NMR Restraints Grid
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NMR Restraints Grid |
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Result table
| image | mrblock_id | pdb_id | bmrb_id | cing | stage | program | type |
|
|
551432 |
2lx5   |
18659 | cing | 2-parsed | STAR | comment |
data_2lx5_MR_file_constraints
save_Conversion_project
_Study_list.Sf_category study_list
_Study_list.Entry_ID parsed_2lx5
_Study_list.ID 1
loop_
_Study.ID
_Study.Name
_Study.Type
_Study.Details
_Study.Entry_ID
_Study.Study_list_ID
1 "Conversion project" NMR . parsed_2lx5 1
stop_
save_
save_entry_information
_Entry.Sf_category entry_information
_Entry.ID parsed_2lx5
_Entry.Title "Original constraint list(s)"
_Entry.Version_type original
_Entry.Submission_date .
_Entry.Accession_date .
_Entry.Last_release_date .
_Entry.Original_release_date .
_Entry.Origination .
_Entry.NMR_STAR_version 3.1
_Entry.Original_NMR_STAR_version .
_Entry.Experimental_method NMR
_Entry.Experimental_method_subtype .
loop_
_Related_entries.Database_name
_Related_entries.Database_accession_code
_Related_entries.Relationship
_Related_entries.Entry_ID
PDB 2lx5 "Master copy" parsed_2lx5
stop_
save_
save_global_Org_file_characteristics
_Constraint_stat_list.Sf_category constraint_statistics
_Constraint_stat_list.Entry_ID parsed_2lx5
_Constraint_stat_list.ID 1
loop_
_Constraint_file.ID
_Constraint_file.Constraint_filename
_Constraint_file.Software_ID
_Constraint_file.Software_label
_Constraint_file.Software_name
_Constraint_file.Block_ID
_Constraint_file.Constraint_type
_Constraint_file.Constraint_subtype
_Constraint_file.Constraint_subsubtype
_Constraint_file.Constraint_number
_Constraint_file.Entry_ID
_Constraint_file.Constraint_stat_list_ID
1 2lx5.mr . . "MR format" 1 comment "Not applicable" "Not applicable" 0 parsed_2lx5 1
1 2lx5.mr . . DYANA/DIANA 2 distance NOE simple 197 parsed_2lx5 1
1 2lx5.mr . . DYANA/DIANA 3 "dihedral angle" "Not applicable" "Not applicable" 18 parsed_2lx5 1
1 2lx5.mr . . n/a 4 comment "Not applicable" "Not applicable" 0 parsed_2lx5 1
1 2lx5.mr . . "MR format" 5 "nomenclature mapping" "Not applicable" "Not applicable" 0 parsed_2lx5 1
stop_
save_
save_MR_file_comment_4
_Org_constr_file_comment.Sf_category org_constr_file_comment
_Org_constr_file_comment.Entry_ID parsed_2lx5
_Org_constr_file_comment.ID 1
_Org_constr_file_comment.Constraint_file_ID 1
_Org_constr_file_comment.Block_ID 4
_Org_constr_file_comment.Details "Generated by Wattos"
_Org_constr_file_comment.Comment
;
