Hi all, I'm a new user of modeller, I want to know how to conserve residue numbering between my target sequence and the MODEL? I will try to build a final Model using two parts of my protein sequence but I want to conserve the numbering. One of my alignment files looks like this: >P1;2hydA structureX:2hydA:1:A:578::::: ----------------------------------------------MIKRYLQFVKPYKY RIFATIIVGIIKFGIPMLIPLLIKYAIDGVINNHA----------------LTTDEKVHH LTIAIGIALFIFVIVRPPIEFIRQYLAQWTSNKILYDIRKKLYNHLQALSARFYA--NNQ VGQVISRVINDVEQTKDFILTGLMNIWLDCITIIIALSIMFFLDVKLTLAALFIFPFYIL TVYVFFGRLRKLTRERSQALAEVQGFLHERVQGISVVKSFAIEDNEAKNFDKKNTNFLTR ALKHTRWNAYSFAAINTVTDIGPIIVIGVGAYLAISGSITVGTLAAFVGYLELLFGPLRR LVASFTTLTQSFASMDRVFQLIDEDYDIKNG-VGAQPIEIKQGRIDIDHVSFQYNDN-EA PILKDINLSIEKGETVAFVGMSGGGKSTLINLIPRFYDVTSGQILIDGHNIKDFLTGSLR NQIGLVQQDNILFSDTVKENILLG-RPTATDEE-VVEAAKMANAHDFIMNLPQGYDTEVG ERGVKLSGGQKQRLSIARIFLNNPPILILDEATSALDLESESIIQEALDVLSKDRTTLIV AHRLSTITHADKIVVIENGHIVETGTHRELIAKQGAYEHLYSIQNL----* >P1;1pgp sequence:1pgp:43: :630::::: --------------------------------------------SNWLDKLYMVVGTLAA IIHGAGLPLMMLVFGEMTDIFANAGNLEDLMSNITNRSDINDT---GFFMNLEEDMTR-- ----YAYYYSGIGAGVLVAAYIQVSFWCLAAGRQIHKIRKQFFHAIMRQEIGWFD--VHD VGELNTRLTDDVSKINEGIGDKIGMFFQSMATFFTGFIVGFTRGWKLTLVILAISPVLGL SAAVWAKILSSFTDKELLAYAKAGAVAEEVLAAIRTVIAFGGQKKELERYNKNLEEAKRI GIKKAITANISIGAAFLLIYASYALAFWYGTTLVLSGEYSIGQVLTVFFSVLIGAFSVGQ ASPSIEAFANARGAAYEIFKIIDNKPSIDSYSKSGHKPDNIKGNLEFRNVHFSYPSRKEV KILKGLNLKVQSGQTVALVGNSGCGKSTTVQLMQRLYDPTEGMVSVDGQDIRTINVRFLR EIIGVVSQEPVLFATTIAENIRYGREN--VTMDEIEKAVKEANAYDFIMKLPHKFDTLVG ERGAQLSGGQKQRIAIARALVRNPKILLLDEATSALDTESEAVVQVALDKARKGRTTIVI AHRLSTVRNADVIAGFDDGVIVEKGNHDELMKEKGIYFKLVTMQT-----*
Regards, A
Anis PhD Student iBiTec-S/SB2SM Laboratoire Stress oxydant et Détoxication CEA-SACLAY, 91191 Gif-sur-Yvette cedex e-mail: anis.bessadok@cea.fr Tel (33)1-69084432, Fax (33)1-69088717
BESSADOK Anis wrote: > I'm a new user of modeller, I want to know how to conserve residue > numbering between my target sequence and the MODEL?
By default, Modeller numbers the output model sequentially starting from 1. It does not use the residue numbering from the template. There is a good reason for this - how would you number residues that are not aligned with your template? For example, in the second line of your sequence you have the primary sequence 'NRSDINDT---GFFMN' which is aligned with gaps in your template. So what would the residue numbers be?
Secondly, you cannot define residue numbering for a sequence in your alignment file:
>> P1;1pgp > sequence:1pgp:43: :630:::::
The various fields in the alignment header instruct Modeller how to read structural information from a PDB file. They don't make any sense (and are ignored) for a sequence that has no structure. So you may as well say "sequence:::::::::" here. The 1pgp, 43, and 60 fields are not used. A sequence does not have residue numbers - they are a property of the structure.
If all you want to do is have your final model be numbered sequentially starting at residue number 43, that is straightforward. There is a rename_segments() command that will do that - see http://salilab.org/modeller/9v6/manual/node177.html for an example. You can either postprocess your models with this command, or add it into automodel.special_patches() or automodel.user_after_single_model() to do it automatically for each generated model.
If you really want to take residue numbering from a template, there is a res_num_from() command that will do that. But remember that regions in your model that are not aligned with a template will not be renumbered.
Ben Webb, Modeller Caretaker
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BESSADOK Anis -
Modeller Caretaker