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Why PMB? Well this started as a place to put programs being
developed for the Gulf Coast Structural Genomics Consortium
(GCSCC). Never heard of the GCSCC? Well that explains why PMB
does not include any model-building tools. However, I started to
include our automated structure refinement tools in the PMB
suite, and the name PMB remains. The murky origin of this
software lies deep within the ancient past of protein structure
refinement with Alec Hodel and Paul Harkins of Robert Fox's group
at Yale. If you use these utilities please cite:
Emily E. Scott, Mark A. White, You Ai He, Eric F.
Johnson, C. David Stout, and James R. Halpert, Structure of
mammalian cytochrome P450 2B4 complexed with 4-(4
chlorophenyl)imidazole at 1.9 A resolution: Insight into the
range of P450 conformations and coordination of redox partner
binding J. Biol. Chem 279, 26, 27294-301, 2004.
(PDF)
A more detailed description of PMB and the improved CNS
routines included in pmb_bncs.f will be available when our Acta
Cryst. D paper is published.
Best Regards,
Mark A. White
white@xray.utmb.edu
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DOWNLOADS
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Image and data processing programs - from our web-server
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PMB_CNS_utils.tar.gz
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CNS utilities. Last updated Sept. 26, 2006. A typical
installation will be placed in /usr/local/PMB (cd
/usr/local ; tar -xzvf PMB_CNS_utils.tar.gz). Then
add these lines to your .cshrc (/etc/csh.chrc) files:
setenv
PMB_HOME /usr/local/PMB/
setenv
PMB_BIN $PMB_HOME/linux #OR#
setenv
PMB_BIN $PMB_HOME/irix
The instructions on how to recompile CNS with the new
restraint routines are located in the file:
/.../PMB/CNS/other/pmb_bncs.f
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PMB_BRUKER_utils.tar.gz
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Bruker image and data processing
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PMB_DIP2030_utils.tar.gz
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Macscience calibration utility
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PMB_HKL_utils.tar.gz
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HKL utilities
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INDEX
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An index of programs and utilities in PMB
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pmb_sca2cns |
pmb_CNS |
pmb_refine |
pmb_cns2phs |
pmb_start |
pmb_resolve |
pmb_check |
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PROGRAM DESCRIPTIONS
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The most current versions are installed on our main server in
$PMB_HOME
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pmb_sca2cns
scalepack.sca
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This program converts a SCALEPACK merged HKL file into a CNS
format CV file with a 5% test set. The test set is picked using a
THIN SHELL algorithm, which is prefered when there is NCS. The
files Fobs.o.cv and Fobs.cv are also generated. This utility also
prints a $PMB_HOME/pmb_CNS command line for you to cut and
paste or edit, if the parameters need adjustment. Normally only
the high_res parameter may need to be changed, but check the
syntax of the "Space(Group)" entry.
BUG: Automatically runs pmb_CNS with default values.
Rerun pmb_CNS with revised values to overwrite all CNS input files.
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pmb_CNS a b c
alpha beta gamma "Space(Group)" SG_Number Resolution
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This com file sets up ALL the CNS 1.1 input files using the
given command line inputs. It also copies the necessary PMB
refinement utilities into your current directory. The BINDIVIDUAL
refinement script utilizes the improved B-factor restraints
developed at UTMB by Mark A. White (Acta Cryst D submitted,
2006). Note the syntax of the "SpaceGroup" entry, which
needs to be in quotes to be recognized as a single text string.
