From: Yuri Pompeu
Date: 31 August 2011 01:32
Quick newbie question,
After i get my output file from baverage containing the average b-factor and rms by residues,
How can I calculate and display the average (and or mean) B-factors?
Is there a way of calculating it by protein, ligands and solvent separately?
thank you
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From: Pavel Afonine
Hi Yuri,
a possible option:
phenix.model_vs_data model.pdb data.mtz will do it. Look for lines like this in the output:
ADP (min,max,mean):
all (136 atoms): 4.4 97.6 25.3
side chains (48 atoms): 4.9 96.8 21.0
main chains (64 atoms): 4.4 97.6 28.3
macromolecule (112 atoms): 4.4 97.6 25.2
ligands (1 atoms): 6.6 6.6 6.6
solvent (23 atoms): 8.8 44.1 26.8
mean bonded (Bi-Bj) : 27.91
number_of_anisotropic : 0
number_of_non_positive_definite : 0
Pavel
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From: Eric Pettersen
Chimera's Render by Attribute tool can depict atoms by their B-factor or residues by their average B-factor (assuming you have a PDB file with a B-factor column). It also shows a histogram of the B-factor values. You can use the Attribute Calculator tool to compute the average B-factor of any part of your structure and write it to a file.
Some links:
Chimera: www.cgl.ucsf.edu/chimera
Render by Attribute: www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/render/render.html
Attribute Calculator: www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/calculator/calculator.html
a tutorial focused on coloring by B-factor: www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html
--Eric
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From: Eleanor Dodson
Look at the plots..
Eleanor
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