Hi Hena - 

If you're not seeing the effects of the "alter" statement, try issuing the command "rebuild" afterward and see if that helps.

Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
550 First Ave MSB 398
New York, NY 10016
212-263-7898

On Jul 10, 2012, at 2:09 PM, Hena Dutta wrote:

Hi Jared,

As I have only C-alpha coordinates. I used
set cartoon_trace, 1

Then I can see a connected smooth ribbon like diagram. I can change the color as follows:
color blue resi 10-23

and this working for all identical chains simultaneously. But, the problem is when I am using
alter resi 10-23, ss='H'
is not working at all.

Hena

On Tue, Jul 10, 2012 at 1:50 PM, Sampson, Jared <Jared.Sampson@nyumc.org> wrote:
Hi Hena - 

You can type the following commands in the command line of the pymol graphics window, one at a time.

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

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?
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