http://wiki.docking.org/index.php?action=history&feed=atom&title=Blastermaster_CLI 2026-04-05T03:21:08Z Revision history for this page on the wiki MediaWiki 1.39.1 http://wiki.docking.org/index.php?title=Blastermaster_CLI&diff=7533&oldid=prev 2014-03-25T16:09:47Z

<p>Created page with &quot;Command line arguments for <a href="/index.php?title=Blastermaster" title="Blastermaster">Blastermaster</a>. &lt;pre&gt; Usage: blastermaster.py [options] Turns pdb files into dockable grids &amp; spheres.Rewrite of MakeDOCK/DOCKblaster into non-...&quot;</p> <p><b>New page</b></p><div>Command line arguments for [[Blastermaster]].<br /> <br /> &lt;pre&gt;<br /> Usage: blastermaster.py [options]<br /> <br /> Turns pdb files into dockable grids &amp; spheres.Rewrite of MakeDOCK/DOCKblaster<br /> into non-makefile form<br /> <br /> Options:<br /> --version show program&#039;s version number and exit<br /> -h, --help show this help message and exit<br /> -v, --verbose lots of debugging output<br /> --elecapp lots of electrostatics debugging files<br /> -r RECEPTOR, --receptor=RECEPTOR<br /> receptor input pdb file, (default: rec.pdb)<br /> -l LIGAND, --ligand=LIGAND<br /> crystal ligand input pdb file, (default: xtal-lig.pdb)<br /> -b DOCKBASE, --dockbase=DOCKBASE<br /> DOCKBASE path for finding necessary programs,<br /> (default: /raid4/people/tskobilka/code/DOCK)<br /> -w WORKINGDIR, --working=WORKINGDIR<br /> working directory for extra files (default: working)<br /> -o OUTPUTDIR, --output=OUTPUTDIR<br /> output directory for DOCK input files (default:<br /> dockfiles)<br /> --vdw=VDWPREFIX vdw grid output filename prefix (default: vdw)<br /> --liganddesolv=LIGANDDESOLV<br /> ligand desolvation output filename (default:<br /> ligand.desolv)<br /> --defaultFiles=DEFAULTFILES<br /> default files (default:<br /> /raid4/people/tskobilka/code/DOCK/proteins/defaults)<br /> --filterParams=FILTERPARAMS<br /> input filter parameters, for binding site (default: /<br /> raid4/people/tskobilka/code/DOCK/proteins/defaults/fil<br /> t.params)<br /> --filterProgram=FILTERPROGRAM<br /> input filter program, for binding site (default: /rai<br /> d4/people/tskobilka/code/DOCK/proteins/filt/bin/filt)<br /> --filterLog=FILTERLOG<br /> filter logfile, for binding site (default:<br /> filter.log)<br /> --bindsiteResidues=BINDSITERESIDUES<br /> binding site residues file (default: rec.site)<br /> --msProgram=MSPROGRAM<br /> molecular surface program (default: /raid4/people/tsko<br /> bilka/code/DOCK/proteins/dms/bin/dms)<br /> --msOutput=MSOUTPUT molecular surface output (default: rec.ms)<br /> --msLog=MSLOG molecular surface logfile (default: dms.log)<br /> --sphgenProgram=SPHGENPROGRAM<br /> sphere generation program (default: /raid4/people/tsko<br /> bilka/code/DOCK/proteins/sphgen/bin/sphgen)<br /> --sphgenOutput=SPHGENOUTPUT<br /> sphere generation output (default: all_spheres.sph)<br /> --pdbsphProgram=PDBSPHPROGRAM<br /> pdb to sphere program (default: /raid4/people/tskobilk<br /> a/code/DOCK/proteins/pdbtosph/bin/pdbtosph)<br /> --pdbsphOutput=PDBSPHOUTPUT<br /> ligand spheres output (default: xtal-lig.match.sph)<br /> --addhProgram=ADDHYDROGENSPROGRAM<br /> add polar hydrogens program (default: /raid4/people/ts<br /> kobilka/code/DOCK/proteins/Reduce/reduce)<br /> --addhDict=ADDHYDROGENSDICT<br /> add polar hydrogens heteroatom dictionary (default:<br /> reduce_wwPDB_het_dict.txt)<br /> --addhOptions=ADDHYDROGENSOPTIONS<br /> add polar hydrogens heteroatom options (default: -OH<br /> -HIS -ALLALT -NOROTNH3 -Keep -METALBump1.5<br /> -NONMETALBump-5.0 )<br /> --addhFirst add polar hydrogens before processing (default: True)<br /> --addhFirstOptions=ADDHYDROGENSFIRSTOPTIONS<br /> add first polar hydrogens heteroatom options (default:<br /> -OH -HIS -ALLALT -ROTNH3 -Keep )<br /> --chargedPdbOutput=CHARGEDPDBOUTPUT<br /> charged pdb structure name (default: rec.crg.pdb)<br /> --addhLog=ADDHLOG add polar hydrogens logfile (default: addh.log)<br /> --lowdielectricSpheresProgram=LOWDIELECTRICSPHERESPROGRAM<br /> create low dielectric spheres program (default: /raid4<br /> /people/tskobilka/code/DOCK/proteins/makespheres1/make<br /> spheres1.cli.pl)<br /> --lowdielectricSpheresOutput=LOWDIELECTRICSPHERESOUTPUT<br /> low dielectric spheres output name (default:<br /> lowdielectric.sph)<br /> --lowdielectricSpheresLog=LOWDIELECTRICSPHERESLOG<br /> low dielectric spheres logfile (default:<br /> lowdielectric.spheres.log)<br /> --minLowdielectricSpheres=MINLOWDIELECTRICSPHERES<br /> minimum number of low dielectric spheres (default: 25)<br /> --sphtopdbProgram=SPHTOPDBPROGRAM<br /> sphere to pdb program (default: /raid4/people/tskobilk<br /> a/code/DOCK/proteins/showsphere/doshowsph.csh)<br /> --lowdielectricPdbOutput=LOWDIELECTRICPDBOUTPUT<br /> low dielectric spheres pdb file output name (default:<br /> lowdielectric.sph.pdb)<br /> --lowdielectricPdbLog=LOWDIELECTRICPDBLOG<br /> low dielectric pdb logfile (default:<br /> lowdielectric.sph.pdb.log)<br /> --matchingSpheresProgram=MATCHINGSPHERESPROGRAM<br /> create matching spheres program (default: /raid4/peopl<br /> e/tskobilka/code/DOCK/proteins/makespheres3/makesphere<br /> s3.cli.pl)<br /> --matchingSpheresOutput=MATCHINGSPHERESOUTPUT<br /> matching spheres output name (default:<br /> matching_spheres.sph)<br /> --matchingSpheresLog=MATCHINGSPHERESLOG<br /> matching spheres logfile (default:<br /> matching_spheres.log)<br /> --matchingSpheresDist1=MATCHINGSPHERESDIST1<br /> matching spheres distance cutoff 1 (default: 1.5)<br /> --matchingSpheresDist2=MATCHINGSPHERESDIST2<br /> matching spheres distance cutoff 2 (default: 0.8)<br /> --matchingSpheresMax=MATCHINGSPHERESMAX<br /> matching spheres maximum number (default: 45)<br /> --boxProgram=BOXPROGRAM<br /> create box surrounding binding site program (default: <br /> /raid4/people/tskobilka/code/DOCK/proteins/makebox/mak<br /> ebox.smallokay.pl)<br /> --boxOutput=BOXOUTPUT<br /> box output name (default: box)<br /> --boxLog=BOXLOG make box logfile (default: makebox.log)<br /> --receptorLowdielectricOutput=RECEPTORLOWDIELECTRICOUTPUT<br /> output name of charged receptor plus low dielectric<br /> spheres (default: receptor.crg.lowdielectric.pdb)<br /> --qnifftProgram=QNIFFTPROGRAM<br /> electrostatics program (default: /raid4/people/tskobil<br /> ka/code/DOCK/proteins/qnifft/bin/qnifft22_193_pgf_32)<br /> --qnifftOut=QNIFFTOUT<br /> qnifft output name (default:<br /> qnifft.electrostatics.phi)<br /> --qnifftTrimOut=QNIFFTTRIMOUT<br /> qnifft trimmed output name (default:<br /> trim.electrostatics.phi)<br /> --qnifftPdbOut=QNIFFTPDBOUT<br /> qnifft pdb logfile with charges and radii (default:<br /> qnifft.atm)<br /> --qnifftLog=QNIFFTLOG<br /> qnifft logfile (default: qnifft.log)<br /> --qnifftGrid=QNIFFTGRID<br /> qnifft grid size (default: 193)<br /> --chargeFile=CHARGEFILE<br /> qnifft charge file (default: amb.crg.oxt)<br /> --radiusFile=RADIUSFILE<br /> qnifft radius file (default: vdw.siz)<br /> --vdwProgram=VDWPROGRAM<br /> vdw program name (default: /raid4/people/tskobilka/cod<br /> e/DOCK/proteins/chemgrid/bin/chemgrid)<br /> --vdwLog=VDWLOG vdw logfile (default: vdw.log)<br /> --vdwprottable=VDWPROTEINTABLE<br /> vdw protein table (default: prot.table.ambcrg.ambH)<br /> --vdwparameters=VDWPARAMETERS<br /> vdw parameters (default: vdw.parms.amb.mindock)<br /> --solvmapProgram=SOLVMAPPROGRAM<br /> ligand desolvation program (default: /raid4/people/tsk<br /> obilka/code/DOCK/proteins/solvmap/bin/solvmap)<br /> --solvmapLog=SOLVMAPLOG<br /> ligand desolvation logfile (default: solvmap.log)<br /> --solvmapHydrogenRadius=SOLVMAPHYDROGENRADIUS<br /> ligand desolvation hydrogen radius (default: 1.0)<br /> --solvmapHeavyRadius=SOLVMAPHEAVYRADIUS<br /> ligand desolvation heavy atom radius (default: 1.8)<br /> --solvmapProbeRadius=SOLVMAPPROBERADIUS<br /> ligand desolvation probe radius (default: 1.4)<br /> --solvmapHydrogenName=SOLVMAPHYDROGENNAME<br /> ligand desolvation hydrogen suffix (default:<br /> .hydrogen)<br /> --solvmapHeavyName=SOLVMAPHEAVYNAME<br /> ligand desolvation heavy atom suffix (default: .heavy)<br /> -s, --sge use sge submission for long tasks that can be done in<br /> parallel<br /> -f, --flexibleReceptor<br /> flexible receptor grid building, off by default<br /> --flexibleResidues=FLEXIBLERESIDUES<br /> flexible residues in format &#039;55+56,66,87&#039; groups<br /> separated by commas, residues separated by +.<br /> --indockName=INDOCKNAME<br /> indock filename (default: INDOCK)<br /> --flexibleReadme=FLEXIBLEREADME<br /> flexible explanation filename (default:<br /> flexible.explanation.txt)<br /> --partReadme=PARTREADME<br /> part explanation filename (default:<br /> part.explanation.txt)<br /> <br /> &lt;/pre&gt;<br /> <br /> <br /> [[Category:DOCK 3.7]]</div>

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