Programs

Programs and documentations developed by Roberto Togawa under Dr. Goran Nesic supervision.
These programs were developed in the Barry Honig's Laboratory

fsc- Change strings in file

Ex: fsc ATOM HEATOM 1fat.pdb > output-file

Change string "ATOM" by string "HEATOM" in the file 1fat.pdb and redirect to the file output-file

Program source developed in shell script and SED

convert - Convert images in RGB format to GIF format using togif program in the current directory

Ex: convert

Convert all files with RGB format (rgb extention) to GIF format (gif extention).

Program convert keeps the RGB format files

Program source developed in perl

sumc - sum charges in PDB file format. PDB file should be created using GRASP program (option - write - pdb&charge coordinates). Program also shows if any aminoacid has non unique charge at diferent sequence position

Ex: sumc file.pdb

sumc makes a list of all aminoacids with sum of their charges. If there are a different charges in a particular aminoacid,them these aminoacids are listed for all positions throughout sequence.

note: the PDB file is not a original file in PDB database, it was creaded by GRASP program with a charge columm.

programa source developed in perl

gen - Separate a PDB file by chains using TER separator an create a new mol.pdb file.

Ex:

a) gen /pdb/1fat.pdb/1+2,3+4/

b) gen /pdb/1fat.pdb/1,4/

a)

1+2 means that chain #1 and chain #2 in original PDB file will be grouped together and treated as new chain A.

3+4 means that chain #3 and chain #4 in original PDB file will be grouped together and treated as new chain B.

The new chains A and B are now part of the newly created mol.pdb file.

b)

1,4 menas that chain #1 and chain #4 are grouped and are now treated as chain A and B respectively , and are part of the newly created mol.pdb file

Note: the program default is gen /pdb/file.pdb/1,2/

program source developed in perl.

listhb_hbplus - Count hydrogen bonds using two files: mol.hb2 (created by hbplus program) and mol.pdb (created by gen program)

Ex: listhb_hbplus mol.hb2 mol.pdb

Program flowchart:

1) gen /pdb/1fat.pdb

2) clean

3) hbplus mol.new

4) listhb_hbplus mol.hb2 mol.pdb

1)- gen is executade to create a mol.pdb file.

2) - clean program prepares mol.pdb for use in hbplus program. When executed it is necessary to type "mol.pdb" when file name is requested.

3) - The hbplus program is executed with "mol.new" parameter. mol.hb2 will be created containing list of hydrogen bonds identified at mol.new file (original /pdb/*.pdb)

4) - listhb_hbplus program requires two files: mol.hb2 and mol.pdb for execution

The following files will be criated: list, list1, list2, html, html1, html2, sort_relat, sort_relat1, sort_relat2, relatorio

list1 - File containg a list of hydrogen bonds between chains A-B.

list2 - File containg a list of hydrogen bonds between chains A-B with interplay of one water molecule (A-H-B).

list3 - File containg a list of hydrogen bonds between chains A-B with interplay of two water molecules (A-H-H-B).

html - File containing sorted list of hydrogen bonds between chains A-B. This file wil be used by make_html program that generates a html file.

html1 - File containing sorted list of hydrogen bonds between chains A-B with interplay of one water molecule (A-H-B). This file wil be used by make_html program that generates a html file.

html2 - File containing sorted list of hydrogen bonds between chains A-B with interplay of two water molecules (A-H-H-B). This file wil be used by make_html program that generates a html file.

sort_relat - Formated output file sorted by -u parameter for uniqueless of the string.

sort_relat1 - Formated output file sorted by -u parameter for uniqueless of the string.

sort_relat2 - Formated output file sorted by -u parameter for uniqueless of the string.

relatorio - Formated output in text format.

Program source developed in perl

make_html - Makes a html file using list_hbplus program output

Ex: make_html

Reads html, html1, html2 files and creates a *.html file.

When program is executed the "tabela_hb.html" file will be created.

This program is part of the "hb_script" script.

Program source developed in perl.

hb_script - Script to count a Hydrogen Bonds

Ex:

a) hb_script /pdb/1slu.pdb

b) hb_script /pdb/1fat.pdb 1+3,2+4

c) hb_script 1ose.pdb

a) Run program using a /pdb/1slu.pdb file, it will be used a TER separator to get each chain. In this case the program will be work using the first two chains. The "relatorio" and "1slu_hb.html" files will be created.

b) Run program using a /pdb/1fat.pdb. In this case chain #1 and chain #3 will be grouped and treated as chain A and chain #2 and chain #4 will be grouped and treated as chain B. The "relatorio" and "1fat_hb.html" files will be created.

c) Run program using a local 1ose.pdb file. In this case is necessary to put a TER separator before water molecules sequence. Is necessary a manual intervention to analise a PDB file. The "relatorio" and "1ose_hb.html" files will be created.

The "relatorio" file is in text form and "*.html" is in HTML format.

Note: When clean program will be executed is necessary to type "mol.pdb" when file name is requested

- hb_script will use the following programs: gen, clean, hbplus, make_html, listhb_hbplus

program source developed in shell script