August 2016 - Chimera-users - RBVI Mailing Lists

Hidden water molecules
by Michael Sharkey 11 Apr '19

11 Apr '19

Hi I'm trying to visualise water molecules associated with the crystal structure of an enzyme (specifically PDB ID: 1C1D). They're listed when I open the pdb as a text file using WordPad, but I can't for the life of me get them to appear on the screen when I try to visualise the structure in Chimera (v. 1.10.2). What am I missing? Thanks in advance Mike --

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Constrainted fitting
by Christoph Wigge 22 Mar '19

22 Mar '19

Dear all, I would like to fit two protein monomers that form a dimer into an em density map. I know from previous mutagenesis studies that the binding takes place with two tryptophan residues and the counterpart binding pocket. How can I set this interaction as fixed so that chimera fits the rest of the molecule according to the density map without continuously changing this part of the essential protein protein interaction? I would like to fit that interaction manually and then exclude it from the automatic procedure. Thank you very much in advance. Bests Christoph Wigge

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Measuring angles and distances between planes defined by two aromatic rings
by George Tzotzos 26 Sep '16

26 Sep '16

Having generated a 100ns trajectory, I’m interested in measuring the time evolution of the distance between to aromatic ring centroids as well as the angle between the planes of these two rings. The idea is to determine if I’m dealing with pi-pi stacking interactions. I’ve check past correspondence and tried various permutations of commands to no avail. Maybe my best option is to do this for selected snapshots and define for each snapshot two centroids (e.g. c1 and c2) and measure the distance c1 c2. I haven’t managed to find a solution for measuring the angles between the two planes defined by the ring atoms. I’d appreciate any suggestions on possible solutions to the problem described above. I’m attaching a snapshot of measuring distances between two atoms (not really a good solution). Thanks in advance George

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Recursive structure matching and acquisition of descriptive numbers
by Healey, Joe 20 Sep '16

20 Sep '16

Hi, I have several hundred structure simulations that were performed on our HPC resource. Each simulation has approximately 5 models associated with it. I also have HMM model homologies for each of these proteins. I would like to use chimera's matchmaker function to compare the simulated structured to their nearest 'real' counterpart with a resolved structure. In order to do this I plan to script chimera to pull in the simulated models as well as the near homolog and then run the matchmaker algorithm. My question is: can the RMSD value that is returned in the reply log be 'accessed directly' such that for each match that is performed, I can obtain the RMSD and thus a ranking for the best fitting structures - or will it require parsing the reply log? Thanks Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey(a)warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfield…> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey>

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Deleting invisible structures?
by max taylordavies 31 Aug '16

31 Aug '16

Hello all, Is there any way to selectively delete the 'invisible' (undisplayed) parts of a structure and keep the visible parts without having to use the usual atom-spec approach? For example, if I run per-model clipping on a protein, is there any way to delete the part that has been rendered invisible by the clipping? If this isn't possible, is there a way to export only the visible/displayed components of a scene? Many thanks in advance, Max Taylor-Davies

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ETA ChimeraX
by Chris Sander 30 Aug '16

30 Aug '16

Just curious when ChimeraX will appear and what it will be able to do! Keep up the good work. Chris Sander www.evfold.org

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Integrating chimera into a database
by McCafferty, Caitlyn (NIH/NEI) [F] 29 Aug '16

29 Aug '16

Hi, I have a number of colored protein structures from chimera that are saved as python files. I would like to put these structures on a database so other users may access them. Is there a way (preferably using html) that a user could click on the python file and it would open up in chimera through the database-- even if the user does not have chimera installed? Thank you, Caitlyn McCafferty Postbaccalaureate Fellow Ophthalmic Genetics and Visual Function Branch National Eye Institute Bldg. 10 Rm. 6-3350 Tel: (301) 402-7058 Email: caitlyn.mccafferty(a)nih.gov

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bond formation
by A G Szabo 26 Aug '16

26 Aug '16

I am working with a PDB file that has two proteins docked together. As this is a model the two proteins do not have a bond between them. The model number is the same for the two chains designated A and B. I have looked through the various tutorials, functions and tools to figure out how to actually place a bond between two residues that link the two chains. It is well established as to how the two proteins would be linked if the bond had been formed. The linkage is between the S of a Cysteine and carbonyl carbon at the C-terminal of the other protein. I think I have managed to select both atoms, but cannot determine how to include a bond. Your assistance is appreciated. Arthur Szabo

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Creating and saving Multiscale Models using Python functions
by Jon David 24 Aug '16

24 Aug '16

Hi Friends, I would like to use Python to perform operations equivalent to the following GUI operations; I'd like to be able to do this as a batch script (e.g., I don't want the Chimera GUI to appear because I don't want to have to close it.): 1) Open a PDB file (I know how to do this part). 2) Tools > Higher-Order Structure > Multiscale Models (this opens the MultiScale Models popup window). 3) Click on the "Make models" button. 4) File > Export Scene... (this opens the Export Scene popup window) 5) In the Export Scene popup window, select File type to be "OBJ [.obj]", enter file name "test.obj" 6) Click on the "Save" button. I have used Python to open a PDB file, and translate, and rotate it around before. But I don't know where to begin with selecting Multiscale Models' parameters. Any tips? Any help would be much appreciated. Thanks, --Jon

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volume viewer - planes
by Michael Elbaum 24 Aug '16

24 Aug '16

Hi. I'm using the volume viewer and the Planes function is extremely useful in order to see a subsection of the volume. Often I want to compare different processing or filtering of the same dataset. When I load several datasets, all the visualization parameters are set individually. Normally this is good, for example in setting different colors, but for Planes it's problematic. In order to switch among the various representations and see the same section of the volume I have to scan them individually, and when two are visible I can move only one. Is there a way to link the Planes among the maps? Perhaps there's a command line trick? thanks, Michael

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