Re: [modeller_usage] Help!!

[Nataraj Balkrishnan <natarajmtech AT yahoo.co.uk>]

hi,

       check it out whether your protein contains any segment name ,since it is missing in alignment file, since  0 residue number in pdb and message of protein not accepted indicates there is a problem in pdb format ,change the format such as ent or pdb and try again and also let me know what happened...(don't use atom format)

B.Nataraj 

"Chaitanya Reddy.A" <chaitanya AT msitprogram.net> wrote:

> Dear all,
> We are modelling a molecule but we are facing a problem to
> which i am unable to find it. We hope you can help me in
> this regard. We want to model a map kinase 8 using the map
> kinase 10 molecule which shows 93% homology. We aligned
> using clustalx and we submitted to modeller as .ali file.
>
> Below is the alignment file we obtained from clustalx
>
> >P1;1jnk
> structureX:1jnk:1 : :346 : :C-JUN N-TERMINAL KINASE::-1.00:
>  2.30
> ------DNQFYSVEVGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAVLDRNVAIKKLSRPFQNQTHAKRAYRELV
> LMKCVNHKNIISLLNVFTPQKTLEEFQDVYLVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHR
> DLKPSNIVVKSDCTLKILDFGLA-----SFMMTPYVVTRYYRAPEVILGMGYKENVDIWSVGCIMGEMVRHKILF
> PGRDYIDQWNKVIEQLGTPCPEFMKKLQPTVRNYVENRPKYAGLTFPKLFPDSLFPADSEHNKLKASQARDLLSK
> MLVIDPAKRISVDDALQHPYINVWYDPAEVEAPPP-----QLDEREHTIEEWKELIYKEVMN-------------
> ----------------------------------------------------*
> >P1;output
> sequence:output:1 : :427 : :JNK mitogen-activated
>  protein
> kinase:2.40:-1.00:-1.00
> MSRSKRDNNFYSVEIGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAILERNVAIKKLSRPFQNQTHAKRAYRELV
> LMKCVNHKNIIGLLNVFTPQKSLEEFQDVYIVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHR
> DLKPSNIVVKSDCTLKILDFGLARTAGTSFMMTPYVVTRYYRAPEVILGMGYKENVDLWSVGCIMGEMVCHKILF
> PGRDYIDQWNKVIEQLGTPCPEFMKKLQPTVRTYVENRPKYAGYSFEKLFPDVLFPADSEHNKLKASQARDLLSK
> MLVIDASKRISVDEALQHPYINVWYDPSEAEAPPPKIPDKQLDEREHTIEEWKELIYKEVMDLEERTKNGVIRGQ
> PSPLGAAVINGSQHPSSSSSVNDVSSMSTDPTLASDTDSSLEAAAGPLGCCR*
>
> After submitting to modeller, the following is the error..
>
> The error message
>
> rdabrk__288W> Protein not accepted: 1
> rdabrk__290E> Number of residues in the alignment and pdb files are
> different:
> 346 0
> For alignment entry: 1
> recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
>
> Please help me in solving this problem.
>
> But we manually examined the number of residues in both pdb files and
> alignment files and we found no
>  difference.
>
> Regards
> Chaitu
>
>
> _______________________________________________
> modeller_usage mailing list
> modeller_usage@listsrv.ucsf.edu
> http://salilab.org/mailman/listinfo/modeller_usage


B.Nataraj,
Final year M.Tech.(Bioinformatics),
SASTRA Deemed University,
(www.sastra.edu)
Thanjavur,
Tamil Nadu,
India.
Email:nataraj AT biotech2.sastra.edu
Email:natarajmtech AT yahoo.co.uk

---

Yahoo! Messenger - Communicate instantly..."Ping" your friends 
today! Download Messenger Now