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.