Hi,
I'm looking for a free programme that will allow me to superimpose a short protein sequence/a motif on its structure or a structural model to verify if it's water accessible or not. A possibility for a visual inspection would be great.
Thank you.
You can do that by following:
1. Find structures and download PDB file or prepare a PDB file if you have a model.
2. Run STRIDE.
http://webclu.bio.wzw.tum.de/cgi-bin/stride/stridecgi.py
3. Check solvent accessible surface area
4. Color by SAS in PyMOL.
Thank you, Woonghee.
I wonder whether one can do these analyses automatically searching for accessible areas en masse. Is there a way to automatically focus on THE specific fragment in such circumastances?
PyMOL can do many things.
http://www.pymolwiki.org/index.php/Practical_Pymol_for_Beginners
Thats a link to their beginners website, they have many useful hints and tutorials.
I have also attached a user manual and tutorial.
As to your last question... You should be able to pick specific AA residues and manipulate them as you wish...I amsure one of these guides will be able to help you.
We did similar stuff to what you want to investigate in tutorials with our third years...
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