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ID | Project | Category | View Status | Date Submitted | Last Update | ||||||||
0000085 | PyRosetta | [All Projects] Input Handling | public | 2012-08-21 17:41 | 2013-04-03 11:15 | ||||||||
Reporter | jecorn | ||||||||||||
Assigned To | evanbaugh | ||||||||||||
Priority | normal | Severity | major | Reproducibility | always | ||||||||
Status | assigned | Resolution | open | ||||||||||
Platform | OS | OS Version | |||||||||||
Product Version | |||||||||||||
Fixed in Version | |||||||||||||
Summary | 0000085: Pyrosetta pose_from_rcsb assumes dimer | ||||||||||||
Description | pose_from_rcsb (the called cleanCRYS method) seems to assume that an input PDB is a dimer containing two chains of different sequence. So importing 1YY8 (the stock PyRosetta example) works, since it takes a crystal tetramer into a biologically relevant dimer. But importing 1UBQ (or any other monomer) crashes with an error about "not a 2.0-mer", unless CRYS=False is provided. So the current implementation will not monomerize an incoming pdb structure that contains multiple copies with identical sequence. This behavior is not documented. Since most Rosetta work is done with monomers, it might make more sense to default to monomer input (removing other members of the AU), and allow the user to specify multimers to pass to cleanCRYS. This could be done by modifying pose_from_rcsb to take a *-mer int as an argument, then passing that on to cleanCRYS. | ||||||||||||
Tags | No tags attached. | ||||||||||||
Application(s) Affected | PyRosetta | ||||||||||||
Command Line Used | all | ||||||||||||
Developer Options | |||||||||||||
Fixed in SVN Version | |||||||||||||
Attached Files | |||||||||||||
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 |
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 |
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