|Data Analysis||Parameter Preparation|
|Improving MCCE runs||Exporting and Debug|
All programs are located at /home/mcce/mcce1.0/bin unless otherwise stated.
MCCE web analysis tool uses mean field approach to eastimate residue-residue interaction. The breakdown analysis helps understanding why a conformer is occupied and why a residue is ionized.
MFE approximation of residue ionization energy. This is the command line version of the web-interfaced analysis tool.
Synopsismfe.py res_id titration_point [pH_cutoff]
res_id is the identification string of an ionizable residue, as appeared in file "pK.out"
titration_point is the titration point that mfe is carried out. If this number is between two titration values of Monte Carlo simulations, a linear interpolation will be performed.
pH_cutoff is the cutoff value in unit pH of printing residue pairwise interaction. It is an optional argument, without which all pairwise interactions will be printed out.
This program measures distance of each atom to [x,y,z], and print out those pdb lines within the threshold.
Synopsiscloseup pdbfile x y z threshold
pdbfile is your input pdb file
x y z are coordinate of a point where distances are measured, you can copy x y z from the pdb line and paste it here
threshold is the distance limit of printing the atoms. Only those within this threshold are printed out.
The serial number field of an ATOM line in the output will be replaced by the atom distance.
This program prints out the RMSD between the specified conformer and other conformers in the same residue.
Synopsisres_confs.py IDstring1 [IDstring2 [IDstring3 ...]]
IDstring1 is the identification string that appeared in the ATOM line of that conformer in step3_out.pdb
IDstring2 is optional identification string to help uniquely identify a conformer
IDstring3 and more are more optional identification string to help uniquely identify a conformer
This program expects file "step3_out.pdb" so it must be called in a working directory. The ID strings are not sensitive to the order.
Exampleres_confs.py res_confs.py GLU A0073_051
This program finds the residues with strong interations.
Synopsisgetinfo residue [threshold]
This program is trying to guess coupled residues for the input residue, you need to run it in the directory with head3.lst and opp files in energies/.
residue: the residue you want to analyze, it can be the residue number (for example: 212) or it can be a string defining the residue (for example: L0212, GLUL0212 etc., L212 would not be recognized in this case)
threshold: energy threshold for deciding if two residues are coupled (in pK units), default value is 2.
This program reads in step3_out.pdb and fort.38, then remove all unoccupied conformers except the native conformers which have "O000" in the history string. The resulted ATOM lines are printed out, which can be redirected to file step2_out.pdb. The purpose is to use this step2_out.pdb as the input of step3 for better dielectric boundary in DelPhi calculation.
This program expects file "step3_out.pdb" so it must be called in a working directory.
Examplereduce_conf.py > step2_out.pdb
This program merges several mcce formatted pdb files into one, duplicated conformers are deleted.
Synopsismerge_pdb -i input_list_file -o output.pdb -p param_directory
-i input_list_file, input_list_flie is a text file with a list of pdb files you want to merge, each line has one pdb file
-o output.pdb, output.pdb is the merged pdb file
-p param_directory, param_directory is the location of the parameter directory, if you have extra residues need new.tpl, put new.tpl in the local directory where this program runs
This program takes head3.lst and opp files under energies/ directory as input and complete the opp file if they are asymmetric.
-d: If you have this flag in the command line, and opp file has extra line than head3.lst (for example some conformers in step2_out.pdb has been deleted), then those extra conformers in opp file will be deleted. Otherwise, if -d is not in the command line, then those extra line are kept at the end of the opp file, but not deleted.
This program updates the derived entries (CONFLIST, NATOM, IATOM, and ATOMNAME) of a parameter (tpl) file from the connectivity table.
Synopsismk_iatom input.tpl output.tpl
input.tpl is the input tpl file.
output.tpl is the output tpl file.
unpdb is unformatted pdb file such as fort.13.
column_in_fort.38 is the column number counted from 1 in the file "fort.38".
The program reads in fort.38 and step3_out.pdb, then picks up the backbone atoms and the most occupied conformer at the pH/Eh specified by column_in_fort.38.
[-t threshold] : threshold for printing, default = 0.05
[-hl n_headline] : skip first n lines, default = 1
[-hc n_headcolumn] : using first n columns for matching lines between two files
[-cf n_column_per_field] : use every n column as one field to get numbers, default = delimited by space
[-c column_file1 column_file2] : only compare one defined column from each file
to compare two sum_crg.out:cmp_yf.py sum_crg.out.1 sum_crg.out.2
to compare two fort.38:cmp_yf.py fort.38.1 fort.38.2 -hc 14
to compare two opp files:cmp_yf.py file1.opp file2.opp -hl 0 -hc 20 -t 1.0
This program reduces conformers of step2_out.pdb by eliminating "similar" conformers. Similar conformers are defined by geometry, vdw pairwise interaction vector and ele pairwise interaction vector. If the atom distance difference in Angstroms, the vdw and ele pairwise interactions in Kcal/Mole of two conformers are all under the threshold values, then the second conformer is a "similar" conformer and will be deleted. Note any big vdw interaction (> 50) all treated as identical values.
Synopsisprune [geometry ele vdw]
The first line is the threshold values of pruning and the number of deleted conformers. The rest is a mcce pdb file which can be used as a new step2_out.pdb. This program will take a few minutes for a 2000-conformer step2_out.pdb.
geometry: threshold of geometry difference, default = 0.5
ele: threshold of electrostatic pairwise interaction difference, default = 1.0
vdw: threshold of vdw pairwise interaction difference, default = 8.0. In Monte Carlo sampling the vdw is scaled down by the protein dielectric constant. So 8.0 here is actually 1.0 viewed by Monte Carlo step when epsilon is 8.
to prune step2_out.pdb and write the result to a file:prune 2 1 8 > temp.pdb
to do it with default valuesprune > temp.pdb
Type the following at unix prompt "perl cutnmr.pl". It will prompt you for your pdb file that contains many structures. Then it will make individual files out of them.