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: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html#pa...
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 3DRS. I hope this helps, Elaine ----- 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