Hello again
In follow up to my own question I have found that the issue only really
occurs when i try to include the water, either with the other ligand or
even without (after re ordering of the pdb file) Does the water in the
pdb file have to have H atoms attached or is a crystallographic O
sufficient?
My log with the hetatms only no water, is:
delete__442E> One or more atoms absent from MODEL: O: 522: C: 522: N: 523: CA: 523:
delete__442E> One or more atoms absent from MODEL: O: 523: C: 523: N: 524: CA: 524:
delete__443_> Restraints marked for deletion were removed.
Total number of restraints before, now:
51172 47475
which still shows these atoms absent errors which i don't understand.
When adding just the water and no other ligand my top and aln files are
appended and my log error is an out of bounds as before. SO it aapears
that the water is the problem, I have also tried in my log file with
only the water changing the line SET HETATM_IO = on, WATER_IO = on to just SET WATER_IO = on but this maks no difference.
delete__442E> One or more atoms absent from MODEL: O: 522: C: 522: N: 523: CA: 523:
delete__443_> Restraints marked for deletion were removed.
Total number of restraints before, now:
48782 45085
nselat__596E> Atom index is out of range (iatm,natm): 4009 4008
recover____E> ERROR_STATUS >=
STOP_ON_ERROR:
1 1
TOP
INCLUDE
SET ALNFILE = 'CcHh1-Bamu.ali'
SET KNOWNS = 'Bamu'
SET SEQUENCE = 'CcHh1'
SET STARTING_MODEL = 1
SET ENDING_MODEL = 1
SET HETATM_IO = on, WATER_IO = on
CALL ROUTINE = 'model'\
ALIGNMENT
>P1;Bamu
structureX:Bamu:1::515::undefined:undefined:-1.00:-1.00
GTHEEEQYLFAVNNTKAEYPRDKTIHQLFEEQVSKRPNNVAIVCENEQLTYHELNVKANQLARIFIEKGIGKDTL
VGIMMEKSIDLFIGILAVLKAGGAYVPIDIEYPKERIQYILDDSQARMLLTQKHLVHLIHNIQFNGQVEIFEEDT
IKIREGTNLHVPSKSTDLAYVIYTSGTTGNPKGTMLEHKGISNLKVFFEN-SLNVTEKDRIGQFASISFDASVWE
MFMALLTGASLYIILKDTINDFVKFEQYINQKEITVITLPPTYVVHL-----DPERILSIQTLITAGSATSPSLV
NKWKE--KVTYINAYGPTETTICATTWVATKETIGHSVPIGAPIQNTQIYIVDENLQLKSVGEAGELCIGGEGLA
RGYWKRPELTSQKFVDNPFVP-GEKLYKTGDQARWLSDGNIEYLGRIDNQVKIRGHRVELEEVESILLKHMYISE
TAVSVHKDHQEQPYLCAYFVSE---KHIPLEQLRQFSSEELPTYMIPSYFIQLDKMPLTSNGKIDRKQLPEPDLT
F/w*
>P1;CcHh1
sequence:CcHh1:1::523::::0.00: 0.00
GPAERLELLAGWNDTDADRAR-PGLVEMFREQARARPDAVAVVDERRTLTYRQVEKLSAQLAHQLLARGLAVEDV
VGISLERSAEMVIGLLAVLRAGGAFVPLDPHWPAERRAVVIEDAGVVVQLDASGEPAPG---EPEAVAVDLGDWR
FGDRPTEDTGVTVPGDALAYVIFTSGSTGRPKGAMIRHEAISERLLWQIHEILGFGHDDASLFKAPLSFDISINE
IFLPLVSGGRLVVLRPGGERDPHHLLSVIDEQRVTFTYLVSSMLDVLLEMAGDSGRLDSLRHVWCGGEVLTPELY
ERFRTRLDIPLYHGYGPAETTIGVSHVVYRGAAERLSTSIGRANPNTRLYVLDDELRPVPVGVGGELYAGGLLLG
RGYVNAPGLTASRFVANPFADDGSRLYRTGDLARFAPDGSLDFLGRADNQVKIRGMRLEIEDVEVGLAEHPRVRH
TCVVARKNTAGGTYLVGYVIPAAGHEDLRADEVKAWAGEHMVEYMVPTHVVVMTEFPLTANGKLDRNALPEPVIP
A/w*
Sorry to post so many mails, I'm really struggling to figure this out!
Jo