I have built a protein structure using MODELLER and would like to compare it with the actual crystal structure using the COMPARE routines. The MODELLER protein and XRAY protein have the same sequence but the MODELLER protein is numbered from 1-494 and the XRAY protein is numbered from 7-500 and contains multiple chains. So MODELLER complains:
sequence difference between alignment and pdb
compare_W> some residues are without DISTANCE_ATOMS atom
So is there something simple I can do to make this compare script work?
I am thinking that I can delete the other chains and renumber the residues in the xray structure file to make it look similar to the MODELLER produced file but was hoping there was something easier to do.
Any help would be much appreciated.
Thanks to all who contributed to the discussion on solving the problem with the COMPARE scripts. I deleted the extra chains, etc from the xray PDB and then renumbered the residues so that they matched with the MODEL pdb. This solved the problem when comparing the model and the actual structures. But when I tried to add the template to the comparison (just like they do in the example script) along with reading in the alignment file, MODELLER complains. The error seems to be with the MODEL and xray pdb, not the template... that seems weird since it was successful without the template or the alignment file. I'll look into it some more.
Again thanks for the responses.