VMD-L Mailing List

From: John C. H. Chao (f93223037_at_ntu.edu.tw)
Date: Fri Jul 03 2009 - 04:42:10 CDT

Dear Leo and Axel.,

Thank you so much for your reply. It does help me to force VMD illustrate
what secondary structural features that I want.

I use windows version of VMD and enter those script in Extensions > Tk
Console and finally got the correct result.

Thanks again.

Cheers,

John Chao
2009/7/3

-----Original Message-----

>> Dear All,

>dear john chao,
 
>>
>> If there is a way to assign secondary structures on residues read from
>> pdb file and finally displayed by VMD in NewCartoon as what I assign.

>yes. you can create a selection with atomselect and then assign
>structure codes to all atoms/residues using the "structure" keyword.

>example:

>set sel [atomselect top "residue 0 to 5"]
>$sel set structure H

>this will flag the first six residues as helix.

>please give it a try and let us know if this solves
>your problem.

>cheers,
>axel.

>You can do that by creating an atom selection and setting its structure
attribute. For example, to force a certain selection to be drawn as helix
you can do:
>$sel set structure H

>Here are the structure codes (copied from AtomSel.C):

>case SS_HELIX_ALPHA: data[i] = "H"; break;
>case SS_HELIX_3_10 : data[i] = "G"; break;
>case SS_HELIX_PI : data[i] = "I"; break;
>case SS_BETA : data[i] = "E"; break;
>case SS_BRIDGE : data[i] = "B"; break;
>case SS_TURN : data[i] = "T"; break;
>default:
>case SS_COIL : data[i] = "C"; break;
>
>Cheers,
>Leo

>> VMD auto assign those features, however, I just want to illustrate why
>> some secondary structures are not possible in my system.
>>
>> Hence, the assigned secondary structure may NOT be realistic.

>> Thanks for any suggestion,
>>
>> John Chao

>> John Ching-Hao Chao (JCH Chao)
>> Email Address: f93223037_at_ntu.edu.tw
>> ssNMR Lab in Dept. of Chemistry
>> National Taiwan University
>> No. 1, Sec. 4, Roosevelt Road, Taipei, Taiwan, R.O.C. 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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