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X-Ray Crystallographic data queries

X-Ray Crystallographic data queries - Protocols and Methods Forum

X-Ray Crystallographic data queries - Post Any Protocol, Method, Technique, Procedure or Tips / Troubleshooting for any Molecular Biology Technique.


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Old 11-09-2006, 07:32 AM
tarun gupta
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Default X-Ray Crystallographic data queries



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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 wetake NMR Structures for Docking analysis ?

3. Why Beta factor is ZEROin NMR Structures?

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

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

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

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

Any explainations/suggestion arehighly appreciated.

Many Regards,
Tarun
B.Sc(Hons)Bioinformatics
GGDSD College
Panjab University
Chandigarh-India
[Only registered users see links. ]


On Wed, 08 Nov 2006 [Only registered users see links. ] wrote :



B.Sc.(hons)Bioinformatics
GGDSD College of Post Graduation
(Panjab University)
Sector-32/C
Chandigarh-160031
Mob: 91-9888237906

[Only registered users see links. ]

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