This repository contains the nucleic acid model building software Nautilus, and is the site where any further developments on the software will be held. The original Nautilus software was written by Kevin Cowtan and this work is part of a PhD studentship funded by the Biotechnology and Biological Sciences Research Council (BBSRC) awarded to Jordan Dialpuri.
You must have
- Clipper
- MMDB2
installed, which come included in the CCP4. To ensure they are in your path, you must source the appropriate script. To do this run:
source /opt/xtal/ccp4-X.X/bin/ccp4.setup-sh
where X.X is your CCP4 version.
To compile this, just simply run:
make
and the executable 'cnautilus' should be created in the root directory of the project.
To run the executable run:
./cnautilus <PARAMS>
The available parameters are
-mtzin <filename>
-seqin <filename>
-pdbin <filename>
-pdblistin <filename>
-pdblistdir <filepath>
-pdbout <filename>
-predicted-phos-map <filename>
-xmlout <filename>
-colin-fo <colpath>
-colin-hl <colpath> or -colin-phifom <colpath>
-colin-fc <colpath>
-colin-free <colpath>
-cycles <number>
-anisotropy-correction
-fragments <number>
-resolution <resolution/A>
-pdbin-ref <filename>
-cif
-search-step <float>
-verbose <number>
mtzin - the input reflections data from the experiment e.g. 1hr2.mtz
seqin - the sequence of the nucleic acid e.g. 1hr2.fasta
pdbin - the filepath of an input model
pdblistin - the list of PDB files for use in the library
pdblistdir - the directory containing all PDB files in the pdblistin
pdbout - the filepath of the output model e.g. 1hr2_output.pdb
predicted-phos-map - the filepath of a predicted phosphate map
xmlout -
colin-fo - column headings for Fobs e.g. FP, SIGFP
coln-hl - column headings for Hendrickson-Lattman coefficients (ABCD) e.g. sfcalc.A, sfcalc.B, sfcalc.C, sfcalc.D
colin-fc - column headings for Fcalc e.g FWT, PHWT
colin-free - column heading for Free R Flag
cycles - number of cycles to run
anisotropy-correction - apply anisotropy correction
-fragments - number of hits to be found in the first step
-resolution - the resolution of the data
-pdbin-ref - single PDB file for use as the library
-cif - output model in CIF format only
-search-step - the step used in the fragment fitting angle search
-verbose - level of logging output