- Chimera-users - RBVI Mailing Lists

Docking problem in my Protein ligand
by MUHAMMAD FURQAN AKBER 27 Aug '20

27 Aug '20

Hi hope you are fine? I cant find out the final result by protein ligand docking by chimera. This shows the error with pdb receptor. What can i do ?

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This Chimera plugin "sounds" interesting
by Eric Pettersen 27 Aug '20

27 Aug '20

Sonification for Structural Biology and Structure-based Drug Design - Paul Vickers <https://paulvickers.github.io/chison/>

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How to fit an atomic model into a topographic height volume
by Lee, Yun-Tzai (NIH/NCI) [F] 24 Aug '20

24 Aug '20

Dear Chimera developers, I am a research fellow who works at Frederick Biophysics Laboratory and working on an image processing project. I used Chimera to generate a topographic height volume data from a single plane image. You can find the attached file and use a command following to generate the topographic surface. % topography #0 height -40 smoothingIteration 5 But there is no option for me to fit the atomic model into the surface height volume by using Fit in Map tools. Can someone help me figure out what’s the issue? Is that possible to fit an atomic model into a height volume created by a single plane image or just simply need multiple planes? Thanks in advance. Best, Yun-Tzai

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INQUIRY
by Samiha I Amer 21 Aug '20

21 Aug '20

Hello Please how do I prevent chimera from renumbering my protein residue sequence in cases where I am working with a pdb structure that does not cover all the residues? For example, the attached pdb protein file (5trf.pdb) was downloaded from the pdb database with the first 9 residues missing. The first residue in the pdb structure is the 10th residue and this was numbered accordingly but whenever I upload such structures on Chimera, the numbering of the residues tend to scatter because chimera automatically numbers the first residue in the structure as 1, just as it appeared in the attached mol2 file. Please how do I avoid/correct such Thank you.

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Cannot dock molecule to targeted region?
by 孙业平 20 Aug '20

20 Aug '20

Dear all, I am trying to fit an antibody molecule to the cryo-EM density map for an antigen-antibody complex. The related files can be found at the following link https://drive.google.com/drive/folders/16ELIDsUxiNwRGp9ely2SRn-zjAdHCudH?us…. I first segmented the map ("emd_22158.map") and get the segment map ("emd_22158.seg") in chimera. Then I selected the regions corresponding to the antibody and use the "Fit to segments" tool of chimera to fit the antibody molecule. The "image1.png" shows the inital antibody postion and the expected docking postion in the segmented complex density (indicated by the red arrow). However, the antibody molecule cannot be fitted into the selected target region after this operation, but moved to the position shown in "image2.png (only the target regions are shown). I have tried to ungoup and regroup the target region to make its overall shape more simial to the antibody, and place the antibody into the region and ajust its orienation, but whatever I tried, the results are the same: the antibody will move to the position shown in "image2.png" after performing the "Fit to segments" action. I wonder whether it is impossible to dock the antibody to the expected position with chimera or there is anything wrong with my operation. Could you help me with this issue? I will appreciate any help from you. Best regards, Yeping Sun

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Fw: Open MTZ file
by Williams, Joanne 20 Aug '20

20 Aug '20

Hello! Can you help with the inquiry below? thanks, Jo ________________________________ From: Sharyn Endow, Ph.D. <sharyn.endow(a)duke.edu> Sent: Thursday, February 22, 2018 5:01 AM To: chimera(a)cgl.ucsf.edu Subject: Open MTZ file Is it possible to open an .mtz file in Chimera? ~~~~~~~~~~~~~~~~~~~~~~~~~~ Sharyn A. Endow, PhD Professor of Cell Biology, DUMC Professor of NBD, Duke-NUS PO Box 3709 450 Sands Bldg/Research Drive Durham, NC 27710 USA T 919 684-4311 F 919 681-9929 ~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Minimized Structures vs. Unminimized
by Jordan Harriman 17 Aug '20

17 Aug '20

Hi there, I have a protein I'm modifying, for a total of 28 unique mutations. My question is if it's possible to tell the energetic difference between a minimized structure vs. an unminimized structure. Following that, if it's possible to rank minimized structures in terms of greatest stability. Is there some quantifiable output I can use to compare structures? Best, Jordan

