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[ccp4bb]: question
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Dear Colleagues,
I have a question not related to ccp4. Are there some people who have calculated the cavity volume of a protein using program "Voidoo"?
Recently, I try to calculate the cavity volume of a dimer of T.thermophillus MnSOD with "voidoo". But I can't understand the following output file. Meanwhile, its cavity volume is about 30 angstrom*3 per monomer in a published article. Could anyone tell me wether my results is true or not?
Thanks a lot!
King Lau
liaojt@moon.ibp.ac.cn
ps:
*** VOIDOO ***
- Vanderwaals radii
ELEM N 1.75 C 1.85 O 1.60 S 2.00
ELEM H 1.00 P 2.10 NA 0.95 MG 0.65
ELEM CL 1.80 CA 1.00 MN 1.10 FE 1.10
ELEM ZN 1.20 CD 1.20
ATOM NZ 1.85 TEST 1.00
SPAT TYR OH 1.65 THR OG1 1.65 SER CB 1.92 ASN CB 1.92
SPAT GLN CB 1.92 GLN CG 1.92 LEU CB 1.92 ARG CB 1.92
SPAT ARG CG 1.92 ARG CD 1.92 ILE CG1 1.92 PHE CB 1.92
SPAT TYR CB 1.92 CYS CB 1.92 MET CB 1.92 MET CG 1.92
SPAT HIS CB 1.92 GLU CB 1.92 GLU CG 1.92 ASP CB 1.92
SPAT TRP CB 1.92 LYS CB 1.92 LYS CG 1.92 LYS CD 1.92
SPAT LYS CE 1.92 PRO CB 1.92 PRO CG 1.92 PRO CD 1.92
SPAT ALA CB 2.00 THR CG2 2.00 LEU CD1 2.00 LEU CD2 2.00
SPAT ILE CG2 2.00 ILE CD1 2.00 VAL CG1 2.00 VAL CG2 2.00
SPAT MET CE 2.00
- Residue types
RESI ALA ARG ASN ASP CYS GLN GLU GLY
RESI HIS ILE LEU LYS MET PHE PRO SER
RESI THR TRP TYR VAL CPR CSS CSH PYR
RESI PCA HPR
- PDB file
mds_dimer.pdb
- LOG file
cavity.log
- Plot files
cavity_#.o
- Grid & cavity parameters
Max nr of cavity-detection cycles : 10
Will do detection cycles until first best
Vanderwaals growth factor : 1.050
Probe radius : 1.400
Min nr of voxels in "real" cavities : 5
Max nr of volume-refinement cycles : 10
Will calculate probe-accessible volumes
Will use probe in cavity-volume calculations
Grid shrink factor : 0.900
Min size of secondary grid : 10
Grid for plot files : 0.700
Volume-convergence tolerance (A3) : 0.100
Volume-convergence tolerance (%) : 0.100
Primary grid spacing : 0.500
Grid sizes : 139 133 123
Lower X/Y/Z limits : -9.500 15.000 -34.500
Upper X/Y/Z limits : 59.500 81.000 26.500
No plot file for protein surface will be made
Plot grid spacing : 0.700
Representation: New-EZD
Determining number of cavities
... Cycle 1 | Vdw-factor 1.00000 | Cavities 4
... Cycle 2 | Vdw-factor 1.05000 | Cavities 1
Best Vdw-factor 1.00000 gives 4 cavities
Refining cavity volumes
Cavity
# 1 Starts at 8.500 48.000 -3.500
Cavity box 5.100 13.400 44.600 51.900 -6.900 0.900
Cycle Grid V(vox) #Vox Cavity volume
1 0.50000 0.12500 7 8.75000E-01
2 0.45000 0.09112 10 9.11250E-01
Centre of cavity gravity 9.225 48.465 -3.330
Nr of calcns/average/sigma volume 2 0.893 0.018
Lining > CG2 ILE A 20 @ 6.477 51.101 -3.154
Lining > CD1 ILE A 20 @ 6.481 49.172 -0.934
Lining > CG2 THR A 24 @ 9.408 51.650 -6.164
Lining > SD MET A 25 @ 5.298 48.251 -5.102
Lining > ND1 HIS A 28 @ 10.749 47.235 -6.196
Lining > CE1 HIS A 28 @ 11.763 46.612 -5.629
Lining > CE2 PHE A 86 @ 9.775 45.099 -2.386
Lining > CZ PHE A 86 @ 9.900 45.183 -1.040
Lining > CA ALA A 171 @ 13.172 50.102 -4.004
Lining > C ALA A 171 @ 12.526 51.290 -3.297
