In silico modeling of arch-3: Medeller and RosettaCM model building.

Here are all the files nessesary for prediction of archaerhodopsin-3 structure using Medeller or RosettaCM algorithms. 

For modeling using  Medeller  please read README_MEDELLER file for all the information. For RosettaCM:

Please, before using these scripts adjust them for you cluster. You will need the recent version of Rosetta package installed.

Let's take for example stucture P96787 (arch-3) as a query, 1UAZ_full.pdb as a template.

Also, you'll need grishex.script, thread.script, hybridize.script, relaxate.script, stage1_membrane.wts, stage2_membrane.wts, stage3_rlx_membrane.wts, uuu.grishin, rosetta_cm.options, rosetta_cm.xml, relax.options, cluster.options that are located in the  "GENERAL" folder here. Let's assume they are located in the workfolder.

Create an alignment file. For pairwise alignement use AlignMe/MP-T. Copy the alignment information in the file P96787_1UAZ.aln in the workfolder.

Put in the workfolder attached P96787_3.frags P96787_9.frags attached here -- fragment files for Rosetta.
Put in the workfolder attached P96787.octopus.

mv 1UAZ_full.pdb 1UAZ.pdb

Open the grish.script and check: "target" and "templateA" which describe each line of the alignment file change on the names of the lines in your alignment file!
For example for AlignMe it will be P96787 1UAZ.
./grishex.script P96787 1UAZ

./thread.script P96787 1UAZ

Run the hybridize script: ./hybridize.script P96787 1UAZ 500
It will take several days.

It will create file hybridized_P96787.out -- a binary silent file of 500 structures with the rebuilt loops and inserted fragments, if
there were gaps. It will take several days also.

Run the ./relax.script P96787 50
 
It will create file relaxed_P96787.out -- a binary silent file of 25000 structures -- 50 for each hybridized.

Time to evaluate the results.

Clustering.

Run ./do.script P96787
open LISTIK
delete the _0001 in the end of each line.
Run ./resulting1.script

In the folder PDBSS open cluster_summary.txt.
The first structure in the list is the best one. It is located in the folder PDBSS.