# ------ read input files ------
read seq tb.seq
read upl submission.upl # read upper distance bounds
read aco tb.aco # read dihedral angle restraints
# ------ structure calculation ------
calc_all 100 steps=40000 # calculate conformers
# ------ structure calculation ------
overview demo.ovw structures=40 pdb # write overview file and 40 best conformers
name:= tb
rmsdrange:=1..18
cyanalib
read seq tb.seq
# Copyright (c) 2002-05 Peter Guntert. All rights reserved.
## 7MACROS: caliba - CYANA macro
##
## Parameters: dmin=dmin (default: 2.4)
## dmax=dmax (default: 5.5)
## vmin=Vmin (default: 0.0)
## bb=A (default: calculated automatically)
## sc=B (default: A/dmin2)
## methyl=C (default: B/3)
## weight=w (default: 1.0)
## avedis=d (default: 3.4)
## plot=file (required)
##
## Calibrates a peak list, i.e. derives upper limit distance constraints from
## all assigned peaks and adds them to the list of current distance
## constraints. The values dmin and dmax give the minimal and the maximal
## value in A for a distance constraints before possible pseudo atom
## corrections are added. Optionally, only peaks with volume larger than Vmin
## or from a peak list with given filename (without extension) may be
## considered. Peaks are classified into three calibration classes:
## class peaks/constraints function
## backbone all HN/Ha - HN/Ha, and HN/Ha - Hb between residues (i, j) with
## |i - j| < 5 V = A/d6
## sidechain not "backbone" and not "methyl" V = B/d4
## methyl all involving methyl groups V = C/d4
##
## The parameters A, B and C are either given by the user or calculated
## automatically as follows:
## The function calsca is used to calculate A by assuming an average distance
## of d A for all constraints from the class "backbone". By default, the
## scalar B is set to B = A/dmin2 in order to intersect the backbone
## calibration curve at dmin, and C is set to B/3 (see also Mumenthaler et
## al., 1997).
## Optionally, the resulting distance constraints may be given the relative
## weight w. Also optionally, a logarithmic plot of volumes versus
## corresponding minimal distances in the selected structures can be
## created.
var echo plt f
syntax dmin=@r=2.4 dmax=@r=5.5 vmin=@r=100.0 bb=@r=-1.0 sc=@r=-1.0 \
methyl=@r=-1.0 weight=@r=1.0 avedis=@r=3.4 plot=@f.ps=
echo:=off
plt='$plot'.ne.' '
print
print " Calibration class: backbone"
print
peaks select "H HN HA* HB* QA QB - METHYL, H HN HA* QA - METHYL levels=0..4" info=none
peaks select "+ H HN HA* QA - METHYL, H HN HA* QA - METHYL levels=5.." info=none
peaks select "/ *,*"
f:=1/d**6
if (bb.le.0.0) bb=calscale('$f',avedis,vmin)
print " Calibration function: $bb(1PE10.2) * $f"
calibrate bb*$f $dmin $dmax weight=$weight \
plot=$if(plt,'caliba_bb.grf',' ') log dmin qfactor
print
print " Calibration class: side-chain"
print
peaks select "! - METHYL, *"
peaks select "/ *, *"
f:=1/d**4
if (sc.le.0.0) sc=bb/(dmin)**2
print " Calibration function: $sc(1PE10.2) * $f"
calibrate sc*$f $dmin $dmax weight=$weight \
plot=$if(plt,'caliba_sc.grf',' ') log dmin qfactor
print
print " Calibration class: methyl"
print
peaks select "METHYL ,*" info=none
peaks select "/ *, *"
f:=1/d**4
if (methyl.le.0.0) methyl=sc/3.0
print " Calibration function: $methyl(1PE10.2) * $f"
calibrate methyl*$f $dmin $dmax weight=$weight \
plot=$if(plt,'caliba_me.grf',' ') log dmin qfactor
print
if (plt) then
print "x0=-160 y0=150 x1=210 y1=350" >$plot(1:indexr('$plot','.'))grf
print "marksize=4" >>
print file=caliba_bb.grf >>
print " " >>
print "x0=-160 y0=-100 x1=210 y1=100" >>
print file=caliba_sc.grf >>
print " " >>
print "x0=-160 y0=-350 x1=210 y1=-150" >>
print file=caliba_me.grf >>
print " " >>
print "X0=0 X1=100 Y0=0 Y1=100 " >>
print "x0=-250 x1=250 y0=-350 y1=350 " >>
print "clip off " >>
print "rotate=on " >>
print "textsize=14 " >>
print "weight=bold " >>
print "text 6 78 \"Backbone class\" " >>
print "text 6 42 \"Side-chain class\" " >>
print "text 6 5 \"Methyl group class\" " >>
print "rotate=off " >>.
graf $plot replace
remove caliba_bb.grf caliba_sc.grf caliba_me.grf
end if
;
save_
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