Re: [modeller_usage] Selection criteria for building sequence database - pdball.pir
To: Praveen Raj <>
Subject: Re: [modeller_usage] Selection criteria for building sequence database - pdball.pir
From: Modeller Caretaker <>
Date: Thu, 05 Nov 2009 10:07:13 -0800
Cc:
Praveen Raj wrote:
I'm trying to rebuild the pdball.pir file from a set of pdb files, using
the model.make_chain() as mentioned in modeller website and I noticed
certain filter criteria as parameters to make_chain() such as
And while processing I found that certain pdb files are skipped due to
this filter criteria. My query is
1) Are these the standard criteria for building pir file?
They're what we use internally to build the database, yes.
2) Or adjusting the values to 0 (except min. res) will alter the purpose ?
You can certainly change these values if you like. The filtering is
there simply to remove "bad" structures, such as those that are not
proteins, are very short chains, or are at very low resolution.