the ligand bound as in the best pose . I want to save the best pose as a pdb file wherein the protein and ligand are present. I gave a filename Test.pdb . Chimera returned the following error message: "You must provide a filename that contains either $name or $number , which will be changed to the model name or model number (respectively) in the final saved file name." I do not understand what this means. I tried using the pose number and also the protein name but it gave the same error. I don't understand what is meant by $name and $number - what do they refer to ? What do I need to do to save a single pose containing protein and the ligand to a unique file not containing other poses? The screenshot below is what I see: Note that in the models list I selected the best pose #0.1 and also the protein, which is at the bottom of the list, hence it is not visible in the picture. What is the filename syntax that I need to use to save a pose with protein to a single PDB file? Stated more plainly: Can you give a viable example of what I need to enter as a filename that will allow saving of the file? Or am I going about this all wrong? Sorry for the verbose email. [image: image.png]

3 3

Stereo Red Cyan
by Angus McDonald 21 Sep '20

21 Sep '20

I am looking at some cryo em data. When I try to view a a 3D stack of em dat with the Red-Cyan stereo setting I seem to only get Red and grayscale. The data is in 32-bit floating point and is in MRC2014 header format. I cannot figure out what I am doing wrong. Is anything obvious? Thanks for your time. -- Angus McDonald amcdonald(a)boisestate.edu

3 2

Using iBabel to convert Chimera's pdb to pdbqt
by Jatin Kashyap 19 Sep '20

19 Sep '20

Dear UCSF Chimera Community, I am trying to minimize a complex[1] and saving it in a pdbqt format. I minimize it in Chimera and saved in pdb[2], followed by using iBabel (GUI of open babel for Mac) to convert pdb into pdbqt. Here are two things: first, if I convert without using any flag then output gives me pdbqt file with BRANCH information which is not supported by Vina. To solve it I am using -XR flag in iBabel to trim the BRANCH information so that resulting pdbqt file can be read by Vina. But in that case iBabel is giving me weird looking structure and upon inspection of pdbqt file[3] I realized the complex was split into different models. I had successfully followed the same workflow for other minimization code i.e. YASARA. Can anybody please help me to fix it. I am attaching files below with corresponding citations. Thank you. [1] [2] [3] —— Jatin Kashyap Ph.D. Student Dr. Dibakar Datta Group Department of Mechanical and Industrial Engineering New Jersey Institute of Technology (NJIT) University Heights Newark, NJ 07102-1982 Phone- (201)889-5783 Email- jk435(a)njit.edu

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Setting a pathway/trajectory for a molecule
by Rani Wiswedel 18 Sep '20

18 Sep '20

Good day, I am an honours student attempting to set up my first molecular dynamics simulation, and am having some trouble trying to understand how to set a pathway for a substrate through a pore in Chimera. I am very unsure of how to do this, and was wondering if you could provide some help. I tried following the Trajectory and Ensemble Analysis tutorial, but essentially cannot get past the first step of downloading leap.top etc. I am also not sure if this is the correct tutorial to follow for what I am looking to do? Any advice would be greatly appreciated, I am in way over my depth. Thank you Kind regards, Rani Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://www.uct.ac.za/main/email-disclaimer or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://csirt.uct.ac.za/page/report-an-incident.php.

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Re: [Chimera-users] alpha carbon atom as sphere
by Elaine Meng 18 Sep '20

18 Sep '20

On Sep 18, 2020, at 1:58 PM, Ruchika <Ruchika(a)ucsf.edu> wrote: > Hi Elaine > I am trying to select just alpha carbon on the atom and show it as a sphere, but I am having hard time doing that. When I select the atom, and go to actions and sphere, I must show the side chain and then going to sphere, shows the whole side chain as a sphere instead of just alpha carbon as sphere. Could you please help me with this issue ? > Thanks a lot !! > Regards > Ruchika Hi Ruchika, Assuming you are using Chimera, we recommend sending such questions to chimera-users(a)cgl.ucsf.edu (CC'd here) or else they may fall through the cracks. It doesn't make sense to me that you would need to show the sidechain. I can only guess that maybe you're showing ribbon and that is causing the confusion. If you are showing ribbon, you cannot see or select the alpha-carbon with the mouse, because ribbon normally hides the backbone atoms. If you select the ribbon it selects the whole residue. If you want to show backbone atoms at the same time as ribbon, use command "ribbackbone" or alternatively, just hide the ribbon, and then show whatever atoms you want. Select only the CA and then change it to sphere. Explanation of "ribbackbone" <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ribbackbone.html> Example commands: open 1gcn ribbackbone show :5@CA repr sphere :5@CA 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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Backbone RMSD
by Zhang, Bixia 18 Sep '20

18 Sep '20

Hi, I am trying to get the backbone RMSD between two structures. However I tried selecting backbone and use matchmaker, it gives me same value with the whole protein. So there must be something wrong. Could you please teach me a command that can do this? Thank you so much for helping! Best, Bixia

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Re: [Chimera-users] Molecular Dynamics
by Jean-Didier Pierre Marechal 18 Sep '20

18 Sep '20

Dear Edmund, Elaine is completely right about everything. This interface was first developed for our lab for our own needs (training, short MD and Teaching) then we work with the Chimera’s team to make it look the way it looks today (a lot better than the initial shot). It can do a lot of things but in its actual state it remains a simple tool for first insights on the system and not necessarily convenient for all systems (especially if you look for large systems with long MDs). Typical time scale of MDs in today standards are difficult to performe with this interface. The main application we make of it is on small molecules and for teaching purposes it is fantastic. You could eventually look look for short MDs on a complex protein-ligand but I would reckon to go for standard MD drivers. We did not continue on this project because ChimeraX, that already integrates openMM, was about to be relased. Hope this help, JeanDI ***************************** Prof. Dr. Jean-Didier Maréchal (JeanDi) Associate Professor Insilichem Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es personal webpage: http://gent.uab.cat/jdidier insilichem webpage: http://www.insilichem.com

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Molecular Dynamics
by Edmund Marinelli 18 Sep '20

18 Sep '20

Hello: Very new to Chimera and to modeling in general. 1.) Does the Molecular Dynamics Tool allow simulation of a protein ligand complex? 2.) Does a protein ligand docking pose generated by Autodock, for example, qualify as a 'model' that can be read by the MD Tool and be employed in a MD run? Is there a comprehensive tutorial or manual discussing in detail the setting of MD run within Chimera? Any help would be appreciated. Thanks. Edmund R Marinelli, PhD

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measurement of arc-length (geodesic distance) between atoms on a protein surface?
by Wiener, Michael C (mcw2s) 17 Sep '20

17 Sep '20

New subscriber here, with a question about whether Chimera currently can measure arc-length (geodesic distance) between atoms on a protein surface (or, for example, generate a Calpha-Calpha distance matrix of this). I am (very) interested in measuring/obtaining distances between pairs of Calpha carbons (or pairs of other atoms, I suppose) of different amino acids that are on the surface of a protein. While the difference between arc-length (geodesic) distance and cartesian/Euclidean distance will be negligible if, for example, the two solvent-exposed Calpha atoms are on the same solvent-exposed face of an alpha-helix, the difference could be significant for residues on opposite “sides” of the protein. I did see that there are ways in Chimera to get distances between an atom and a molecular surface, or to place markers on the surface & obtain the lengths between these for a distance, but I am VERY interested in whether one can simply select two atoms and get the arc-length (geodesic) distance or generate an arc-length (geodesic distance) matrix of all surface-exposed Calpha pairs. Several computational methods have been developed for this sort of thing, via graph theoretical or other approximation method, and have been published (Hall et al., Biophysical Chemistry 190-191 [2014] 50-55). However, I have not yet (?) found this to be in any graphics/analysis program. I’m thinking that this could perhaps be useful to someone besides me? Any assistance would be greatly appreciated. My lab and I are (much) more on the user side than the developer side, so are not currently well-positioned to code it in-lab. Regards, -MW (btw, if anyone in the “Chimera Group” wants to know more about why I am interested in this, don’t hesitate to send me an email. This type of distance calculation is related to some experimental technology/assay development that we are doing.) ----- Michael C. Wiener. Ph.D., Professor Department of Molecular Physiology and Biological Physics University of Virginia Charlottesville, VA 22908-0886 434-243-2731 (office); 434-243-2730 (lab)

