vicinity.pl

Usage

usage:   vicinity.pl [options] [file(s)]
options: [-l min:max[=min:max=...]]
         [-hard value[:force]]
         [-soft value[:force]]
         [-f filelist]
         [-[no]margin]

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Description

This script is used for loop or fragment modeling to find residues that are located within a cutoff of a given residue subset in a larger protein. The output consists of two lines. The first line contains a residue specification for all residues that are within the cutoff (including the loop residues) that can be used with -l as command line argument in other MMTSB tools. The second line contains a residue specification including restraint force constants for use in minCHARMM.pl, for example, to run minimizations where only the neighboring residues of the modeled loop or fragment are kept flexible. The loop residues are not included in the second residue list.

One or more PDB files (with different conformations for the same protein) are read as input. The loop or fragment residues are specified with -l as a list of residue ranges. The cutoff is changed with -hard (default value: 16.0 A). A second, soft cutoff is set to 12.0 A by default and can be changed with -soft. Residues within this smaller cutoff are expected to be restrained with a smaller force constant while residues beyond the soft cutoff but within the main cutoff are restrained to a much larger extent to allow for stress relief but no significant structural rearrangements beyond the immediate loop neighborhood. Force constants used in the second line of output are by default 0.5 kcal/mol for residues within the soft cutoff and 10.0 kcal/mol beyond. They can be changed by appending the new force constant to the cutoff in the -hard and -soft options.

The -f option is available to read a list of files with different protein conformations from an external file (or standard input if - is given as the file name).

Options

-help 

usage information

-l min:max[=...] 

list of reference set of residues

-hard value[:force] 

outer cutoff distance and force for restraint list generation

-soft value[:force] 

inner cutoff distance and force for restraint list generation

-f filelist 

list of files to be read to determine residues within cutoffs from reference residues in any of the structures

-[no]margin 

follow cutoff criteria strictly (nomargin) or generate a minimum one-residue margin for residues in inner cutoff list to be restrained with hard restraint (margin)

Examples

vicinity.pl -l 71:81 1poa.exp.pdb
determines the residues within the default cutoffs of the loop at 71 through 81

1:19=21=28=39:40=42:44=46:55=57:103
16:19_10=21=28=39:40=42:44=46=48:49=52:53=55=57:61=63:64=103=1:15_0.5=47=50:51=54=62=65:70=82:102

vicinity.pl -l 71:81 -hard 12:1.0 -soft 10:0.2 1poa.exp.pdb
determine the residues within a 12 A from the loop at 71 through 81. The soft cutoff is also reduced to 10 A and modified force constants of 0.2 and 1.0 kcal/mol are used in the output.

1:15=47=50:51=54=62=64:102
1:2_1.0=15=47=50:51=54=62=64=102=3:14_0.2=65:70=82:101

vicinity.pl -nomargin -l 71:81 -hard 12:1.0 -soft 10:0.2 1poa.exp.pdb
determine the residues within a 12 Å from the loop at 71 through 81. The soft cutoff is also reduced to 10 Å and modified force constants of 0.2 and 1.0 kcal/mol are used in the output. No margin is generated and cutoff criteria are followed strictly.

1:15=47=50:51=54=62=65:102
1:2_1.0=15=47=50:51=54=62=102=3:14_0.2=65:70=82:101