Hi Hena,

if you only have CA atoms, you probably need this as well:

# assign secondary structure
alter all, ss="L"
alter resi 10-36, ss="H"
alter resi 50-56, ss="S"

# show cartoon
set cartoon_trace_atoms
as cartoon

# and eventually...
set cartoon_discrete_colors

Cheers,
   Thomas

Sampson, Jared wrote, On 07/10/12 19:50:
> Hi Hena - 
> 
> You can type the following commands in the command line of the pymol 
> graphics window, one at a time.
> 
> 
> color red, ss h
> color yellow, ss s
> color white, ss l+''
> 
> 
> If you don't mind the loops being green, you could also use the first 
> preset under the Color menu for your object.
> 
> [C] > by ss > helix sheet loop (choose the colors you want)
> 
> Hope that helps,
> Jared
> 
> --
> Jared Sampson
> Xiangpeng Kong Lab
> NYU Langone Medical Center
> 550 First Ave MSB 398
> New York, NY 10016
> 212-263-7898
> http://kong.med.nyu.edu/
> 
> On Jul 10, 2012, at 1:39 PM, Hena Dutta wrote:
> 
>> Hi,
>>
>> Sorry, I forgot to mention that, I have only C-alpha coordinates of 60 
>> chains in one pdb file.
>>
>> I have 60 identical chains. Each chain is about 140 residues. Residues 
>> from 10-36 is helix and residues from 50-56 is beta sheet. I want to 
>> prepare a cartoon diagram displaying helix and sheet in red and yellow 
>> color respectively and the rest part(loop) in white. I need to do this 
>> for all 60 chains in diagram. Can someone help me? what commands I can 
>> use for this?
>> Regards... 

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

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