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generate helical symmetry mates around an axis
by sadeem ahmad 17 Sep '20

17 Sep '20

Hi all, I am trying to generate a helical trimer from the monomer pdb around a central double-stranded RNA. The rise and twist are 46 A and 74.0 deg respectively. I opened my monomer pdb in chimera *(Screenshot-0)* and used the following command to generate an axis around the central RNA double helix: *define axis #0:.X,.Y* where X and Y are the chain IDs for the 2 RNA strands This command helped me generate an axis named *a1* along the RNA duplex *(Screenshot-1)*. Now I want to generate a helical trimer along the RNA duplex with rise=46A and twist=74deg. For this I used the command: *sym #0 group H,46,74,3 axis a1* However, it is not placing the symmetric copies around axis a1 but around a distant axis *(Screenshot-2)*. I am not sure how to generate the helical trimer along the a1 axis. Any help in this regard would be appreciated. Thanks. -Sadeem -- :-)

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Re: [Chimera-users] Chimera-users Digest, Vol 209, Issue 27
by Jatin Kashyap 17 Sep '20

17 Sep '20

Eric, Following are steps I followed: load the structure> del H > run Dock Prep(Add Hydrogen - ticked, Write Mol2 - unticked) > del :10.P@h :8.T@h > minimize (while deselecting the add hydrogen option) I got a warning that I am not sure about. I am pasting the log below[1], can you please confirm that I followed the correct steps and warning can be ignored in the log. [1] Model 0 (7bv2_nsp12-7.pdb) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. Model 0 (7bv2_nsp12-7.pdb) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. Residues with incomplete side chains: LYS 98.A ASP 100.A ASP 218.A ASP 824.A GLU 50.C Replacing each by 'swapaa same (residue atom spec) lib Dunbrack preserve True' LYS 98.A: phi -78.3, psi 128.2 trans Chi angles for LYS 98.A: ASP 100.A: phi -70.1, psi -6.8 trans Chi angles for ASP 100.A: ASP 218.A: phi -127.8, psi 120.9 trans Chi angles for ASP 218.A: ASP 824.A: phi -92.0, psi 1.6 trans Chi angles for ASP 824.A: GLU 50.C: phi -60.9, psi -45.8 trans Chi angles for GLU 50.C: Applying LYS rotamer (chi angles: -62.5 -75.3 99.0 -88.6) to LYS 98.A Applying ASP rotamer (chi angles: -67.2 -26.9) to ASP 824.A Applying ASP rotamer (chi angles: -70.6 -17.9) to ASP 100.A Applying GLU rotamer (chi angles: -170.8 -83.2 -29.7) to GLU 50.C Applying ASP rotamer (chi angles: -175.9 -11.3) to ASP 218.A No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain A; guessing terminii instead No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain C; guessing terminii instead No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain P; guessing terminii instead No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain T; guessing terminii instead Chain-initial residues that are actual N terminii: VAL 31.A, LYS 2.C, G 10.P, U 8.T Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: U 20.P, C 21.T Chain-final residues that are not actual C terminii: THR 929.A, GLY 64.C 856 hydrogen bonds Removing spurious proton from 'C' of THR 929.A Removing spurious proton from 'C' of GLY 64.C Hydrogens added Charge model: AMBER ff14SB Non-standard atom names: G H (G 10.P H) U H (U 8.T H) Total charge for #0: -30.384 The following residues had non-integral charges: U 20.P -0.6919 C 21.T -0.6919 Correct charges are unknown for 2 non-standard atom names in otherwise standard residues Charges of 0.0 were assigned to the unknown atoms 1 model(s) had non-integral total charge Details in reply log No incomplete side chains Charge model: AMBER ff14SB Total charge for #0: -30.384 The