VMD-L Mailing List

From: Qmer_AN?= (bounlu_at_gmail.com)
Date: Mon Jun 06 2011 - 12:30:04 CDT

Hi,

I have XY homodimer complex structure obtained from docking. Although the inital structures are identical (X=Y), their coordinates are apparently changed after several steps of docking even if slightly. Then by using measure fit command in VMD, I superimposed the Y of one complex with the X of another and so. So my structure goes like X-(YX)-(YX)-...-(YX)-Y. Here Y is translated onto the X so that their RMSD is minimized by measure fit function but still I have the coordinates of X and Y separately. Now I want to creatae one PDB file containing the coordinates of the chain X-A-A-...-A-Y where A is the combined averaged (?) coordinates of X and Y that are superimposed. Is it possible? How can I obtain these new coordinates of superimposed structure as single file?