{eg. P4(1), P2(1)2(1)2(1), C2(1), P3(1)21 }
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pmb_refine -c5 -g -w2
-n -r -a -b -l -s22 -o -q -d -k -h [MODEL.pdb]
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An automated CNS refinement program with several
command line flags:
FLAGS:
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| -c{#} | (Cycles {opt#cycles}) -Default 1 cycle of refinement
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| -g | (Generate new topology files) - Do this after model building (1)
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| -w{#} | (pick waters {opt#rounds}) - Default 1 round water pick
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| -n | (NCS-shake) - Relaxes NCS restraints for 1 round: "NCS Annealing"
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| -r | (Rigid body refinement) - Normally only used after MR
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| -a | (Simulated Annealing) - Do this with your initial models! (*See pmb_param.inp)
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| -b | (Use H-bond restraints) - For low resolution models (*See pmb_param.inp)
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| -l | (LocalScale OFF flag) - Turns OFF local scaling: PHS files are still generated (2)
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| -s{#} | (Stereochem optimize ) - Optimize bond rmsd to Engh & Huber (*See pmb_param.inp) (3)
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| -o | (A composit Omit Map) - Generate a Composit Omit Map after refinement
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| -q | (Occupancy refinement) - qindividual of selected atoms!
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| -d{%} | (Density modification) - Use RESOLVE to generate a MAP (CCP4) (4)!
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| -k | (ChecK structure) - Use PROCHECK & SFCHECK to check model(CCP4) (4)!
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| -h | (HELP) - View this help message
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Each refinement cycle continues until the freeR value stops
decreasing. This routine utilizes the Czerwinski/Matthews/Hynes
local scaling program to correct for absorption and anisotropic
scattering. It generates an XtalView format PHS file for generating a “map” in xfit or
COOT. The MTZ file new_sa.mtz generated with the -d flag (using pmb_resolve) is recommended for use in COOT.
(1) Run ./pmb_start on your rebuilt model OR specify your MODEL.pdb as the last entry on the command line.
(2) Local scaling should be turned off when the model is incomplete (<80%).
(3) See pmb_param.inp for bond_trgt and refined wa_scale value. Enter 0 to
automatically determine or a bond_trgt value in thousanths of an A (3-25). A
negative value will reset the wa_scale to CNS defaults.
(4) This option requires CCP4! RESOLVE: Input %Solvent or else let CNS determine.
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pmb_cns2phs
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A com file which launches the Czerwinski/Matthews/Hynes local
scaling program pmb_cns2phs.I65, written in FORTRAN. This program
uses the output of the CNS script FoFc_calc.inp (fo.sfo.fc.fob),
which calculates Fc, Fbulk and phases, to produce an XtalView PHS
format file (pmb_lscale.phs) and a corrected Fobs.cv
(fobs_lscale.fob) file. The inclusion of the local scaling
correction and bulk solvent component produces superior quality
maps!
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pmb_start PDB_file
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Configures your PDB file for generate to create the
connectivity and stereo chemical restraints list. This splits
your PDB file into the necessary components for generate.inp:
start.protein.pdb, start.ion.pdb, start.ligand.pdb, and start.water.pdb.
The start.ion.pdb and start.ligand.pdb files may need manual
editing to insert the necessary TER cards between each ion or
ligand. The pmb_start com file may be edited to do this
automatically for you.
For example this the line to parse the TRIS (TRS) ligand, and automatically add the TER
card after the last ATOM of each molecule "O3 TRS":
awk '/ TRS / {print $0 }; /O3 TRS/{printf"TER\n"}' $1 >> start.ligand.pdb
This function is now called if you specify the PDB file at the end of the \"pmb_refine -g\" command.
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pmb_resolve
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Create a solvent-flipped map (CCP4+RESOLVE). This runs
RESOLVE using your latest model (minimize.pdb) and phases (pmb_lscale.phs).
The MTZ files new_sa.mtz and resolve.mtz generated by pmb_resolve are
recommended for use in COOT. This script is run after refinement with the
pmb_refine -d flag.
BUG: Requires CCP4.
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pmb_check
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Check the Quality of your Model (CCP4) This runs both
PROCHECK and SFCHECK on your latest model (minimize.pdb). This script is run after refinement with the
pmb_refine -k flag.
BUG: Requires CCP4.
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File Naming Conventions
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generate.mtz(pdb), minimize.pdb, bindividual.pdb
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The output files of generate.inp, minimize.inp and
bindividual.inp. They are used as the input files for iterative
minimization/b-factor refinement. The pmb_param.inp
file can override the defaults set in these input files:
(minimize, bindividual, anneal)
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Fobs.o.cv, Fobs.cv
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The ORIGINAL CV format data file, and the locally scaled file
used by most refinement scripts.
