[phenixbb] I seem to be unable to select the map_coeff_labels for phenix.cut_out_density
Pietro Roversi
pietro.roversi at path.ox.ac.uk
Sun Jul 31 09:50:34 PDT 2011
Dear Tom
I am trying to run phenix.cut_out_density
but I seem to be unable to select the map_coeff_labels:
viscount:~/sharpfiles/logfiles/Japanin-ID29-Phaser714.15> phenix.cut_out_density cycle_best_13.pdb eden_flat_55.0pc.mtz << EOF
map_coeff_labels="FBshasol SIGFPsha PHIBshasol FOMshasol"
EOF
The output (see below) says I did not give SIGFP and it also picks the default F,PHI and FOM from
columns 4,5,6
What am I doing wrong?
Thanks!
Pietro
# cutout
#
# Cut out density from a map
# Type phenix.doc for help
Cutting out density
Miller arrays in mtz_in: ['H', 'K', 'L', 'Fcentsha', 'PHIcentsha', 'FOMsha', 'HLA', 'HLB', 'HLC', 'HLD', 'FHsha', 'PHIHsha', 'FreeR_flag', 'FPsha', 'SIGFPsha', 'Fcentshasol', 'PHIcentshasol', 'FBshasol', 'PHIBshasol', 'PHIshasol', 'FOMshasol', 'HLAshasol', 'HLBshasol', 'HLCshasol', 'HLDshasol', 'FCshasol', 'PHICshasol']
Setting FP and PHI from map_coeffs
Setting FP and PHI from map_coeffs
Setting FP and PHI from map_coeffs
Setting FP and PHI from map_coeffs
Setting FP and PHI from map_coeffs
Center of cutout region will be from model center at: [62.32560090909093, 43.68719545454543, 32.72059636363636]
------------------------ COPYRIGHT NOTICE ---------------------------------
Los Alamos National Laboratory
This program was prepared by Los Alamos National Security, LLC at
Los Alamos National Laboratory (the University) under Contract No.
W-7405-ENG-36 with the U.S. Department of Energy (DOE). The University has
certain rights in the program pursuant to the contract and the program should
not be copied or distributed outside your organization. All rights in the
program are reserved by the DOE and the University. Neither the U.S.
Government nor the University makes any warranty, express or implied, or
assumes any liability or responsibility for the use of this software.
*******************************************************
* --- RESOLVE --- *
* *
* Statistical density modification *
* Automated model-building *
* *
* For on-line help *
* see "http://solve.lanl.gov" *
* *
* This software uses library routines from the *
* CCP4 suite (http://www.ccp4.ac.uk) for which *
* the author is very thankful! *
*******************************************************
(version 2.15 of 20-Mar-2010)
(size = 6)
Tom Terwilliger, Los Alamos National Laboratory, "terwilliger at LANL.gov"
>pdb_in_memory
Reading pdb_in from memory
If "no_reuse_model" is not set then this model will also be used as starting point for model-building
>no_build
Model will not be built
>mask_cycles 1
Number of mask/image cycles: 1
>minor_cycles 0
Number of minor cycles per mask/image cycle: 0
>no_build
Model will not be built
>cutout
Cutting out density near cutout_center and writing to P1 cell
>fine_grid
FFT grid will be extra fine (1/5 of resolution)
>no_sort
The atoms in pdb_in will not be sorted.
>resolution 1000 2.13352593412
Resolution range (A) is: 2.133526 to 1000.000
>cell1 15.0 15.0 15.0 90 90 90
Cell for cutout (cell1) is 15.00000 15.00000 15.00000 90.00000 90.00000 90.00000
>cutout_center 62.3256009091 43.6871954545 32.7205963636
Center of density for cutout (cutout_center) is 62.32560 43.68719 32.72060
>padding 5.0
Padding around cutout of density: 5 A
>cutout_mask 1
Cutout mask type (1=box, 2=sphere, 3=mask around model): 1
>cutout_sphere 10.0
Radius of cutout of density around cutout_center: 10 A
>rad_mask 5.0
Radius for creating solvent model: 5.000000
>
All done with inputs
Not writing any files as information returned in memory
Building protein
Setting up for building protein
Standard fill-in residues: ALA A GLY G
Standard main-chain atoms: N CA C O CB
All main-chain atoms: N CA C O
Max dist between adjacent N atoms: 6.000000
List of all residues: GLY ALA SER VAL ILE LEU MET CYS PHE TYR LYS ARG TRP HIS GLU ASP GLN ASN PRO THR
List of 1-letter code of residues: GASVILMCFYKRWHEDQNPT
List of number of atoms in side-chains: 0 1 2 3 4 4 4 2 7 8 5 7 10 6 5 4 5 4 3 3
checking license file.. solve2.access
The date today is 31-jul-11. Your license is good until 15-dec-96.
