Hi Yong and Blaine, The "alignto" command actually does allow you to specify the "mobile" objects.
PyMOL>alignto ? Usage: alignto [ target [, method [, selection [, quiet ]]]] For example, you could disable all excluded objects and then use "enabled" as the selection: disable obj1 obj2 obj3 alignto ref, super, enabled The alternative for such a heavy task would be a custom loop in Python: python for name in cmd.get_object_list(): if name != "ref": cmd.super(name, "ref") python end By the way, "alignto" is just a wrapper for "extra_fit", with different argument order and default arguments. See also: https://pymolwiki.org/index.php/Extra_fit Cheers, Thomas > On Jun 4, 2020, at 12:12 AM, Mooers, Blaine H.M. (HSC) > <blaine-moo...@ouhsc.edu> wrote: > > Hi Yong, > > Maybe you tried this already, but you might try reducing the use of RAM by > superposing all 500 structures represented as CA traces > ('ribbons' in PyMOL) or even show the CA atoms as lines (show lines, name ca > and i. *) and then switch representation after alignment. > > Best regards, > > Blaine > > Blaine Mooers, Ph.D. > Associate Professor > University of Oklahoma Health Sciences Center > Oklahoma City, OK 73104-5419 > > ________________________________________ > From: Yong Tang [liutan...@gmail.com] > Sent: Wednesday, June 03, 2020 3:55 PM > To: pymol-users@lists.sourceforge.net > Subject: [EXTERNAL] [PyMOL] protecting a group during subsequent aligment > > Dear all, I have a task to overlay 500+ structures onto a reference structure > "ref", as the body of data is big, I decided to do them in chunks, 100 at a > time (after crashing pymol on my Windows laptop for a few times attempting > it). This is the commend that I used for the first 100: > > alignto ref, method=super. > > This worked perfectly for most entries, but not for all, so I manually > adjusted some entries, and then grouped them into chunck1. > > Now I'm ready to move on to the next chunk; I realized I wanted to protect > the processed entries from being moved/aligned again as the alignto doesn't > allow specification of the "mobile". I applied the /Actions/Movement/Protect > on group chunk1, but that didn't seem to prevent the entries in there to be > moved/aligned again. > > Any clue how to fix my problem? > > Many thanks, -yong > > > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe