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)
> <[email protected]> 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 [[email protected]]
> Sent: Wednesday, June 03, 2020 3:55 PM
> To: [email protected]
> 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
>
>
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--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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