The :2:@:363:@: you are talking about are the residue number and chain ID, not the coordinates. In the second line of each entry in the alignment file you have : - first colum defines if the alignment is for a template or for the model - second colum gives the file name corresponding to the PDB - 3rd col. is the residue number of the first residue in the PDB file - 4th col. is the chain identifier of the first residue in the PDB file - 5th col. is the residue number of the last residue in the PDB file - 6th col. is the chain identifier of the last residue in the PDB file - 7th col. is the protein name - 8th col. can be used to specify other information - 9th col. is the resolution (in the casde of a template) - 10th col. is the B-factor (in the casde of a template)
Colums 7-10 are optionnal.
Note that this means that Modeller reads the coordinates of the atoms in the pdb file corresponding to the name given in the 2nd col, not directly from the alignment file.
On Sun, 15 Jun 2003, christos Kouriniadis wrote:
> Hello everybody, > > I am doing a project on comparative modelling, by using > modeller. My problem is the following: > > I am trying to make an input file with PDB structures aligned > in PIR format. > However, when I am reading the modeller manual, I see that the worked > example is in the form: > > P1;2ald > structureX:2ald:2:@:363:@:aldolase:human muscle:2.00:0.17 > * > > If you go to the section "display/download file", in the PDB > website, you will get the usual big file. > But when I have a look at this file, I see that ATOM has > three coordinates: > -20.521 45.890 70.464 > > How from these coordinates I get the :2:@:363:@: ??? > Is there a formula that transforms it? > > I would be grateful if you could give me a hint on this. > > Thanks, > > Christos Kouriniadis > > _________________________________________________________________ > Add photos to your e-mail with MSN 8. Get 2 months FREE*. > http://join.msn.com/?page=features/featuredemail >