Program : PROF
Version : 961212
Author : Gerard J. Kleywegt & T. Alwyn Jones,
Dept. of Cell and Molecular Biology,
Uppsala University, Biomedical Centre, Box 590,
SE-751 24 Uppsala, SWEDEN
E-mail : gerard@xray.bmc.uu.se
Purpose : generate electron-density profiles
Package : RAVE
Reference(s) for this program:
* 1 * T.A. Jones (1992). A, yaap, asap, @#*? A set of averaging programs. In "Molecular Replacement", edited by E.J. Dodson, S. Gover and W. Wolf. SERC Daresbury Laboratory, Warrington, pp. 91-105.
* 2 * G.J. Kleywegt & T.A. Jones (1994). Halloween ... Masks and Bones. In "From First Map to Final Model", edited by S. Bailey, R. Hubbard and D. Waller. SERC Daresbury Laboratory, Warrington, pp. 59-66.
* 3 * G.J. Kleywegt & R.J. Read (1997). Not your average density. Structure 5, 1557-1569. [http://www4.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=9438862&form=6&db=m&Dopt=r]
* 4 * G.J. Kleywegt & T.A. Jones (2037 ?). Convenient single and multiple crystal real-space averaging. To be published ???
* 5 * G.J. Kleywegt & T.A. Jones (1999 ?). Chapter 25.2.6. O and associated programs. Int. Tables for Crystallography, Volume F. To be published.
0.1 - 961127 - first version
0.2 - 961209 - improvements
0.3 - 961210 - always use 0.5 A grid for profile (use skew-averaging
routine)
0.4 - 961212 - first production version (Uppsala)
PROF is a program to calculate electron-density profiles. It reads a library of rigid fragments (e.g., of amino-acid residues), and for each fragment finds all copies in your model, retrieves their densities, averages them (to yield the "profile map"), and calculates how well each copy's density fits the profile map.
Required input:
- a map in CCP4 format which covers the entire model
- your model in PDB format
- a library file to define the rigid fragments
Output:
- a new map in CCP4 format of the profile density
- a new PDB file of your model, with the B-factors replaced by the
correlation coefficient of the profile density and the local
density, multiplied by 100.
The following shows an example run of the program:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ... *** PROF *** PROF *** PROF *** PROF *** PROF *** PROF *** PROF *** PROF ***Allocate maps of size : ( 10000000) Allocate masks of size : ( 5000000) Allocate mini maps/masks of size : ( 500000) Max nr of atoms in model : ( 10000) Max nr of profile groups : ( 100) Max nr of atoms per group : ( 100) Max nr of occurences : ( 1000) Atom masking radius (A) : ( 1.600)
Input CCP4 map file ? ( ) ../p2ave/p2_10_mola.E Input CCP4 map file : (../p2ave/p2_10_mola.E) Read header Input map : (../p2ave/p2_10_mola.E) ... Name of model PDB file ? (m1.pdb) p2_mola.pdb Name of model PDB file : (p2_mola.pdb) Number of atoms : ( 1039) Nr of H stripped : ( 0)
Name of PROF library file ? (/nfs/public/lib/prof.lib) Name of PROF library file : (/nfs/public/lib/prof.lib) Group : (ALA N CA (C) CB) Group : (ALA (CA) C O) Group : (ARG N CA (C)) ... Group : (VAL (CA) C O) Group : (VAL CB CG1 CG2)
Output CCP4 map file ? (prof.E) Output CCP4 map file : (prof.E)
Output PDB file ? (prof.pdb) Output PDB file : (prof.pdb)
Origin : ( -17 -32 -31) Extent : ( 95 70 62) Calculated map/masksize : ( 412300)
*****************************************
Group : (ALA N CA (C) CB) Nr of map points : ( 317) Average density : ( 1.036E+01) ALA A 22 ... CC = 0.924 ... R = 0.457 ... LSQ-RMSD = 0.015 A ALA A 28 ... CC = 0.872 ... R = 0.385 ... LSQ-RMSD = 0.011 A ALA A 36 ... CC = 0.922 ... R = 0.539 ... LSQ-RMSD = 0.041 A ALA A 75 ... CC = 0.917 ... R = 0.309 ... LSQ-RMSD = 0.018 A ALA A 87 ... CC = 0.842 ... R = 0.489 ... LSQ-RMSD = 0.023 A
...
