Hi all, I have a little problem with Modeller 8v0. Usually it patches disulfide bonds automatically. But when I try to make model of my protein, it patches only one disulfide instead of five. When I try to define these bonds manually (like in FAQ p.3), the procedure stops and says: TypeError: special_patches() takes exactly 1 argument (2 given) .log file ends immediately. What can be the root of problem? Input files are here. The template is a protein with pdb id 1yi5, slightly minimized in Sybyl. When I use pdb id 1ux2 as a template, there are no problems, and disulfide bonds are on their place.

>P1;1yi5_min structureX:1yi5_min:.:A:.:E: : : : LDRADILYN----IRQTSRPDV--IPTQRDRPVAVSVSLKFINILEVNE ITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVP--ISSLWVPDLAAYNAI S--KPEVLTP-QLARVVSDGEVLYMPSIRQRFSC--DVSGVDTESGATCRI KIGSWTHHSREISVDPT----SDDSEYFSQYSRFEILDVTQKKNSVTYSCC PEAYEDVEVSLNFRKKG-/ LDRADILYN----IRQTSRPDV--IPTQRDRPVAVSVSLKFINILEVNE ITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVP--ISSLWVPDLAAYNAI S--KPEVLTP-QLARVVSDGEVLYMPSIRQRFSC--DVSGVDTESGATCRI KIGSWTHHSREISVDPTT-N-SDDSEYFSQYSRFEILDVTQKKNSVTYSCC PEAYEDVEVSLNFRKKG-/ LDRADILYN----IRQTSRPDV--IPTQRDRPVAVSVSLKFINILEVNE ITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVP--ISSLWVPDLAAYNAI S--KPEVLTP-QLARVVSDGEVLYMPSIRQRFSC--DVSGVDTESGATCRI KIGSWTHHSREISVDPT----SDDSEYFSQYSRFEILDVTQKKNSVTYSCC PEAYEDVEVSLNFRKKGR/ LDRADILYN----IRQTSRPDV--IPTQRDRPVAVSVSLKFINILEVNE ITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVP--ISSLWVPDLAAYNAI S--KPEVLTP-QLARVVSDGEVLYMPSIRQRFSC--DVSGVDTESGATCRI KIGSWTHHSREISVDPTTEN-SDDSEYFSQYSRFEILDVTQKKNSVTYSCC PEAYEDVEVSLNFRKKG-/ LDRADILYN----IRQTSRPDV--IPTQRDRPVAVSVSLKFINILEVNE ITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVP--ISSLWVPDLAAYNAI S--KPEVLTP-QLARVVSDGEVLYMPSIRQRFSC--DVSGVDTESGATCRI KIGSWTHHSREISVDPT--N-SDDSEYFSQYSRFEILDVTQKKNSVTYSCC PEAYEDVEVSLNFRKKG-/ *

>P1;r1 sequence:r1:.:A:.:E: : : : PDITKSPLTKSEQLLRIDDHDFSMRPGFGGPAIPVGVDVQVESLDSISE VDMDFTMTLYLRHYWKDERLSFPSTNNLSMTFDGRLVKKIWVPDMFFVHSK RSFIHDTTTDNVMLRVQPDGKVLYSLRVTVTAMCNMDFSRFPLDT-QTCSL EIESYAYTEDDLMLYWKKGNDSLKTDERISLSQFLIQEFHTTTKLAFYSS- TGWYNRLYINFTLRRHI/ PDITKSPLTKSEQLLRIDDHDFSMRPGFGGPAIPVGVDVQVESLDSISE VDMDFTMTLYLRHYWKDERLSFPSTNNLSMTFDGRLVKKIWVPDMFFVHSK RSFIHDTTTDNVMLRVQPDGKVLYSLRVTVTAMCNMDFSRFPLDT-QTCSL EIESYAYTEDDLMLYWKKGNDSLKTDERISLSQFLIQEFHTTTKLAFYSS- TGWYNRLYINFTLRRHI/ PDITKSPLTKSEQLLRIDDHDFSMRPGFGGPAIPVGVDVQVESLDSISE VDMDFTMTLYLRHYWKDERLSFPSTNNLSMTFDGRLVKKIWVPDMFFVHSK RSFIHDTTTDNVMLRVQPDGKVLYSLRVTVTAMCNMDFSRFPLDT-QTCSL EIESYAYTEDDLMLYWKKGNDSLKTDERISLSQFLIQEFHTTTKLAFYSS- TGWYNRLYINFTLRRHI/ PDITKSPLTKSEQLLRIDDHDFSMRPGFGGPAIPVGVDVQVESLDSISE VDMDFTMTLYLRHYWKDERLSFPSTNNLSMTFDGRLVKKIWVPDMFFVHSK RSFIHDTTTDNVMLRVQPDGKVLYSLRVTVTAMCNMDFSRFPLDT-QTCSL EIESYAYTEDDLMLYWKKGNDSLKTDERISLSQFLIQEFHTTTKLAFYSS- TGWYNRLYINFTLRRHI/ PDITKSPLTKSEQLLRIDDHDFSMRPGFGGPAIPVGVDVQVESLDSISE VDMDFTMTLYLRHYWKDERLSFPSTNNLSMTFDGRLVKKIWVPDMFFVHSK RSFIHDTTTDNVMLRVQPDGKVLYSLRVTVTAMCNMDFSRFPLDT-QTCSL EIESYAYTEDDLMLYWKKGNDSLKTDERISLSQFLIQEFHTTTKLAFYSS- TGWYNRLYINFTLRRHI/ *

# Homology modelling by the automodel class

from modeller.automodel import * # Load the automodel class

log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in

# directories for input atom files env.io.atom_files_directory = './'

a = allhmodel(env, alnfile = 'align.ali', # alignment filename knowns = '1yi5_min', # codes of the templates sequence = 'r1') # code of the target

# Very thorough VTFM optimization: a.library_schedule = 1 a.max_var_iterations = 300

# Very thorough MD optimization: a.md_level = refine.very_slow

# Repeat the whole cycle 3-times and do not stop unless obj.func. > 1E6 a.repeat_optimization = 3 a.max_molpdf = 1e6

a.make() # do the actual homology modelling