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start.pdb, start.ion.pdb, start.ligand.pdb, start.water.pdb
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The input files for generate containing your protein model,
the ions, any ligand, and the waters.
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ligand.top, ligand.param
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These ligand parameter and topology files must exist in your
working directory. They may be empty if you do not have a ligand.
(Look in $PMB_HOME/CNS/other for some examples)
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HOW TO
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A roughly cronological order of how to use the PMB utilities
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WHAT TO DO
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HOW TO DO IT.
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Convert Scalepack to CNS
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Run $PMB_BIN/pmb_sca2cns ScalePack.sca to generate your
Fobs.cv file. This utility also copies the output file
"ScalePack.sca.cv" to the two required CV files for
you:Fobs.o.cv and Fobs.cv
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Make the CNS input files
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Run $PMB_HOME/pmb_CNS a b c alpha beta gamma “S(G)”
SG_No. Res to automatically produce the required CNS
input files and copy all the PMB utilities into your current
directory.
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Set up PDB for CNS
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Then run "pmb_start My_Model.pdb" to set up
your CNS input models. The start.ion.pdb file may need manual
editing to insert the necessary TER cards between each ion. The script
pmb_start
may be edited to add your ligand to the list of automatically recognized ones:
For example this the line to parse the TRIS (TRS) ligand, and automatically add the TER
card after the last ATOM of each molecule "O3 TRS":
awk '/ TRS / {print $0 }; /O3 TRS/{printf"TER\n"}' $1 >> start.ligand.pdb
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Refine your model in CNS
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To refine the model and generate a map run: "pmb_refine
-g |tee LogFile.log" The pmb_refine program uses the
current directory name as the PROJECT name. It creates data and
log files with a date/project stamp for easy project management.
The pmb_param.inp file can
override the defaults set in these input files: (minimize,
bindividual, anneal). This program has many flags to modify its
behavior. To see the current list of flags type: pmb_refine -h
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Build the Model
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XtalView may be run using the "sharefonts;xtalmgr &" command.
You will need to create a project name and crystal
data entry from the XTALMGR menu before using XFIT "xfit
minimize.pdb pmb_lscale.phs" to examine your model there
are links to local copies of the XtalView HowTo webpages on our
web-server under SOFTWARE.
To use COOT for your model building it is recommended that you run pmb_resolve
in order to generate a MTZ file (new_sa.mtz or resolve.mtz).
(Use the -d flag in pmb_refine)
COOT can display PHS files, but there is a problem using the resulting map with
COOT's refinement tools.
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Use NCS and Solvent Flattening in RESOLVE/CCP4
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Edit pmb_resolve to have the correct CELL and SG
number. Pick suitable residues to use as the basis of NCS and
edit the default selection criteria accordingly. Note that you do
not want too many nor too few atoms to be selected. Note that
this script requires that the model has been refined at least
once in order to generate PHIC.
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EXAMPLES
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WHAT TO DO
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A cut and paste example of how to do it.
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Convert Scalepack to CNS CV
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$PMB_BIN/pmb_sca2cns My_Data.sca
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Set up files for CNS
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$PMB_HOME/pmb_CNS 47.812 47.812 62.134 90.000 90.000
90.000 "P4(1)" 76 1.7
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Prepare PDB model for CNS
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pmb_start 1STN.pdb
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Refine your model in CNS
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pmb_refine -g -r -a -s 1STN.pdb |tee MMDDHH_My_Project_log
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Build the Model in XTALVIEW
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sharefonts;xtalmgr &
xfit minimize.pdb pmb_lscale.phs
xfit MMDDHHx.Project.pdb MMDDHHx.Project.phs
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Use NCS and Solvent Flattening in RESOLVE
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pmb_resolve
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Mark A.
White, white@xray.utmb.edu
X-RAY | SCSB
| UTMB
Department of Biochemistry and Molecular Biology
© 2001,2002,2003,2004,2005
UTMB | Disclaimer
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