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Thanks everybody for putting good comments.
When I executed
$to_cns my.sca my.cns
the output looks like this
{* CNS file junk1.cns converted from hkl file my.sca
Converted by program to_cns *}
NREFlections= 22723
ANOMalous= TRUE
DECLare NAME=IOBS DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=SIGI DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=FOBS DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=SIGMA DOMAin=RECIprocal TYPE=REAL END
INDEx= 0 0 4 IOBS= 105.80 SIGI= 5.70
FOBS= 10.29 SIGMA= 0.28
INDEx= 0 0 6 IOBS= 446.60 SIGI= 19.10
FOBS= 21.13 SIGMA= 0.46
Then I used this my.cns file in "make.cv" to get my.hkl required for
"model_map.inp".
output is as follows
NREFlection= 22723
ANOMalous=FALSe { equiv. to HERMitian=TRUE}
DECLare NAME=FOBS DOMAin=RECIprocal TYPE=COMP END
DECLare NAME=SIGMA DOMAin=RECIprocal TYPE=REAL END
DECLare NAME=TEST DOMAin=RECIprocal TYPE=INTE END
INDE -43 1 12 FOBS= 101.600 0.000 SIGMA= 6.210 TEST=
0
INDE -43 1 13 FOBS= 17.600 0.000 SIGMA= 8.720 TEST=
0
INDE -43 1 14 FOBS= 40.600 0.000 SIGMA= 13.950 TEST=
0
I would like to know how I can get HL coefficients (A, B, C, D) required for
model_map.inp, as none of the above two ways I could get them.
{* Hendrickson-Lattman coefficients A,B,C,D *}
{* required for the "mlhl" target and phase combined or observed maps *}
{+ table: rows=1 "HL coefficients" cols=4 "A" "B" "C" "D" +}
{===>} obs_pa="pa";
{===>} obs_pb="pb";
{===>} obs_pc="pc";
{===>} obs_pd="pd";
(2)
I like know how "xmin, xmax, ymin, ymax, zmin and zmax calculated. These
parameters also required for "model_map.inp"
{* limits in orthogonal angstroms for box mode or
fractional coordinates for fract mode *}
{+ table: rows=3 "x" "y" "z" cols=2 "minimum" "maximum" +}
{===>} xmin="";
{===>} xmax="";
{===>} ymin="";
{===>} ymax="";
{===>} zmin="";
{===>} zmax="";
(3)
To get Hg atoms in the generate.pdb, a output file of generate.inp
tail part of the input PDB I used is as follows.
ATOM 1420 CB ALA B 493 38.802 -25.838 3.557 1.00 39.63 BBBB
C
ATOM 1421 C ALA B 493 39.574 -27.476 1.780 1.00 39.63 BBBB
C
ATOM 1422 O ALA B 493 38.867 -28.550 1.816 1.00 39.63 BBBB
O
ATOM 1501 HG Hg B 757 26.937 -0.022 18.702 1.00 35.00 BBBB
ATOM 1502 HG Hg B 758 16.790 -15.955 15.878 1.00 35.00 BBBB
ATOM 1503 HG Hg B 759 36.504 2.463 7.478 1.00 35.00 BBBB
ATOM 1505 HG Hg A 761 -4.105 35.153 22.774 1.00 35.00 AAAA
ATOM 1506 HG Hg A 762 3.201 48.512 34.441 1.00 35.00 AAAA
ATOM 1507 HG Hg A 763 -2.505 40.737 12.738 1.00 35.00 AAAA
But the tail part of the output (generate.pdb) is as follows which is
without Hg.
ATOM 2841 N GLY 492 35.052 -23.501 0.595 1.00 39.63 BBBB
ATOM 2842 CA GLY 492 35.914 -24.607 0.159 1.00 39.63 BBBB
ATOM 2843 C GLY 492 37.357 -24.746 0.615 1.00 39.63 BBBB
ATOM 2844 O GLY 492 38.225 -23.951 0.198 1.00 39.63 BBBB
ATOM 2845 N ALA 493 37.626 -25.822 1.368 1.00 39.63 BBBB
ATOM 2846 CA ALA 493 38.952 -26.061 2.046 1.00 39.63 BBBB
ATOM 2847 CB ALA 493 38.802 -25.838 3.557 1.00 39.63 BBBB
ATOM 2848 C ALA 493 39.574 -27.476 1.780 1.00 39.63 BBBB
ATOM 2849 O ALA 493 38.867 -28.550 1.816 1.00 39.63 BBBB
So I am not getting Hg atoms in the output of generate.inp
The topology and parameter files of generate.inp used are as follows.
{================== protein topology and parameter files
===================}
{* protein topology file *}
{===>} prot_topology_infile="CNS_TOPPAR:protein.top";
{* protein linkage file *}
{===>} prot_link_infile="CNS_TOPPAR:protein.link";
{* protein parameter file *}
{===>} prot_parameter_infile="CNS_TOPPAR:protein_rep.param";
{================ nucleic acid topology and parameter files
=================}
{* nucleic acid topology file *}
{===>} nucl_topology_infile="CNS_TOPPAR:dna-rna.top";
{* nucleic acid linkage file *}
{* use CNS_TOPPAR:dna-rna-pho.link for 5'-phosphate *}
{===>} nucl_link_infile="CNS_TOPPAR:dna-rna.link";
{* nucleic acid parameter file *}
{===>} nucl_parameter_infile="CNS_TOPPAR:dna-rna_rep.param";
{=================== water topology and parameter files
====================}
{* water topology file *}
{===>} water_topology_infile="CNS_TOPPAR:water.top";
{* water parameter file *}
{===>} water_parameter_infile="CNS_TOPPAR:water_rep.param";
{================= carbohydrate topology and parameter files
===============}
{* carbohydrate topology file *}
{===>} carbo_topology_infile="CNS_TOPPAR:carbohydrate.top";
{* carbohydrate parameter file *}
{===>} carbo_parameter_infile="CNS_TOPPAR:carbohydrate.param";
{============= prosthetic group topology and parameter files
===============}
{* prosthetic group topology file *}
{===>} prost_topology_infile="";
{* prosthetic group parameter file *}
{===>} prost_parameter_infile="";
{=================== ligand topology and parameter files
===================}
{* ligand topology file *}
{===>} lig_topology_infile="";
{* ligand parameter file *}
{===>} lig_parameter_infile="";
{===================== ion topology and parameter files
====================}
{* ion topology file *}
{===>} ion_topology_infile="CNS_TOPPAR:ion.top";
{* ion parameter file *}
{===>} ion_parameter_infile="CNS_TOPPAR:ion.param";
For HG, instead of ATOM, HETATM also used at the begining of the line of
input PDB used. Still I do not find any difference in the output.
Taking Hg in a seperate PDB file (as hg.pdb) mentioned at
{* ion coordinate file *}
{===>} ion_coordinate_infile_1="hg.pdb";
I am still missing Hg atoms in the output of generate.inp.
I use CNS version 1.1.
Look for the suggestion and help.
Many thanks.
Sam
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