- Chimera-users - RBVI Mailing Lists

New Install of Chimera on RHEL 9
by Evan Kantrowitz 12 Sep '24

12 Sep '24

I have been working with my IT department to port a script that uses Chimera from an old linux machine to a new Linux machine running RHEL. I setup my own test node at home with RHEL (same version). I got the script working on my test node. I am now moving the system to the IT node. When I reinstalled the same version of Chimera (Chimera64-2024-04-12) on that machine and run the script when Chimera starts I get Tkinter errors and others (see below). What do I need to do to get this version of Chimera running? Any suggestions would be appreciated. Should I try a more current build? ERRORS: Traceback (most recent call last): File "/opt/viewmotions/chimera64/share/__main__.py", line 73, in <module> value = chimeraInit.init(sys.argv) File "/opt/viewmotions/chimera64/share/chimeraInit.py", line 680, in init import chimera File "/opt/viewmotions/chimera64/share/chimera/__init__.py", line 2782, in <module> from SimpleSession import BEGIN_RESTORE_SESSION, END_RESTORE_SESSION File "/opt/viewmotions/chimera64/share/SimpleSession/__init__.py", line 14, in <module> from save import saveSession, sessionID, noAutoRestore, autoRestorable, \ File "/opt/viewmotions/chimera64/share/SimpleSession/save.py", line 13, in <module> from chimera import replyobj, selection, SessionPDBio, version File "/opt/viewmotions/chimera64/share/chimera/replyobj.py", line 24, in <module> import Tkinter File "/opt/viewmotions/chimera64/lib/python2.7/lib-tk/Tkinter.py", line 39, in <module> import _tkinter # If this fails your Python may not be configured for Tk ImportError: libXss.so <http://libxss.so/>.1: cannot open shared object file: No such file or directory Thanks Evan ----------------------------------------------------------------------------- Evan R. Kantrowitz, Ph.D evan.kantrowitz(a)bc.edu <mailto:evan.kantrowitz@bc.edu> Emeritus Professor of Chemistry Cell: 617-775-9915 Boston College www2.bc.edu/evan-kantrowitz <http://www2.bc.edu/~kantrow> -----------------------------------------------------------------------------

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Announcement: Release of DOCK 6.12
by Scott Brozell 12 Sep '24

12 Sep '24

We are pleased to announce the release of DOCK 6.12. DOCK is a suite of programs for molecular docking. The source code for DOCK 6.12 is available for download and free for academic users at https://dock.compbio.ucsf.edu/DOCK_6/index.htm This release includes several major new features: A new implementation of the hierarchical database search method of DOCK 3 which samples ligand degrees of freedom from precomputed conformations, a new covalent docking algorithm called attach-and-grow which aligns covalent residues and dummy atoms on ligands to grow conformations, a new receptor desolvation scoring function based on GIST, and updates to the chemgrid scoring function to match DOCK 3.7. For full information on what is new in DOCK 6.12, please visit: https://dock.compbio.ucsf.edu/DOCK_6/new_in_6.12.txt Sincerely, The DOCK Team Please visit us at the DOCK Web site. https://dock.compbio.ucsf.edu

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How to move ions along with protein structure
by Amir Mehdi 10 Sep '24

10 Sep '24

Hi, I am MEHDI I am trying to make a fusion between two proteins but when I am joining them by using build structure->joint structure (C-N peptide bonds) it will only move the protein structure but not the ions attached with the structure, can you suggest me something what to do in this case? Thank you

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morph command in chimerax
by Hansen, Bryan (NIH/NIAID) [E] 09 Sep '24

09 Sep '24

Hi, I'm using ChimeraX v 1.8 (2024-06-10) and I'm having a problem with the morph command. No matter how I format the command I'm getting the same error message of "Require at least 2 structures for morph" I've tried morph #3,4 core 0.1 frames 75 wrap t and morph #3#4 core 0.1 frames 75 wrap t These are 2 electron density maps so there's no sequence info docked in yet. Thanks for any tips or advice on what I'm doing wrong. Bryan Hansen Computational Biologist / Electron Microscopist NIH/NIAID/RTB/RML/EMU Rocky Mountain Laboratories 903 S. 4th St Hamilton, MT 59840 406.363.9202 *********************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information.It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error, please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ***********************************************************

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Chimera interface to Modeller
by Vonderviszt Ferenc 03 Sep '24

03 Sep '24

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

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

29 Aug '24

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

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display cartoon and H-bonds
by Bryan Sutton 27 Aug '24

27 Aug '24

I can't for the life of me figure out how to display ONLY a cartoon representation of my protein and backbone H-bonds. ChimeraX keeps forcing side-chain:backbone bonds.. I don't want that. I can do it if I show the backbone atoms, but I don't want to do that either. I only want it to show ONLY backbone H-bonds.

