VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue Dec 19 2017 - 12:09:13 CST

If you want the distance between selections, the easiest thing to do is to measure the distance between the center of the selections:

veclength [vecsub [measure center $sel1] [measure center $sel2]]

Measure bond works on atomic indices. So if you wanted to get the distance between the first atoms in two selections, you could do something like this:

measure bond [lindex [$sel1 get index] 0] [lindex [$sel2 get index] 0]

-Josh

On 12/19/2017 06:12 AM, Ashar Malik wrote:
Now $sel1 and $sel2 are the selections. But the documentation of the measure bond says:

The atoms are specified in form of a list of atom indexes

Not selections of atom themselves. So you need to get the index of the atoms.

You can do this:

set seltext1 "name CG and resid 26"
set sel1 [[atomselect top "$seltext1"] get index]
set seltext2 "name CG and resid 30"
set sel2 [[atomselect top "$seltext2"] get index]
measure bond [list $sel1 $sel2]

I am not sure since I haven't tried this - but it shoudl theoretically work.

On Tue, Dec 19, 2017 at 10:03 PM, $BK\B<H%(B <h-motomura_at_bioreg.kyushu-u.ac.jp<mailto:h-motomura_at_bioreg.kyushu-u.ac.jp>> wrote:
I am sorry, I corrected my script.

vmd > set seltext1 "name CG and resid 26"
vmd > set sel1 [atomselect top "$seltext1"]
vmd > set seltext2 "name CG and resid 30"
vmd > set sel2 [atomselect top "$seltext2"]
vmd > measure bond {$sel1 $sel2}
expected integer but got "$sel1" measure bond: bad atom index

> 2017/12/19 17:42$B!"(BAshar Malik <asharjm_at_gmail.com<mailto:asharjm_at_gmail.com>>$B$N%a!<%k(B:
>
> I didn't have a detailed look at this but
>
> vmd > set seltext1 "name CG and resid 26$B!I(B
> vmd > set seltext2 "name CG and resid 30$B!I(B
> vmd > measure bond {$sel1 $sel2}
>
> what is $sel1 and $sel2???
>
> your selections are called seltext1 and seltext2 not sel1 and sel2.
>
> On Tue, Dec 19, 2017 at 8:56 PM, $BK\B<H%(B <h-motomura_at_bioreg.kyushu-u.ac.jp<mailto:h-motomura_at_bioreg.kyushu-u.ac.jp>> wrote:
> Dear all,
>
> I would like to measure bond length with $B!H(Bname ** and resid **$B!I(B in scripts.
>
> vmd > set seltext1 "name CG and resid 26$B!I(B
> vmd > set seltext2 "name CG and resid 30$B!I(B
> vmd > measure bond {$sel1 $sel2}
> expected integer but got "$sel1" measure bond: bad atom index
>
> However the following command succeed.
> vmd > measure bond {113 140}
> 11.772942543029785
>
> I configured that the above atoms existed.
> How can I measure bond length with $B!H(Bname ** and resid **" in scripts?
>
> Sincerely,
> Hajime Motomura
>
>
>
>
> --
> Best,
> /A 

--
Best,
/A