VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon May 28 2007 - 15:58:26 CDT

Ah, good point--my apologies. I should've been paying more attention to
the specific case.
Thanks,
Peter

Cesar Luis Avila wrote:
> 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
>>>>
>>>> ------------------------------------------------------------------------
>>>>
>>>> Sick sense of humor? Visit Yahoo! TV's Comedy with an Edge
>>>> <http://us.rd.yahoo.com/evt=47093/*http://tv.yahoo.com/collections/222>to
>>>>
>>>> see what's on, when.
>>
>>