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Problem of starting Chimera
by 郭家瑞 24 Aug '24

24 Aug '24

Hello, This is the first time I am stalling Chimera, but I meet the problem of starting the software. According to the Debug command, I have tried update my graphic driver, installed Gzip and tried different Chimera releases including 1.18, 1.17 and 1.14. However, the software still cannot be started. The content of debug log is copied as following: D:\Chimera 1.14\share\chimeraInit.py:99: UnicodeWarning: Unicode equal comparison failed to convert both arguments to Unicode - interpreting them as being unequal if chimera_env.get(e) == _original_environ.get(e): initializing general preferences loading Tix initializing graphics Return code: -1073741819 I am looking forward to any guidance or help for solving the problem. My graphic is NVIDIA Geforce 3050Ti and the opperation system is Windows 10. If necessary, more details can be supplied. Sincerely Appreciated, Jiarui Guo from China

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Mac Version
by Gonzalo de Prat Gay 22 Aug '24

22 Aug '24

Hello I have downloaded Chimaera 1.18 for Mac I am running Ventura 13.4.1, and it tells me the file is corrupted when I try to open de dmg Is there any compatibility issue or should it run on this OS X? Thanks Gonzalo

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chimera
by 2719354821＠qq.com 13 Aug '24

13 Aug '24

After installing and opening the UCSF Chimera software, pythonw.exe keeps popping up new windows, causing the software to malfunction. I have tried downloading various versions of the UCSF Chimera software, but after installation, when I double-click to open it, various interfaces keep popping up. At the same time, Microsoft Edge also continuously opens web pages, rendering both the software and the computer unusable. I found that a few years ago, someone in the community had the same experience. How can this be resolved? Most concerning is that, like them, I am also using a Honor laptop.

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Chimera
by Kotin, Robert 13 Aug '24

13 Aug '24

Good afternoon – I’d appreciate advise for virus capsid viewing. Adeno-associated viruse structures, e.g., 1lp3, consist of the asymmetric unit repeated 60x to form the icosahedral capsid (T=1). I’d like to highlight the equivalent residue in each of the 60 subunits but haven’t figured out how to do that (except by manually going through each of the 60 chains). Please let me know if there are commands that can specify the residue in chains 1, 2, 3,…60. Thank you Robert Kotin

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.crd file not opening
by safi ch 05 Aug '24

05 Aug '24

Greetings, hope you are doing well. I want your guidance on how can I open a .crd file on UCSF Chimera. I am working on a protein and its mutants and performed their docking via Swiss Dock, it gave results in form of .crd file that I cannot open. My supervisor also has no idea how to open it, so please help me in this regard, I need to open it to work further on my research. Waiting for your kind response please.

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August 1 Chimera(X) website downtime
by Elaine Meng 01 Aug '24

01 Aug '24

Planned downtime for server maintenance: The Chimera and ChimeraX websites, Toolshed, web services (Blast Protein, Modeller, ...) and cgl.ucsf.edu e-mail will be unavailable August 1, 3-6 pm PDT. Apologies for any inconvenience, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

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column selection: chimera vs chimeraX
by 7mkf 22 Jul '24

22 Jul '24

Hi there, I'm an avid user of chimera and have begun transitioning to chimeraX. A feature I find very useful in chimera is expand selection to columns within the multialignviewer. Is there a way to do this in ucsf chimeraX? Many thanks, Mike

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molmap onGrid option
by Hernando J Sosa 18 Jul '24

18 Jul '24

Dear Chimera I am using the molmap command with the option onGrid but the results are not what I would have expected. With a loaded map (#0) and an atomic model(#1) The command: molmap #1 6.0 onGrid #0 generates a map with a voxel size of 6.768 even though the loaded map #0 has a voxel size of 0.846 Trying to force the voxel size with molmap #1 6.0 onGrid #0 gridSpacing 0.846 produces the same result as the onGrid option overrides the gridSpacing option. How can I produce a map using molmap that has exactly the same dimensions and voxel size of map #0? Thanks H. _

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Internal Server Error. Can Not Download chimera 1.18
by Setyanto Md 17 Jul '24

17 Jul '24

Dear Chimera User and Development Team, I tried to download ucsf-chimera version 1.18. However, the message 500 Internal Server Error appears. Is this error from our internet network, or is it from the chimera server? Thank you ------- Setyanto Tri Wahyudi ------- Computational Biophysics Group, Department of Physics, IPB University - Indonesia Gedung Fisika Wing-S Lt.2 Jl. Meranti Kampus IPB Darmaga Bogor - 16680 Indonesia

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Docking with auto dock fails for a ligand containing a Boron atom
by Patrone Marco 15 Jul '24

15 Jul '24

Dear All, I’m trying to dock a ligand containing a boronate substituent using Auto Dock Vina within Chimera v. 1.13.1 The process fails as the B in the pdb instance is not recognized for Boron and the following syntax error is printed “Parse error on line 27 in file "ligand.pdbqt": ATOM syntax incorrect: "B" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive” Is there any way to overcome this? Are there newer/different libraries that inlcude also Boron element I can update my ADV with? Many thanks for your time and best regards, marco -- Marco Patrone – PhD Biocrystallography Unit Division of Immunology, Transplantation, and Infectious Disease (DITID) DIBIT – San Raffaele Scientific Institute Via Olgettina, 58 20132 Milano Italy phone: +39 0226434921 fax: +39 0226434153 http://www.hsr.it/research/organzation/massimo-degano [https://p.hsr.it/5xmille/b2024.jpg]<https://www.5xmille.org/?utm_source=firmamail&utm_medium=email&utm_campaign…> CODICE FISCALE 07636600962 Scopri di più su www.5xmille.org<https://www.5xmille.org/?utm_source=firmamail&utm_medium=email&utm_campaign…> Rispetta l’ambiente: non stampare questa mail se non è necessario. Respect the environment: print this email only if necessary.

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Covalent substrate modeling and minimization
by wh-kelvin.chung＠polyu.edu.hk 14 Jul '24

14 Jul '24

Good day I am a researcher studying antibiotic interaction and trying to make a model with a substrate covalently bound to the active site. There is a homolog with a crystal structure (PDB: 4KQO), and I am going to add the bound substrate in this pdb file to my target protein where the mode was generated by alphafold server. Although the workflow shall be simple, I still have some problems, could you kindly help? 1. Firstly, I would like to check whether the model of 4KQO is good enough for modeling, by examining the electron density map (open 4KQO, open 4KQO from eds). However, I found that it is a bit different from the tutorial (https://www.cgl.ucsf.edu/chimerax/docs/quickstart/index.html, pdb:1a0m) that the electron density of 4KQO did not cover the substrate molecule. I am totally ignorant in crystallography, so, how could I visualize the electron density of the substrate? by any symmetry operation / command so that I could check whether there is "electron density in the substrate" ? 2. I aligned 4KQO with the alphafold generated model, and I deleted the protein from 4KQO, and combined the two model, make a bond between the active residue with the substrate, however, I am not sure how to (1) check the bond length and angle is appropriately assigned, and (2) do energy minimization to reorientate side change to eliminate the crash with the substrate. Thank you very much for your help in advance Have a nice weekend

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Capturing output of measure center command
by ldreher＠smith.edu 12 Jul '24

12 Jul '24

Hello, I am trying to write a python script to prepare proteins for molecular docking, and as part of that I want to be able to identify and save the center coordinates of each protein. using runCommand('measure center #0') works fine, but I am at a loss as to how to capture the output of that command. Ideally I would like to save the output as a string in python. Any advice on how to go about this would be appreciated! Thanks! Laura

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Difference between command line and menus
by edith.gincel＠u-paris.fr 09 Jul '24

09 Jul '24

Dear all I am trying to check contacts between ligands and protein. I tried to use the command line, to be able to do it semi-automatically, but I don't find any contact. When I use the command line, I find contacts. Has someone experienced such problems? Thank you for your help

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Stereo in ChimeraX
by Engelhardt, Peter 01 Jul '24

01 Jul '24

Hi chimera team, We can’t get any stereo to work in ChimeraX though several trials. In the earlier Chimera all worked perfectly. We are especially interested in red-cyan stereo as it’s most suitable for a large public and easy to use even with colors. Could you please let us know how to install e.g. red-cyan stereo for ChimeraX. We thank you in advance Cheers Peter __________________________ Peter Engelhardt PhD., Docent Adjunct Professor in Molecular Genetics Unit of Molecular Electron Tomography and Nanoscopy Nanomicroscopy Center (NMC), Otanano Aalto University, School of Science and Technology, Puumiehenkuja 2, FI02150 Espoo Finland Mobil Phone: +358 400193342 Email: Peter.Engelhardt(a)Helsinki.Fi<https://webmail.helsinki.fi/horde/imp/dynamic.php?page=message&buid=2535&ma…> Email: Peter.Engelhardt(a)Aalto.Fi<mailto:Peter.Engelhardt@Aalto.Fi> Sent from my iPhone

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script for comparing surfaces bits
by chiarini＠takisbiotech.it 24 Jun '24

24 Jun '24

Dear all, I'm trying to come up with some method to compare surfaces of the same protein area over some trajectory. A simple RMSF doesn't cover the analysis as a roto-traslation of some parts might retain the surface form and shape, whereas a residue might have a complete rearrangement of its surrounding without undergoing large RMSF changes. Some software based on Masif are available, tough they do not confront between trj frames. Are there any turnarounds in chimera to do this? A function similar to RMSD but for surfaces that maybe could be emplyed in this specific case? Thank you all, Valerio Chiarini -- Dr. Valerio Chiarini _Senior Scientist_ Proteins & Monoclona Antibodies Department b Takis Biotech c/o Tecnopolo Via di Castel Romano, 100 00128 Rome, Italy Tel.: +39 06-50576077 Fax: +39 06-50576710 Email: chiarini(a)takisbiotech.it Web: http://www.takisbiotech.it 196/03_ _Le informazioni contenute in questa comunicazione e gli eventuali documenti allegati hanno carattere confidenziale, sono tutelate dal segreto professionale e sono ad uso esclusivo del destinatario. Nel caso questa comunicazione Vi sia pervenuta per errore, Vi informiamo che la sua diffusione e riproduzione C( contraria alla legge e preghiamo di darci prontamente avviso e di cancellare quanto ricevuto. __Grazie._ _This e-mail message and any files transmitted with it are subject to attorney-client privilege and contain confidential information intended only for the person(s) to whom it is addressed. If you are not the intended recipient, you are hereby notified that any use or distribution of this e-mail is strictly prohibited: please notify the sender and delete the original message. __Thank you._

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(no subject)
by furkan calapoğlu 20 Jun '24

20 Jun '24

How can i do organometalic ligand and protein docking ?