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Dock-preparation
by JAVAD KARIMBAYLI 17 Aug '20

17 Aug '20

Hi! I have got a problem and searched all previous posts for solutions but failed to find one. Therefore, I would be very much thankful to have your guidance. I have generated my protein model in I-Tasser and now I would like to do dock-prep. (Attached model-PDB file) However, when I run it: *Tools .. Strct edit .. Dockprep **All selected ** Add hydrogens (also consider H-bonds)* *Incomplete side chains:replace(Dunbrack 2010 rotamer library)* *Protonation states fro: his (residue-name-based)* *standart residues: AMBER ff14SB* *other residues: AM1-BCC* *Output:* No incomplete side chains No SEQRES records for model1 (1).pdb (#0) chain A; guessing terminii instead Chain-initial residues that are actual N terminii: MET 1.A Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: Chain-final residues that are not actual C terminii: LEU 522.A 470 hydrogen bonds Removing spurious proton from 'C' of LEU 522.A Hydrogens added Charge model: AMBER ff14SB Non-standard atom names: ILE HD3 (ILE 18.A HD3, ILE 31.A HD3, ILE 42.A HD3 + 26 others) ILE HD1 (ILE 18.A HD1, ILE 31.A HD1, ILE 42.A HD1 + 26 others) ILE HD2 (ILE 18.A HD2, ILE 31.A HD2, ILE 42.A HD2 + 26 others) Total charge for #0: 9.382 The following residues had non-integral charges: ILE 18.A -0.0558 ILE 31.A -0.0558 ILE 42.A -0.0558 ILE 77.A -0.0558 ILE 96.A -0.0558 ILE 132.A -0.0558 ILE 136.A -0.0558 ILE 151.A -0.0558 ILE 153.A -0.0558 ILE 163.A -0.0558 ILE 184.A -0.0558 ILE 193.A -0.0558 ILE 223.A -0.0558 ILE 236.A -0.0558 ILE 250.A -0.0558 ILE 256.A -0.0558 ILE 284.A -0.0558 ILE 297.A -0.0558 ILE 321.A -0.0558 ILE 370.A -0.0558 ILE 378.A -0.0558 ILE 401.A -0.0558 ILE 416.A -0.0558 ILE 436.A -0.0558 ILE 447.A -0.0558 ILE 450.A -0.0558 ILE 480.A -0.0558 ILE 489.A -0.0558 ILE 495.A -0.0558 Correct charges are unknown for 3 non-standard atom names in otherwise standard residues Charges of 0.0 were assigned to the unknown atoms So, please kindly help me to solve the issue. Yours Sincerely Javad Karimbayli

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Modeling of mutlichain protein complex
by amit gaur 16 Aug '20

16 Aug '20

Hi, I am trying to model a multichain protein complex using modeller extension in chimera. But, I do.nt know how to do that? Can some one help me with this ? Thanks -- *Dr. Amit Gaur* *Post Doctoral ResearcherPI: Dr. Ji-Fang ZhangThomas Jefferson University* *1020, Locust Street, Suite 418* *Philadelphia, PA 19107*

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The command like volume zone in X
by Zheng, Fengwei 14 Aug '20

14 Aug '20

Dear Developer, I am wodering if there is a command of Chimera can achieve the same function like "volume zone" in ChimeraX? I tried the command "vol zone #2 near #0:.a range 2", but the chimera always said "unknow keyword #2"~ Another thing is that I wonder if there is a command of ChimeraX can achieve the same function like "turn z 2 360 precess 20" in Chimera (to achieve the Wobble motion / "wiggle-rock" motion, like nutation in pymol)~ The I tried 1.14, 1.15 and the latest daily built versions of Chimera. The ChimeraX version I used is 1.0, Many thanks! Best, Fengwei

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Coordinate bond problem
by Xelha ap 13 Aug '20

13 Aug '20

Hi! I have had problems minimizing the structure of a molecule that contais cordination bonds. Chimera does not recognizes the bond. The structure is a BODIPY, and its characteristics is the coordination bond between Boron atom and one nitrogen. Can you help me to minimize mi structure? is there in chimera any option to select coordination bonds? When i tried to minimize it, i selected that the boron atom is tetrahedral and subtituents but, with the following conditions to select dis not work for me. I get "Failure running ANTECHAMBER for residue UNKCheck reply log for details". I have been changed the next selections and I get the same answer. Can you help me please? M. en C. Xelha Araujo Padilla Estudiante de Doctorado del Programa de Biomedicina y Biotecnología Molecular Lab. de Citopatologia Ambiental, Depto. de Morfología, Escuela Nacional de Ciencias Biológicas-IPN, Zacatenco. Ciudad de México Tel. +52(55) 57296300 Ext. 52399.

