Hi Chung-Ming Yu,

You can change the secondary structure identifiers as follows:

alter helix_selection,ss='H'
alter sheet_selection,ss='S'
alter loop_selection, ss='L'

The RMS deviation gives you information about the quality of the fit. The lower the number, the better the fit.

Cheers,

Tsjerk

On 10/8/05, yucmbuu <yucmbuu@gate.sinica.edu.tw> wrote:
Dear All:

I made two protein models from one known pdb by using SWISS-MODEL server. I
superimpose these three pdb with pymol. However, I need to modified the
secondary structure of these structures after "procheck". How could I using
"alter" command to modified one structure at once? Is it meaningful that
RMS scores were obtained by using "align" command in pymol? Thanks for your
help.

Chung-Ming Yu
Inst. Biol. Chem.
Academia Sinica




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--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336