Hi Rodrigo, If a PDB file doesn't have HELIX and SHEET information in it, the ksdssp program is used to detect the secondary structure. Ksdssp uses the 3D structure (it doesn't matter what the sequence is). However, even if the 3D structure looks almost the same in the new model as in the original, there are reasons the assignments might be different: (a) the original structure has HELIX and SHEET information in it, and the person who determined that information used a different method than ksdssp, or different parameters (b) the structures are slightly different, causing the strands not to be predicted in the new structure There are some ways you can change the HELIX and SHEET assignments if you feel they are not right: (a) select the residues you think should be in beta-strands, open the Selection Inspector (click the button on the bottom right corner of the Chimera window), Inspect "Residue", set "is strand" to "true" (b) re-run the ksdssp algorithm but with different parameters. Open the Model Panel (Favorites... Model Panel), switch to the "infrequently used" list of functions, choose "compute SS". Try Apply-ing different parameters. If you want particular values of these parameters to always be used (for any proteins without HELIX and SHEET info), you can click "Save as Defaults" I hope this helps, Elaine On Dec 8, 2005, at 4:26 PM, rquiroga@immf.uncor.edu wrote:
Greetings,
I have some concerns with Chimera's secondary structure detection/ depiction.
I am using Modeller to predict some 3D structures.
I open my predicted structure in pdb file in Chimera along with the original structure I based my prediction on, and find that my predicted structure lacks two beta sheets that the model protein has, though the AA that compose the B-sheet are identical for the two proteins when I compare sequences with Matchmaker.
I tried opening my predicted structure in MolMol and it detects the B-sheet, though I hugely prefer Chimera, so if you could solve this problem for me I would be very greatful.
Thanks in advance, and regards
Rodrigo Quiroga _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html