Re: [PyMOL] [EXTERNAL] protecting a group during subsequent aligment

[Thomas H. <tho...@sc...>]

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) <Bla...@ou...> 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 [liu...@gm...]
> Sent: Wednesday, June 03, 2020 3:55 PM
> To: pym...@li...
> 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.