VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 09 2009 - 16:41:32 CST

Hi,
  I believe this is caused by a bug in some old "fall back" code that
handles cases with fewer than 4 atoms. I haven't tested your example
yet, but it may or may not work with the current test versions of VMD
1.8.7, I'll have to try and see. I didn't write the code in question
so I'll have to dig into it to see what can be done to work around this
and a couple of other bugs that have cropped up. As I recall, the fall-back
code is just translating the first atoms to coincide, and then rotating
around that one to place the second, and then rotating along that bond
to place the third. As I recall the code will not deal with cases where
the order of atoms is different in the two structures, though your note
didn't indicate that as a possibility in the problem you encounterd.
Anyway, I'll try and look at this next week and get back to you on it.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Feb 03, 2009 at 01:51:02PM -0800, Leontyev Igor wrote:
> I used VMD tool for matching structures without any problem until tried to
> fit atom triplets. For these structures the command "measure fit" in a
> script produces irrelevant transformation matrix. Program move second
> structure far away (to almost infinity) instead of aligning the structures.
> Use of graphical RMSD Tool leads to the same result. The structures are
> given bellow. I use VMD with WindowsXP. How the problem can be fixed?
>
> seltriplet0.pdb:
>
> CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
> ATOM 1 C18 HEA X 516 41.696 310.454 201.293 1.00 0.00
> ATOM 2 C19 HEA X 516 40.504 310.822 201.821 1.00 0.00
> ATOM 3 C27 HEA X 516 40.284 312.095 202.581 1.00 0.00
> END
>
>
>
> seltriplet1.pdb
>
> CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
> ATOM 1 C18 HEA X 515 47.812 311.246 202.665 1.00 0.00
> ATOM 2 C19 HEA X 515 47.564 312.299 203.472 1.00 0.00
> ATOM 3 C27 HEA X 515 46.342 313.148 203.243 1.00 0.00
> END 

-- 
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