X-Ray Crystallographic data queries

tarun gupta via methods%40net.bio.net (by hotbacteria At rediffmail.com)
Thu Nov 9 02:32:43 EST 2006


  

HI All,

I have been working on pdb files for x-ray data validation. I am encountering some problems which are as follows: 

1. Procheck perform various checks on pdb files and ceates a .SUM file along with many other files. Now I want to ask if .NEW files (corrected files generated by procheck) be used as input files for further analysis instead of original .pdb files? If Yes, Is there any .new to .pdb convertor?

2. Can we take NMR Structures for Docking analysis ?

3. Why Beta factor is ZERO in NMR Structures?

4. What should be the ideal threshold R value and R-Free value in an 
   Ideal structure ?

5. In NMR structures, there are various MODELS for same chain (e.g. – 
   1MO7.pdb). What is the significance of these models for docking?

6. Why beta factors differ so rapidly for all residues in a structure?

7. What does a ZERO B-Factor Structure Imply (e.g. – 1JQ2.pdb)?

Any explainations/suggestion are highly appreciated.

Many Regards,
Tarun
B.Sc(Hons)Bioinformatics
GGDSD College
Panjab University
Chandigarh-India
http://hotbacteria.tripod.com 


On Wed, 08 Nov 2006 methods-request At oat.bio.indiana.edu wrote :
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>Message: 1
>Date: Tue,  7 Nov 2006 19:03:00 +0200
> From: Yoram Gerchman <gerchman At research.haifa.ac.il>
>Subject: Newbie HPLC system
>To: methods At magpie.bio.indiana.edu
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>Greetings all
>I am looking for a newbie HPLC system. Should be easy to use, low maintenance,
>and upgradeable (and not very expensive...). It will be used mainly for
>separation of proteins and protein complexes. Does anyone have a
>recommendation? Does anyone know the SRI model 210 HPLC (I had good experience
>with the 310 GC)?
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>Thanks Yoram
>
>Yoram Gerchman
>Haifa University-Oranim
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B.Sc.(hons)Bioinformatics 
GGDSD College of Post Graduation 
(Panjab University) 
Sector-32/C 
Chandigarh-160031 
Mob:  91-9888237906

http://hotbacteria.tripod.com


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