I have sent my crystal for synchrotron and now I have diffraction images. I want to start the data processing. It is my first time and I need to know the step by step protocols (for MR or SeMet) and the needed software for each steps from diffraction images until pdb file submitting.
Welcome to the club of structure hunters !!
Your question is a very general one implementing thousands of sub questions and strategies and several possible programs of data processing for each step. Better find somebody around you who knows and has the time to explain details for your first structure as well as for a the dozen to come.
the steps are :
1. LOOK with great attention your images
2. INDEX your data and find the adequate SPACE GROUP ...
3. INTEGRATE your data considering this SPACE GROUP
4. IMPORT & SCALE the integrated data within a data processing program (PHENIX, CCP4, ...etc)
5. PHASE the data by MOLECULAR REPLACEMENT or EXPERIMENTAL PHASING and find a molecular MODEL
6. REFINE the molecular MODEL
7. DEPOSITE to the pdb...
Each protein is a new adventure with new problems and new desicions and strategies to apply. And it's an amazing job I tell you..!
Hi
Congratulations for your crystals and diffraction data.
Nicolas already answer very well to your question.
I would like just add that you could participate in the CCP4BB,
where you can post questions about protein crystallography.
If you are at the data processing level, I will suggest you use XDS
and try to figure out your Space Group (or the possible ones) .
If you are in MR option go in CCP4 and try Balbes or Phaser.
if you have anomalous signal try AutoSharp.
And later for the refinement, use Coot and Refmac ...
But all theses programs are my very personal-preferred ones.
If you have a specific question about a step, let us know or
search in the CCP4BB archive.
Good luck and welcome to the club
The aforementioned answers provide excellent advice. HKL3000 is a pretty decent option for an all inclusive suite of programs. Subroutines can analyze the data to ensure data quality. SeMET and MR phasing is easily performed through the PHENIX GUI (included in HKL3000). Furthermore, MOLPROBITY is implemented throughout the refinement process which has become the standard for model quality. Macros are included with COOT allowing for clashscores to be calculated and displayed on the fly.
MR is a fantastic way to derive phases, but phase bias is important to consider. Also, not all data sets can be solved quickly with MR. There are some de novo phasing programs (e.g. Acrimboldo) that might work for you, although SeMet provides experimental phasing and is a better choice for structure solution.
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