Lining > O ALA A 171 @ 11.370 51.215 -2.937
Lining > CB ALA A 171 @ 13.541 49.050 -2.973
Lining > CE1 TYR A 183 @ 10.764 50.299 0.644
Lining > OH TYR A 183 @ 11.678 48.180 0.072
Nr voxels/Voxel volume/Cavity volume on plot grid 1 0.3429999 0.343
Cavity
# 2 Starts at 9.000 53.000 -1.500
Cavity box 5.600 12.900 49.600 57.400 -5.900 1.900
Cycle Grid V(vox) #Vox Cavity volume
1 0.50000 0.12500 5 6.25000E-01
2 0.45000 0.09112 10 9.11250E-01
3 0.40500 0.06643 11 7.30731E-01
4 0.36450 0.04843 16 7.74841E-01
Centre of cavity gravity 9.204 53.468 -2.050
Nr of calcns/average/sigma volume 4 0.760 0.103
Lining > CA ILE A 20 @ 5.247 52.775 -1.668
Lining > CG1 ILE A 20 @ 6.284 50.636 -0.746
Lining > CG2 ILE A 20 @ 6.477 51.101 -3.154
Lining > OD1 ASP A 21 @ 7.446 55.116 -4.500
Lining > O ALA A 171 @ 11.370 51.215 -2.937
Lining > CA TYR A 172 @ 12.828 53.511 -2.299
Lining > CD2 TYR A 176 @ 10.232 55.777 0.575
Lining > CE2 TYR A 176 @ 8.950 55.345 0.952
Lining > CD1 TYR A 183 @ 10.851 51.488 1.298
Lining > CE1 TYR A 183 @ 10.764 50.299 0.644
Nr voxels/Voxel volume/Cavity volume on plot grid 3 0.3430000 1.029
Cavity
# 3 Starts at 20.500 61.500 -13.000
Cavity box 17.100 25.400 58.100 65.400 -16.900 -9.100
Cycle Grid V(vox) #Vox Cavity volume
1 0.50000 0.12500 6 7.50000E-01
2 0.45000 0.09112 6 5.46750E-01
3 0.40500 0.06643 9 5.97871E-01
Centre of cavity gravity 21.060 61.695 -12.960
Nr of calcns/average/sigma volume 3 0.632 0.086
Lining > CA ILE B 20 @ 22.323 65.400 -14.410
Lining > CG1 ILE B 20 @ 24.532 64.224 -14.342
Lining > CG2 ILE B 20 @ 23.205 64.666 -12.206
Lining > OD1 ASP B 21 @ 18.890 64.145 -12.021
Lining > O ALA B 171 @ 22.925 60.188 -10.679
Lining > CA TYR B 172 @ 20.954 58.462 -11.547
Lining > C TYR B 172 @ 19.460 58.132 -11.498
Lining > CB LYS B 175 @ 17.254 62.263 -14.230
Lining > CD2 TYR B 176 @ 19.910 59.738 -15.695
Lining > CE2 TYR B 176 @ 20.461 60.868 -16.292
Lining > CD1 TYR B 183 @ 24.064 59.232 -14.671
Lining > CE1 TYR B 183 @ 24.995 59.626 -13.705
Nr voxels/Voxel volume/Cavity volume on plot grid 3 0.3429999 1.029
Cavity
# 4 Starts at 25.000 62.500 -10.000
Cavity box 21.600 29.400 58.600 66.400 -13.900 -6.600
Cycle Grid V(vox) #Vox Cavity volume
1 0.50000 0.12500 8 1.00000E+00
2 0.45000 0.09112 12 1.09350E+00
Centre of cavity gravity 25.500 62.475 -10.275
Nr of calcns/average/sigma volume 2 1.047 0.047
Lining > CG2 ILE B 20 @ 23.205 64.666 -12.206
Lining > CD1 ILE B 20 @ 25.844 63.950 -13.699
Lining > CG2 THR B 24 @ 21.594 62.920 -8.667
Lining > SD MET B 25 @ 25.415 66.739 -9.853
Lining > ND1 HIS B 28 @ 25.695 61.971 -6.806
Lining > CE1 HIS B 28 @ 26.433 60.872 -6.749
Lining > CE2 PHE B 86 @ 29.065 61.764 -9.645
Lining > CZ PHE B 86 @ 29.394 61.237 -10.885
Lining > CD1 LEU B 90 @ 29.352 65.085 -11.679
Lining > CA ALA B 171 @ 23.478 58.877 -8.801
Lining > C ALA B 171 @ 22.661 59.195 -10.005
Lining > O ALA B 171 @ 22.925 60.188 -10.679
Lining > CB ALA B 171 @ 24.890 58.314 -9.271
Lining > CE1 TYR B 183 @ 24.995 59.626 -13.705
Lining > CZ TYR B 183 @ 25.900 58.669 -13.187
Lining > OH TYR B 183 @ 26.818 59.051 -12.249
Nr voxels/Voxel volume/Cavity volume on plot grid 5 0.3430001 1.715
*** VOIDOO ***