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The following files will be found in each pdb/chain directory whose run finished successfully:

seq.fas : amino acid sequence of the selected chain in fasta format. : psi-blast output (zippped) for the sequence. The database which was used can be found at the beginning of the file, in the line begins with: 'Database'.

seq_homologs.fasta : file containing the sequences selected by the screening process, in fasta format.

cd-hit.out.clstr : output of the program cd-hit, which is showing the clusters found from all the selected sequences.

seq_rejected.txt : file containing the sequences rejected by the screening process and the reason for their rejection.

seq_final.fasta : The final file which details the screened sequences in fasta format.

TheTree.txt : Tree in newick format, which was constructed in the neighbor joining method from the chosen sequences.

TheTree.txt : Tree in HTNL format - for online view

msa_orig.aln : Multiples Sequence Alignment, created using MAFFT.

color_msa.html : ConSurf Color-Coded Multiples Sequence Alignment - HTML file

msa.aln : Multiples Sequence Alignment, created using MAFFT in Clustalw format.

msa_aa_variety_percentage.csv : table which details the amino acid variety in each position in the MSA (best viewed with an editor that respects Comma-Separated Values).

r4sOrig.res : Rate4Site output, before the normalization.

r4s.res : Rate4Site output, after the normalization.

consurf.grades : A summary of the ConSurf run: The conservation grades of the positions in the MSA and residues in the PDB, the normalized score from rate4site, residue variety per position and more.

rasmol.scr : a rasmol script which colors each ATOM in the PDB with the relevant conservation grade. The estimated scores are presented for all the amino acid positions, even if the confidence is low, e.g., due to insufficient data.

isd_rasmol.scr : same as rasmol.scr, only in this script the insufficient data will be shown as light yellow color.

(pdbid_chain)_ConSurf_DB_pipe.pdb : Header which should be added to the beginning of the PDB file in order to view the PDB molecule with FirstGlance in JMOL. (Please note that the line beginning with the word 'HEADER' should be removed from the PDB file).

(pdbid_chain)_ConSurf_DB_tempFactor.pdb : Conservation scores added to tempFactor field in order to view the PDB molecule with Pymol and Chimera.

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