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IDProjectCategoryView StatusDate SubmittedLast Update
0000085PyRosetta[All Projects] Input Handlingpublic2012-08-21 17:412013-04-03 11:15
Assigned Toevanbaugh 
PlatformOSOS Version
Product Version 
Fixed in Version 
Summary0000085: Pyrosetta pose_from_rcsb assumes dimer
Descriptionpose_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.
TagsNo tags attached.
Application(s) AffectedPyRosetta
Command Line Usedall
Developer Options
Fixed in SVN Version
Attached Files

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-  Notes
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.

> pose.dump_pdb(pdb_file[:-4]+'.mono.pdb')
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
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
jecorn (Developer)
2012-10-04 18:59

Reminder sent to: evanbaugh

Hi Evan. Any progress on this?
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.
jecorn (Developer)
2013-04-03 11:15

Reminder sent to: evanbaugh


- 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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