Import Dunbrack PISCES lists instead of PDBselect (Feature #1502)


Added by Donnie Berkholz - almost 5 years ago. Updated almost 5 years ago.


Status:Closed Start date:
Priority:Blocker Due date:
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Category:Splicer Spent time: -
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Description

We're gonna start using lists from http://dunbrack.fccc.edu/Guoli/pisces_download.php instead of the current ones, so we'll need to know how to read those. The two that will directly replace our existing ones are:

http://dunbrack.fccc.edu/Guoli/culledpdb/cullpdb_pc25_res3.0_R1.0_d090606_chains6414.gz
http://dunbrack.fccc.edu/Guoli/culledpdb/cullpdb_pc90_res3.0_R1.0_d090606_chains16437.gz

The file naming is described on that page. Basically, pcXX is equivalent to our threshold, res is resolution, R is the R-factor, d is the release date, and chains just says how many proteins are in the file.

The format is also straightforward:

IDs         length Exptl.  resolution  R-factor [[FreeRvalue]]
7ODCA 424 XRAY 1.600 0.20 0.23
2AXPA 173 XRAY 2.500 0.26 0.29
2QUDA 125 XRAY 1.600 0.16 0.20
1WBAA 175 XRAY 1.800 0.19 1.00
1M2ZB 21 XRAY 2.500 0.27 0.27

The "ID" field is the PDB code + the chain ID. We can also easily get the resolution, R-factor and R-free from this instead of hacking around with mmLib.


History

Updated by almost 5 years ago

Implemented a Pydra Task for selecting using these files.

One thing to note is that the filenames can change based on how many proteins are in the file. I'm using threshold list, resolution, and r-factor to build a regex to match files to download and process. This may need to be expanded upon to give greater flexibility for selecting from the pre-culled files.

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