August 2020 - Chimera-users - RBVI Mailing Lists

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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