Re: [ccp4bb]: xplor on DNA from NMR data

[Saxena Neetu <neetupbs@iitr.ernet.in>]

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Dear all,
 I am a postgraduate student from India. Neetu Saxena, Department
of Biotechnology, IIT-Roorkee, Roorkee, INDIA. i am working on xplor(0.5)
for dna modeling through nmr data. i am using sgi origin O-2 .
        My problem is that when i run the file gen_new.inp by giving a
...pdb file of DNA and using parallhdg.dna andtopallhdg.dna as input files as parameter and topology files as these are
required for producing hydrogens . Besides this, I am also setting
hydrogen flags to be true . Still it gives the following error at the site
of hydrogen flags asked in the input file:CNSrefine> if
(&hydrogen_flag=false) then
  1461 NEXTCD: condition evaluated as false
  1462 CNSrefine> delete selection=( hydrogen ) end
  1463 CNSrefine> end if
  1464 CNSrefine>
  1465 CNSrefine> identity (store1) (none)
  1466 SELRPN:  0 atoms have been selected out of 0
  1467 CNSrefine>
  1468 CNSrefine> identity (store1) (&atom_build)
  1469 SELRPN:  0 atoms have been selected out of 0
  1470 CNSrefine> if ( &hydrogen_build = "all" ) then
  1471 NEXTCD: condition evaluated as false
  1472 CNSrefine> identity (store1) (store1 or hydrogen)
  1473 CNSrefine> elseif ( &hydrogen_build = "unknown" ) then
  1474 NEXTCD: condition evaluated as true
  1475 CNSrefine> identity (store1) (store1 or (not(known) and hydrogen))
  1476 %SELRPN-RECAll-ERR: Store empty
  1477 SELRPN:  0 atoms have been selected out of 0
  1478 CNSrefine> end if
  1479 CNSrefine>
  1480 CNSrefine> show sum(1) (store1)
  1481 %SELRPN-RECAll-ERR: Store empty
  1482 SELRPN:  0 atoms have been selected out of 0
  1483 SHOW: zero atoms selected
 

%SELRPN-RECAll-ERR: Store empty
  1646 SELRPN:  0 atoms have been selected out of 0
  1647 SHOW: zero atoms selected
  1648 CNSrefine> do (b=$result) (store1 and (attr b < 0.01))
  1649 %SELRPN-RECAll-ERR: Store empty
  1650 SELRPN:  0 atoms have been selected out of 0

CNSrefine> write coordinates output=dnacoordinate_outfile end
  1659 CWRITE: zero atoms specified. No file created
    

             I am unable to understand why it is not able to select any
atom? If any body has appropriate answer for it, please inform me.


NEETU SAXENA
Department Of Biosciences & Biotechnology
IIT-Roorkee
Roorkee