pymol-users

[PyMOL] How to rotate entire section of structure relative to rest

[Alex T. <at...@bu...>]

Hi All,

I'm relatively new to this software, and even though I've been using it for
a few months, I haven't really had to use some of the more advanced options
yet. This would be my first foray into actual manipulation.

That being said, I'm trying to figure out how to move a small section at
the N-terminus of my protein while keeping the rest static. That is, I'd
just like to be able to rotate one bond and fix the relative positions and
structures of the entire rest of the protein. I did some googling, and
there was something about a Sculpting feature, but when I tried it,
sections lit up that I was not interested in, and I was basically moving
tiny sections at a time without preserving the structures I wanted. Is
there a way to just manipulate the angle so I can swing that section out
and away from its current position? I'll deal with the positions of those
individual residues if this cannot method cannot resolve my problem.

Thanks,
Alex

Re: [PyMOL] How to rotate entire section of structure relative to rest

[David H. <li...@co...>]

If you are comfortable with the command line interface, you can use http://pymolwiki.org/index.php/Set_Dihedral 

-- 
David Hall


On Monday, October 22, 2012 at 4:27 PM, Alex Truong wrote:

> Hi All,
> 
> I'm relatively new to this software, and even though I've been using it for a few months, I haven't really had to use some of the more advanced options yet. This would be my first foray into actual manipulation.
> 
> That being said, I'm trying to figure out how to move a small section at the N-terminus of my protein while keeping the rest static. That is, I'd just like to be able to rotate one bond and fix the relative positions and structures of the entire rest of the protein. I did some googling, and there was something about a Sculpting feature, but when I tried it, sections lit up that I was not interested in, and I was basically moving tiny sections at a time without preserving the structures I wanted. Is there a way to just manipulate the angle so I can swing that section out and away from its current position? I'll deal with the positions of those individual residues if this cannot method cannot resolve my problem.
> 
> Thanks,
> Alex
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Re: [PyMOL] How to rotate entire section of structure relative to rest

[Thomas H. <sp...@us...>]

Hi Alex,

sculpting is not the right tool for your task. PyMOL has all the basic 
editing features like rotating around a bond etc. Enter "Editing" mode, 
pick a bond with the mouse and rotate around the bond by pressing CTRL 
and click-dragging a second atom.

You can enter Editing Mouse Mode by clicking on the lower-right panel.

Hope that helps.

Cheers,
   Thomas

On 22.10.2012 22:27, Alex Truong wrote:
> Hi All,
>
> I'm relatively new to this software, and even though I've been using it
> for a few months, I haven't really had to use some of the more advanced
> options yet. This would be my first foray into actual manipulation.
>
> That being said, I'm trying to figure out how to move a small section at
> the N-terminus of my protein while keeping the rest static. That is, I'd
> just like to be able to rotate one bond and fix the relative positions
> and structures of the entire rest of the protein. I did some googling,
> and there was something about a Sculpting feature, but when I tried it,
> sections lit up that I was not interested in, and I was basically moving
> tiny sections at a time without preserving the structures I wanted. Is
> there a way to just manipulate the angle so I can swing that section out
> and away from its current position? I'll deal with the positions of
> those individual residues if this cannot method cannot resolve my problem.
>
> Thanks,
> Alex

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen