Hello Kim,
at first:
http://salilab.org/cgi-bin/lwgate/lwgate/MODELLER_USAGE/archives/modeller_usage.archive.99/date/article-47.html
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:
> 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
--
,
Andras Fiser, PhD # phone: (212) 327 7216
The Rockefeller University # fax: (212) 327 7540
Box 270, 1230 York Avenue # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras