Program : FLOOD
Version : 981109
Author : Gerard J. Kleywegt, 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 : fill a cavity with solvent molecules
Package : VOIDOO
Reference(s) for this program:
* 1 * G.J. Kleywegt & T.A. Jones (1993). Biomacromolecular Speleology. CCP4/ESF-EACBM Newsletter on Protein Crystallography 29, November 1993, pp. 26-28. [http://alpha2.bmc.uu.se/usf/factory_2.html]
* 2 * G.J. Kleywegt & T.A. Jones (1994). Detection, delineation, measurement and display of cavities in macromolecular structures. Acta Cryst D50, 178-185. [http://www.iucr.ac.uk/journals/acta/tocs/actad/1994/actad5002.html]
* 3 * G.J. Kleywegt & T.A. Jones (1999 ?). Chapter 25.2.6. O and associated programs. Int. Tables for Crystallography, Volume F. To be published.
Version 0.1 @ 930930 - first version & documentation
Version 0.2 @ 931007 - fixed bug in mask reading
Version 1.0 @ 931117 - add END record to output PDB files
960415 - 1.0.2 - minor bug fixes
981030 - 1.1 - changed such that grid and cell axes no longer
have to be identical for X, Y, and Z; cell
angles must still all be 90 degrees, though;
changed default for HOH oxygen name from " O1 "
to " O "; added instructions on how to fill
a molecular envelope (mask) with water molecules
981109 - 1.1.1 - changed maximum mask size to 6 MWord
FLOOD is VOIDOO's little sister. With FLOOD you can take
a cavity (in the form of an EZD file, for example) and find
out how many solvent molecule probes you can put inside
the cavity.
An UPPER estimate of this number is obtained by dividing
the volume of the Vanderwaals or the probe-occupied cavity
by the volume of one probe sphere.
A LOWER estimate is obtained by running FLOOD using your
probe-ACCESSIBLE cavity.
Before using FLOOD, you must run VOIDOO in order to obtain an EZD file (for example) containing a mould of your cavity.
Example of a VOIDOO run prior to running FLOOD:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ... Type of calculation (C/V/R) ? (C) Do you want extensive output ? (N) ... Library file ? (cavity.lib) ../cavity.lib ... PDB file name ? (in.pdb) m26.pdb ... Primary grid spacing (A) ? ( 1.000) Probe radius (1.4 A for water) ? ( 1.400) ... Nr of detection cycles ? ( 10) Growth factor for Vanderwaals radii ? ( 1.100) Min size of "real" cavities (voxels) ? ( 1) 5 Are you looking for a specific cavity ? (N) y Enter coordinates of a cavity point : ( 0.000 0.000 0.000) 17.069 4.685 -1.182 Do you want a MASK file ? (N) LOG file name ? (cavity.log) Do you want to refine the cavities ? (Y) Nr of volume-refinement cycles ? ( 10) You may calculate one of these type of cavity volumes: (V) Vanderwaals: not occupied by the molecule (A) Probe-accessible: available to the probe centre (O) Probe-occupied: occupied by rolling probe Type of cavity volume (V/A/O) ? (A) Grid-shrink factor ? ( 0.900) Min size of secondary grid ? ( 10) Convergence criterion (A3) ? ( 0.100) Convergence criterion (%) ? ( 0.100) Create protein-surface plot file ? (N) Do you want plot files ? (Y) First part of plot file names ? (cavity) Grid for plot files ? ( 0.700) 0.35 You may choose from the following types of graphical representations for your cavities: E * generate EZD files N * generate New-EZD files D * draw dots for all cavity points 3 * 3-sweep contour (fairly quick) 1 * 1-sweep contour (quick and dirty) C * connect all surface points (fast/big objects) T * tiles (ie, poly-triangles; not implemented yet) Graphical representation (C/1/3/D/T/E/N)? (E) ... NEW CAVITY ! Nr of points : ( 171) Zero-order volume : ( 1.710E+02) ... >>> CONVERGENCE <<<Last change (A3/%) : ( 1.159E-01 6.626E-02) Centre of cavity gravity 17.069 4.685 -1.182 Nr of volume calculations : ( 3) Average volume (A3) : ( 1.736E+02) Volume corresponds to a sphere of radius (A) : ( 3.461E+00) Standard deviation (A3) : ( 1.839E+00)
Looking for atoms inside this cavity ... Inside > C2 RTL 200 @ 16.591 8.960 1.071 ... Inside > C20 RTL 200 @ 16.235 -0.847 -4.081 Inside > O1 HOH 230 @ 19.829 0.266 -4.738 Nr found : ( 18)
Looking for atoms lining this cavity ... Nr of candidates : ( 346) Lining > CE MET 10 @ 10.344 2.937 3.204 Lining > ND2 ASN 13 @ 12.907 2.627 6.205 ... Lining > NE2 GLN 128 @ 13.639 0.922 2.746 Lining > CZ PHE 130 @ 9.311 1.843 -0.235 Nr found : ( 110)
Nr of plot grid points : ( 42 53 47) Setting up grid ... Nr of points in grid : ( 104622) Not the protein : ( 5794) The protein itself : ( 98828) 23 CPU total/user/sys : 11.9 11.6 0.3 Nr of points "zapped" : ( 4049) Nr of points "zapped" for plot : ( 4049) Volume per voxel (A3) : ( 4.287E-02) Cavity volume on plot grid (A3) : ( 1.736E+02) Volume corresponds to a sphere of radius (A) : ( 3.461E+00) 33 CPU total/user/sys : 4.9 4.8 0.1
Summary : Nr of cavities found : ( 1) Nr of original grid points in cavities : ( 171) Total cavity volume : ( 1.748E+02) ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Note that we have calculated the probe-accessible cavity, creating
an EZD file on a grid of 0.35 A, which is 1/4 of the probe radius
(1.4 A for a water molecule) ! If you ensure that :
{ probe_radius / plot_file_grid_spacing }
is an integer number, then this will improve FLOOD's ability
to pack your solvent molecules as tightly as possible.
VOIDOO has created the following files for us:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- 2 -rw-r--r-- 1 gerard 601 Sep 30 1993 cavity_1.omac 211 -rw-r--r-- 1 gerard 107592 Sep 30 1993 cavity_1.ezd 21 -rw-r--r-- 1 gerard 10646 Sep 30 1993 cavity.log ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----*** FLOOD *** FLOOD *** FLOOD *** FLOOD *** FLOOD *** FLOOD *** FLOOD ***
Version - 930930/0.1 (C) 1993 - Gerard J. Kleywegt, Dept. Mol. Biology, BMC, Uppsala (S) User I/O - routines courtesy of Rolf Boelens, Univ. of Utrecht (NL) Others - T.A. Jones, G. Bricogne, Rams & W.A. Hendrickson Others - W. Kabsch, CCP4, PROTEIN, etc. etc.
Started - Thu Sep 30 22:22:32 1993 User - gerard Mode - interactive Host - rigel ProcID - 2747 Tty - /dev/ttyq0
*** FLOOD *** FLOOD *** FLOOD *** FLOOD *** FLOOD *** FLOOD *** FLOOD ***
Max size of cavity map : ( 4194304) Max nr of solvent molecules : ( 50000) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Read E(zd), N(ew-ezd) or M(ask) ? (E) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Enter the type of file produced by VOIDOO
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- File type : (E)Name of cavity file ? (cavity.ezd) cavity_1.ezd ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Enter the name of the cavity file you're interested in
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Name of cavity file : (cavity_1.ezd) Read map header Input map : (cavity_1.ezd) Scale constant : ( 1.000E+00) Size 104622 ED min, max, total 0.0000E+00 1.0000E+00 4.0490E+03 ED ave, var, stdev 3.8701E-02 3.7203E-02 1.9288E-01Parameters as read from the map file Origin ...................... 29 -13 -27 Extent ...................... 42 53 47 Grid ........................ 100 100 100 Cell axes ................... 35.00 35.00 35.00 Cell angles ................. 90.00 90.00 90.00 UVW (fast, medium, slow) .... Y X Z
Map read okay Nr of points in map : ( 104622) Nr of grid points in cavity : ( 4049) Cell volume : ( 4.288E+04) Voxel volume : ( 4.287E-02) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
After reading the map, the following is checked:
* was the map read okay ?
* is the number of grid points identical in all three
directions ?
* are the cell axes identical in all three directions ?
* are all three cell angles equal to 90 degrees ?
* are all points set to either ZERO or ONE
These checks are done to make sure that you are really feeding
FLOOD a cavity map created by VOIDOO; if so, there shouldn't
be any problems.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Radius for solvent molecule ? ( 1.400) 1.39 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Enter a number which is equal to OR slightly smaller than the probe radius you used in VOIDOO
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Radius for solvent molecule : ( 1.390) Volume of one solvent mol : ( 11.249)Output solvent PDB file ? (sol.pdb) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The optimal set of solvent molecules will be written to a PDB file; enter the name for this file
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Output solvent PDB file : (sol.pdb)Solvent molecule name in O ? (SOLV) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
FLOOD will create an O macro; enter a name for the solvent molecule inside O
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Solvent molecule name in O : (SOLV)Solvent residue name ? (HOH) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Enter the residue name for your solvent molecules (e.g, HOH, WAT, SOL, SUL, ..)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Solvent residue name : (HOH)Solvent atom name ? ( O1) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Enter the name of the central atom in your solvent molecules; note that the first TWO characters must be the name of the chemical element (e.g., ' C', ' S', ' O')
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Solvent atom name : ( O1)Nr of first solvent residue ? ( 500) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This determines the numbering of the solvent molecules (in this case, one would get HOH 500, HOH 501, HOH 502, ...)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Nr of first solvent residue : ( 500)Output O macro file ? (sol.omac) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Enter the name of the O macro file that FLOOD will create for you
Now, FLOOD will make SIX attempts at packing as many as possible
solvent molecules as tightly as possible.
The major simplifying limitation in FLOOD is that solvent
molecule centres may only lie on cavity grid points (this
explains why it is beneficial to have a probe radius which
is an integer multiple of the grid spacing !).
FLOOD will try all six combinations of varying X, Y and Z
fastest, intermediate and slowest. Since the grid is discrete,
this may (and usually will) give different results. The one
that yields the highest number of placed solvent molecules
wins.
For each order, it loops over all grid points inside the cavity.
If it finds one which is labelled '1', it checks if there is no
previously placed solvent molecule within 2*radius of that point.
If this is successful, a solvent molecule is added, and all grid
points with 'radius' are 'zapped' (set to '-1'). Then it will
continue its search for grid points labelled '1', etc.
Afterwards, it makes one more round through the grid points, just
in case ...
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Output O macro file : (sol.omac)Trying order XYZ Nr of solvent molecules : ( 23) Total volume of solvent molecules : ( 258.738) Cavity points available : ( 4049) Volume (A3) : ( 173.601) Cavity points occupied by solvent : ( 2087) Volume (A3) : ( 89.480) Utilisation % : ( 51.544)
Trying order XZY Nr of solvent molecules : ( 24) Total volume of solvent molecules : ( 269.988) Cavity points available : ( 4049) Volume (A3) : ( 173.601) Cavity points occupied by solvent : ( 2121) Volume (A3) : ( 90.938) Utilisation % : ( 52.383)
Trying order YZX Nr of solvent molecules : ( 24) Trying order YXZ Nr of solvent molecules : ( 24) Trying order ZXY Nr of solvent molecules : ( 23) Trying order ZYX Nr of solvent molecules : ( 26) Total volume of solvent molecules : ( 292.487) Cavity points available : ( 4049) Volume (A3) : ( 173.601) Cavity points occupied by solvent : ( 2304) Volume (A3) : ( 98.784) Utilisation % : ( 56.903) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Order XYZ gave 23 solvent molecules initially. Order XZY gave
24 and the initial PDB file was overwritten. Details regarding
the utilisation of the cavity volume are printed.
Orders YZX, YXZ and ZXY gave no improvement in the number of
placeable solvent molecules, but the last order, ZYX, gave 26
possible solvent molecules. Again, the PDB file is overwritten
and details are printed.
