The following bug report has been submitted: Platform: windows Chimera Version: 1.8.1 Description Hi, I found some strange behavior in saving pdb file by script file. I tried to modify the orientation of pdb file ‘tst.pdb’ (#1) in reference to axis coordinate (#0), then save the atomic coordinates in pdb file. When I typed in the commands through either command line window or IDLE, transformed coordinates were saved. It worked fine. However, the exact identical commands (inside the brancket) or lines (rc(’..’)) were run by script file shown in below, the untransformed coordinates were saved. This is also the case for “Midas.write method”. I wondered this might be a bug. Regards, Tetsuro Sample.py: ---------------------------------------------- from chimera import runCommand as rc rc('open axis.bild') rc('open tst.pdb') rc('rock y 60 1 center #1 coord #0 models #1') # orientation of tst.pdb was modified rc('focus') rc('write relative #0 #1 tstA.pdb') # write current coordinates to tstA.pdb rc('open tstA.pdb') # opened tstA has original untransformed orientation -----------------------------------------------