MCSG

UVA

Map to Model Correspondence

map2mod is a set of programs for evaluation of agreement between a protein model and crystallographic electron density maps. It is useful for validation and refinement of protein models. Upload files with 2Fo-Fc and Fo-Fc electron density maps or a file with structure factors in ccp4 format and a file with 3-D coordinates of protein's atoms in pdb format, set up specified below parameters (or use default values) and selest the mode in which you want the data to be processed. The results will be printed on the screen and sent by email (if provided) within several seconds.

Manual


Required data to be processed:

upload pdb file with the model
map processing mtz processing

upload a file with 2Fo-Fc electron density map
upload a mtz format file containing phases for maps calculation

upload a file with Fo-Fc (difference) electron density map 		F PHI FOM



Optional parameters:


2Fo-Fc density cutoff 2Fo-Fc density radius
Fo-Fc density cutoff (positive) Fo-Fc density radius (positive)
Fo-Fc density cutoff (negative) Fo-Fc density radius (negative)
check only
remove side chains which are out of 2Fo-Fc density or in the negative Fo-Fc density
remove only water out of 2Fo-Fc density or in the negative Fo-Fc density
check B-factor
overall for atoms and hetatoms separately Å
print atoms having B-factor more less than sigmas from the average
print atoms having B-factor more less than (absolute value)
check R/Rfree value in comparison with the average R Rfree Å
extract values from provided pdb file
check model to the data confidency (pdb and mtz files are required)


if you want the modified pdb file was sent to you please provide your email address:




Contact for questions and problems