Now, FLOOD writes the O macro and voila.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----Max nr of solvent molecules : ( 26)
*** FLOOD *** FLOOD *** FLOOD *** FLOOD *** FLOOD *** FLOOD *** FLOOD ***
Version - 930930/0.1 Started - Thu Sep 30 22:22:32 1993 Stopped - Thu Sep 30 22:23:16 1993
CPU-time taken : User - 12.8 Sys - 0.3 Total - 13.1
*** FLOOD *** FLOOD *** FLOOD *** FLOOD *** FLOOD *** FLOOD *** FLOOD ***
>>> This program is (C) 1993, GJ Kleywegt & TA Jones <<< E-mail: "gerard@xray.bmc.uu.se" or "alwyn@xray.bmc.uu.se"
*** FLOOD *** FLOOD *** FLOOD *** FLOOD *** FLOOD *** FLOOD *** FLOOD ***
STOP ... Toodle pip ... statement executed 12.777u 0.379s 0:44.04 29.8% 0+0k 2+4io 9pf+0w ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
FLOOD gave us the following files:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- % 194 gerard rigel 23:06:19 cavity/crbpm26 > ls sol* 1 -rw-r--r-- 1 gerard 209 Sep 30 1993 sol.omac 4 -rw-r--r-- 1 gerard 1824 Sep 30 1993 sol.pdb ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- % 195 gerard rigel 23:06:19 cavity/crbpm26 > cat sol.pdb REMARK Created by FLOOD V. 930930/0.1 at Thu Sep 30 22:23:15 1993 for user gerard ATOM 1 O1 HOH 500 14.700 2.800 -7.350 1.00 20.00 ATOM 2 O1 HOH 501 14.000 -0.350 -7.000 1.00 20.00 ATOM 3 O1 HOH 502 18.550 0.000 -6.300 1.00 20.00 ATOM 4 O1 HOH 503 15.750 1.050 -5.250 1.00 20.00 ATOM 5 O1 HOH 504 15.400 -1.750 -4.200 1.00 20.00 ATOM 6 O1 HOH 505 19.600 -1.050 -3.850 1.00 20.00 ATOM 7 O1 HOH 506 18.200 1.400 -3.850 1.00 20.00 ATOM 8 O1 HOH 507 16.100 3.500 -3.500 1.00 20.00 ATOM 9 O1 HOH 508 19.600 8.400 -3.500 1.00 20.00 ATOM 10 O1 HOH 509 15.050 1.050 -2.450 1.00 20.00 ATOM 11 O1 HOH 510 15.400 7.700 -2.450 1.00 20.00 ATOM 12 O1 HOH 511 17.500 5.600 -2.100 1.00 20.00 ATOM 13 O1 HOH 512 19.600 1.750 -1.400 1.00 20.00 ATOM 14 O1 HOH 513 17.850 8.400 -1.050 1.00 20.00 ATOM 15 O1 HOH 514 16.800 2.450 -0.700 1.00 20.00 ATOM 16 O1 HOH 515 13.300 2.800 -0.350 1.00 20.00 ATOM 17 O1 HOH 516 15.400 4.900 -0.350 1.00 20.00 ATOM 18 O1 HOH 517 18.900 4.200 0.000 1.00 20.00 ATOM 19 O1 HOH 518 14.000 8.050 0.000 1.00 20.00 ATOM 20 O1 HOH 519 20.300 6.650 0.350 1.00 20.00 ATOM 21 O1 HOH 520 19.950 9.450 0.700 1.00 20.00 ATOM 22 O1 HOH 521 16.100 9.800 0.700 1.00 20.00 ATOM 23 O1 HOH 522 17.150 6.650 1.050 1.00 20.00 ATOM 24 O1 HOH 523 14.000 4.200 2.100 1.00 20.00 ATOM 25 O1 HOH 524 14.350 7.000 2.800 1.00 20.00 ATOM 26 O1 HOH 525 20.650 7.700 3.150 1.00 20.00 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- % 196 gerard rigel 23:06:19 cavity/crbpm26 > cat sol.omac ! Created by FLOOD V. 930930/0.1 at Thu Sep 30 22:23:15 1993 for user gerard s_a_i sol.pdb SOLV mol SOLV zo ; end centre_zone SOLV 500 525 db_set_data .cpk_radii 8 8 1.390000 sketch_cpk SOLV bell message Done ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This macro will:
* read the solvent PDB file
* draw the solvent molecule
* centre at its centre-of-gravity
* set the appropriate CPK radius, PROVIDED the central chemical
element was one of ' C', ' N', ' O' or ' S' (if not, ALL CPK
radii are set to your probe radius !!)
* make a CPK model of your solvent molecule
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ... MAPMAN > read m1 cavity_1.ezd ezd Read header Input map : (cavity_1.ezd) Scale constant : ( 1.000E+00) Size 104622 ED min, max, total 0.0000E+00 1.0000E+00 4.0490E+03 ED ave, var, stdev 3.8701E-02 3.7203E-02 1.9288E-01Parameters as read from the map file Origin ...................... 29 -13 -27 Extent ...................... 42 53 47 Grid ........................ 100 100 100 Cell axes ................... 35.00 35.00 35.00 Cell angles ................. 90.00 90.00 90.00 UVW (fast, medium, slow) .... Y X Z
Header done Sum of density in map : ( 4.049E+03) Map read into memory CPU total/user/sys : 1.9 1.8 0.2 MAPMAN > mappage m1 cav.map Opening DSN6 file : (cav.map) Big-endian machine; will NOT swap bytes Scale constant for cell : ( 80) Pages along X, Y and Z : ( 6 7 6) Nr of records written : ( 253) CPU total/user/sys : 1.3 1.2 0.0 MAPMAN > quit ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ... O > @cavity_1.omac O > Macro in computer file-system. O > Cavity-molecule name ? m26 O > O > O > O > @sol.omac O > Macro in computer file-system. Sam> File type is PDB Sam> Database compressed. Sam> Space for 61312 atoms Sam> Space for 10000 residues Sam> Molecule SOLV contained 26 residues and 26 atoms O > O > As4> SOLV 500 525 SOLV As4> Centering on zone from 500 to 525 O > O > Sketch> SOLV Sketch> ....making the object O > O > map_fil cav.map map_obj cav O > map_par 30 30 30 Map> Define contour level [ 0.100]: 0.01 Map> Colour? [blue]: Map> Define map intensity, fore & aft [ 0.50 0.00]: Map> Define line type [5]: O > ma_ac ma_dr setransp called max 255.000000 min 0.000000 contour value is : 2.550000 number of points : 3680 number of triangles : 7348 ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Hence, with a minimum of effort you now have the following on the screen:
(1) INS_1 - an object containing residues which lie (partly) inside
your cavity
(2) LIN_1 - an object containing all residues which have at least one
atom lining the cavity
(3) SOLV - the solvent molecules placed by FLOOD
(4) CPK_SOLV - a CPK model of these solvent molecules
(5) CAV - a semi-transparent (SGI only) map of your cavity
The procedure to fill a molecular envelope (mask) with atoms is very similar to the normal use of FLOOD:
- generate a mask
- make absolutely sure that the cell on which you generate the mask has only 90 degree angles. If this is not the case, transfer the mask to an orthogonal dummy grid in MAMA using the NEw commands; e.g., use a cell of 100 100 100, 90 90 90, select an appropriate grid (e.g., 100 100 100 would give a 1 Å grid spacing), and then use NEw UNit_cell to do the transfer.
- since FLOOD assumes that the "cavity" is probe-accessible, you may want to use the CUt command in MAMA to peel off the outer layer of the mask
- save the mask
- run FLOOD as usual (see example below)
- start up O; read and draw the mask; execute the O macro created by FLOOD
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Read E(zd), N(ew-ezd) or M(ask) ? (E) M File type : (M)Name of cavity file ? (cavity.mask) p2.mask Name of cavity file : (p2.mask) Read map header Input map : (p2.mask) Reading mask (O format) Format : compressed Grid points : ( 360594) Stretches : ( 1458) Mask points : ( 30854) Number of points in mask : ( 30854)
Parameters as read from the map file Origin ...................... 21 34 -1 Extent ...................... 67 69 78 Grid ........................ 100 110 64 Cell axes ................... 91.80 99.50 56.50 Cell angles ................. 90.00 90.00 90.00 UVW (fast, medium, slow) .... Y X Z
Map read okay Closing MASK on unit : ( 11) ERROR --- Grid not the same for x,y,z ERROR --- Cell axes not the same for x,y,z Nr of points in map : ( 360594) Nr of grid points in cavity : ( 30854) Cell volume : ( 5.161E+05) Voxel volume : ( 7.331E-01)
Radius for solvent molecule ? ( 1.400) Radius for solvent molecule : ( 1.400) Volume of one solvent mol : ( 11.494)
Output solvent PDB file ? (sol.pdb) Output solvent PDB file : (sol.pdb)
Solvent molecule name in O ? (SOLV) Solvent molecule name in O : (SOLV)
Solvent residue name ? (HOH) Solvent residue name : (HOH)
Solvent atom name ? ( O) Solvent atom name : ( O)
Nr of first solvent residue ? ( 500) 1 Nr of first solvent residue : ( 1)
Output O macro file ? (sol.omac) Output O macro file : (sol.omac)
Trying order XYZ Nr of solvent molecules : ( 982) Total volume of solvent molecules : ( 11287.147) Cavity points available : ( 30854) Volume (A3) : ( 22617.941) Cavity points occupied by solvent : ( 16420) Volume (A3) : ( 12036.903) Utilisation % : ( 53.218)
Trying order XZY Nr of solvent molecules : ( 966) Trying order YZX Nr of solvent molecules : ( 993) Total volume of solvent molecules : ( 11413.582) Cavity points available : ( 30854) Volume (A3) : ( 22617.941) Cavity points occupied by solvent : ( 16626) Volume (A3) : ( 12187.914) Utilisation % : ( 53.886)
Trying order YXZ Nr of solvent molecules : ( 972) Trying order ZXY Nr of solvent molecules : ( 991) Trying order ZYX Nr of solvent molecules : ( 975)
Max nr of solvent molecules : ( 993) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
None, at present.
Created at Fri Dec 18 19:42:11 1998
by MAN2HTML version 971024/1.6