Re: [modeller_usage] PDB updates for Modeller

[Bruno Afonso <brunomiguel@dequim.ist.utl.pt>]

Eswar Narayanan wrote:
> > Since I know this PDB is probably a good model and it won't come up in 
> > seq_search I was wondering how I could manually update CHAINS_all.seq 
> > or create my own sequence database.
>
> The latest release of MODELLER (version 7v7, released last month) has a 
> new command called SEQFILTER that can be used to cluster PDB sequences. 
> You can use MAKE_CHAINS (also in the latest release) to collect the PDB 
> chains prior to running SEQFILTER.
There was a mistake in my previous e-mail. :) The PDB sequence is 
missing, which is *bad*, not good. I'm sorry to ask this questions, but 
I'm still puzzled as to how to deal with this:
1) What's the criteria for make chains_all.seq? I ask this because 
clearly not all of PDB is there :) and there are sequences there with 
resolutions as high as 5.0 angstroms...
2) Can't I make a chains_all.seq alike with MY criteria without making 
my own script? ie, is there a "right way"(TM) to do it?
3) I can use MAKE_CHAINS and then load the .chn as a database, but that 
involves having me first finding the good PDBs that aren't on the 
modeller's DB, which is kind of misses the whole point. I was using 
modeller to try to find the good ones in the first place.
Thanks for the tip on seqfilter, but my problem was the sequence missing 
in the modeller's default database in the first place ;-)
sorry for the inconvenience,
BA

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Bruno Afonso
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