Abhinav's Programs

Crystallography Related Programs (in fortran)

The program Dealpdb helps manipulate PDB files and lets you perform a number of operations on them.

The program Dealmap helps manipulate CCP4 map files and lets you perform a number of operations on them.

The program Mask_ovlp helps check a mask for the presence of overlaps arising from crystallographic and/or NCS symmetry relations. The overlaps can be viewed through O and then corrected interactively through the program.

The program Matrix helps manipulate 4X3 matrices (rotation+translation). The program can read/write the matrices in a number of formats including XPLOR, RAVE, O, and FREE formats.

Other Programs (in Perl)

The program Rare Codons checks the presence of rare codons in a gene sequence for expression in E. coli .

The program Mol Weight computes amino acid sequence analysis from a given protein sequence.

The program MAD Signal from Se atoms computes the strength of MAD signal arising from Selenium substituted protein in a MAD crystallography experiment.

The program Show Residues highlites selected residues in a given protein sequence.

The program Format Sequence formats a DNA/Protein sequence for printing etc.

The program invert_complement generates Invert/Complement of a DNA Sequence.

The program kd binding calculates percent binding saturation of a ligand to a protein (useful for forming complexes).

The program Superdex 200 MW computes the estimated molecular weight of a protein from Size Exclusion elution profile on a Superdex 200 HR column.

Please let me know if you download any program.

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DEALPDB

You can EITHER download dealpdb.tar.gz , which includes all files.

To install you need to do the following:

 gzip -dc dealpdb.tar.gz | tar -pxf -

This would create the following files:

 dealpdb.f               (Main source code) 
 fortran_util_sgi/dec.f  (Library source codes) 
 dealpdb_sgi             (SGI executible) 
 dealpdb_dec             (DEC executible)

To compile dealpdb, simply type

 f77 -o dealpdb dealpdb.f fortran_util_sgi/dec.f

(or use your own favorite fortran compiler)

OR you can download the individual files one at a time.

        (try SHIFT+CLICK if CLICK doesn't work)

 dealpdb.f            (Main source code)
 fortran_util_sgi.f   (Library source code for SGI)
 fortran_util_dec.f   (Library source code for DEC)
 dealpdb_sgi          (SGI executible)
 dealpdb_dec          (DEC executible)

And compile the program as above.

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DEALMAP

Download dealmap.tar.gz

To install you need to do the following:

 gzip -dc dealmap.tar.gz | tar -pxf -

This would create the following files:

 dealmap.f               (Main source code)
 ccp4_rw.f               (CCP4 map read/write source code: 
                                 -- courtesy Kevin Cowton)
 fortran_util_sgi.f      (my library)  
 dealmap                 (SGI executible)

To compile dealmap, simply type

 f77 -o dealmap dealmap.f ccp4_rw.f fortran_util_sgi.f $CLIB/libccp4.a

($CLIB is the CCP4 library directory)

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MASK_OVLP

Download mask_ovlp.tar.gz (Only for SGI currently)

To install you need to do the following:

 gzip -dc mask_ovlp.tar.gz | tar -pxf -

This would create the following files:

 mask_ovlp.f           (Main source code)
 mask_rw.f             (mask read/write code: borrowed from Gerard Kleywegt)      
 mask.inc              (parameter file)
 libfortran_util_sgi.a (Library)
 mask_ovlp             (SGI executible)

To compile mask_ovlp, simply type

 f77 -o mask_ovlp mask_ovlp.f mask_rw.f libfortran_util_sgi.a

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MATRIX

Download matrix.tar.gz

To install you need to do the following:

 gzip -dc matrix.tar.gz | tar -pxf -

This would create the following files:

 matrix.f               (Main source code)
 libfortran_util_sgi.a  (SGI Library) 
 libfortran_util_dec.a  (DEC Library) 
 matrix_sgi             (SGI executible)
 matrix_dec             (DEC executible)

To compile matrix, simply type

 f77 -o matrix matrix.f libfortran_util_sgi/dec.a

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