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Problem opening Chimera "vop zFlip" mrc map in CADD MOE
by Paul Miller 13 Aug '20

13 Aug '20

Hi I opened an MRC file in UCSF Chimera 1.13.1 and used the "vop zflip" command and then saved the flipped map. The original map opened in CADD MOE, but the flipped map would not open. Is this a known issue? Just wondering if there's a solution. Cheers, Paul Paul Miller, PhD University Lecturer in Pharmacology Department of Pharmacology University of Cambridge Tennis Court Road Cambridge CB2 1PD +44 1223 761267 https://www.phar.cam.ac.uk/research/miller

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Using python to run rotamer
by mailman-bounces＠cgl.ucsf.edu 12 Aug '20

12 Aug '20

From: benjamintam <benjamintam(a)um.edu.mo <mailto:benjamintam@um.edu.mo>> Subject: Using python to run rotamer Date: August 5, 2020 at 12:49:55 AM PDT To: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu <mailto:chimera-users-bounces@cgl.ucsf.edu>> Dear all, I am trying to simplify tedious and repetitive work through using Chimera. My work has to substitute a list of residue on a protein. For each row of the list, after the substitution, I need to save it as a separate file. Since I am a beginner of python coding, I would like to ask the following question before I attempt to code: -From what I said, is it possible to do it in Chimera? -Do I just call the Rotamer program out by using “useRotamers()”? If it is using that, how do I provide the residue number and residue type into the program? Thanks for your time and help. Best regards, Ben

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Blast protein analysis
by Bernadette Ataku 12 Aug '20

12 Aug '20

Hi, I have been using Chimera for some time and lately I can't seem to blast my protein sequence. "BLAST Database error: No alias or index file found for protein database [/databases/mol/blast/db_current/pdbaa] in search path [/wynton-local/usr.local/opal25-tomcat7/webapps/ROOT/appBlastProtein2Service1597130953690-1008200060::]" This statement is generated when I try to blast my protein sequences. What could be the problem? and how can I fix it. Kind regards, Bernadette Kutima

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Question related to chimera
by Malimige Aponso 12 Aug '20

12 Aug '20

Hi, I've been using chimera (Platform: Windows; Chimera version: 1.12/build 41623) for my research purposes and it has been a great tool. But now I have encountered an issue when providing the executable location. When I select the opal web service, it shows that the website is down. Alternatively, when I select the local pathway for vina.exe, chimera indicates that the running failed. Can I kindly get assistance to resolve this matter as soon as possible? Thank you. Kind regards, Minoli Aponso. --

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Chimera launches multiple instances on Mac OS X Catalina
by Oliver Clarke 07 Aug '20

07 Aug '20

Hi, After upgrading to Mac OS X Catalina, Chimera now launches a new instance of the application every time I open a new file. Previously, if I for example double-clicked an MRC or PDB file, it would open in the existing instance of Chimera; Now, it launches a new instance each time, which pretty quickly leads to me having 20+ copies of Chimera running simultaneously. Has anyone else encountered this and found a way to revert to the original behavior? Cheers Oli

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AFTER DOCKING I AM SAVING THE PDB FILES, BUT IN THAT PDB FILE THE LIGAND AND RECEPTOR ARE HAVING THE SAME NAME
by Shinjini Ghosh 07 Aug '20