Space group name: Point group:
Space group number : 96 Symmetry operators: 8
Done with lookup
FP taken from column 4
No dataset found matching ID = 0
PHIB taken from column 5
FOM taken from column 6
Using HLA HLB HLC HLD coefficients
WARNING: No SIGFP input data--output SIGFP column will be SIGFP=1.0 for all HKL!
Reading in FreeR_flag
Total of 5695 reflections read from file
Guessing FreeR_flag corresponding to free reflections
This can be set with free_id xx
Free R reflections are those with FreeR_flag= 0
Total of 251 of 5695 reflections in test set
High-resolution limit of input phased data: 3.21
Adding F000 term (0.0) to this list
Closed mtz file
Starting resolution: 3.20 max: 3.20
Space group is 96
Using symmetry operations from input MTZ file
MATRICES:
SYMMETRY ELEMENT 0
1 0 0 0
0 1 0 0
0 0 1 0
SYMMETRY ELEMENT 1
0 -1 0 0.5
1 0 0 0.5
0 0 1 0.75
SYMMETRY ELEMENT 2
0 1 0 0.5
-1 0 0 0.5
0 0 1 0.25
SYMMETRY ELEMENT 3
1 0 0 0.5
0 -1 0 0.5
0 0 -1 0.25
SYMMETRY ELEMENT 4
-1 0 0 0.5
0 1 0 0.5
0 0 -1 0.75
SYMMETRY ELEMENT 5
-1 0 0 0
0 -1 0 0
0 0 1 0.5
SYMMETRY ELEMENT 6
0 1 0 0
1 0 0 0
0 0 -1 0
SYMMETRY ELEMENT 7
0 -1 0 0
-1 0 0 0
0 0 -1 0.5
SPACE GROUP SYMBOL: P 43 21 2
CHECK ON SPACE GROUP SYMBOL: P 43 21 2
HALL SYMBOL : P 4nw 2abw
Extra fine grids used for FFT
Transformations from orthogonal to fractional and back:
Orthogonal to fractional
fractional x= 0.01183 X + -0.00000 Y + -0.00000 Z
fractional y= 0.00000 X + 0.01183 Y + -0.00000 Z
fractional z= 0.00000 X + 0.00000 Y + 0.01123 Z
Fractional to orthogonal
Orthogonal X= 84.50000 x + 0.00010 y + 0.00010 z
Orthogonal Y= 0.00000 x + 84.50000 y + 0.00010 z
Orthogonal Z= 0.00000 x + 0.00000 y + 89.05000 z
Estimated # of atoms in au: 2510
Not separating out FREE set from other reflections for main cycles. Using all data.
Results of wilson scaling:
Scale on I = 3.274
B-value = 47.194
Scaling data with value of 3.274
Reading model density histograms from /software/xtal/PHENIX/phenix-1.7.1-743/solve_resolve/ext_ref_files/segments/rho.list
Read total of 6 sets of density functions
Highest value of ix, iy, iz in a.u: 143 143 18
nu nv nw: 144 144 144 Number of grid points in au: 373320
Mean fom of this map was: 0.84
Summary of starting FOM vs resolution
RES FOM FOM-smoothed N
29.25 0.89 0.86 27
17.82 0.79 0.86 42
13.27 0.71 0.86 72
10.48 0.85 0.86 120
8.83 0.89 0.85 118
7.63 0.84 0.85 206
6.65 0.85 0.85 243
5.96 0.88 0.85 268
5.43 0.85 0.85 306
5.03 0.88 0.85 313
4.67 0.89 0.85 415
4.38 0.86 0.84 348
4.15 0.88 0.84 445
3.91 0.86 0.84 567
3.67 0.84 0.84 701
3.46 0.82 0.84 675
3.28 0.78 0.83 829
Mean fom of this map was: 0.84
Starting phases assumed to be experimental
(To override, use "phases_from_resolve")
Estimating optimal initial smoothing radius using the function:
R=2.41 * (dmin**0.90) * (fom**-0.26)
with dmin = 3.200273 and fom = 0.8443282
Leading to R= 7.174512
To override, set "wang_radius_cycle", "wang_radius", or "wang_radius_start"
Setting final smoothing radius to 4.000000
To override, set "wang_radius_cycle", "wang_radius", or "wang_radius_finish"
Using pdb_in from memory
Center of molecule read in with 1081
atoms is 62.275337 43.672276 32.612022
Read 1081 atoms from
PDB file for use in model-building MEMORY
Solvent content will be 0.40
Using database entry 5 for histograms (" 3 A dehalogenase model ")
Using all data for tests due to low number in test set (override with "use_free_for_test")
Total mask cycles: 1
Total density modification mask cycles: 1
Cycle Ref NCS Use NCS Build image solvent Extend Cycles Test
1 NO NO NO NO YES NO 0
Mask cycle 1
Weighting this cycle: 1.000000
Histogram DB entry # 5 (" 3 A dehalogenase model ")
