Re: [PyMOL] Drawing secondary structure for PDB with only Calpha atoms

[Thomas H. <sp...@us...>]

Hi Jon,

this can be done by enabling "cartoon_trace_atoms".

set cartoon_trace_atoms
show cartoon

You can also enable it for your particular object, if you have other 
objects loaded for which the setting should not apply.

set cartoon_trace_atoms, 1, yourcaonlyobject

Hope that helps.

Cheers,
   Thomas

On 11/15/2012 10:14 AM, Jonathan Grimes wrote:
>
>     I have a pdb file, with only Alpha carbon atoms.
>
>     I want to display the secondary structure.   Given that pymol
>     uses the backbone to define SS elements is there a way
>     i can draw the cartoon.
>
>     i have tried explicitly defining ss using alter command
>     but without success. i want to avoid generating the backbone
>     using an external piece of software.
>
>      thanks
>      jon
>
> Dr. Jonathan M. Grimes,
> NDM Senior Reseach Fellow
> University Research Lecturer
> Division of Structural Biology
> Wellcome Trust Centre for Human Genetics
> University of Oxford
> Roosevelt Drive,
> Oxford OX3 7BN, UK
>
> Email: Jon...@st..., Web: www.strubi.ox.ac.uk
> Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547