07 Aug '20

For analysis, I want to have a PDB file of let's say with the first docked ligand in chimera which I did with autodock vina. I was able to save and open it in chimera. But the receptor and the ligand are both having the same name which I am using to save my PDB file. How can I change the names of receptor and ligand in the PDB file so that it is considered as different molecules in that particular PDB file. I want to give two different names to the receptor and the ligand in that particluar PDB file. This I need for my project. Please help me with this. Thank you. -- Shinjini Ghosh. Student of Master of Science, Biophysics and Molecular Biology' Rajabazar Science College, University of Calcutta. <https://mailtrack.io/?utm_source=gmail&utm_medium=signature&utm_campaign=si…> Sender notified by Mailtrack <https://mailtrack.io/?utm_source=gmail&utm_medium=signature&utm_campaign=si…> 08/07/20, 08:02:34 PM <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…> <x-msg://5/#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Server maintenance
by Eric Pettersen 06 Aug '20

06 Aug '20

Hi all, The servers that usually host the Chimera web site and web services will be undergoing maintenance Monday and Tuesday of next week (August 10/11), but we have jury-rigged a temporary solution that should allow the web site and services to continue to function through the maintenance window. Nonetheless, do not be shocked if the site/services wind up being down on those days. Also, mail to the Chimera mailing lists and Chimera bug reports will be not be fully processed until the servers fully come back up on Wednesday. Such mail/reports will be accepted but spooled during the maintenance window, and delivered afterward. So you probably will not get any responses until Wednesday/Thursday. --Eric Eric Pettersen UCSF Computer Graphics Lab

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How to prepare increase visible detail characteristics in cryo-EM structure with chimera?
by sunyeping 04 Aug '20

04 Aug '20

Dear all, I am trying to learn preparing publishable figures of cryo-EM protein structure. I try to reproduce a figure (fig. 4A) from a paper published in Nature (https://doi.org/10.1038/s41586-020-2571-7) Could you please find the original figure in the publication and the one I prepared in the following link？ https://drive.google.com/file/d/1dwQYT9-bGbs7OHi8e351SmE0FYr6FLK4/view?usp=… The original figure (a) is for EMD-22156. I download the map for EMD-22156 form https://www.ebi.ac.uk/pdbe/emdb/, loaded it in Chimera, adjusted the range, hide the dusted, performed segmentation, and get images like (b). The orignal figure (a) has plenty of structural detailed, and the helix can be clearly seen, but the images I prepared do not like that and look ugly. Could you give me some detailed step-by-step instruction on how this original figure was prepared in chimera? With many many thanks Yeping Sun

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Help in protein minimization
by Aishah Hisham 03 Aug '20

03 Aug '20

Hi, I'm doing protein minimization using Chimera 1.14However, I'm not sure if something was wrong with my structure or the software as it takes hours to run, the software is not responding and sometimes the structure went missing after running. Here I attached the protein needed to be minimized. I use the default setting with Gasteiger charges. Thank you. Best regards.

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Splitting, addh, save only saves secondary structure for first model
by Brian Wiley 03 Aug '20

03 Aug '20

Hi, It a multisubunit complex such as 2ast, Chimera will indicate it's better to split the model to add the hydrogens. However when after split and adding hydrogens I would like to save as 1 model which I can do but then I only get the secondary structure helices and sheets for first model. You will see there should be around 20-23 total "HELIX" for all 3 structures A,B,C in total (authors split continuous helices for some reason). However I only get the helices and sheets for model A (159 residue protein) when "saving multiple models in a single file". Is this a functionality request so that all HELIX from all models are included after split as in the original PDB file? Brian JHU

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Scripting Question
by Helmick, Harrison Dale Brent 03 Aug '20

03 Aug '20

To the Chimera Team, Hello, my name is Harrison Helmick, and I am a PhD student in Purdue University's department of food science. I hope that you all are doing well. I am interested in developing more relationships between bioinformatic models and end use properties of foods, helping us understand and predict characteristics like emulsification, gelling, denaturation, etc. I have been using Chimera to run molecular dynamic simulations, as well as analyze the protein structures and compare those to experimental properties. I'd like to see if there are predictable functional differences based on intermediate steps of denaturation of common seed storage proteins used in food. I have found Chimera to be super interesting and helpful in terms of my learning so far. One of the characteristics I'd like to quantify is the change in secondary structure over the course of denaturation. I would like to have a script that returns the number of residues that are identified as the basic secondary structures so that I can graph the relative proportion of these structures of the course of the simulation. I'd also like to see which helices and strands are being degraded first, and I will compare that to their relative surface accessibility. The way I have gone about this is to use the Chimera command per frame scripts KSDSSP, sel hex, and writesel to attempt to generate files for each frame. With a short python code, we could loop over the files to see which residue numbers disappear first and the progression of the destruction of helices, strands, etc. I haven't been able to get the dynamic file writing to work though, so I always write over the original file instead of saving it as a new one. While I could probably figure out the dynamic file writing, this seems inefficient, and I was wondering if you all had a better script this process. Thank you, -- Harrison Helmick Graduate Research Assistant, Ross Fellowship Kokini Lab, Purdue University Philip E. Nelson Hall of Food Science 745 Agriculture Mall Dr. West Lafayette, IN 47907-2009

