[phenixbb] how impose disulphides in phenix.mr_rosetta?

[Elena Seiradake]

Hello,

Would anyone know an easy way of imposing disulphide bridges during the initial rosetta building step of phenix.mr_rosetta? 

One thing I have tried is putting SSBOND information in the header of the input model + renaming the relevant cysteines to CYD. At the start of the rosetta rebuilding, the CYD residues were indeed read with connections as given in the header. But then it went on reverting what I think are the less "geometrically proper" bridges to CYS and subsequently re-connected them wrongly. The resulting models are completely messed up.  

Any help would be greatly appreciated,
Elena



Details: 
This is my input script

#!/bin/sh 
# 
#Running mr_rosetta with a model that is already place in the unit cell
#
setenv PHENIX_ROSETTA_PATH /rosetta/321
set ROSETTA_BIN = /rosetta/321/rosetta_source/bin

phenix.mr_rosetta \
  seq_file= Seq.dat \
  data= rosettatest.mtz \
  search_models= rosettatest.pdb \
  already_placed=True \
  fragment_files = aat000_03_05.200_v1_3.gz \
  fragment_files = aat000_09_05.200_v1_3.gz \
  rescore_mr.relax=False \
  rosetta_models=20 \
  ncs_copies=1 \
  space_group=r32 \
  use_all_plausible_sg=False \
  nproc=3



Excerpt of rebuild.log:

...(first it reads in the header info)
core.conformation.Conformation: Connecting residues: 48 ( CYD ) and 166 ( CYD ) at atoms  SG  and  SG 
core.conformation.Conformation:  with mututal distances: 3.8087 and 0.733173
core.conformation.Conformation: Connecting residues: 83 ( CYD ) and 93 ( CYD ) at atoms  SG  and  SG 
core.conformation.Conformation:  with mututal distances: 3.09896 and 3.52089
core.conformation.Conformation: Connecting residues: 179 ( CYD ) and 222 ( CYD ) at atoms  SG  and  SG 
core.conformation.Conformation:  with mututal distances: 1.70468 and 1.16652
core.conformation.Conformation: Connecting residues: 208 ( CYD ) and 235 ( CYD ) at atoms  SG  and  SG 
core.conformation.Conformation:  with mututal distances: 2.49179 and 3.53666
core.conformation.Conformation: Connecting residues: 237 ( CYD ) and 248 ( CYD ) at atoms  SG  and  SG 
core.conformation.Conformation:  with mututal distances: 3.73229 and 5.15675
core.conformation.Conformation: Connecting residues: 251 ( CYD ) and 265 ( CYD ) at atoms  SG  and  SG 
core.conformation.Conformation:  with mututal distances: 3.38617 and 3.74316
core.conformation.Conformation: Connecting residues: 268 ( CYD ) and 282 ( CYD ) at atoms  SG  and  SG 
core.conformation.Conformation:  with mututal distances: 2.6711 and 2.63
core.conformation.Conformation: Connecting residues: 284 ( CYD ) and 300 ( CYD ) at atoms  SG  and  SG 
core.conformation.Conformation:  with mututal distances: 0.617564 and 2.38221
core.conformation.Conformation: Connecting residues: 341 ( CYD ) and 355 ( CYD ) at atoms  SG  and  SG 
core.conformation.Conformation:  with mututal distances: 4.70923 and 2.94228
core.conformation.Conformation: Connecting residues: 344 ( CYD ) and 352 ( CYD ) at atoms  SG  and  SG 
core.conformation.Conformation:  with mututal distances: 1.53246 and 3.97459

