VMD-L Mailing List

From: Danielle Chandler (dechandl_at_ks.uiuc.edu)
Date: Thu Oct 09 2008 - 14:30:37 CDT

Hi,

I just wanted to point out that selections like "lipids" in VMD are really
just pre-defined atomselect macros. You can create your own macros for
more complex selections like this. For example, here is my macro for
dealing with this for POPE, POPG and POPC - you'll have to change the
selections if you have different lipid preferences:

atomselect macro lipidtails {(resname POPE and not name N HN1 HN2 HN3 C12
H12A H12B C11 H11A H11B P O11 O12 O13 O14 C1 HA HB C2 HS O21 O22 C21 C3 HX
HY O31 O32
C31) or (resname POPC and not name N C12 C13 C14 H21 H22 H23 H31 H32 H33
H41 H42 H43 C11 H11 H12 C15 H51 H52 P1 O1 O2 O3 O4 C1 HA HB O21 O22 C21 C3
HX HY O31 O32 C31) or
(resname POPG and not name C12 O12 H31 H21 H22 C11 H11 O11 H12 C15 H51 H52
P1 O1 O2 O3 O4 C1 HA HB C2 HS O21 O22 C21 C3 HX HY O31 O32 C31)}

I keep these in my .vmdrc file so that they're defined at startup. Then
selections like "lipidtails" will work from then on. This is useful if
you know you'll want to re-use a selection often.

Hope this helps.

On Sat, 4 Oct 2008, BIN ZHANG wrote:

> Hi, All:
> I wonder whether there is an easy way to select the lipid tail of membrane
> in VMD?
> Thanks a lot.
> Bin
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> -------------------------------------------------------------
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