Transfer_xyz question
Hello,
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??
This is the code that i have been using. from modeller import *
env = environ() env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib')
aln = alignment(env, file='alignment.ali',align_codes=('1ji4', 'madeup')) mdl = model(env)
mdl.generate_topology(aln['madeup'])
# Assign the average of the equivalent template coordinates to MODEL: mdl.transfer_xyz(aln)
# Get the remaining undefined coordinates from internal coordinates: mdl.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES')
# Write the final MODEL coordinates to a PDB file: mdl.write(file='madeup.pdb') Regards, Ali Algarrous
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
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
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Ali Algarrous -
Modeller Caretaker