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Source Codes
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Source Codes |
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Various Fortran, and Perl Programs we made |
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| Program | Purpose |
| a.f | to edit near2.out file |
| addchain.f | to add chain identifier to residue number |
| angles.f | to calculate angles and off planes distance on diamond file |
| applysym.f | to apply symmetry to a pdb file(assuming protomer A input) |
| applysymO.f | to do same as above using output from lsqman |
| askte.f | to work with Ten Eyck map |
| average6.f | to average Ten Eyck map |
| averocc.f | to average occupancies in WH file with quantitation .1 |
| averocc2.f | to average occupancies in WH file with quantitation .2 |
| axis.f | to help analyze axis relating chains |
| axis2.f | to make pdb file for above programs by creating axis.pdb |
| chain.f | to add chain Identifier with residue...different from addchain |
| chainwh.f | to change alphabetic chain labels to numbers |
| check.f | to check values in Ten Eyck map |
| checkocc.f | to list atoms with OCC != 1 & writes file with all OCC=1 |
| checkseq.f | to compare sequences in diamond files with alpha & beta sequence |
| checkwat.f | to use cover2 output to determine which waters to check/delete |
| checkwat2.f | to do same as above with only 2 input |
| checkwat3.f | to do same as checkwat, works with pdb & creates a summary |
| checkwatO.f | to do same same checkwat, but uses lsqman datas to calculate |
| checkwh.f | to look through WH file for symmetry related labels |
| chksolv.f | to apply symmetry to potential solvent list & look for redundancy |
| classwat.f | to list waters by numbers of H-bonding main chain partners |
| classwath.f | to go through classwat.out & calculate new histogram |
| compress.f | to compresse residue numbers for solvents |
| compresspdb.f | to do almost similar task as above with different behavior |
| convert_fob.f | to convert reflection file |
| core.f | to extract core of all map for TOMMAP |
| corel.f | to calculate corelation between 2 maps |
| corelb.f | to calculate correlation coefficient of B's with distance from origin |
| correctseq.f | to adjust sequence to agree with gene sequence |
| corrtemap.f | to do same as corel.f & ignore those map points which are 0 |
| cover2.f | to read & store Diamond file & report on density covering atom |
| COVER2.f | to do same as above but works with pointers |
| deapplysym.f | to move protomers B-F onto protomer A from *.pdb to *.nosym. |
| deapplysymO.f | to do same as above but uses output from lsqman |
| deletewat.f | to delete waters using output from checkwat3 using residue numbers |
| deletewat2.f | to do same as above using pdb file |
| editnear.f | to edit near2.out |
| editpdb.f | to change ILE CD1 to ILE CD and adjust PCD sequence for submission |
| fixbfpcd.f | to copy B's to monomers E,F,G,H and set occ = 1 |
| fixocc.f | to set occupancies=0 for residues for whom occupancies are fixed at 1 |
| getcell.f | to read DSN2 file for CELL records |
| getsymm.f | to read DSN2 file for SYMM records |
| homocore.f | to calculate numbers of pariwise sequence identities |
| j.f | to list atoms with OCC != 1 |
| ligands.f | to look for S,N,O atoms near 6 Fe's and calculates stats |
| limits.f | to give limits of WH file |
| limits2.f | to find CM, radii,distances from local symmetry axes in a PDB file |
| limitsdiam.f | to give limits of diamond file |
| listpack.f | to scan packing.log & list protein residues that make contact |
| listpack2.f | to scan packing2.log & list protein residues that make contact |
| makeau.f | to extract unique portion of averaged map |
| makelist2.f | to list points for molecular averaging |
| makemap.f | to create maps.com & start stream of PCD map generation jobs |
| makesolv.f | to make solvent list |
| meanres.f | to calculate between resolution between 2 boundaries |
| near.f | --- |
| near2.f | --- |
| near3.f | --- |
| near4.f | to list waters in interface |
| nearby.f | to read list of peaks/holes & indicate nearby atoms |
| nearby2.f | to see if near potential H-bond partner unless crit<0 |
| nearby2w.f | --- |
| nearby3.f | --- |
| nearres.f | to look for residues that are within criterion in one ORTH |
| newnum.f | to renumber solvent in WH file.compressed input->compressed output |
| newnum2 | to be used for solvent mapping |
| next.f | to make new PROLSQ command file |
| next2.f | to do same as above but later version |
| nohy.f | to remove hydrogens & change CD of ILE to CD1 |
| orthog.f | --- |
| orthtopdb.f | to reformat orthogonal Diamond file into PDB file |
| packing.f | to apply translational components to PCD holoenzyme and looks for contacts in adjacent molecules |
| packing2.f | to list contacts between protomer A and adjacent protomers |
| pdbtodiam.f | to convert pdb file into diamond files |
| peakhole.f | to list peaks above crit and holes below -crit |
| pkstoptn.f | to reformat peaks in PTN file |
| printmap2.f | to read and print map written by FSFOUR2 |
| ptntopdb.f | to reformat ptn file into PDB file |
| putsymm.f | to read DSN2 file for SYMM records and changes C centered to I centered |
| reindexmu.f | to reindex a mulist for monoclinc space group by applying crystallographic two-fold along b* |
| renumpdb.f | --- |
| rotdiam.f | to apply transformation crystallographic two-fold around y-axis to Diamond file. Relabel subunits. |
| rotpdb.f | to do same as above to a PDB file |
| rotwh.f | to do same as rotdiam.f to a WH file |
| saltpack.f | to look for salt links in packing*log files |
| splicealt.f | to copy alternate conformation coordinates from one PDB onto another PDB. Note these conformations MUST BE IN SAME ORDER |
| split.f | to split PDB file into separate molecules + waters for XPLOR for PCD |
| splitA.f | to split out monomer A from PDB files |
| splitCNS.f | to split PDB file to use it on CNS program |
| splitdiam.f | to split diamond file into monomers |
| splitdiam2.f | to do same as above & trim off monomer label |
| splitpdb.f | to split pdb into monomers |
| splitpdb2.f | to do same as above & updated version |
| statau2.f | to calculate stats of maps of final asymmetric unit |
| superdiam.f | to check position of local dyads for PCD |
| superdiam2.f | to do same as above with specified rotation |
| superimpose.f | --- |
| superwat.f | to look for waters obeying local symmetry |
| symm.f | to apply local symmetry to fractional coordinates |
| tweakpdb.f | to move monomers so that Fe's for each protomer match reference PDB |
| undumptemap.f | to restore a dumped Ten Eyck map |
| whtodiam.f | to convert WH file to a Diamond file |
| whtoorth.f | to convert WH file to Diamond file using orthogonal coordinate |
| whtoorth2.f | to do same as above and is an updated version |
| whtopdb.f | to reformat WH file to a pdb file |