VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Nov 02 2007 - 14:29:14 CDT

Hi Sam,
this can be done using the molefacture plugin; just start molefacture
(extensions->modeling->molefacture) on the section of interest in your
molecule, select the bond that is at the center of the angle you want to
rotate (by holding shift and clicking on the atoms defining that bond),
and use the dihedral slider in the gui. Please let me know if you have
any problems.
Best,
Peter

Samuel Flores wrote:
>
> Hi Guys,
>
> I have a quick question.. is there a quick and easy way to adjust
> dihedral angles for my molecule? I am trying to manually close a loop
> on an RNA hairpin to generate a reasonable starting structure which I
> will subsequently equilibrate to try to find a hopefully somewhat
> accurate structure for the molecule. I've heard PYMOL will do it but
> thought I'd find out first if my default modeling package will do it.
> Also I've seen that VMD-XPLOR will do it, but am not sure if I need to
> install this.
>
> Sam
>
>
> On Oct 31, 2007, at 3:25 PM, John Stone wrote:
>
>>
>> Hi,
>> Have you gone through any of the VMD/NAMD tutorials? If you know
>> the transformation you want to apply to the protein, you can use
>> atom selections and '$sel move' commands and their many variants, to
>> perform rotations, translations, and other operations on the structure.
>> The NAMD structure building tutorials should have more useful
>> examples on
>> this specific type of work, even though much of the building is done
>> within VMD:
>> http://www.ks.uiuc.edu/Training/Tutorials/
>>
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>>
>> On Wed, Oct 31, 2007 at 07:14:12PM +0100, maria goranovic wrote:
>>> CORRECTION:
>>>
>>> the protein does not need to be "aligned along the bilayer normal",
>>> it just
>>> needs to be inserted into the membrane, and its orientation in the
>>> protein
>>> is determined by the angle between the bilayer normal and the axis
>>> of one of
>>> its helices (the angle is 30 degrees)
>>>
>>> Sorry if this was not clear the first time
>>>
>>> -maria
>>>
>>>
>>> On 10/31/07, maria goranovic <mariagoranovic_at_gmail.com> wrote:
>>>>
>>>> Hi
>>>>
>>>> I have a multi-segment protein which needs to be aligned along the
>>>> bilayer
>>>> normal. I have information about the angle between the bilayer
>>>> normal and
>>>> one of the helices of the protein. Once I have the principal axes
>>>> of the
>>>> protein aligned with the coordinates axes, how can I go about using
>>>> the
>>>> angle information to reorient the protein in the membrane ?
>>>>
>>>> Thanks a million for the suggestions,
>>>>
>>>> -Maria
>>>>
>>>> --
>>>> Maria G.
>>>> Technical University of Denmark
>>>> Copenhagen
>>>>
>>>
>>>
>>>
>>> --
>>> Maria G.
>>> Technical University of Denmark
>>> Copenhagen
>>
>> --
>> NIH Resource for Macromolecular Modeling and Bioinformatics
>> Beckman Institute for Advanced Science and Technology
>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
>> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078