Solvent content: 0.40 Smoothing radius: 7.17
Using histogram-based mask
Assuming this cycle is unbiased (no previous density modification)
Plot 1
-------------------------------------------------------------------------------
Plot of probability that a grid point is part of protein region
vs percentiles of grid points
All points to the left of the "+" signs are in solvent masked region
those to right are in protein masked region.
The values of p(protein) should change from low to high approximately at the
value of the fraction of solvent indicated by the "+" signs.
The sharper the transition the better.
Note: the mask is only used to make an estimate of the p(protein)
The values of p(protein) are used to weight the contribution of each grid
point to the probability of the map:
p(rho) = p(rho|protein) p(protein) + p(rho|solvent) (1-p(protein))
This says that the probability that we would observe the value "rho" of
electron density at this point is the probability that we
would observe "rho" if this were really protein times the probability
that this is protein, plus the probability that we would observe
"rho" if it were really solvent, times the probability that
it is solvent.
Probability that grid points are in protein region
1.0 ...........................xxxxxxxxxxxxxxxxxxxxxxx
. + xx .
. + x .
. + x .
. + .
. + x .
. + .
p(protein) . xxxxxx .
0.5 . xxxxxxxxxxxxx + .
. + .
. x + .
. + .
.x + .
. + .
. + .
0.0 ....................+.............................
0 20 40 60 80 100
Percentile of grid points
-------------------------------------------------------------------------------
Cutting region containing model out of map
Box to be cut out of density (A) : 15 15 15
Box with padding (A) : 25 25 25
NX NY NZ for cutout box: 36 36 36
NX NY NZ with padding: 60 60 60
Center of cutout region (A): 62.3256 43.6872 32.7206
Using box for cutout mask
Total grid points marked: 46656 not marked: 169344
Mean density in cutout region (no density offset applied ) 0.040 for 46656 points
Number of points in padded region (set to 0.0): 169344
Output array in memory with 3600 reflections
resolve exit_info:
source_file: /net/longnose/scratch2/phenix/phenix-1.7.1-743/solve_resolve/resolve/cutout.cpp
source_line: 252
status: 0
EndOfResolve
Output map coeffs 3600
Writing output mtz: cutout.mtz
Writing output pdb (offset to match output mtz): cutout.pdb
Citations for cutout:
Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung
LW, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ,
Richardson DC, Richardson JS, Terwilliger TC, Zwart PH. (2010) PHENIX: a
comprehensive Python-based system for macromolecular structure solution. Acta
Cryst. D66:213-221.
________________________________________
From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] On Behalf Of Thomas C. Terwilliger [terwilliger at lanl.gov]
Sent: 05 July 2011 17:46
To: PHENIX user mailing list
Subject: Re: [phenixbb] phenix.mr_rosetta: Inconsistent query numbering
Hi Pietro,
There is something that phenix.mr_model_preparation cannot read in
Japanin.hhr (attached):
phenix.mr_model_preparation Japanin.hhr
gives the same error. I'll copy Gabor Bunkoczi and see if he can help with
this.
All the best,
Tom T
>> Dear all,
>>
>> my run of phenix.mr_rosetta stops with:
>>
>> ******************* ERROR ENDING ***************
>> Inconsistent query numbering
>>
>> ******************* ERROR ENDING ***************
>>
>> I attach script and logfiles.
>>
>> Any suggestions?
>>
>> Thanks
>>
>> Pietro
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>
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