Entering edit mode
10.4 years ago
GreenDiamond
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70
I am looking at a small peptide (PDB_ID: 1Y32) that has one alpha helix.
The PDB file shows 14 models, and I am trying to determine how the alpha helix changes throughout the models. I would like to determine which atoms (n=595) and/or residues (n=40) are part of the alpha helix, in each of the 14 models.
Is this achievable, and if so, what would be an effective (and fairly easy - I do not have much experience) method to do so?
Thanking you!
Thanks Joao. So you are confirming that alpha helical position prediction/information is not in the PDB file? I will look at the DSSP server you suggested! Thanks again.
It depends. The PDB file might or might not show secondary structure information explicitly (through HELIX and SHEET records). If you want to try and use the mmCIF format, you can find this information perhaps more easily and more 'parsable'.
Where are your models coming from?
Hi Joao. My models are coming from the PDB file. There are 14 models, each followed by 392 atomic positions. I can look into mmCIF format; I don't think I have used that before. Thank you!
I meant to ask if the models are coming from a structure in the PDB database or from a modelling program. If they are coming from a modelling program you probably need DSSP because there are probably no HELIX/SHEET records. But if they are coming from the PDB database, just parse the records. mmCIF is somewhat easier to parse and there are a few parsers already out there, for example in Python (Biopython).
Also, for help on understanding the mmCIF format: http://mmcif-beta.wwpdb.org/
A word of caution: secondary structure annotations often do not match with that of DSSP/STRIDE.