Dear Modeller Users and Developers,
The WRITE_DATA command can write the selected types of data (such as PSA DIH NGH SSM CRV CAV CROSS-SECTIONS) about the MODEL to a corresponding file. The example script write_data.top in the path 'modeller7v7/example/commands' is:
# Example for: WRITE_DATA
# This will calculate solvent accessibility, dihedral angles, and # residue-residue neighbors for a structure in the PDB file.
SET OUTPUT_CONTROL = 1 1 1 1 1
# Get topology library for radii and the model without waters and # HETATMs: READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib' SET HETATM_IO = off, WATER_IO = off READ_MODEL FILE = '1fas'
# Calculate residue solvent accessibilities, dihedral angles, and # residue-residue neighbors: SET RADII_FACTOR = 1.0 # The default is 0.82 (for soft-sphere restraints) WRITE_DATA FILE = '1fas', OUTPUT = 'PSA DIH NGH SSM CRV'
After I run this script, I can get corresponding files: 1fas.dih 1fas.ngh 1fas.psa 1fas.sol 1fas.ssm. However, when I changed the last line "WRITE_DATA FILE = '1fas', OUTPUT = 'PSA DIH NGH SSM CRV'" into "WRITE_DATA FILE = '1fas', OUTPUT = 'ALL'" or "WRITE_DATA FILE = '1fas', OUTPUT = 'CRV CAV CROSS-SECTIONS'", I can not find 1fas.crv, 1fas.cav in the ouput directory. And there is no information on writing 1fas.crv and 1fas.cav in write_data.log file. Where can I get these two files or information about mainchain curvatures and protein internal cavity volums? is it a bug?
Best regards
Shuqun Liu