[phenixbb] a new PDB clustering tool available in phenix from nightly build dev-756

Francois Berenger berenger at riken.jp
Thu May 26 22:24:40 PDT 2011

Dear Phenix users,

Starting from the nightly build dev-756, a new clustering tool called 
DURANDAL is included in Phenix.
It performs exact clustering of proteins in PDB format, fast.
It is primarily aimed at people working in protein structure prediction
and having to deal with a lot of protein models.

The correspondence used to compute CARMSD for a pair of proteins is 1 to 1.
If two proteins A and B are to be optimally superposed, both PDB files
(A.pdb and B.pdb) must have the same numbers of alpha carbons.
The first alpha carbon in A.pdb will be matched to the first alpha 
carbon in B.pdb, and so on.

Clustering up to 20,000 PDB files should work on most machines.
Workstations with a lot of memory will be able to cluster even more files.


* to perform exact clustering using a fixed cutoff value of 3.0

durandal.cluster_pdbs -i [file_containing_one_PDB_filename_per_line]\
-d 3.0 -o out -s -v

* there is also another tool included, to compute CARMSD of many files
   versus a reference one (the first in the list is considered the

durandal.rank_pdbs [file_containing_one_PDB_filename_per_line]

If you want to know more about how the software is working, you can have 
a look at http://bioinformatics.oxfordjournals.org/content/27/7/939

Don't hesitate to ask if you encounter any problem while using the software.

Best regards,
Francois Berenger.

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