[Chimera-users] To consult the Morph conformation

Elaine Meng meng at cgl.ucsf.edu
Mon Dec 7 10:12:49 PST 2009

Dear Jiraporn,
Sorry, Morph Conformations only includes parts that are in both  
structures in the morphing trajectory.  In your situation, I suggest  
text-editing one of the input PDB files (more details below).

Morph Conformations maps residues in the starting structure to  
residues in the ending structure by creating a sequence alignment.   
Where the residue in the starting structure is aligned with the same  
type of residue in the ending structure, the whole residue will be  
included.  Where the residue in the starting structure is aligned with  
a different type of residue, only the parts that are the same will be  
included, which will include the backbone and sometimes part of the  
sidechain.  Where there are backbone atoms, you can show a ribbon.  If  
the residue is aligned with a gap, it will not be included.

Here is the explanation in the manual:

Currently Morph Conformations will only use the sequence alignment it  
figures out itself.  A future improvement will be to allow the user to  
provide the sequence alignment (perhaps avoiding some of the gaps),  
but that is not available yet.

I took a look at your proteins, 3DRR and 3DRS.  They are the same  
protein, and the only difference is that the 3DRR crystal structure  
has more residues at the C-terminal end, forming a helix.  3DRR ends  
at 557 and 3DRS ends at 548.  I guess you want that end part shown in  
the morphing trajectory.  The structures look nearly the same in the  
residues before the difference, so to do this I would just use a text- 
editor and add the end residues from 3DRR onto the 3DRS structure.   
For example, make a copy of the 3DRR PDB file, then edit it to replace  
543-end with 543-end from the 3DRS PDB file.  Then you would just open  
the new edited 3DRR with the longer tail and then morph from that to  

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Dec 5, 2009, at 1:29 AM, Nok :p wrote:

> Dear Chimera teme,
> First of all, I would like to introduce myself. My name is Jiraporn  
> Yongpisanphop. Now, I am a master student of KMUTT university in  
> Bioinformatics field.
> My thesis topic involve in drug design. A part of my work is  
> concerning about overaly binding pocket of single mutant enzymes  
> (PDB file: 3DRR and 3DRS). And, I
> use Morph Conformation method. It is good but it not complete for my  
> work. Because the intermedate structure was generate from compare of  
> same amino acid
> of both structures. However, the difference amino acid was kept only  
> reference model. Therefore, I would like to consult you how I will  
> keep amino acid that
> differece of both structures into intermediate structure.
> Thank you very much for your kind.
> Best regards,
> Jiraporn

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