Parameter File Format

Introduction

The parameter file is a text file that may be created automatically by the RSRef2000 GUI editor or manually in a text editor. It contains information that will be used by rsref.py  (see Running RSRef2000) for real-space refinement of local regions of macromolecules. Explanation for each entry is given in documentation for the RSRef2000 GUI editor.

An example of a parameter file is in the sample directory.  It is largely self-documenting (see example), but the following may help the uninitiated.  More detailed comments are in the standalone rsref module (RSRef2.0) documentation. Note that most of the options of the standalone  rsref module are not implemented in RSRef2000.

Remarks

1. If a “remote” machine (compute-server - see Running RSRef2000) is used for refinement:

• Run_script should be set to ‘-r’
• The remote machine should have the Map file and NCS (non-crystallographic symmetry operator) file and the full paths should be specified in corresponding fields

• The rest of the files should be on the local “front end” machine. Full path should be specified if they are not in the directory from which rsref.py is called.

• Output files will be written to the “front end” machine.

2. A Region containing several residues starting from First_res and ending at Last_res is called a Zone.

Example

Note: parameters are fully documented in the page for the RSRef2000 GUI editor.

*RSRef parameter file.

*Set any parameter you do not use to "none". 

Parameter_file = ak.prm 

Run_script = -r 

>>>>============================== Resolution range 

Low_res_limit = 6.0 

High_res_limit = 1.2 

>>>>========================= Files used in real-space refinement 

Starting_coord = ak.pdb 

Output_coord= ak_refined.pdb 

Map_file= Maps/anneal1.2final2.dsn6  

Log_file= ak.log 

>>>>============================== Crystallographic data 

symmetry_file= none 		=(replace "none" with the name of the symmetry-operator file) 

Atomsize = 3.4

Refsize = 1.6

>>>>============================= "Local Refinement" information 

Region =  zone 		=(region to be refined. Choice: zone, sphere)

>> First_res and Last_res must be specified if a zone is to be refined 

First_res = 2 

Last_res = 3 

Margin = 1.5 		=(of unrefined atoms that contribute to the calculated energy.)

>>>>============================== Minimization information 

w_a=40.0 			=(weight for Electron Density component) 

ref_scheme=slowcool 	=(choice: conjugate, slowcool, constant) 

>>>>=============== Molecular dynamics data 

md_type = torsion 		=(molecular dynamics type. Choice: cartesian, torsion)

start_temp=1700.0 		=(for slow-cooling, or constant-temperature)

cool_rate=500.0 		=(drop temperature; recommended cool_rate=500)

>>>>============================== end of parameter file.