- Chimera-users - RBVI Mailing Lists

Batch Processing of Molecular Attributes
by Benjamin Feinsilver 01 Nov '18

01 Nov '18

Hello, Is it possible to pass a CSV file to Chimera containing a list of SMILEs, then output their molecular attributes in a new CSV file? For example, volume, surface area, the number of surface points with positive electrostatic potential, and the energy of the molecule's current 3D conformation. If so, would you please let me know how I would accomplish this? Thanks, Ben

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Chimera use
by Hui Min 31 Oct '18

31 Oct '18

Hi there, Sorry to disturb you. I have a question of how to use the Chimera software. If I've already got a .pdb file and use SMART to predict the domains, how can I mark the 3D structure with user defined color？ Thank you in advance for your help -- *Hui Min* Postdoctoral Scholar Research, Department of Internal Medicine, College of Medicine, University of South Florida, Tampa, FL 33612 minh8(a)health.usf.edu

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How can I load a list of residues of protein?
by Paris Tzou 30 Oct '18

30 Oct '18

Dear all, I want to load a file containing a lit of residues of protein which is already shown in Chimera. I don't want to manually select the residues under investigation through "Favorite -- Sequence". Is there a way of doing this ? I know I can do it using command line like:select #0:15-17.C,263-265, 300-310.A. Instead, I can have a text file with content like: 15,C 16,C 17,C 263,A 264,A 265,A Thank you very much. Paris Tzou

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Split map from command line
by armoelle 29 Oct '18

29 Oct '18

Dear Chimera Team, I am trying to call the split map command directly from a script but somehow I don’t seem to be able to get it to run - maybe you can help me? I am calling scolorzone (which works perfectly) and then ( as suggested in the mailing list) use the accelerator command ac sm to split the map. However, generally nothing happens - sometimes though (I don’t know what triggers it - and I am not doing anything different) it runs perfectly fine. I am a bit puzzled as the same is the case no matter if I run form command line or I use the keyboard shortcuts gui. Many thanks for your help! cheers Arne ________________________________ Dr. Arne Moeller Independent Research Group Leader Department of Structural Biology Max-Planck-Institute of Biophysics Affiliated Researcher DANDRITE, Aarhus University, DK www.moeller-lab.com www.biophys.mpg.de/en/moeller.html Arne.Moeller(a)biophys.mpg.de 0049 69 63033057 Max-von-Laue-Strasse 3 D-60438 Frankfurt am Main Office L.1.015

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CUDA on Mac OSX 10.14 Mojave
by David Bhella 26 Oct '18

26 Oct '18

Dear All I just learned (after updating) that nVidia CUDA support is not in place for the latest Mac OS X release. I have a 2010 Mac Pro with a Quadro 4000 card in - which is still fine as a desktop. Chimera throws an error now - complaining about the graphics settings being incorrect: "Display misconfiguration. Please increase the color quality (24 bit color or greater), update your display (graphics) driver, and/or upgrade your graphics card. Also see chimera installation instructions." Presumably because the graphics driver is not working correctly. Has anyone succeeded in resolving this? Or do I need to roll back to 10.13? A quick scan of the Mac/nVidia Forums suggests that CUDA support may not be forthcoming anytime soon, but I thought I would check if anyone has resolved this before going through the hassle of downgrading. Thanks, D Dr David Bhella Director - Scottish Centre for Macromolecular Imaging MRC-University of Glasgow Centre for Virus Research Sir Michael Stoker Building Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK) Telephone: 0141-330-3685 Skype: d.bhella

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Dynamic Protein
by Alex Nazlidis 25 Oct '18

25 Oct '18

Dear Elaine, is there any way in chimera to produce a clip similiar to this ( https://www.youtube.com/watch?v=zm-3kovWpNQ at 5:44)? You know animating the dynamic nature of a protein and its folding process. Thank you very much in advance, Alex

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defining planes and axes based on existing ones
by ChuHui Fu 25 Oct '18

25 Oct '18

Hello, I am trying to define planes and axes that are orthogonal to the planes and axes that I have previously defined. I have an alpha helix, and I only managed to define one plane and two orthogonal axes around the helix. Is it possible to define the rest of the axes and planes? Thanks! -- ChuHui Fu B.S.Candidate in Chemistry Haverford College, Class of 2019 cfu(a)haverford.edu

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Saving a moved PDB only moved in a new session
by Marta Perez Illana 25 Oct '18

25 Oct '18

Hi all I am working with chimera, and I have a map and a pdb. 1) I have split the pdb into several fragments in order to fit them into the map 2) I have successfully moved the PDBs and fitted them into the map 3) I have "write each PDB" "relative to the map, which seems to make sense :) 4) In the current session I keep the map and the moved PDB open ...plus I open the just saved "wrote PDB" (intended to be on the same position I moved it). To me both, the opened PDB (which I have moved) and the just saved PDB, might be in the same position, fitting into the map... But... the just save-written PDB is clearly somewhere else... :( 5) But... If I make a NEW session, opening the map and the "wrote PDB", everything make sense, and the PDB is where I in fact moved to keep it fitted... Why is that that in the current session the written-PDB is not where it was "moved"; but when a new session is opened it is displayed where it was moved? It seems that everything works fine, it is just a bit confusing to me. Thanks in advanced! Marta

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Help SASA
by Andrea Yimena Cardona Barreto 25 Oct '18

25 Oct '18

Good afternoon, my name is Andrea Cardona and I´m a student of a magister in Human Genetics at Universidad Nacional de Colombia. In my thesis I´m interested in obtain the surface accessible solvent area of a homotetrameric protein (fumarate hydratase) but I have some troubles with Chimera. Can you give some help? -- Andrea Yimena Cardona Barreto Maestría en Genética Humana Universidad Nacional de Colombia

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Accessible surface area and ASA per residue
by anastasia＠campus.technion.ac.il 25 Oct '18

25 Oct '18

Dear User, I'll appreciate your help. I've worked with Chimera previously, but have not used it recently. Now I try to repeat some of the analysis I've done, but I don't see the option ,solvent accessible surface, in the software (I guess I've installed a newer version). I would like to color all the exposed (to the solvent) residues like in the image below and export a table with these values per atom and residue. [cid:7c648fa9-c7cf-4dab-bf40-f0b4a95b8f47] What I tried to do this time is : 1. Show a molecular surface.. 2. Depiction --> render by attr , when attr is set to areaSAS on residues [cid:f46b071c-36ab-4792-bfc2-31eb50fc2be3] The result I got was: [cid:6b44e796-b2c2-42f8-aac8-1ab725121d38] Am I doing it right? how can export the calculated areaSAS per atom and residue from chimera? How the SAS values calculated in Chimera? Does the higher value means that this residue is more exposed? Thank you for your help, Anastasia

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