Hi all,
I was running the Match application and :
1. I noticed that some outputted PDBs are annotated in the log file as follows (I am using cloudPDB as output format):
protocols.match.output.PDBWriter: (0) beginning writing cloud for group 471
protocols.match.output.PDBWriter: (0) 0 upstream hits and 0 downstream hits for geom cst 1
protocols.match.output.PDBWriter: (0) 0 upstream hits and 0 downstream hits for geom cst 2
protocols.match.output.PDBWriter: (0) A total of 1 models were written for match group 471 in 1 files.
Indeed, after checking some of these outputs, I found that the cst blocks are not (fully) satisfied by the models created.
Is normal behaviour for the match outputter to create cloud groups and models even when it finds no hits? Am I missing something?
Is there a way to filter out (or even better, to not output) these groups showing no hits for my cst?
2. I wanted to play with the collision filters parameters. In particular, I find that in most outputs I have big clashes of my substrate with the side chains of my scaffold. I would like to filter out all matches showing upstream-downstream clashes. Though, I dont seem to manage. By adding, removing any type of collision-related flag or by changing their values, no match gets actually filtered.
About the collision filter flags: does "upstream" refer to all residues of the scaffold or only to the newly introduced residues based on the cst? And are the sidechains included or just collisions with the backbone are filtered out?
By using the flag "-bump_tolerance 0", am I filtering out clashes with both sidechains and backbone of the whole scaffold?
Is there a combination of flags and/or their values that would help me achieve what I want or, at least, matches with small/less clashes with the sidechains?
The output I get in the logfile is the one below:
Created UpstreamCollisionFilter
core.scoring.etable: (0) Starting energy table calculation
core.scoring.etable: (0) smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: (0) smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: (0) smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: (0) Finished calculating energy tables.
Created UpstreamDownstreamCollisionFilter
...
protocols.match.output.MatchProcessor: (0) No matches failed any filter.
Thank you in advance!