Thursday, 15 September 2011

Temperature Factor statistics


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:

a tutorial focused on coloring by B-factor: www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html

--Eric


                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu



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From: Eleanor Dodson
If these are in different chains - Yes.
Look at the plots..
Eleanor

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