I'm sorry but it seems I didn't explain myself clearer.
What I asked for last time is different than what I'm asking now. This time I want the script to transfer the coordinates for aligned residues only and nothing that is not aligned. So the MSFIEKMIG in my sequance is not going to have any coordinates because it was not aligned with anything from my templae.
I hope I explained myself better now.
Regards, Ali
-----Original Message----- >From Modeller Caretaker modeller-care@salilab.org Sent Mon 11/5/2007 2:34 PM To Ali Algarrous algarra@uni.edu Cc modeller_usage@salilab.org Subject Re: [modeller_usage] Transfer_xyz question
Ali Algarrous wrote: > If i have the following alignment > >>P1;1ji4 > structureX:1ji4:FIRST:A:LAST:A:::: > MKTFEILKHLQADAIVLFMKVHNFHWNVKGTDFFNVHKATEEI---------Y > EEFADMFDDLAERIVQLGHHPLVTLSEAIKLTRV-----KEETKTSFHSKDIF > KEILEDYKYLEKEFKELSNTAEKEGDKVTVTYADDQLAKLQKSIWMLQAHL-- > -----A* > > >>P1;madeup > sequence:madeup::::::: > -------------------------------------------MSFIEKMIGS > LNDKREWKAMEARAKAL---PKEYHHAYKAIQKYMWTSGG--PTDWQDTKRIF > GGILDLFEEGAAEGKKVTDLTGE--D--VAAFCDELMKDTKTWMDKYRTKLND > SIGRD-* > > and i want to transfer the coordinates from my template to my sequence > without building the loops. How should I change my code so it would do > that for me??
What's wrong with the script you posted? Looks like it should do exactly what you want to do to me. And how does your question differ from that at http://salilab.org/archives/modeller_usage/2007/msg00200.html ? I thought that had already been resolved.
Ben Webb, Modeller Caretaker
Ali Algarrous wrote: > I'm sorry but it seems I didn't explain myself clearer. > > What I asked for last time is different than what I'm asking now. > This time I want the script to transfer the coordinates for aligned > residues only and nothing that is not aligned. So the MSFIEKMIG in > my sequance is not going to have any coordinates because it was not > aligned with anything from my templae.
That's straightforward - leave out the mdl.build(...) command from your script. transfer_xyz only transfers the known coordinates, so the coordinates for your loop atoms will end up 'undefined' (999).
(On the other hand, if you are calling mdl.build() because you have missing atoms in some of your non-loop residues which you want Modeller to fill in for you, you could leave mdl.build() in to build all coordinates, then select all of your loops using model.loops(), then use selection.unbuild() to reset the coordinates of the loop atoms to 'undefined'.)
Ben Webb, Modeller Caretaker
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Ali Algarrous -
Modeller Caretaker