October 2018 - Chimera-users - RBVI Mailing Lists

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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Chimera bug report submission
by Anas 23 Oct '18

23 Oct '18

The following bug report has been submitted: Platform: osx_x11 Chimera Version: (None given) Description Hello, I am trying to superpose a .pdb file on a density map (.mrc), and save it as .pdb. Chimera saves the file, but when I open it it doesn’t display any density map. Just the pub file which was superposed. I am doing it to start model building, but I am stuck at this. Kindly help.

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MacOS Mojave
by Eric Pettersen 22 Oct '18

22 Oct '18

Hi all, A fix for the non-showing buttons problem on MacOS Mojave (10.14) is now in the Chimera daily build and the 1.13.1 release candidate. If you encounter any problems with the new version please use Chimera’s Help→Report A Bug to let us know about them. Note that the fixed version only runs on Mac OS 10.10 or later, whereas the previous version also ran on 10.8 and 10.9. —Eric Eric Pettersen UCSF Computer Graphics Lab

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Re: [Chimera-users] Chimera problems
by Elaine Meng 20 Oct '18

20 Oct '18

> On Oct 19, 2018, at 8:41 PM, Shriwas, Pratik <ps774614(a)ohio.edu> wrote: > > Hi, > I am trying to use USCF chimera for studying docking between my compound and the receptor called GLUT1 (PDB - 4pyp or 1SUK). My concerns are: > > • I find different scores everytime I use the same compound and receptor Hi Pratik, Sounds like you are using the Autodock Vina interface of Chimera. Chimera does not calculate the docking, it just sends/receives data from an outside web service that is running the Autodock Vina program. It may be that the docking process uses some random numbers, and because the web service does not allow a high amount of sampling, it cannot always find the same top score(s). However, I do not know the details of Autodock Vina and you would have to look at its website <http://vina.scripps.edu/> and/or paper to learn about that. I’m guessing you are using Chimera’s Autodock Vina GUI to enter inputs, not the “vina” command. However, if you are using the command make sure you get a recent version of Chimera, because some problems with the command were fixed. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> > • I am not able to show my hydorgen bonds between compound snd receptor in GUI. Although I can see them in the list box. Maybe the atoms are not shown (for example, if the sidechain is not shown, the H-bond to the sidechain won’t be shown). To make sure the H-bonding atoms are shown, in the H-bond parameters dialog turn on the option “If endpoint atom hidden, show endpoint residue.” However, if that is not the problem, then maybe the graphics on your computer has trouble showing lines. You could try updating your graphics driver, or try showing the H-bonds as sticks instead of lines with command: setattr p drawMode 1. Or maybe it can draw lines but they are too thin for you to see. In that case, in the H-bond parameters dialog increase the “Line width” value. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbo…> > • I am not able to find exact binding energy. This is the central problem of docking! Firstly docking scores are not binding energies, only approximations, and secondly, one has to do a lot of conformational and positional sampling to find the most accurate position. The Autodock Vina website does not allow a high amount of sampling, as it is a shared resource provided for free. If you want to do more intensive docking you can download Autodock Vina (or some other docking progam like DOCK, Gold, ...) and run it directly. > • My ligand is not on pubchem/NIH servers. What is best way to find its smiles string. Different websites have different smiles string and I get different interactions. Usually there are multiple ways of writing the SMILES string for the same compound. As long as the compound looks right to you (has the correct covalent structure, the right elements connected in the right way) then the results should be equally valid even though the coordinates might be slightly different (e.g. rotated or translated or different conformation). Any slight change in inputs will change docking outputs, since sampling is not exhaustive, but the change does not mean one answer is “wrong” and the other is “right". > > Regards, > Pratik Shriwas > Phd Candidate, > Molecular and Cellular Biology program, > Edison Biotechnology Institute, > Ohio University. For future reference, Chimera questions should be sent to chimera-users(a)cgl.ucsf.edu (CC’d here). For Autodock Vina questions, see <http://vina.scripps.edu/questions.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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