- Chimera-users - RBVI Mailing Lists

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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