VMD-L Mailing List

From: Samuel Coulbourn Flores (scflores_at_stanford.edu)
Date: Mon Nov 05 2007 - 02:42:48 CST

HI Guys,

So I used molefacture to rotate the dihedral angles in my molecule.
However the result of this is hard to understand. The dihedral angle
targetted in fact changes, but instead of the entire molecule
downstream rotating together, an (as far as i can tell) aritrary
point is chosen at which to "break" the chain. Everything downstream
of this break remains stationary. How can I make it so the entire
molecule to one side of the dihedral rotates together? Even better
would be to be able to choose which side of the molecule rotates and
which side is the anchor.

Many thanks,

Sam

On Nov 4, 2007, at 11:53 AM, John Stone wrote:

> Hi,
> It was posted just the other day, but for your convenience
> I've attached a copy of it to this email. I'll update the
> script library web page with this version since a lot of people
> need it these days.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Sun, Nov 04, 2007 at 12:46:13PM -0700, Dong Xu wrote:
>> Hi John, I remember you mentioned before about the
>> bigdcd_wait_until_done script. Could you tell me where I can download
>> it from? I have a 50GB trajectory file. bigdcd didn't work well, it
>> only processed a few hundreds frame and quit.
>>
>> Thanks,
>> Dong Xu
>>
>> On 11/3/07, John Stone <johns_at_ks.uiuc.edu> wrote:
>>>
>>> Hi,
>>> Luis' RMSDTT plugin can do the both of the alignments you're
>>> asking about
>>> without having to write scripts etc. Please see the
>>> documentation for
>>> it here:
>>> http://www.ks.uiuc.edu/Research/vmd/plugins/rmsdtt/
>>>
>>> Read the section "calculation type", and "reference molecule" in
>>> particular.
>>>
>>> Cheers,
>>> John Stone
>>> vmd_at_ks.uiuc.edu
>>>
>>> On Thu, Nov 01, 2007 at 03:52:12PM -0600, Zhaochuan Shen wrote:
>>>> Hi all,
>>>>
>>>> I have two quesiotns:
>>>>
>>>> 1) For all the scripts posted on the website and plugins about
>>>> RMSD, there
>>>> are feature about alignment. Why people want to do alignment?
>>>> How people do
>>>> this? The scripts are not very clear. Just "measure fit" and
>>>> then "move".
>>>> 2) I have a long trajectory (100000 frames) and want to find out
>>>> RMSD
>>>> for some alpha carbons. The reference is average coordinate. Is
>>>> there any
>>>> standard process? What I did is exprot the trajectory and then
>>>> use RMSDTT
>>>> plugin directly. Do I need to do the alignment? Or anyone can
>>>> give a
>>>> standard process? Thanks!
>>>>
>>>> Wishes,
>>>> Zhaochuan
>>>
>>> --
>>> 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
>>>
>
> --
> 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
> <mybigdcd.tcl>