July 2015 - Chimera-users - RBVI Mailing Lists

On the fly map sharpening?
by Oliver Clarke 21 Jul '15

21 Jul '15

Hi, just a request for a future chimera version (probably Chimera 2 I guess) - would it be possible to integrate on the fly map sharpening into chimera, perhaps as an option for vop? It would be great to be able to play with different negative B-factors within chimera and thereby get instant feedback on map contrast and detail in different regions. Alternatively, would it be possible to call an external program that does the same thing from within chimera, perhaps bfactor from the Grigorieff lab or similar? Cheers, Oliver,

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Electrostatic Potential based on Poisson-Boltzmann using APBS
by leila karami 18 Jul '15

18 Jul '15

Dear chimera users, I am using chimera 1.10.1. I did following steps to obtain Electrostatic Potential based on Poisson-Boltzmann using APBS: open... pr.pdb action... surface... show to obtain *.dx file, I typed APBS in command line, after minutes, *.dx file was created and surface color window was opened, I pressed color tab. Please see the figure in following link: https://www.dropbox.com/s/99gjecypqu910hu/apbs.png?dl=0 Why are the colors black and white in the surface, instead of blue and red? Any help will highly appreciated.

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RMSD
by Valerio Chiarini 17 Jul '15

17 Jul '15

Hi everyone, I am dealing with an NMR structure and I noticed in literature that among the parameters required for presentation is included "RMSD from the ideal geometry". Does anyone know if is possible to calculate such value from chimera and how? Currently I just know how to calculate RMSD to the mean coordinate... thank you all in advance Val

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question
by leila karami 16 Jul '15

16 Jul '15

Dear chimera users, 1) I want to have electrostatic surface of my protein in chimera. To this, I used *Tools... Surface/Binding Analysis... Coulombic surface coloring* A new window is opened, but apply bottom is inactive. 2) There are ray command in pymol to obtain better image of molecular structures. Is there a similar command or utility in chimera? Any help will highly appreciated. Best wishes, Leila

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adjusting threshold values on volume rendering
by Dougherty, Matthew T 15 Jul '15

15 Jul '15

Hi, I can access threshold values from solid/volume rendering. eg: from VolumeViewer import active_volume v = active_volume() if v==None: return levels = getattr(v, "solid_levels") t,a=levels[0] How can I change a threshold value? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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Error opening file
by Sneha Poondru 10 Jul '15

10 Jul '15

Hello! I’m trying to prepare a receptor for dock6, so I downloaded a file (1tvb_.all.sph) from our cluster onto my desktop. However, when I click to open it, I keep getting this error message from Chimera: non-standard sph header Error while processing /Users/SnehaPoondru/Desktop/Project/1tvb_.all.sph: cannot open file "/Users/SnehaPoondru/Desktop/Project/1tvb_.all.sph": syntax error, line 1832 Any help is appreciated! Thanks! ~Sneha

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Structureviz Cytoscope plugin problem
by Ahmed Ezat 10 Jul '15

10 Jul '15

Dear Sir, I am trying to use structureviz Cytoscope plugin to launch Chimera, but it does not work. I installed Chimera and Cytoscope properly and set the path to Chimera in structureviz settings but it is not working. What can I do? I am using windows 7. I have also a problem to install chimera on Linux. if possible,c Can you send me detailed procedure for the installation process. Best Ahmed A Ezat

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swapaa: choosing rotamers
by roz orchidea 09 Jul '15

09 Jul '15

Dear all, I would like to use swapaa and choose which rotamer I want. Foe example I want from library dynameomics the second rotamer that appears in the pop-up menu of Arg. is it possible? Thank you for your time, Alex

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How to display two EM map and a PBD simultaneously
by 师扬 08 Jul '15

08 Jul '15

Dear all, Recently, I have a task to display two EM density map ('A' and 'B') and one PDB ('C') at the same time. B and C fit in map to A. So, I need to make A and B transparent to observe them simultaneously. However, one strange thing happened when I made A and B transparent. I can only see the density which A is lager than B or B is larger than A, and I could not see the buried density. In another words, when I make both A and B transparent, the map can be changed in to the 'A+B' map, and I could not see any 'A-B' or 'B-A' information. Have anyone met this problem? Do change something in setting can solve this problem? Best regards Yang

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on the movie command “turn y 3 120”
by Smith Liu 07 Jul '15

07 Jul '15

Dear All, For movie command "turn y 3 120", the molecule will turn counter-clockwise. Will you lease tell me the movie command which makes the molecule turn clockwise？ Best regards. Smith

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