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Private lesson
by Sylvia Lee-Huang 31 Jul '20

31 Jul '20

I would like to inquire if you offer private lessons on Chimera X and /or Chimera. If so, what is your rate? Specifically, I would like to learn protein-protein docking using your system. Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Re: [Chimera-users] Where is the 2D Labels gui?
by Elaine Meng 31 Jul '20

31 Jul '20

> On Jul 31, 2020, at 4:58 AM, Chin-Bow, Stephen <stephen.chin-bow(a)yale.edu> wrote: > > Hi Elaine, > I just searched for: > > chimera 2D labels +gui > > but I did not find it. > Is it possible that the 2D Labels GUI was added for ChimeraX users? > Many thanks! > Stephen Hi Stephen, Chimera's 2D Labels tool is in the menu under Tools... Utilities, and also under Tools... Depiction. In general every command manual page also has a crossreference link to its tool, so you could just look at the "2dlabels" command manual page to find out about the tool. We generally just call the graphical interface dialogs "tools" so you wouldn't see the jargon "gui" very often in the documentation or find it in a search. If you just searched for "2d labels" you would find it. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels…> The 2D Labels tool is also mentioned in the "tips on preparing images" and used in many of the image-making tutorials. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#tips> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/convergent.html> Another way to find out about the tool is to look at the Tools index in the User Guide. Each tool's individual manual page says what tool category it is in (which is the submenu under Tools in which it appears). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecontrib.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels…> ChimeraX does not have a 2D Labels GUI (tool dialog) yet, only a 2dlabels command. We changed the syntax of this command between the two programs, to simplify/improve it in ChimeraX. Regarding your other message, we had envisioned new users finding out about Chimera features in these ways: (1) tutorials: numerous in the User Guide and additional ones on our website (2) using menu Help... Search Documentation to search for terms of interest (3) browsing the User Guide (included with download, menu Help... User's Guidef), scanning through tools index, commands index, basic functions outline for topics of interest (e.g. "tips on preparing images") and then following the links to read more details. (4) website feature highlights, image gallery, and animation gallery This does not address learning the programming (python) side of things. Chimera includes a Programmers Guide, but information for programmers is much less detailed than for users. <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/index.html> ChimeraX has much more emphasis than Chimera on supporting programmers (APIs, programmer documentation, ...), as well as a Toolshed online repository for plugins (similar to the Cytoscape App store). I hope this clarifies things. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Is there a way to determine the "screen" window coordinates (x, y) of an "atom-spec"
by Chin-Bow, Stephen 30 Jul '20

30 Jul '20

Hello, It has been only a few weeks since I first started learning Chimera 1.14 (build 42094) on a Linux64 system with X11. I hope my experiences will help you improve both Chimera and ChimeraX. Earlier today, I reported a situation which results in an unexpected handling of a "divide by zero" bug. I am using the experience to also learn some Python. I am sure there are better ways, but I edited your playmorph.py code to record an animation with a morphing sequence played in reverse. I admit that I still do not understand the different coordinate systems used in Chimera. I have a question which can simply be answered using a ruler, but I am hoping there is another more elegant solution. "2D Labels" arrow ends are specified as a percentage of the screen width and screen height (range 0.0 to 1.0). I would like to draw an arrow whose end (x,y) is specified with precision. After I can specify the windowsize Is there a way to request the "window-screen" coordinates of a specific atom-spec? This is useful, because if I have set the windowsize then I can simply divide the coordinates by the window dimensions to get the desired end for the arrow. Many thanks, Stephen

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