VMD-L Mailing List

From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Mon May 28 2007 - 14:04:32 CDT

I am aware of that. Since you are trying to select lipids, and some of
them are composed of more than one residue you should use fragment.

Peter Freddolino escribió:
> For complete residues, you should actually use
> "same residue as within 5 of protein"
>
> fragment will give a set of connected residues (see
> http://www.ks.uiuc.edu/Research/vmd/current/ug/node79.html)
>
> Peter
>
> Cesar Luis Avila wrote:
>
>> "same fragment as within 5 of protein"
>>
>> naga raju escribió:
>>
>>> Dear VMD users,
>>> I want to insert protein in a lipid
>>> bilayer. I aligned protein and lipid bilayer. I used " within 5 of
>>> protein" in graphics representation then it selects atoms within 5 of
>>> protein, but i need complete residues.
>>> would you tell me how to select lipid
>>> residues from protein within perticular distance.
>>> Thank you in advance,
>>>
>>> with regards,
>>>
>>> nagaraju
>>>
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>