- Chimera-users - RBVI Mailing Lists

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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