Hey list,
I'm doing automated modelling of 800+ targets based on 31 templates. 10 structures are produced for each target. Below are the scores (objective function, procheck) for 10 structures of one of the targets.
struct obj func core allow gener disall 1 303.8717 88.20% 11.80% 0.00% 0.00% 2 328.9031 96.10% 3.90% 0.00% 0.00% 3 373.319 88.20% 9.80% 2.00% 0.00% 4 350.9386 94.10% 2.00% 3.90% 0.00% 5 337.4741 90.20% 7.80% 0.00% 2.00% 6 335.0486 90.20% 5.90% 3.90% 0.00% 7 329.6535 96.10% 2.00% 2.00% 0.00% 8 298.5056 96.10% 2.00% 0.00% 2.00% 9 319.118 92.20% 5.90% 2.00% 0.00% 10 333.3913 88.20% 11.80% 0.00% 0.00%
I tried to optimize the refinement of the models and theoretically get better structures. To this end I changed the following parameters:
SET LIBRARY_SCHEDULE = 1 SET MAX_VAR_ITERATIONS = 500 SET MD_LEVEL = 'refine_5' SET REFINE_HOT_ONLY = 0 SET RSTRS_REFINED = 2 SET REPEAT_OPTIMIZATION = 5 SET MAX_MOLPDF = 1E6
Although the calculations took a lot longer, I did not end up with better structures as indicated by the following scores:
struct obj func core allow gener disall 1 773.4081 80.40% 9.80% 7.80% 2.00% 2 973.659 76.50% 7.80% 7.80% 7.80% 3 1356.805 76.50% 9.80% 9.80% 3.90% 4 1084.465 72.50% 15.70% 9.80% 2.00% 5 1073.4241 66.70% 13.70% 9.80% 9.80% 6 1287.894 74.50% 11.80% 7.80% 5.90% 7 823.8506 82.40% 5.90% 11.80% 0.00% 8 1074.581 74.50% 17.60% 7.80% 0.00% 9 909.5347 78.40% 13.70% 5.90% 2.00% 10 1129.2293 80.40% 11.80% 3.90% 3.90%
Is it that refine_5 is not particularly good or is it a combination of the variables that is leading to poor final structures? I would be pleased if somebody could recommend more appropriate parameters for optimizing/refining models.
I have also tried doing external refinement in CNS. However, without any restraints to pass to CNS, the calculations lead to the loss of secondary structure.
I have been comparing the restraint file formats used by MODELLER and CNS. It is not entirely clear to a CNS novice such as myself how one would go about converting a MODELLER formatted restraint file to a CNS acceptable one. Has anybody else looked into this or can recommend another method for external refinement?
Many thanks,
Cvetan