Hi
Is there a problem with automatic disulfides in Modeller 6? My recent models are being produced without the disulfides present in the templates and I don't remember this being a problem with earlier versions. In the log file there is a call to the relevant patch routine
TOP_________> 151 465 PATCH_SS_TEMPLATES
but it doesn't seem to work. The template files have been processed so that they have lost PDB headers but I assume MODELLER figures SS bonds for itself rather than reading SSBOND lines in PDB headers...
We can always define the disulfides manually with the general PATCH command but, as the manual says, they'll be better defined by PATCH_SS_TEMPLATES - generated restraints.
Thanks for your help.
Daniel
+-------------------------------------------------------------------------+ | Dr Daniel John Rigden | | CENARGEN/EMBRAPA | e-mail: daniel@cenargen.embrapa.br | | Parque Estacao Biologica | http://www.cenargen.embrapa.br | | PqEB - Final - Av. W3 Norte | Phone: +55 (61)448-4741 | | 70770-900, Brasilia-D.F.-BRAZIL | Fax: +55 (61)340-3658 | +-------------------------------------------------------------------------+
It should not be a problem. Would you please send me your input top, alignment, and atom files. Thanks, Andrej
-- Andrej Sali, Associate Professor The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399 tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540 e-mail sali@rockefeller.edu; http://salilab.org
-----Original Message----- From: owner-modeller_usage@salilab.org [mailto:owner-modeller_usage@salilab.org] On Behalf Of Daniel John Rigden Sent: Wednesday, January 23, 2002 7:57 AM To: Modeller Usage List Subject: disulfides
Hi
Is there a problem with automatic disulfides in Modeller 6? My recent models are being produced without the disulfides present in the templates and I don't remember this being a problem with earlier versions. In the log file there is a call to the relevant patch routine
TOP_________> 151 465 PATCH_SS_TEMPLATES
but it doesn't seem to work. The template files have been processed so that they have lost PDB headers but I assume MODELLER figures SS bonds for itself rather than reading SSBOND lines in PDB headers...
We can always define the disulfides manually with the general PATCH command but, as the manual says, they'll be better defined by PATCH_SS_TEMPLATES - generated restraints.
Thanks for your help.
Daniel
+----------------------------------------------------------------------- --+ | Dr Daniel John Rigden | | CENARGEN/EMBRAPA | e-mail: daniel@cenargen.embrapa.br | | Parque Estacao Biologica | http://www.cenargen.embrapa.br | | PqEB - Final - Av. W3 Norte | Phone: +55 (61)448-4741 | | 70770-900, Brasilia-D.F.-BRAZIL | Fax: +55 (61)340-3658 | +----------------------------------------------------------------------- --+
Dear Andrej
Thanks for your rapid response. Here's a gzipped tar of the relevant files...
Daniel
+-------------------------------------------------------------------------+ | Dr Daniel John Rigden | | CENARGEN/EMBRAPA | e-mail: daniel@cenargen.embrapa.br | | Parque Estacao Biologica | http://www.cenargen.embrapa.br | | PqEB - Final - Av. W3 Norte | Phone: +55 (61)448-4741 | | 70770-900, Brasilia-D.F.-BRAZIL | Fax: +55 (61)340-3658 | +-------------------------------------------------------------------------+
On Wed, 23 Jan 2002, Andrej Sali wrote:
> It should not be a problem. Would you please send me your input top, > alignment, and atom files. Thanks, Andrej > > -- > Andrej Sali, Associate Professor > The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399 > tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540 > e-mail sali@rockefeller.edu; http://salilab.org > > -----Original Message----- > From: owner-modeller_usage@salilab.org > [mailto:owner-modeller_usage@salilab.org] On Behalf Of Daniel > John Rigden > Sent: Wednesday, January 23, 2002 7:57 AM > To: Modeller Usage List > Subject: disulfides > > > Hi > > Is there a problem with automatic disulfides in Modeller 6? My recent > models are being produced without the disulfides present in the > templates and I don't remember this being a problem with earlier > versions. In the log file there is a call to the relevant patch routine > > TOP_________> 151 465 PATCH_SS_TEMPLATES > > but it doesn't seem to work. The template files have been processed so > that they have lost PDB headers but I assume MODELLER figures SS bonds > for itself rather than reading SSBOND lines in PDB headers... > > We can always define the disulfides manually with the general PATCH > command but, as the manual says, they'll be better defined by > PATCH_SS_TEMPLATES - generated restraints. > > Thanks for your help. > > Daniel > > +----------------------------------------------------------------------- > --+ > | Dr Daniel John Rigden > | > | CENARGEN/EMBRAPA | e-mail: daniel@cenargen.embrapa.br > | > | Parque Estacao Biologica | http://www.cenargen.embrapa.br > | > | PqEB - Final - Av. W3 Norte | Phone: +55 (61)448-4741 > | > | 70770-900, Brasilia-D.F.-BRAZIL | Fax: +55 (61)340-3658 > | > +----------------------------------------------------------------------- > --+ > > > >
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Andrej Sali -
Daniel John Rigden