January 2022 - Chimera-users - RBVI Mailing Lists

Autodock Vina plugin
by Enrico Martinez 12 Jan '22

12 Jan '22

Dear Chimera Users, First Happy New Year to you and your families! I am trying to perform protein-ligand docking using UCSF Chimera 1.16v installed on my iMAC Big Sur. Using the pdb of the receptor and mol2 of the ligand (that I have already tested with VINA 1.2.3!) I got the following error: Model 1 (receptor.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 receptor.pdb (#1) chain A; guessing terminii instead Chain-initial residues that are actual N terminii: #1 SER 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: #1 THR 304.A 278 hydrogen bonds Removing spurious proton from 'C' of #1 THR 304.A Hydrogens added Wrote test.receptor.pdb into /Users/gleb/Desktop/docking_tuto adding gasteiger charges to peptide Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/vina/ws.py", line 395, in prepareReceptor execfile(scriptPath, d) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/AutoDockTools/Utilities24/prepare_receptor4.py", line 172, in <module> delete_single_nonstd_residues=delete_single_nonstd_residues) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/AutoDockTools/MoleculePreparation.py", line 533, in __init__ version=version, delete_single_nonstd_residues=delete_single_nonstd_residues) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/AutoDockTools/MoleculePreparation.py", line 140, in __init__ self.addCharges(mol, charges_to_add) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/AutoDockTools/MoleculePreparation.py", line 226, in addCharges chargeCalculator.addCharges(mol.allAtoms) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/MolKit/chargeCalculator.py", line 80, in addCharges babel.assignHybridization(atoms) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/PyBabel/atomTypes.py", line 127, in assignHybridization a.babel_atomic_number = self.get_atomic_number(a.babel_type) File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/PyBabel/atomTypes.py", line 103, in get_atomic_number (name,_name) ) ValueError: Could not find atomic number for Hn Hn Receptor preparation for AutoDock Vina failed; please look in Reply Log to see error messages.cannot prepare receptor for AutoDock Vina; please look in Reply Log and/or run Chimera with --debug flag to see errors. So here are my questions: 1) May this error be related to the version of OSX installed on my imac (I can not run MGL tools on the Big Sur for instance) ?? 2) Alternatively may I use the ADT scripts integrated in the Chimera like prepare_receptor4.py for my scripting purposes (outside of the UCSF Chimera) on the same iMAC machine ? Many thanks in advance! Cheers Enrico

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Error on installation on a student's computer
by Kenward Vaughan 11 Jan '22

11 Jan '22

Hello all, As usual I have my students installing Chimera as part of their continuing adventure in organic chemistry, but have one of them reporting an error on attempted startup after installation. So far I have little information (we haven't started classes yet--next week--but she has sent the error message obtained. It is apparently on Windows. I suggested that she try starting from the command line to do the debug run, but this is from a distance at this time and I don't know how savvy she is with such stuff. Is there enough information in just the number noted by this message for someone to know what might be happening with her setup? Many thanks, and cheers! Kenward -- In a completely rational society, the best of us would aspire to be _teachers_ and the rest of us would have to settle for something less, because passing civilization along from one generation to the next ought to be the highest honor and the highest responsibility anyone could have. - Lee Iacocca Any fool can know. The point is to understand. - Albert Einstein

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Problem with the app
by Nicola De Trino 11 Jan '22

11 Jan '22

I have download the chimera-1.16-win64.exe <https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=win64/c…> for Windows 64 bit. I have installed but when i try to launch the program, it appears an error message : *chimera exited abnormally; the exit code was: -1073731819. * I try to install again the program but same result. I don't know how to fix the problem. <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> Mail priva di virus. www.avg.com <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> -- ------------------------ Indirizzo istituzionale di posta elettronica degli studenti e dei laureati dell'Università degli Studi di TorinoOfficial University of Turin email address for students and graduates

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Convenient way to move 2D labels around
by Prathvi Singh 09 Jan '22

09 Jan '22

Hi Elaine, Is there a convenient way (a keyboard or mouse shortcut) to move 2D labels around once the 2D labels window has been closed? Thanks -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Model placement side by side
by George Tzotzos 07 Jan '22

07 Jan '22

Hi, Having superimposed 4 structures using MatchMaker, is there a way to view the aligned structures in a window grid? Moving them manually after superimposition is not optimal. Thanks in advance for any suggestions and best wishes for 2022

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Introduce a-helices into protein structure ab initio
by Chara Spanou 06 Jan '22

06 Jan '22

Hello chimera-users, I would like to introduce a-helices into my protein structure ab initio. Is it possible to do this with chimera? Another option that I have is to take a-helical pieces of sequence from a different model and introduce these into the desired model. Would that be more feasible? There is a chance I also need to introduce loops and turns ab initio to best localize the introduced a-helices within my protein structure. Can you please indicate how can a chimera user build all this ab initio? Thank you in advance for your time and help, Chara SpanouPhD studentUniversity of Cologne

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report rotate and shift value in MatchMaker
by Yanhe Zhao 06 Jan '22

06 Jan '22

Greeting there, Happy New Year! How can find the rotate and shift value after I done the 'MatchMaker' in Chimera? Thanks and regards, Yanhe

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Question: PDB file creation
by Kenji MATSUI 05 Jan '22

05 Jan '22

Dear Chimera company Thank you for allowing me to use your software. I am Japanese, so I hope you will understand that there are some inappropriate expressions. I would like to ask you one question. I would like to know how to overlay the docked protein (osh4)-ligand (cholesterol) complex (the gray one in the figure) and the complex on the PDB. [image: image.png] Aim I would like to know how well the docked data matches the data in the PDB. Methods I have tried I did it based on the following link from Chimera. https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matcha… Thank you for your cooperation. --------------------------------------------------------------------------- 松井健治東京農工大学大学院工学府産業技術専攻修士〒184-8588 東京都小金井市中町2-24-16 Mail: s214903z(a)st.go.tuat.ac.jp Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan Mail: s214903z(a)st.go.tuat.ac.jp

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report rotate and shift in MatchMaker
by Yanhe Zhao 04 Jan '22

04 Jan '22

Greeting there, How can find the rotate and shift value after I done the 'MatchMaker' in Chimera? Thanks and regards, Yanhe

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Opening .py files
by Henry Shook 04 Jan '22

04 Jan '22

Chimera User Support, I'm working on dockprepping the sars-2 main protease and whenever I try and save it as a .py file, I can't open it from sources other than the saved session I wrote. Whenever I try and open it from a dropbox or my finder, I get the message: Error while processing /Users/8642165/Desktop/Research/DC AP Research /[7l0d]DOCKPREPPEDFINAL.py: File "[7l0d]DOCKPREPPEDFINAL.py", line 1 @<TRIPOS>MOLECULE ^ SyntaxError: invalid syntax File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 1325, in _openPython loadFunc(sandboxName, fileName, f) See reply log for Python traceback. Is there any way that I can fix this problem? Thanks, Henry Shook

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