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Difference between revisions of "User talk:Ahnlab"

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Hello PyMOLWiki Users,
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Is there a way to display the amide hydrogens but not the side chain atoms? In other words to display the backbone or main chain hydrogen without the functional group? They seem to show and hide together but I need a way to view only the backbone hydrogens. Thank you for any help.
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I am a graduate student finishing a thesis on MAPK allostery and activation. We are predominantly a signalling and proteomics lab, but I use hydrogen exhcange mass spectrometry (HXMS) as a primary analytical method and thus use high resolution structures for analysis and interpretation. I have a few questions for the community.
 
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One, I am interested in H bond distances & angles. I found the feature that calculates H bond distances (1773045), but I cannot find a way to extract them from the viewer. Is there a way to export these H bond assignments & distances to a txt, csv or other easily manipulated file type? Is there a way to calculate the bond angle and export them as well?
 
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Two, is there a way to calculate the distance from every protein backbone amide to the surface (nearest surface point) and export these as well? Thank you.
 
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Enjoy
 
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In short, PyMOL was never meant to be an analysis tool although it has the capabilities of performing rather complicated calculations when
 
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needed.  Having said that, you can write Python scripts that will do exactly what you want to do and to write the calculated values
 
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directly into a file. This can be challenging if you haven't coded in Python before (with respect to PyMOL) but it is well worth it.
 
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You can get a good idea of how to perform custom calculations by looking in the scripting area.
 
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Good luck!
 

Latest revision as of 04:13, 28 March 2014

Is there a way to display the amide hydrogens but not the side chain atoms? In other words to display the backbone or main chain hydrogen without the functional group? They seem to show and hide together but I need a way to view only the backbone hydrogens. Thank you for any help.

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