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Score decimals question
by VALERIA MARIA CARRILLO RAMIREZ 19 Jun '24

19 Jun '24

Hi, I'm doing a work for college and my professor is asking for an analysis via Autodock Vina. However I have to calculate scores and the program is giving them with only one decimal and I need to report the values with 3 decimals. How can I change that? Thanks a lot :)

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Aligning small molecules in Chimera
by Prathvi Singh 19 Jun '24

19 Jun '24

Hi Elaine, Is it possible to superimpose/align small molecules in chimera/chimeraX? I have isolated a very small part of a polypeptide chain from a PDB file (it contains a CO and NH group engaged in peptide bond formation and both the groups are flanked by C-alpha atoms such that the structure's formula becomes CH3-CO-NH-CH3). I have 10 such PDB files. I want to extract this fragment from each PDB file and superimpose them to know the differences. Thank you Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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RBVI downtime
by Eric Pettersen 13 Jun '24

13 Jun '24

Hi all, The RBVI compute cluster will be down for scheduled maintenance Monday and Tuesday of next week (June 17/18) which means that the Chimera and ChimeraX web sites (including the ChimeraX toolshed) and mailing lists will be down during that time. This also means that web services from Chimera/ChimeraX that access our compute cluster will not work (Blast Protein, Modeller tools, sequence realignment). We are sorry for any inconvenience. --Eric Eric Pettersen UCSF Computer Graphics Lab

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ChimeraX_InfoRequest
by Altan KARA (MAM-GMBE) 09 Jun '24

09 Jun '24

To whom it may concern, How we can create high resolution images with ChimeraX? No matter what I tried still the outputted images are not in high resolution. Thanks Dr. Altan KARA Kd. Uzman Araştırmacı TÜBİTAK MAM Gen Mühendisliği ve Biyoteknoloji Enstitüsü Barış Mah. Dr. Zeki Acar Cad. No.1 P.K. 21 41470 GEBZE / KOCAELİ T +90 262 677 3371 F +90 262 641 2309 www.mam.gov.tr altan.kara(a)tubitak.gov.tr

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Converting a carbonyl group to carboxylic acid group
by Prathvi Singh 06 Jun '24

06 Jun '24

Hi Elaine, I have a SER residue which is in the middle of a polypeptide chain. Is there a way in chimera/chimeraX to specifically extract this residue such that the carbonyl group bonded to its N-terminal NH group also gets extracted but is converted to carboxylic acid group (-COOH group) before extracting? Thanks in advance, Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Help saving models as .pdb file
by Jacek Jagodzinski 03 Jun '24

03 Jun '24

I have constructed model of pentameric protein by exchanging one of the chains with a very closely related chain from other variant of such pentameric protein. Chimera recognizes that my model consists of parts of two proteins. I would like to save it as a single protein file. When I attempt to save model as a single file (option in save dialog) a PDB file is produced. However, when I open this file in other application (such as Cresset Flare) to explore molecular dynamics or docking in this newly constructed hybrid system - it opens as two different proteins. Is it possible to “merge” the parts to become a single pentameric protein, that would behave as single entity during docking or MD computations? Jacek Jagodzinski PS. I am not computational chemist, I am medicinal chemist by training and long career.

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Using Chimera/AutoDock Vina for oligomers
by Ballanah Torbett 24 May '24

24 May '24

Hello, I hope this email finds you well! I had a question about using the Chimera and its AutoDock Vina interface, as I'm relatively new to using these programs. I've been able to dock substrate onto one binding site of my protein of interest, but I'd like to apply it to the other three binding sites of the tetramer as well. I wouldn't be able to work with the monomer since the active sites are formed from the interactions between the N and C termini. I have also tried saving the session as a new PDB file and docking a new substrate, but it bound to the already-occupied site. Is there a way to dock substrate onto the other sites while "ignoring" the occupied site? Thank you! Sincerely, Ballanah Torbett 3rd Year PhD Student Gaucher Group Georgia State University

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Saving symmetry model in pdb format
by Kailash Singh Bisht 17 May '24

17 May '24

Hello ChimeraX team I am trying to export the symmetry structure of the protomer virus protein as a pdb file but whenever I am saving that model it only saves the same protomer instead of the whole symmetry structure. Can you please help? How to export those symmetry models as PDB files -- With Regards Thanking You Kailash Singh Bisht Ph.D. Student

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Displaying angles in chimera
by Prathvi Singh 16 May '24

16 May '24

Hi Elaine, Is it possible in chimera/chimeraX to display angles between two covalent bonds like in pymol? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Difficulty with Ribbon Visualization in Chimera Software
by 罗舒月 15 May '24

