Re: [modeller_usage] how to analyse the output file of align2d.py

[Modeller Caretaker <>]

On 01/29/2012 08:25 PM, Naresh wrote:
> mkapsa__637W> No residue topology library is in memory.
> Better radii would be used if topology.read() is called first.
>
> iup2crm_280W> No topology library in memory or assigning a BLK residue.
> Default CHARMM atom type assigned: N --> N
> This message is written only for the first such atom.

This is just warning you that you didn't read in the CHARMM topology 
library (env.libs.topology.read('${LIB}/top_heav.lib')). Without this, 
Modeller cannot map PDB atom names (such as CB) to CHARMM atom types 
(such as CT2) so it has to guess (it just matches the first letter, C). 
It needs to get the CHARMM atom type to determine the atomic radius, and 
it needs the radius in order to calculate the solvent accessible surface 
area, which is one of the properties that align2d() uses. For standard 
amino acids, Modeller's guess is almost always correct, and the radius 
doesn't dramatically affect the alignment, so you can probably ignore 
these warnings.

	Ben Webb, Modeller Caretaker
--
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