Thanks Blaine and Thomas for the timely helps - what a life saver! Much appreciated, -yong
On Thu, Jun 4, 2020 at 3:09 AM Thomas Holder <thomas.hol...@schrodinger.com> wrote: > 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. > >
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