Hello<br>
<br>
I apologise if this message is posted more than once, I am having difficulties with my email system.<br>
<br>
My questions regards the process for modelling with ligands.<br>
<br>
>From the tutorial i understand that you have the ligands in the pdb
file template and then you manually alter the alignment to take account
of these ligands, for me that means adding /..w* to the end of the
structure and seqeunce alignments (i'm unsure if you add it to the
seqeunce, if you want it included). This also means changing the number
of residues in the structure file in the alignment to include the 3
BLK/water items, as even if they are included in the pdb prior to
alignment they are not included in the residue number line in the
alignment (i.e. in alignment below changing original 514 to 517).<br>
<br>
I then do the modelling using the alignment, as appended below and the
model.top script (7v7 user!) also below and get the following error
which i do not understand.<br>
<br>
check_ali___&gt; Checking the sequence-structure alignment.<br>
<br>
Implied target CA(i)-CA(i+1) distances longer than&nbsp; 8.0 angstroms:<br>
<br>
ALN_POS&nbsp; TMPL&nbsp; RID1&nbsp; RID2&nbsp; NAM1&nbsp; NAM2&nbsp;&nbsp;&nbsp;&nbsp; DIST<br>
----------------------------------------------<br>
&nbsp;&nbsp;&nbsp; 134&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp; 134&nbsp;&nbsp;
138&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; G&nbsp;&nbsp;&nbsp;&nbsp;
E&nbsp;&nbsp;&nbsp; 8.407<br>
END OF TABLE<br>
<br>
<br>
delete__442E&gt; One or more atoms absent from MODEL:&nbsp; O: 522: C: 522: N: 523: CA: 523:<br>
delete__442E&gt; One or more atoms absent from MODEL:&nbsp; O: 523: C: 523: N: 524: CA: 524:<br>
delete__442E&gt; One or more atoms absent from MODEL:&nbsp; O: 524: C: 524: N: 525: CA: 525:<br>
delete__443_&gt; Restraints marked for deletion were removed.<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
Total number of restraints before, now:&nbsp;&nbsp;&nbsp;
51247&nbsp;&nbsp;&nbsp; 47550<br>
nselat__596E&gt; Atom index is out of range (iatm,natm):&nbsp;&nbsp;&nbsp;&nbsp; 4033&nbsp;&nbsp;&nbsp;&nbsp; 4032<br>
recover____E&gt; ERROR_STATUS &gt;=
STOP_ON_ERROR:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1<br>
<br>
Dynamically allocated memory
at&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; finish
[B,kB,MB]:&nbsp;&nbsp;&nbsp;&nbsp; 26700639&nbsp;&nbsp;
26074.844&nbsp;&nbsp;&nbsp; 25.464<br>
Starting
time&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
: 2006/01/02&nbsp; 21:50:15.029<br>
Closing
time&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
: 2006/01/02&nbsp; 21:50:35.218<br>
Total CPU time
[seconds]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 20.18<br>
&nbsp;<br>
I unerstand distance table and know which region of my alignment this
points to but I do not understand the missing atoms or the out of range
error, as I have 4142 atoms and no missing atoms. Could anyone help
with where I am going wrong?! And also tell me if my procedure is
correct, should the alignment automatically include the 3 BLK/water
residues in the resdiue number if it is in the pdb file? and if i want
the ligands in the output model is it correct to state /..w* at the end
of this sequence in the alignment too? Also in the alignment is it
correct for the seqeunce line to read:
sequence:CcHh1:&nbsp;&nbsp;&nbsp;&nbsp; : :&nbsp;&nbsp;&nbsp;&nbsp; :
:::-1.00:-1.00 ?<br>
<br>
Any feedback would be greatly appreciated.<br>
<br>
Thanks<br>
Jo<br>
<br>
ALIGNMENT<br>
&gt;P1;Bamu<br>
structureX:Bamu:&nbsp;&nbsp; 1 : : 517 : :undefined:undefined:-1.00:-1.00<br>
GTHEEEQYLFAVNNTKAEYPRDKTIHQLFEEQVSKRPNNVAIVCENEQLTYHELNVKANQLARIFIEKGIGKDTL<br>
VGIMMEKSIDLFIGILAVLKAGGAYVPIDIEYPKERIQYILDDSQARMLLTQKHLVHLIHNIQFNGQVEIFEEDT<br>
IKIREGTNLHVPSKSTDLAYVIYTSGTTGNPKGTMLEHKGISNLKVFFEN-SLNVTEKDRIGQFASISFDASVWE<br>
MFMALLTGASLYIILKDTINDFVKFEQYINQKEITVITLPPTYVVHL-----DPERILSIQTLITAGSATSPSLV<br>
NKWKE--KVTYINAYGPTETTICATTWVATKETIGHSVPIGAPIQNTQIYIVDENLQLKSVGEAGELCIGGEGLA<br>
RGYWKRPELTSQKFVDNPFVP-GEKLYKTGDQARWLSDGNIEYLGRIDNQVKIRGHRVELEEVESILLKHMYISE<br>
TAVSVHKDHQEQPYLCAYFVSE---KHIPLEQLRQFSSEELPTYMIPSYFIQLDKMPLTSNGKIDRKQLPEPDLT<br>
F/..w*<br>
<br>
&gt;P1;CcHh1<br>
sequence:CcHh1:&nbsp;&nbsp;&nbsp;&nbsp; : :&nbsp;&nbsp;&nbsp;&nbsp; : :::-1.00:-1.00<br>
GPAERLELLAGWNDTDADRAR-PGLVEMFREQARARPDAVAVVDERRTLTYRQVEKLSAQLAHQLLARGLAVEDV<br>
VGISLERSAEMVIGLLAVLRAGGAFVPLDPHWPAERRAVVIEDAGVVVQLDASGEPAPG---EPEAVAVDLGDWR<br>
FGDRPTEDTGVTVPGDALAYVIFTSGSTGRPKGAMIRHEAISERLLWQIHEILGFGHDDASLFKAPLSFDISINE<br>
IFLPLVSGGRLVVLRPGGERDPHHLLSVIDEQRVTFTYLVSSMLDVLLEMAGDSGRLDSLRHVWCGGEVLTPELY<br>
ERFRTRLDIPLYHGYGPAETTIGVSHVVYRGAAERLSTSIGRANPNTRLYVLDDELRPVPVGVGGELYAGGLLLG<br>
RGYVNAPGLTASRFVANPFADDGSRLYRTGDLARFAPDGSLDFLGRADNQVKIRGMRLEIEDVEVGLAEHPRVRH<br>
TCVVARKNTAGGTYLVGYVIPAAGHEDLRADEVKAWAGEHMVEYMVPTHVVVMTEFPLTANGKLDRNALPEPVIP<br>
A/..w*<br>
<br>
MODLE.TOP<br>
<br>
INCLUDE<br>
SET ALNFILE = 'CcHh1-Bamu.ali'<br>
SET KNOWNS = 'Bamu'<br>
SET SEQUENCE = 'CcHh1'<br>
SET STARTING_MODEL = 1<br>
SET ENDING_MODEL = 1<br>
SET HETATM_IO = ON, WATER_IO = ON<br>
CALL ROUTINE = 'model'<br>