following residues had non-integral charges: U 20.P -0.6919 C 21.T -0.6919 1 model(s) had non-integral total charge Details in reply log Using main parameter file parm10.dat modified by heme-iron.frcmod, frcmod.ff14SB, frcmod.ionsjc_tip3p Initial energy: -45283.236153 kJ/mol Step 12 Potential energy: -58447.379716, Gradient norm: 758.031360 Updated 15035 atoms. RMSD: 0.037342 Finished 10 of 100 steepest descent minimization steps Step 12 Potential energy: -64213.179928, Gradient norm: 362.328469 Updated 15035 atoms. RMSD: 0.018132 Finished 20 of 100 steepest descent minimization steps Step 12 Potential energy: -65930.345155, Gradient norm: 417.614654 Updated 15035 atoms. RMSD: 0.012606 Finished 30 of 100 steepest descent minimization steps Step 12 Potential energy: -67901.748990, Gradient norm: 190.328174 Updated 15035 atoms. RMSD: 0.010435 Finished 40 of 100 steepest descent minimization steps Step 12 Potential energy: -68928.640793, Gradient norm: 79.670023 Updated 15035 atoms. RMSD: 0.007430 Finished 50 of 100 steepest descent minimization steps Step 12 Potential energy: -70504.551913, Gradient norm: 192.974949 Updated 15035 atoms. RMSD: 0.016225 Finished 60 of 100 steepest descent minimization steps Step 12 Potential energy: -71243.383589, Gradient norm: 95.907393 Updated 15035 atoms. RMSD: 0.006255 Finished 70 of 100 steepest descent minimization steps Step 12 Potential energy: -71661.708391, Gradient norm: 193.911209 Updated 15035 atoms. RMSD: 0.006283 Finished 80 of 100 steepest descent minimization steps Step 12 Potential energy: -72255.311758, Gradient norm: 199.037193 Updated 15035 atoms. RMSD: 0.007288 Finished 90 of 100 steepest descent minimization steps Step 12 Potential energy: -72873.927407, Gradient norm: 84.768251 Updated 15035 atoms. RMSD: 0.005517 Finished 100 of 100 steepest descent minimization steps Step 12 Potential energy: -79350.452189, Gradient norm: 206.369396 Updated 15035 atoms. RMSD: 0.114423 Finished 10 of 10 conjugate gradient minimization steps —— Jatin Kashyap > On Sep 16, 2020, at 6:41 PM, chimera-users-request(a)cgl.ucsf.edu wrote: > > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://plato.cgl.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..." > > > Today's Topics: > > 1. Re: Error "No MMTK name for atom "H" in standard residue ?G"" > (Eric Pettersen) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 16 Sep 2020 15:41:33 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > To: Jatin Kashyap <jk435(a)njit.edu> > Cc: Chimera User Help <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Error "No MMTK name for atom "H" in > standard residue ?G"" > Message-ID: <9B74E727-F918-4A68-9E48-83F05E6B329E(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="utf-8" > > Ah I see. Because you also have missing side chains you have to do things a little differently. Namely run Dock Prep (Tools?Structure Editing?Dock Prep) first, keeping "Add hydrogens" on but "Write Mol2" off; then use the delete command to delete the two unwanted protons; then run Minimize. > > --Eric > >> On Sep 16, 2020, at 2:54 PM, Jatin Kashyap <jk435(a)njit.edu> wrote: >> >> I am sorry for the confusion. Actually I did that step by GUI options (Tools>Structure Editing>AddH). But I did it again by issuing ?addh? from command line along with other steps. >> But still I am getting the same error. >> >> ?? >> Jatin Kashyap >> >> >>> On Sep 16, 2020, at 5:49 PM, Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: >>> >>> It's "addh" not "add H". >>> >>> --Eric >>> >>>> On Sep 16, 2020, at 2:44 PM, Jatin Kashyap <jk435(a)njit.edu <mailto:jk435@njit.edu>> wrote: >>>> >>>> Hi Eric, >>>> >>>> Just for the