On 07/19/2010 07:45 AM, Diane Lynch DLLYNCH wrote:
I understood that modeler will assign the radii based on the element in the BLK residue (since there are no parameters or topology for it, e.g. question 1 below). But I think I am misunderstanding how exactly modeler assigns radii for BLK residues, because when i put the following in my python script. m.write(file='outGRASP.pdb', model_format='GRASP') the GRASP.pdb file output has the radii 1.70 for all the atoms in my BLK ligand,e.g. in the outGRASP.pdb for one of the ligand atoms: HETATM 2643 C1 CP5 B 334 -6.583 0.667 16.488 1.70 0.000 e.g. it seems to be assigned the radii of an UNDF atom (not a C atom?) For clarification, how does modeler assign radii (from the radii.lib file) for BLK residues?
You are absolutely right - in fact, both answers are correct in different circumstances (the manual is a bit confusing in this regard - I have checked it against the code and rephrased this section to remove the confusion).
All BLK atoms *in your model* get the CHARMM UNDF atom type. The radius for each BLK atom is thus the radius defined in radii.lib for the UNDF type, as you have observed.
All atoms in non-standard residue types (such as BLK) in template structures will have their CHARMM atom types guessed from the first letter of their PDB atom names. These atom types are, however, only used for calculating template properties such as accessible surface area.
And maybe there are some comments on whether this makes much difference in any case?
I doubt it would make much difference - and in a situation where it did make a difference, it's probably not a good idea to be using BLK residues anyway (since all the other parameters will likely be inaccurate too).
Ben Webb, Modeller Caretaker
--
http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage