Very difficult to say in general, but I would try a couple of combinations:
0 2 0 3 0 4
0 x ensure that only those pairs of calphas that are within 2 times x are aligned.
Best, andrej
-- Andrej Sali, Professor Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research Mission Bay Genentech Hall 600 16th Street, Suite N472D University of California, San Francisco San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier) Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4239 Email sali@salilab.org; Web http://salilab.org
> -----Original Message----- > From: owner-modeller_usage@salilab.org > [mailto:owner-modeller_usage@salilab.org] On Behalf Of Chris de Graaf > Sent: Thursday, February 27, 2003 4:10 AM > To: modeller_usage@salilab.org > Subject: gap creation and extension penalties > > > Dear Modellers, > > I am working on a structural alignment between 6 protein > structures with an average seq. identity of approx. 25 % and > average homology of approx. 45 %. Usage of default values for > gap creation and extension penalties for structure/structure > superposition (0.0 and 1.75 respecrtively) result in the > introduction of multiple (relatively) large gaps in the > multiple sequence alignment. Of course I can "avoid" this by > increasing both gap creation and extension penalties, but > what I would like to know which penalty values are > "reasonable" in this case. > > Thanking you in advance and with kind regards, > > Chris de Graaf > > > -- > drs. C. de Graaf > LACDR - Division Molecular Toxicology > Department Pharmacochemistry > Vrije Universiteit Amsterdam > De Boelelaan 1083 > 1081 HV Amsterdam > Tel. (31) 020-4447608 > Fax. (31) 020-4447610 > >