...(now it goes through the given list and rejects some)
core.conformation.Conformation: Found disulfide between residues 48 166
core.conformation.Conformation: current variant for 48 CYD
core.conformation.Conformation: current variant for 166 CYD
core.conformation.Conformation: current variant for 48 CYD
core.conformation.Conformation: current variant for 166 CYD
core.conformation.Conformation: Found disulfide between residues 83 93
core.conformation.Conformation: current variant for 83 CYD
core.conformation.Conformation: current variant for 93 CYD
core.conformation.Conformation: current variant for 83 CYD
core.conformation.Conformation: current variant for 93 CYD
core.conformation.Conformation: Found disulfide between residues 179 222
core.conformation.Conformation: current variant for 179 CYD
core.conformation.Conformation: current variant for 222 CYD
core.conformation.Conformation: current variant for 179 CYD
core.conformation.Conformation: current variant for 222 CYD
core.conformation.Conformation: Found disulfide between residues 208 235
core.conformation.Conformation: current variant for 208 CYD
core.conformation.Conformation: current variant for 235 CYD
core.conformation.Conformation: current variant for 208 CYD
core.conformation.Conformation: current variant for 235 CYD

...(next one is rejected)
core.conformation.Conformation: Reverting out-of-date disulfide CYD to CYS at resid 237
core.conformation.Conformation: Reverting out-of-date disulfide CYD to CYS at resid 248
core.conformation.Conformation: Found disulfide between residues 251 265
core.conformation.Conformation: current variant for 251 CYD
core.conformation.Conformation: current variant for 265 CYD
core.conformation.Conformation: current variant for 251 CYD
core.conformation.Conformation: current variant for 265 CYD
core.conformation.Conformation: Found disulfide between residues 268 282
core.conformation.Conformation: current variant for 268 CYD
core.conformation.Conformation: current variant for 282 CYD
core.conformation.Conformation: current variant for 268 CYD
core.conformation.Conformation: current variant for 282 CYD
core.conformation.Conformation: Found disulfide between residues 284 300
core.conformation.Conformation: current variant for 284 CYD
core.conformation.Conformation: current variant for 300 CYD
core.conformation.Conformation: current variant for 284 CYD
core.conformation.Conformation: current variant for 300 CYD
core.conformation.Conformation: Reverting out-of-date disulfide CYD to CYS at resid 341
core.conformation.Conformation: Reverting out-of-date disulfide CYD to CYS at resid 344
core.conformation.Conformation: Reverting out-of-date disulfide CYD to CYS at resid 352
core.conformation.Conformation: Reverting out-of-date disulfide CYD to CYS at resid 355

...(now it starts re-connecting, but in the wrong way)
core.conformation.Conformation: Found disulfide between residues 48 222
core.conformation.Conformation: current variant for 48 CYS
core.conformation.Conformation: current variant for 222 CYS
core.conformation.Conformation: current variant for 48 CYD
core.conformation.Conformation: current variant for 222 CYD
core.conformation.Conformation: Found disulfide between residues 83 352
core.conformation.Conformation: current variant for 83 CYS
core.conformation.Conformation: current variant for 352 CYS
core.conformation.Conformation: current variant for 83 CYD
core.conformation.Conformation: current variant for 352 CYD
core.conformation.Conformation: Found disulfide between residues 93 251
core.conformation.Conformation: current variant for 93 CYS
core.conformation.Conformation: current variant for 251 CYS
core.conformation.Conformation: current variant for 93 CYD
core.conformation.Conformation: current variant for 251 CYD
core.conformation.Conformation: Found disulfide between residues 166 282
core.conformation.Conformation: current variant for 166 CYS
core.conformation.Conformation: current variant for 282 CYS
core.conformation.Conformation: current variant for 166 CYD
core.conformation.Conformation: current variant for 282 CYD
core.conformation.Conformation: Found disulfide between residues 179 237
core.conformation.Conformation: current variant for 179 CYS
core.conformation.Conformation: current variant for 237 CYS
core.conformation.Conformation: current variant for 179 CYD
core.conformation.Conformation: current variant for 237 CYD
core.conformation.Conformation: Found disulfide between residues 265 344
core.conformation.Conformation: current variant for 265 CYS
core.conformation.Conformation: current variant for 344 CYS
core.conformation.Conformation: current variant for 265 CYD
core.conformation.Conformation: current variant for 344 CYD
core.conformation.Conformation: Found disulfide between residues 268 284
core.conformation.Conformation: current variant for 268 CYS
core.conformation.Conformation: current variant for 284 CYS
core.conformation.Conformation: current variant for 268 CYD
core.conformation.Conformation: current variant for 284 CYD
...