[modeller_usage] disulfide bonds

[Dmitry Osolodkin <dmitry_o@org.chem.msu.su>]

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