15 May '24

Dear Chimera Software Team,     I hope this email finds you well. I am writing to seek assistance regarding a challenge I am facing while using the Chimera software. Specifically, I am experiencing difficulties in visualizing my protein structure in ribbon mode.     When I load my PDB file and choose the ribbon representation, the resulting visualization appears as linear segments rather than the desired helical structure. I am unsure whether this issue is related to my file or if there is a specific step or setting I am overlooking.    I would greatly appreciate it if you could provide me with guidance on how to achieve the desired helical ribbon model in Chimera or any insights on potential issues with my file. To assist you in troubleshooting, I have attached the PDB file in question, as well as an image showing the current ribbon visualization.    Thank you in advance for your time and support. I look forward to your prompt response.  Best regards, Shuyue Luo the result of my file the effect I want 发自我的企业微信

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Difficulty with Ribbon Visualization in Chimera Software
by 罗舒月 14 May '24

14 May '24

Dear Chimera Software Team,      I hope this email finds you well. I am writing to seek assistance regarding a challenge I am facing while using the Chimera software. Specifically, I am experiencing difficulties in visualizing my protein structure in ribbon mode.      When I load my PDB file and choose the ribbon representation, the resulting visualization appears as linear segments rather than the desired helical structure. I am unsure whether this issue is related to my file or if there is a specific step or setting I am overlooking.    I would greatly appreciate it if you could provide me with guidance on how to achieve the desired helical ribbon model in Chimera or any insights on potential issues with my file. To assist you in troubleshooting, I have attached the PDB file in question, as well as an image showing the current ribbon visualization.     Thank you in advance for your time and support. I look forward to your prompt response.   Best regards, Shuyue Luo the result of my file the effect I want 发自我的企业微信

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Preparing molecular structures for panel of figures
by Prathvi Singh 10 May '24

10 May '24

Hi Elaine, I want to create a panel containing 4 figures. Each figure in the panel will be a ball and sticks representation of an amino acid residue. I have tried using the "Tile Structures" feature in UCSF chimera to create the panel. Although it does ease the job a lot, I find it difficult in aligning residue labels or 2D labels. Is there a grid based feature which can display a grid on the chimera workspace so that I can use its lines as a guide to better align my labels? Thanks in advance Prathvi, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Chimera scripting
by Flip Jansen 06 May '24

06 May '24

Hello Chimera dev team, I am a junior specialist from across the hall working at the Fraser Lab and I have some questions about using chimera scripting for omitting densities and generating reference maps. One of the issues I have been having has been that using the molMap function in Chimera generates a non-cubic output and I am aware that I can use onGrid with a pre-existing map with the desired dimensions. However, in the workflow, I am setting up I do not yet have a reference map and I am in most scenarios starting with just a PDB or an adapted from PDB map. Is there a way to let Chimera(X) generate a cubic output map from PDB without requiring another map from an external program like cryoSPARC? Another question I have is regarding the loss of secondary structural information when saving a map in Chimera. Is there a way to save a map while maintaining that information? Any help is highly appreciated, I would also be happy to come by an talk in person. Best, Flip Jansen

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Issues installing chimera on linux
by Conor Bonal 02 May '24

02 May '24

Hello, I tried to follow the tutorial to install Chimera on Linux. I'm using a computer with Ubuntu 18.04.5 and it is 64-bit. I followed the tutorial word for word then substituted "chimera-installer.bin" with the file name "chimera-1.17.3-linux_x86_64.bin" and I continued to get the same error message telling me the file or directory does not exist, although I can clearly see it in my downloads folder. Can you provide any assistance with installing the software? Thank you! Conor Bonal

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

29 Apr '24

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

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Ligand has no chain ID after saving docked complex
by kalabamelisa＠yahoo.com 24 Apr '24

24 Apr '24

Hello. I want to use PRODIGY web server to predict the binding affinity of my docked complexes, and the server requires a single PDB file containing both the docked ligand and the protein. I open the .pdbqt file containing the docking results using ViewDock and then I open my receptor file in .pdb format. I combine the two (receptor and the best ligand) and then save the complex as a PDB file. The server requires the ligand's name and what chain it's on, but when I open the complex in Chimera the ligand has no chain ID, it just shows up as "het". How do I assign a chain ID to my ligand in this situation?

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Problem in Docking Output
by Mrs Kumud Pant 22 Apr '24