clarification I am double checking it here, first I loaded the structure > del H > add H > del :10.P@h :8.T@h > minimize (while deselecting the add hydrogen option). >>>> >>>> But it is throwing the error [1]. >>>> >>>> >>>> [1] >>>> Model 0 (7bv2_nsp12-7.pdb) appears to be a protein without secondary structure assignments. >>>> Automatically computing assignments using 'ksdssp' and parameter values: >>>> energy cutoff -0.5 >>>> minimum helix length 3 >>>> minimum strand length 3 >>>> Use command 'help ksdssp' for more information. >>>> No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain A; guessing terminii instead >>>> No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain C; guessing terminii instead >>>> No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain P; guessing terminii instead >>>> No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain T; guessing terminii instead >>>> Chain-initial residues that are actual N terminii: VAL 31.A, LYS 2.C, G 10.P, U 8.T >>>> Chain-initial residues that are not actual N terminii: >>>> Chain-final residues that are actual C terminii: U 20.P, C 21.T >>>> Chain-final residues that are not actual C terminii: THR 929.A, GLY 64.C >>>> 852 hydrogen bonds >>>> Removing spurious proton from 'C' of THR 929.A >>>> Removing spurious proton from 'C' of GLY 64.C >>>> Hydrogens added >>>> Residues with incomplete side chains: >>>> LYS 98.A >>>> ASP 100.A >>>> ASP 218.A >>>> ASP 824.A >>>> GLU 50.C >>>> Replacing each by 'swapaa same (residue atom spec) lib Dunbrack preserve True' >>>> LYS 98.A: phi -78.3, psi 128.2 trans >>>> Chi angles for LYS 98.A: >>>> ASP 100.A: phi -70.1, psi -6.8 trans >>>> Chi angles for ASP 100.A: >>>> ASP 218.A: phi -127.8, psi 120.9 trans >>>> Chi angles for ASP 218.A: >>>> ASP 824.A: phi -92.0, psi 1.6 trans >>>> Chi angles for ASP 824.A: >>>> GLU 50.C: phi -60.9, psi -45.8 trans >>>> Chi angles for GLU 50.C: >>>> Applying ASP rotamer (chi angles: -67.2 -26.9) to ASP 824.A >>>> Applying LYS rotamer (chi angles: -178.9 71.3 178.8 68.6) to LYS 98.A >>>> Applying ASP rotamer (chi angles: -175.9 -11.3) to ASP 218.A >>>> Applying GLU rotamer (chi angles: -170.8 -83.2 25.9) to GLU 50.C >>>> Applying ASP rotamer (chi angles: -70.6 -17.9) to ASP 100.A >>>> Charge model: AMBER ff14SB >>>> Total charge for #0: -32.172 >>>> The following residues had non-integral charges: >>>> LYS 98.A -0.6068 >>>> ASP 100.A -1.0636 >>>> ASP 218.A -1.0636 >>>> ASP 824.A -1.0636 >>>> GLU 50.C -0.9909 >>>> U 20.P -0.6919 >>>> C 21.T -0.6919 >>>> 1 model(s) had non-integral total charge >>>> Details in reply log >>>> >>>> Residue #0:98.A (LYS/lysine) is missing atoms H_gamma_3, H_epsilon_2, H_zeta_3, H_delta_2, H_epsilon_3, H_alpha, H_beta_3, H_gamma_2, H_delta_3, H_beta_2, H_zeta_1 and H_zeta_2 >>>> >>>> >>>> ?? >>>> Jatin Kashyap >>>> >>>> >>>>> On Sep 16, 2020, at 5:32 PM, Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: >>>>> >>>>> Hi Jatin, >>>>> I you don't delete those phosphates, then Chimera will add spurious protons to them, which is what is causing the problem. In order to get this to work, you will have to run Add Hydrogens "by hand" before your minimization, delete the spurious protons, and then run your minimization -- being careful to skip adding hydrogens as part of the minimization process. >>>>> The command (Favorites?Command Line) to delete the unwanted protons in your case is "del :10.P@h :8.T@h". >>>>> >>>>> --Eric >>>>> >>>>> Eric Pettersen >>>>> UCSF Computer Graphics Lab >>>>> >>>>> >>>>>> On Sep 16, 2020, at 2:10 PM, Jatin Kashyap <jk435(a)njit.edu <mailto:jk435@njit.edu>> wrote: >>>>>> >>>>>> Dear Chimera Community Members, >>>>>> >>>>>> I am