User talk:Ahnlab - Revision history

Bell: 5 revisions

2014-03-28T04:13:32Z

5 revisions

Ahnlab: backbone hydrogens

2011-01-14T22:33:03Z

backbone hydrogens

Slaw at 04:16, 14 December 2009

2009-12-14T04:16:59Z

Ahnlab at 22:14, 10 December 2009

2009-12-10T22:14:04Z

Slaw at 18:47, 10 December 2009

2009-12-10T18:47:11Z

Ahnlab: PyMOL calculations

2009-12-09T21:56:04Z

PyMOL calculations

New page

Hello PyMOLWiki Users,
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.
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?
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.

Enjoy

← Older revision		Revision as of 22:33, 14 January 2011
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−	~~Hello PyMOLWiki Users,~~	+	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.
−	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.
−	~~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~~?
−	~~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.~~
−
−	~~Enjoy~~
−
−	~~In short, PyMOL was never meant to be an analysis tool although it has the capabilities of performing rather complicated calculations when~~
−	~~needed. Having said that, you can write Python scripts that will do exactly what you want~~ to do and ~~to write the calculated values~~
−	~~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.~~
−	~~You can get~~ a ~~good idea of how~~ to ~~perform custom calculations by looking in~~ the ~~scripting area~~.
−
−	~~Good luck!~~
−
−
−	Thank you for the response. While learning python has been on my list of things to do, it is not yet checked off. I imagine learning how to script these two calculations is not trivial for a novice, but we do have experts around that can help~~. Do you know of any sortware that can perform the calculations in question? Thank you!~~
−
−
−	If you're analyzing PDB files then you might as well write a simple script (using any language of your choice) to process the PDB file. In fact, you can simply use AWK to extract the two sets of coordinates that you're interested in (for a distance calculation) and run it through a script to calculate the distance. This can be the same thing for an angle (with the exception that you'll have 3 sets of coordinates). For simulation trajectory files, there's a set of tools called the MMTSB toolset which is very handy but may take you some time to learn.

← Older revision		Revision as of 04:16, 14 December 2009
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	Thank you for the response. While learning python has been on my list of things to do, it is not yet checked off. I imagine learning how to script these two calculations is not trivial for a novice, but we do have experts around that can help. Do you know of any sortware that can perform the calculations in question? Thank you!		Thank you for the response. While learning python has been on my list of things to do, it is not yet checked off. I imagine learning how to script these two calculations is not trivial for a novice, but we do have experts around that can help. Do you know of any sortware that can perform the calculations in question? Thank you!
		+
		+
		+	If you're analyzing PDB files then you might as well write a simple script (using any language of your choice) to process the PDB file. In fact, you can simply use AWK to extract the two sets of coordinates that you're interested in (for a distance calculation) and run it through a script to calculate the distance. This can be the same thing for an angle (with the exception that you'll have 3 sets of coordinates). For simulation trajectory files, there's a set of tools called the MMTSB toolset which is very handy but may take you some time to learn.

← Older revision		Revision as of 22:14, 10 December 2009
Line 12:		Line 12:

	Good luck!		Good luck!
		+
		+
		+	Thank you for the response. While learning python has been on my list of things to do, it is not yet checked off. I imagine learning how to script these two calculations is not trivial for a novice, but we do have experts around that can help. Do you know of any sortware that can perform the calculations in question? Thank you!

← Older revision		Revision as of 18:47, 10 December 2009
Line 5:		Line 5:

	Enjoy		Enjoy
		+
		+	In short, PyMOL was never meant to be an analysis tool although it has the capabilities of performing rather complicated calculations when
		+	needed. Having said that, you can write Python scripts that will do exactly what you want to do and to write the calculated values
		+	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.
		+	You can get a good idea of how to perform custom calculations by looking in the scripting area.
		+
		+	Good luck!

← Older revision	Revision as of 04:13, 28 March 2014
(No difference)