Group : (VAL CB CG1 CG2) Nr of map points : ( 260) Average density : ( 8.451E+00) VAL A 11 ... CC = 0.824 ... R = 0.450 ... LSQ-RMSD = 0.010 A VAL A 25 ... CC = 0.893 ... R = 0.420 ... LSQ-RMSD = 0.004 A VAL A 40 ... CC = 0.955 ... R = 0.410 ... LSQ-RMSD = 0.002 A VAL A 84 ... CC = 0.971 ... R = 0.474 ... LSQ-RMSD = 0.006 A VAL A 94 ... CC = 0.934 ... R = 0.370 ... LSQ-RMSD = 0.007 A VAL A 109 ... CC = 0.841 ... R = 0.465 ... LSQ-RMSD = 0.011 A VAL A 114 ... CC = 0.980 ... R = 0.332 ... LSQ-RMSD = 0.004 A VAL A 115 ... CC = 0.960 ... R = 0.428 ... LSQ-RMSD = 0.007 A VAL A 122 ... CC = 0.894 ... R = 0.528 ... LSQ-RMSD = 0.005 A VAL A 123 ... CC = 0.786 ... R = 0.682 ... LSQ-RMSD = 0.006 A VAL A 131 ... CC = 0.874 ... R = 0.442 ... LSQ-RMSD = 0.006 A
Stamp : (Created by PROF V. 961212/0.4 at Thu Dec 12 17:52:04 1996 for user gerard) (Q)QOPEN allocated # 1 User: gerard Logical Name: prof.E Status: UNKNOWN Filename: prof.E
File name for output map file on unit 11 : prof.E logical name prof.E
Minimum density in map = -27.00774 Maximum density = 70.51029 Mean density = 0.36923 Rms deviation from mean = 3.26598
Map written out
Writing PDB file with B = CC (group dens, profile dens)
*** PROF *** PROF *** PROF *** PROF *** PROF *** PROF *** PROF *** PROF ***
Version - 961212/0.4 Started - Thu Dec 12 17:51:08 1996 Stopped - Thu Dec 12 17:52:15 1996
CPU-time taken : User - 22.2 Sys - 0.4 Total - 22.6
*** PROF *** PROF *** PROF *** PROF *** PROF *** PROF *** PROF *** PROF *** ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The program lists for each copy of each fragment:
- correlation coefficient between profile and local density
- unscaled R-factor between these two densities
- RMSD for the least-squares superpositioning of the library fragment
and the copy in your model
A high correlation coefficient means that the local density is "typical"; a low correlation coefficient means it is "atypical" (usually, this means that the density is very poor).
A high RMSD means that the geometry of the fragment in your model is poor (the library fragments have virtually ideal Engh & Huber geometry).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Group : (MET (CG SD) CE) Nr of map points : ( 250) Average density : ( 2.501E+01) MET A 20 ... CC = 0.900 ... R = 0.334 ... LSQ-RMSD = 0.021 A MET A 113 ... CC = 0.951 ... R = 0.336 ... LSQ-RMSD = 0.015 A MET A 119 ... CC = 0.655 ... R = 0.418 ... LSQ-RMSD = 0.013 A ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
To view the profile map, do the following:
- mappage the profile map (e.g., with MAPMAN)
- start up O
- read the library in as a molecule (sam_atom_in prof.lib prof pdb)
- draw it and centre on it (mol prof zo ; end ce_zo prof 1 20)
- draw the profile map at the same level at which you contour the original
map of your model that went into PROF
The resulting map shows you what a typical copy of each residue type looks like (of course, if your model contains no histidines, there will be no density for the histidine in the profile map). Because of the averaging process (unless you have only one copy of a residue type in your model), the profile map will usually look better than any individual copy.
To see how well your model fits the profile map, read in the new PDB file produced by PROF and colour-ramp it according to B-factor (sam_atom_in newfile.pdb new mol new pai_ramp atom_b 0 100 red blue). For a good model, one would expect to see a large blue core, with some green at the surface and the occasional yellow or red sidechain pointing into the solvent. Out-of-register errors may be detectable as continuous regions of green/yellow/red. Completely "bogus" models will have green and blue all over the place (as opposed to a blue core with some green on the surface).
The default library contains one copy each of the 20 standard amino acids, with near-ideal Engh & Huber geometry. They are arranged as two 10-residue beta-strands to make it easy to produce 2D plots.
The library file is set up such that it can be read into O as a PDB file. The file may contain any number of REMARK records at the top. Fragments are demarcated by PROFIL and ENDPRO records:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- PROFIL ALA (CA) C O REMARK 2 CA ALA 1 1.678 1.980 -2.775 1.00 20.00 6 ATOM 3 C ALA 1 2.837 2.669 -2.062 1.00 20.00 6 ATOM 4 O ALA 1 4.001 2.456 -2.400 1.00 20.00 8 ENDPRO ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The PROFIL line contains the name of the fragment (free text). The atoms
in each fragment fall into two categories:
- those that are only needed to do the least-squares superpositioning;
these are labelled as REMARK records, but have the same format as
ATOM records (in this way, O will ignore them)
- those that are used for the superpositioning, but are also to be
included in the profile calculations; these are given on ordinary
ATOM records
Some guidelines for generating your own library entries:
- each atom should occur on an ATOM record exactly once (it may occur
on REMARK records more often, or not at all)
- each fragment should be a rigid entity, i.e. there should be no
free conformational torsion angle between any of the atoms, both
those defined with ATOM and those defined with REMARK records
- each fragment should contain at least two ATOM records (ideally,
three or more)
- make sure that all fragments have "ideal" geometry (e.g., Engh & Huber)
For example, a PHE residue gives rise to three rigid fragments:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- PROFIL PHE N CA (C) ATOM 104 N PHE 14 19.250 0.514 0.331 1.00 20.00 7 ATOM 105 CA PHE 14 20.079 -0.097 1.360 1.00 20.00 6 REMARK 106 C PHE 14 20.937 -1.213 0.775 1.00 20.00 6 ENDPRO PROFIL PHE (CA) C O REMARK 105 CA PHE 14 20.079 -0.097 1.360 1.00 20.00 6 ATOM 106 C PHE 14 20.937 -1.213 0.775 1.00 20.00 6 ATOM 107 O PHE 14 22.126 -1.317 1.073 1.00 20.00 8 ENDPRO PROFIL PHE CB CG CD1 CD2 CE1 CE2 CZ ATOM 108 CB PHE 14 19.208 -0.625 2.501 1.00 20.00 6 ATOM 109 CG PHE 14 18.419 0.443 3.202 1.00 20.00 6 ATOM 110 CD1 PHE 14 17.171 0.821 2.735 1.00 20.00 6 ATOM 111 CD2 PHE 14 18.926 1.067 4.328 1.00 20.00 6 ATOM 112 CE1 PHE 14 16.443 1.804 3.379 1.00 20.00 6 ATOM 113 CE2 PHE 14 18.203 2.051 4.977 1.00 20.00 6 ATOM 114 CZ PHE 14 16.960 2.420 4.502 1.00 20.00 6 ENDPRO ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
- the output profile map is always on a fixed, orthogonal grid with a spacing of 0.5 A in all three directions
- the "integration radius" for density around any atom is fixed at 1.6 A
- the algorithm is roughly as follows:
(1) loop over all groups in the library
(2) for each group, generate a mask with a radius of 1.6 A around the
ATOMs on the 0.5 A grid
(3) loop over all copies of the group in the user's model
(4) for each copy, retrieve the appropriate atoms; do a least-squares
superpositioning to get the operator into the user's map; extract
the density around the copy (using a skew-averaging routine to
account for the different grids etc.), and accumulate the profile
density for this group
(5) average the profile density for this group; accumulate the complete
profile density map
(6) loop over all copies of the group again
(7) for each copy, extract the density again, and calculate the correlation
coefficient and unscaled R-factor between the local density and the
profile density; put 100 times the correlation coefficient into the
B-factor field of each ATOM in this copy of the group
(8) adjust the complete profile density map (divide each density value
by the number of times it was set; this is to avoid artefacts due
to overlap of neighbouring fragments)
PROF allocates memory for maps and masks dynamically. This means that you can increase the size of maps and masks that the program can handle on the fly:
1 - through the environment variables MAPSIZE and MASKSIZE (must be in capital letters !), for example put the following in your .cshrc file:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- setenv MAPSIZE 8000000 setenv MASKSIZE 3000000 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
2 - by using command-line arguments MAPSIZE and MASKSIZE (need not be in capitals), for example:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- run prof mapsize 10000000 masksize 5000000 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Note that command-line arguments take precedence over environment variables. So you can set the environment variables in your .cshrc file to "typical" values, and if you have to deal with a map and/or mask which is bigger than that, you can use the command-line argument(s).
If sufficient memory cannot be allocated, the program will print a message and quit. In that case, increase the amount of virtual memory (this will not help, of course, if you try to allocate more memory than can be addressed by your machine (for 32-bit machines, something 2**32-1 bytes, I think), or reduce the size requirements.
PROF needs space for 2 maps and 1 mask, and for 2 "mini-maps" and 2 "mini-masks" which are 10% of the size of a normal mask.
PROF is sensitive to the environment variable CCP4_OPEN. If this variable has *not* been set, you will not be able to create any CCP4 maps. If this happens, the program will abort execution on startup. To fix this, put the following line in your .cshrc file: setenv CCP4_OPEN UNKNOWN
PROF uses the environment variable GKLIB to set the default location of its library file. If you set GKLIB in your .cshrc file to /nfs/public/lib (Uppsala only), the program will always come up with the correct default name for this file.
None, at present.
None that I know of ;-)
Created at Fri Dec 18 19:42:22 1998
by MAN2HTML version 971024/1.6