facing an error while minimizing a protein that have 5? terminal phosphates attached to it. >>>>>> Chimera is showing the warning that AMBER is unable to parametrize the phosphates and if you do not delete it, 0 charges will be assigned to it. >>>>>> I selected the option not to delete it but then it throws error[1] on the following step. I am pasting my log below [2]. >>>>>> >>>>>> Thank you for helping me to understand this. >>>>>> >>>>>> [1] >>>>>> No MMTK name for atom "H" in standard residue ?G" >>>>>> >>>>>> [2] >>>>>> Model 0 (7bv2_nsp12-7.pdb) appears to be a protein without secondary structure assignments. >>>>>> Automatically computing assignments using 'ksdssp' and parameter values: >>>>>> energy cutoff -0.5 >>>>>> minimum helix length 3 >>>>>> minimum strand length 3 >>>>>> Use command 'help ksdssp' for more information. >>>>>> Residues with incomplete side chains: >>>>>> LYS 98.A >>>>>> ASP 100.A >>>>>> ASP 218.A >>>>>> ASP 824.A >>>>>> GLU 50.C >>>>>> Replacing each by 'swapaa same (residue atom spec) lib Dunbrack preserve True' >>>>>> LYS 98.A: phi -78.3, psi 128.2 trans >>>>>> Chi angles for LYS 98.A: >>>>>> ASP 100.A: phi -70.1, psi -6.8 trans >>>>>> Chi angles for ASP 100.A: >>>>>> ASP 218.A: phi -127.8, psi 120.9 trans >>>>>> Chi angles for ASP 218.A: >>>>>> ASP 824.A: phi -92.0, psi 1.6 trans >>>>>> Chi angles for ASP 824.A: >>>>>> GLU 50.C: phi -60.9, psi -45.8 trans >>>>>> Chi angles for GLU 50.C: >>>>>> Applying LYS rotamer (chi angles: -62.5 -75.3 99.0 -88.6) to LYS 98.A >>>>>> Applying ASP rotamer (chi angles: -67.2 -26.9) to ASP 824.A >>>>>> Applying ASP rotamer (chi angles: -175.9 -11.3) to ASP 218.A >>>>>> Applying ASP rotamer (chi angles: -70.6 -17.9) to ASP 100.A >>>>>> Applying GLU rotamer (chi angles: -170.8 -83.2 -29.7) to GLU 50.C >>>>>> No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain A; guessing terminii instead >>>>>> No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain C; guessing terminii instead >>>>>> No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain P; guessing terminii instead >>>>>> No SEQRES records for 7bv2_nsp12-7.pdb (#0) chain T; guessing terminii instead >>>>>> Chain-initial residues that are actual N terminii: VAL 31.A, LYS 2.C, G 10.P, U 8.T >>>>>> Chain-initial residues that are not actual N terminii: >>>>>> Chain-final residues that are actual C terminii: U 20.P, C 21.T >>>>>> Chain-final residues that are not actual C terminii: THR 929.A, GLY 64.C >>>>>> 856 hydrogen bonds >>>>>> Removing spurious proton from 'C' of THR 929.A >>>>>> Removing spurious proton from 'C' of GLY 64.C >>>>>> Hydrogens added >>>>>> Charge model: AMBER ff14SB >>>>>> Non-standard atom names: >>>>>> G H (G 10.P H) >>>>>> U H (U 8.T H) >>>>>> Total charge for #0: -30.384 >>>>>> The following residues had non-integral charges: >>>>>> U 20.P -0.6919 >>>>>> C 21.T -0.6919 >>>>>> Correct charges are unknown for 2 non-standard atom names in otherwise standard residues >>>>>> >>>>>> Charges of 0.0 were assigned to the unknown atoms >>>>>> >>>>>> 1 model(s) had non-integral total charge >>>>>> Details in reply log >>>>>> >>>>>> No MMTK name for atom "H" in standard residue "G" >>>>>> >>>>>> >>>>>> ?? >>>>>> Jatin Kashyap >>>>>> New Jersey Institute of Technology >>>>>> >>>>>> _______________________________________________ >>>>>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>>>>> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >>>>> >>>> >>>> _______________________________________________ >>>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>>> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >>> >> > >

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