22 Apr '24

Dear Developers, I am facing problem of incomplete docking. The error statement is pasted below. Also attaching receptor and ligand file for your perusal. Since I am new to this software therefore, detailed explanation is requested in eliminating the problem. #0, chain A: prostaglandin G/H synthase 1 Model 0 (oxidoreductase.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 incomplete side chains Terminii for oxidoreductase.pdb (#0) chain A determined from SEQRES records 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: LEU 599.A Chain-final residues that are not actual C terminii: 595 hydrogen bonds Hydrogens added Charge model: AMBER ff14SB Total charge for #0: -2.000 No incomplete side chains Terminii for oxidoreductase.pdb (#0) chain A determined from SEQRES records 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: LEU 599.A Chain-final residues that are not actual C terminii: 566 hydrogen bonds Hydrogens added Charge model: AMBER ff14SB Total charge for #0: -2.000 Wrote C:\Users\GEU\Downloads\new dock\oxidoreductase.pdb #1, chain A: prostaglandin G/H synthase 1 Terminii for oxidoreductase.pdb (#1) chain A determined from SEQRES records Chain-initial residues that are actual N terminii: #1 MET 1.A Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: #1 LEU 599.A Chain-final residues that are not actual C terminii: 566 hydrogen bonds Hydrogens added Wrote oxidoaspirin.receptor.pdb into C:\ProgramData\Chimera adding gasteiger charges to peptide Wrote oxidoaspirin.ligand.pdb into C:\ProgramData\Chimera Autodock Vina ligand docking initiated for oxidoreductase.pdb Status file contents: 1639 1713445280.81 1713445293.84 Terminii for oxidoreductase.pdb (#1) chain A determined from SEQRES records Chain-initial residues that are actual N terminii: #1 MET 1.A Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: #1 LEU 599.A Chain-final residues that are not actual C terminii: 566 hydrogen bonds Hydrogens added Wrote oxidoaspirin.receptor.pdb into C:\ProgramData\Chimera adding gasteiger charges to peptide Wrote oxidoaspirin.ligand.pdb into C:\ProgramData\Chimera Autodock Vina ligand docking initiated for oxidoreductase.pdb Running AutoDock Vina for oxidoreductase.pdb failed; see Reply Log for more information Application stderr ----- [no output] ----- Application stdout ----- [no output] ----- Status file contents: 1639 1713445301.94 1713445303.83 Running AutoDock Vina for oxidoreductase.pdb failed; see Reply Log for more information Application stderr ----- [no output] ----- Application stdout ----- [no output] ----- Search error: couldn't compile regular expression pattern: invalid escape \ sequence Probably an error in regular expression. Search error: couldn't compile regular expression pattern: invalid escape \ sequence Probably an error in regular expression. #1, chain A: prostaglandin G/H synthase 1 Terminii for oxidoreductase.pdb (#1) chain A determined from SEQRES records Chain-initial residues that are actual N terminii: #1 MET 1.A Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: #1 LEU 599.A Chain-final residues that are not actual C terminii: 566 hydrogen bonds Hydrogens added Wrote oxidoaspirin.receptor.pdb into C:\ProgramData\Chimera adding gasteiger charges to peptide Wrote oxidoaspirin.ligand.pdb into C:\ProgramData\Chimera Autodock Vina ligand docking initiated for oxidoreductase.pdb Status file contents: 1639 1713447116.49 1713447119.45 Running AutoDock Vina for oxidoreductase.pdb failed; see Reply Log for more information Application stderr ----- [no output] ----- Application stdout ----- [no output] ----- Terminii for oxidoreductase.pdb (#1) chain A determined from SEQRES records Chain-initial residues that are actual N terminii: #1 MET 1.A Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: #1 LEU 599.A Chain-final residues that are not actual C terminii: 566 hydrogen bonds Hydrogens added Wrote oxidoaspirin.receptor.pdb into C:\ProgramData\Chimera adding gasteiger charges to peptide Wrote oxidoaspirin.ligand.pdb into C:\ProgramData\Chimera Autodock Vina ligand docking initiated for oxidoreductase.pdb Status file contents: 1639 1713447148.99 1713447151.35 Running AutoDock Vina for oxidoreductase.pdb failed; see Reply Log for more information Application stderr ----- [no output] ----- Application stdout ----- [no output] ----- Thank you in advance Dr. Kumud Pant Associate Professor Department of Biotechnology Graphic Era (Deemed to be) University Dehradun

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i can´t installate chimera.
by Suilma Ivette Pérez Pineda 14 Apr '24

14 Apr '24

hi! i cannot installate chimera, when i acept "terms and conditions", the windows says tht "i dessagree", when im agree. Suilma Ivette Pérez Pineda

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AutoDockVina: Merge charges
by limbuingso2112＠gmail.com 12 Apr '24

12 Apr '24

Hi all, Beginner to molecular docking. I tried to find answers to my question but to no avail and was hoping this site would help me in some ways. When conducting autodockVina after DockPrep, Tools > Surface/Binding Analysis > AutoDockVina. In the receptor/ligand options, there are two sections where you can merge charges Straight from the documentation: Merge charges and remove non-polar hydrogens (true/false) - note AutoDock Vina does not use charges or nonpolar hydrogens, so this setting is not expected to affect results except for the presence or absence of nonpolar hydrogens in the processed receptor Merge charges and remove lone pairs (true/false) - note AutoDock Vina does not use charges or lone pairs, so this setting is not expected to affect results except for the presence or absence of lone pairs in the processed receptor (and there may not have been any lone pairs to start with) While there is a caveat that it might affect results in some ways. I have been trying to dig deeper into this merge charges aspect of docking and could not find much explanation or documentation on it. My question stems from the fact that im docking a protein [5A8K] with 1 ligand. When i put false for the merge charges for both ligand and receptor, i get a negative score but with a absurd binding pose but when i put true for the merge charges [default] for both ligand and receptor, i get a negative score with a good binding pose which has matched literature. I initially placed false because i got the idea that merging charges was an approximation/simplification and i wanted to model the system better without merging charges. If autodock does not use charges at all, why does my result differ so much when i change those settings. Any insights into this matter is highly appreciated. TIA

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AutoDockVina: Merge charges
by limbuingso2112＠gmail.com 11 Apr '24

11 Apr '24

Hi all, Beginner to molecular docking. I tried to find answers to my question but to no avail and was hoping this site would help me in some ways. When conducting autodockVina after DockPrep, Tools > Surface/Binding Analysis > AutoDockVina. In the receptor/ligand options, there are two sections where you can merge charges Straight from the documentation: Merge charges and remove non-polar hydrogens (true/false) - note AutoDock Vina does not use charges or nonpolar hydrogens, so this setting is not expected to affect results except for the presence or absence of nonpolar hydrogens in the processed receptor Merge charges and remove lone pairs (true/false) - note AutoDock Vina does not use charges or lone pairs, so this setting is not expected to affect results except for the presence or absence of lone pairs in the processed receptor (and there may not have been any lone pairs to start with) While there is a caveat that it might affect results in some ways. I have been trying to dig deeper into this merge charges aspect of docking and could not find much explanation or documentation on it. My question stems from the fact that im docking a protein [5A8K] with 1 ligand. When i put false for the merge charges for both ligand and receptor, i get a negative score but with a absurd binding pose but when i put true for the merge charges [default] for both ligand and receptor, i get a negative score with a good binding pose which has matched literature. I initially placed false because i got the idea that merging charges was an approximation/simplification and i wanted to model the system better without merging charges. If autodock does not use charges at all, why does my result differ so much when i change those settings. Any insights into this matter is highly appreciated. TIA

1 0

Protein Modeling with Model/Refine Loops Tool
by Ecem Güngör 09 Apr '24

09 Apr '24

Hello all, I have encountered an issue while working with a protein in complex with ligands. There are some missing regions in the protein structure, and I attempted to model these regions using the "Model/Refine Loops" tool in UCSF Chimera (version 1.17.3). However, I observed that when I saved the modeled structures as PDB files, the ligands were not included in the file. Additionally, in some models, the modeled C-terminal extended into the binding pocket in an unusual manner. I am curious whether this tool takes into account the presence of ligands or molecules in the structure while modeling missing regions. How can I prevent such issues from occurring? How can I model the missing long C-terminal in Chimera while ensuring that the presence of other ligands or molecules is also considered? Thanks in advance. Ece.

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Bug
by Anoop B S 09 Apr '24

09 Apr '24

Sometimes its not responsive.How to resolve that

2 1

Opening chimera within MS powerpoint
by Prathvi Singh 08 Apr '24

08 Apr '24

Hi Elaine, I was wondering whether it it possible (either directly or via a plugin) to open a UCSF chimera/chimeraX window within a Microsoft powerpoint slide so that I can open a PDB file directly within the slide and perform different types of operations (showing distance between 2 atoms which someone from the audience demanded to know, for example)? This way, I would be able to satisfy the doubts of the audience without breaking the flow of the presentation. Thank you, -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Fw: Chimera numpy error
by Garrett Scapellato 01 Apr '24

01 Apr '24

Garrett Scapellato Research Technician II Edwards Lab DHVI Duke University [cid:133a3af9-3314-4e94-9c72-9d0bc6ffe6cc] ________________________________ From: Garrett Scapellato <garrett.scapellato(a)duke.edu> Sent: Friday, March 29, 2024 2:24 PM To: pett(a)cgl.ucsf.edu <pett(a)cgl.ucsf.edu> Subject: Re: Chimera numpy error Eric, Apologies for sending so many emails. I was able to delete all numpy modules from Chimera. Now when I try to open Chimera I get this error. Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/__main__.py", line 73, in <module> value = chimeraInit.init(sys.argv) File "/Applications/Chimera.app/Contents/Resources/share/chimeraInit.py", line 680, in init import chimera File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 2782, in <module> from SimpleSession import BEGIN_RESTORE_SESSION, END_RESTORE_SESSION File "/Applications/Chimera.app/Contents/Resources/share/SimpleSession/__init__.py", line 14, in <module> from save import saveSession, sessionID, noAutoRestore, autoRestorable, \ File "/Applications/Chimera.app/Contents/Resources/share/SimpleSession/save.py", line 13, in <module> from chimera import replyobj, selection, SessionPDBio, version File "/Applications/Chimera.app/Contents/Resources/share/chimera/selection/__init__.py", line 1033, in <module> from chimera import oslParser File "/Applications/Chimera.app/Contents/Resources/share/chimera/oslParser.py", line 690, in <module> import numpy ImportError: No module named numpy I tried reinstalling numpy the same way I installed pandas, but I get the same error as above. How can I fix this issue? Thanks, Garrett Scapellato Research Technician II Edwards Lab DHVI Duke University [cid:5a4e481b-169d-4789-87e0-4c616c5183fc] ________________________________ From: Garrett Scapellato Sent: Friday, March 29, 2024 2:11 PM To: pett(a)cgl.ucsf.edu <pett(a)cgl.ucsf.edu> Subject: Chimera numpy error Eric, I get the following error whenever I try to open chimera. I tried uninstalling numpy with a pip installer, and that didn't work, I assume because it doesn't uninstall the module from chimera specifically. DHVI-F5KJC04Q:~ edwardslab$ chimera Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/__main__.py", line 73, in <module> value = chimeraInit.init(sys.argv) File "/Applications/Chimera.app/Contents/Resources/share/chimeraInit.py", line 680, in init import chimera File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 2782, in <module> from SimpleSession import BEGIN_RESTORE_SESSION, END_RESTORE_SESSION File "/Applications/Chimera.app/Contents/Resources/share/SimpleSession/__init__.py", line 14, in <module> from save import saveSession, sessionID, noAutoRestore, autoRestorable, \ File "/Applications/Chimera.app/Contents/Resources/share/SimpleSession/save.py", line 13, in <module> from chimera import replyobj, selection, SessionPDBio, version File "/Applications/Chimera.app/Contents/Resources/share/chimera/selection/__init__.py", line 1033, in <module> from chimera import oslParser File "/Applications/Chimera.app/Contents/Resources/share/chimera/oslParser.py", line 690, in <module> import numpy File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/numpy/__init__.py", line 142, in <module> from . import core File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/numpy/core/__init__.py", line 91, in <module> raise ImportError(msg.format(path)) ImportError: Something is wrong with the numpy installation. While importing we detected an older version of numpy in ['/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/numpy']. One method of fixing this is to repeatedly uninstall numpy until none is found, then reinstall this version. I also tried rm -rf ~/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/numpy/ repeatedly, but that didn't work. I couldn't use Finder to navigate to the python2.7 folder to delete the files manually, either. Any help would be appreciated. Thanks, Garrett Scapellato Research Technician II Edwards Lab DHVI Duke University [cid:570bb78a-e702-4643-995c-11d5cdaf82fd]

