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For your comment (1)
>From the header lines you pasted below (reflection file), I don't
see any header info or columns containing HL-coefficients (pa,
pb, pc, pd). You also need to read in the file containing the HL
coefficients.
------------
For (2)
"xmin, xmax, ymin, ymax, zmin and zmax" are not at all 'required'
to be specified UNLESS you have asked CNS to calculate the map in
the 'fract' mode.
You can just as easily tell the input file the extent of the map
by specifying the foll. (found in the input file just above the
stuff you pasted)
{* extent of map *}
{+ choice: "asymmetric" "box" "unit" "molecule" "fract" +}
{===>} map_mode="asymmetric";
This would be the easiest way to proceed.
-------------
For (3)
Here's what you have:
>ATOM 1422 O ALA B 493 38.867 -28.550 1.816 1.00 39.63
>ATOM 1501 HG Hg B 757 26.937 -0.022 18.702 1.00 35.00
Here are some changes:
>ATOM 1422 O ALA B 493 38.867 -28.550 1.816 1.00 39.63
>ATOM 1501 HG Hg B 757 26.937 -0.022 18.702 1.00 35.00
>ATOM 1501 HG HG B 757 26.937 -0.022 18.702 1.00 35.00
>ATOM 1501 HG+2 HG2 B 757 26.937 -0.022 18.702 1.00 35.00
Keep the precise column position of 'atom' name and 'residue'
name in columns 3 and 4. See aligment wrt line 1.
The 'single space' before Hg might most likely fix your problem.
HETATM is not needed for Hg.
-------------
HTH.
Raji
>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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---------End of Included Message----------
Raji Edayathumangalam
Postdoctoral Fellow
The Rockefeller University
Box 224, 1230 York Avenue
New York, NY 10021
