[Chimera-users] Problems detecting a left-handed helix

Felipe Vasquez anfelvas at gmail.com
Wed Jun 10 09:24:13 PDT 2015


I am trying to visualize several of the secondary structure details on a
protein of interest, and I recently had notice (by several research papers)
about the existence of a left-handed helix on it. However, I could not
detect the helix using UCSF Chimera (it is simply considered as a loop).
Why could this happen and how could be resolved? I have tried to modify the
ksdssp cut-off parameter, but it was unsuccessful, so I think now that
maybe the specific nature of the helix (left-handed polyproline-like type
II) could be a bit tricky for the program. What would you suggest?

Thanks in advance for your help an patience.

Best regards,

*Andrés Felipe Vásquez J., BSc, MSc.*
Grupo de Fisiología Molecular
Subdirección de Investigación Científica y Tecnológica
Dirección de Investigación en Salud Pública
Instituto Nacional de Salud
Avenida calle 26 No. 51-20 - Zona 6 CAN
+57 (1) 2207700 ext. 1419
Bogotá, D.C., Colombia
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