This worked--thanks. I have another ? that may have been addressed previously but do not know the answer. Is there a way to do an alignment (or maybe docking is a better word) on two structures/selections and input a constraint for that alignment? For example, i am working on generating a model RE a dimer of two molecules, and I have some data suggesting a range of distances between certain residues of the selection. Is there a way to input that data into Pymol before it completes the alignment, or do I need to use other docking programs to do that? Hope that makes sense. Thanks.
From: Lapolla, Suzanne M (HSC)
Sent: Friday, April 04, 2014 5:11 PM
To: Thomas Holder
Subject: RE: [PyMOL] manual superposition with pymol
Thank you! I will try this and get back to you.
From: Thomas Holder [firstname.lastname@example.org]
Sent: Friday, April 04, 2014 3:16 PM
To: Lapolla, Suzanne M (HSC)
Subject: Re: [PyMOL] manual superposition with pymol
looks like you only deprotected the CA atoms. If you have this as a named selection, try "A > modify > complete > molecules" and deprotect again. Or type:
PyMOL> deprotect bymol (sele)
Instead of working with one object and protecting/deprotecting of subsets of atoms, I suggest to extract the selection that you want to move to its own object. That's usually easier to handle.
On 04 Apr 2014, at 13:38, Lapolla, Suzanne M (HSC) <email@example.com> wrote:
> I am using pymol 1.3 and having trouble with doing manual superposition with my structures. I am able to download my structures, select the portion I want to move manually and, after deprotecting it using the action menu move it using the shift-mouse editing command. When I do this with my selection shown in cartoon mode, things look great, but then when i switch to show my selected residues as sticks, the sticks become huge --they get bigger and/or smaller as I move the structure. Ideas on what I may be doing wrong? Hope this makes sense. Thanks, Suzanne
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