0000085: Pyrosetta pose_from_rcsb assumes dimer

(0000080)
jecorn (Developer)
2012-08-22 10:30

The easiest fix for this might be to just dump *.mono.pdb regardless of whether or not the the oligomer argument to cleanCRYS is correct. This doesn't fix much, but at least prevents pose_from_rcsb from crashing.

./rosetta/__init__.py
426a427
> pose.dump_pdb(pdb_file[:-4]+'.mono.pdb')

(0000081)
evanbaugh (Developer)
2012-08-22 10:44

cleanCRYS should be deprecated within the week, it was never fully tested and uses a very hacky method to assess identical chains
in any case, cleanCRYS should have an input for specifying the size to check (i.e. 2 for monomer, 3 for trimer, etc.) which defaults to 2
pose_from_rcsb has the "CRYS" option- but it doesn't allow you to specify size so in this context it really means "check for a dimer of sequences"
you should be able to use
load_from_rcsb
cleanATOM
cleanCRYS
pose_from_pdb
to accomplish what you want
a much fancier version of this should be available soon
sorry for the confusion, I'll close this out once its officially deprecated

(0000114)
jecorn (Developer)
2012-10-04 18:59

Reminder sent to: evanbaugh

Hi Evan. Any progress on this?

(0000137)
jecorn (Developer)
2013-01-04 13:09

Hi evan. Still wondering about this bug... I'm teaching a PyRosetta class using non-dimers, and it's causing some problems.

(0000246)
jecorn (Developer)
2013-04-03 11:15

Reminder sent to: evanbaugh

ping

Issue History
Date Modified	Username	Field	Change
2012-08-21 17:41	jecorn	New Issue
2012-08-21 19:20	Labonte	Assigned To	=> evanbaugh
2012-08-21 19:20	Labonte	Status	new => assigned
2012-08-22 10:30	jecorn	Note Added: 0000080
2012-08-22 10:44	evanbaugh	Note Added: 0000081
2012-10-04 18:59	jecorn	Note Added: 0000114
2013-01-04 13:09	jecorn	Note Added: 0000137
2013-04-03 11:15	jecorn	Note Added: 0000246

Notes
(0000080) jecorn (Developer) 2012-08-22 10:30	The easiest fix for this might be to just dump *.mono.pdb regardless of whether or not the the oligomer argument to cleanCRYS is correct. This doesn't fix much, but at least prevents pose_from_rcsb from crashing. ./rosetta/__init__.py 426a427 > pose.dump_pdb(pdb_file[:-4]+'.mono.pdb')

(0000081) evanbaugh (Developer) 2012-08-22 10:44	cleanCRYS should be deprecated within the week, it was never fully tested and uses a very hacky method to assess identical chains in any case, cleanCRYS should have an input for specifying the size to check (i.e. 2 for monomer, 3 for trimer, etc.) which defaults to 2 pose_from_rcsb has the "CRYS" option- but it doesn't allow you to specify size so in this context it really means "check for a dimer of sequences" you should be able to use load_from_rcsb cleanATOM cleanCRYS pose_from_pdb to accomplish what you want a much fancier version of this should be available soon sorry for the confusion, I'll close this out once its officially deprecated

(0000114) jecorn (Developer) 2012-10-04 18:59	Reminder sent to: evanbaugh Hi Evan. Any progress on this?

(0000137) jecorn (Developer) 2013-01-04 13:09	Hi evan. Still wondering about this bug... I'm teaching a PyRosetta class using non-dimers, and it's causing some problems.

(0000246) jecorn (Developer) 2013-04-03 11:15	Reminder sent to: evanbaugh ping

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