VMD-L Mailing List

From: Samuel Flores (samuel.flores_at_yale.edu)
Date: Thu Nov 01 2007 - 13:58:13 CDT

        
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