2 1

Importing Modules into Chimera
by Garrett Scapellato 28 Mar '24

28 Mar '24

Chimera Help, Hello, I hope you are doing well. I am attempting to use the "pandas" module while using Chimera to read python code. I receive this error any time I do. I am able to use pandas while using other python interpreters on my computer. I am also able to use other modules, such as NumPy when using Chimera to run python code. Any help in this issue would be greatly appreciated. Thank you for your time, Garrett Scapellato Research Technician II Edwards Lab DHVI Duke University [cid:d20c0851-a63b-49a0-a3e5-efa576c4dc55]

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Problems installing Chimera for command line use on Centos
by Evan Kantrowitz 25 Mar '24

25 Mar '24

Hi All, I am trying to move our viewmotions.bc.edu <http://viewmotions.bc.edu/> server to a new server running Centos 9. I downloaded the most recent chimera (chimera-1.17.3-linux_x86_64.bin <https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=linux_x…>). Followed the install procedure with no issues. When I ran chimera I got these errors, both in commandline mode or regular. Any help would be appreciated. Thanks kantrow@localhost ~/vm_test]$ chimera --preferences /data/viewmotions/lib/chimeraVMPreferences --script chimera_script.py Traceback (most recent call last): File "/progs/share/__main__.py", line 73, in <module> value = chimeraInit.init(sys.argv) File "/progs/share/chimeraInit.py", line 680, in init import chimera File "/progs/share/chimera/__init__.py", line 2782, in <module> from SimpleSession import BEGIN_RESTORE_SESSION, END_RESTORE_SESSION File "/progs/share/SimpleSession/__init__.py", line 14, in <module> from save import saveSession, sessionID, noAutoRestore, autoRestorable, \ File "/progs/share/SimpleSession/save.py", line 13, in <module> from chimera import replyobj, selection, SessionPDBio, version File "/progs/share/chimera/replyobj.py", line 24, in <module> import Tkinter File "/progs/lib/python2.7/lib-tk/Tkinter.py", line 39, in <module> import _tkinter # If this fails your Python may not be configured for Tk ImportError: libXss.so.1: cannot open shared object file: No such file or directory ----------------------------------------------------------------------------- Evan R. Kantrowitz, Ph.D evan.kantrowitz(a)bc.edu <mailto:evan.kantrowitz@bc.edu> Emeritus Professor of Chemistry Cell: 617-775-9915 Boston College www2.bc.edu/evan-kantrowitz <http://www2.bc.edu/~kantrow> -----------------------------------------------------------------------------

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cannot access Chimera website
by lbmccusker＠retired.ethz.ch 19 Mar '24

19 Mar '24

I am an enthusiastic user of Chimera for non-protein applications (in particular zeolites), and would like to use it in an upcoming workshop on charge flipping. However, when I tried to check the website (https://www.cgl.ucsf.edu/chimera/ to give students instructions for downloading, I got the message Secure Connection Failed An error occurred during a connection to http://www.cgl.ucsf.edu PR_END_OF_FILE_ERROR Error code: PR_END_OF_FILE_ERROR The page you are trying to view cannot be shown because the authenticity of the received data could not be verified. Please contact the website owners to inform them of this problem. Can you check into this? I tried Safari, Firefox and Edge, and all have the same problem. Thanks! Lynne McCusker

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