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
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@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
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B.Nataraj, Final year M.Tech.(Bioinformatics), SASTRA Deemed University, (www.sastra.edu) Thanjavur, Tamil Nadu, India. Email:nataraj@biotech2.sastra.edu Email:natarajmtech@yahoo.co.uk --------------------------------- Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now
Hi,
Residue count in 1JNK goes from 45-400 instead 1-346. It should be:
structureX:1jnk: 45 : :400 : :C-JUN N-TERMINAL KINASE::-1.00: 2.30
Also, you are trying to model a large number of residues for which you don't have a template. I suggest cutting the ends of your alignment to look like this:
... MLVIDPAKRISVDDALQHPYINVWYDPAEVEAPPP-----QLDEREHTIEEWKELIYKEVMN* ... MLVIDASKRISVDEALQHPYINVWYDPSEAEAPPPKIPDKQLDEREHTIEEWKELIYKEVMD*
The same applies to the first 6 residues in your protein.
Hope this helps,
Mensur
On Fri, 7 May 2004, Chaitanya Reddy.A 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
========================================================================== | Mensur Dlakic, Ph.D. | Tel: (406) 994-6576 | | Department of Microbiology | Fax: (406) 994-4926 | | Montana State University | http://www.umich.edu/~mensur/ | | 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur | | Bozeman, MT 59717-3520 | E-mail: mdlakic@montana.edu | ==========================================================================
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Chaitanya Reddy.A -
Mensur Dlakic -
Nataraj Balkrishnan