Re: [PyMOL] Secondary structure labeling

[Thomas H. <tho...@sc...>]

Hi Bishwa,

what you want is to label one representative atom per secondary
structure element. So figure out chain and residue number of those
atoms, and label each of them individually:

PyMOL> label A/42/CA, "beta1"
PyMOL> label A/117/CA, "alpha1"
PyMOL> label A/147/CA, "alpha2"

For changing label font, size, color etc., see:
http://pymolwiki.org/index.php/Label

Cheers,
  Thomas

Bishwa Subedi wrote, On 05/08/13 21:50:
> Dear Thomas,
> 
> Thank you. The one you said is to show molecule as cartoon and color
> according to the secondary structure. But I would like to label/name the
> alpha helices as alpha1...and beta strands as Beta1 and so on. Can that
> be done using Pymol. 
> 
> Best
> 
> Bishwa Subedi, M.Sc Bioinformatics
> University of Turku
> Finland
> 
> On May 8, 2013, at 5:33 PM, Thomas Holder wrote:
> 
>> Hi Bishwa,
>>
>> can you be more precise what you mean by "label"? If the secondary
>> structure is defined in the header of your PDB file, PyMOL can show
>> cartoon representation, show text labels on C-alpha atoms and color by
>> secondary structure.
>>
>> PyMOL> as cartoon
>> PyMOL> label name CA, ss
>> PyMOL> color red, ss H
>> PyMOL> color yellow, ss S
>>
>> Cheers,
>>  Thomas
>>
>> Bishwa Subedi wrote, On 05/08/13 13:33:
>>> Hi All,
>>>
>>> I am using Pymol to make figures for my publication. I am not sure if
>>> there has been a discussion earlier but I would like to know how we
>>> can label the secondary structures (helices and strands) using Pymol.
>>> I have them defined in my header file using DSSP.
>>>
>>> Thank you in advance.
>>>
>>> Bishwa Subedi

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor