Hi
I try to model a chimeric protein based on FAQ 4
To test the method I took a PDB file and cut it in two parts and then try to model the complete molecule again based on an FAQ 4
I get the error:
fit2xyz_E> number of equivalent positions < 3: 0 recover__> ERROR_STATUS >= STOP_ON_ERROR: 1 1
As I understand it there are not enough overlapping residues in the alignment. But that is exactly the point, I try to model a chimeric protein based on the independent fragments exactly as in FAQ 4.
What is wrong?
Does the templates have to be overlapping, and is FAQ 4 wrong?
All files are attached
Thanks in advance
Kim
------------------------------------------------------------------------ Kim Vilbour Andersen, PhD Senior Scientist Maxygen Agern Allé 1 DK-2970 Hørsholm Denmark <<model.top.gz>> <<align.pir.gz>> <<1GR3_A2.pdb.gz>> <<1GR3_A1.pdb.gz>> Tel: +45 7020 5550 Direct: +45 4517 8473 Mobile: +45 2637 3727 Fax: +45 7020 5530
E-mail: kva@maxygen.dk http://www.maxygen.dk/ ------------------------------------------------------------------------
Hello Kim,
at first:
http://salilab.org/cgi-bin/lwgate/lwgate/MODELLER_USAGE/archives/modeller_us...
but it is an old message about and an older version. If you use mod6v2 it will be checked automatically: even if your templates are not overlapping the modeling will be done , but I would like to call your attention on our remark in the manual:
"If no additional information is available about the relative orientation of the two domains the resulting model will probably have an incorrect relative orientation of the two domains when the overlap between A and B is non-existing or short. To obtain satisfactory relative orientation of modeled domains in such cases, orient the two template structures appropriately before the modeling. " best regards Andras
"Andersen, Kim Vilbour (KVA)" wrote: > > Hi > > I try to model a chimeric protein based on FAQ 4 > > To test the method I took a PDB file and cut it in two parts and then try to model the complete molecule again based on an FAQ 4 > > I get the error: > > fit2xyz_E> number of equivalent positions < 3: 0 > recover__> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > As I understand it there are not enough overlapping residues in the alignment. But that is exactly the point, I try to model a chimeric protein based on the independent fragments exactly as in FAQ 4. > > What is wrong? > > Does the templates have to be overlapping, and is FAQ 4 wrong? > > All files are attached > > Thanks in advance > > Kim > > ------------------------------------------------------------------------ > Kim Vilbour Andersen, PhD > Senior Scientist > Maxygen > Agern Allé 1 > DK-2970 Hørsholm > Denmark > <<model.top.gz>> <<align.pir.gz>> <<1GR3_A2.pdb.gz>> <<1GR3_A1.pdb.gz>> > Tel: +45 7020 5550 > Direct: +45 4517 8473 > Mobile: +45 2637 3727 > Fax: +45 7020 5530 > > E-mail: kva@maxygen.dk > http://www.maxygen.dk/ > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------ > Name: model.top.gz > model.top.gz Type: application/x-gzip > Encoding: base64 > Description: model.top.gz > > Name: align.pir.gz > align.pir.gz Type: application/x-gzip > Encoding: base64 > Description: align.pir.gz > > Name: 1GR3_A2.pdb.gz > 1GR3_A2.pdb.gz Type: chemical/x-pdb > Encoding: base64 > Description: 1GR3_A2.pdb.gz > > Name: 1GR3_A1.pdb.gz > 1GR3_A1.pdb.gz Type: chemical/x-pdb > Encoding: base64 > Description: 1GR3_A1.pdb.gz
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Andersen, Kim Vilbour (KVA) -
Andras Fiser