Re: [PyMOL] [EXTERNAL] protecting a group during subsequent aligment
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
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:
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>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
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Re: [PyMOL] [EXTERNAL] protecting a group during subsequent aligment
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)
> 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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Re: [PyMOL] [EXTERNAL] protecting a group during subsequent aligment
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
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