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Extract PDB structures from database

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Extract PDB structures from database
#1

I am using a RosettaScripts which outputs structure coordinates to a database (.db3). I am trying to extract the individual PDB files. I tried using the following command:

score_jd2.static.linuxgccrelease -inout:database_filename struct.db3
 
 
ERROR: Option matching -inout:database_filename not found in command line top-level context
caught exception ERROR: Option matching -inout:database_filename not found in command line top-level context
 
Any idea of what I can do to fix this?
 
In case you need more info, the RosettaScript XML I am using is in the supplementary materials to this paper: https://www.biorxiv.org/content/early/2017/11/17/221689
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Mon, 2018-01-29 09:30
cossio

It looks like there's a typo on that page. The correct option is `-inout:dbms:database_name` -- the default is a SQLite database, which is a file, but if you do the appropriate extras compile, you can also have MySQL and PostgreSQL support.  Those two database types also use the -inout:dbms:database_name option, but it's not a filename.

Also note that the -inout:dbms:database_name option only sets the database file to be used - it can be used both for input and output (or both). To select whether you are doing structure input or output to the database, use the `-in:use_database` or `-out:use_database` (or both) as appropriate.

Tue, 2018-01-30 07:35
rmoretti

This worked fine some months ago. I am now getting strange errors. Could there have been a change in the newer releases of Rosetta affecting this? I am now using the numbered version 3.10. Here is the error output.

 

Error: [ ERROR ] 
Error: [ ERROR ] Treating failure as bad input; canceling similar jobs
protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: 4_0001
protocols.features.ProteinResidueConformationFeatures: Attempting to set atom coordinates for residue '121'.
The pose residue has '18' coordinates but '17' were provided.
The residue type in the database is 'PRO:NtermProteinFull' and it matches the pose residue type.

Error: [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job '40_0001'
Error: [ ERROR ] 

File: src/protocols/features/ProteinResidueConformationFeatures.cc:521
Atom mismatch in ProteinResidueConformation
 

Wed, 2018-10-17 15:59
cossio