On Thu, Mar 24, 2011 at 10:11 PM, Yingjie Lin <[email protected]> wrote:
> Hello Angel,
>
> I almost get what I want with what you suggested, except for some minor
> issues.
> I want to label all residues in a chosen box (x1<x<x2 and y1<y<y2 and
> z1<z<z2),
>
select x > x1 and x < x2 and y > y1 and y < y2 and z > z1 and z < z2
or
boundbox @{point(x1, y1, z1)} @{point(x2, y2, z2)}
select within(boundbox)
or, if you know the points, you can just do something likes this:
boundbox {0 0 0} {10 10 10}
select within(boundbox)
Now, that defines all ATOMS in the box. If you need their residues, just use
instead:
select within(group, within(boundbox))
or if you want only residues that are ENTIRELY within the box, use this:
select not within(group, not within(boundbox))
Usually when people label a residue, they just label the alpha carbon:
select *.ca and not within(group, not within(boundbox))
> Some additional questions:
> 1.
> print {visible}.resno.min;
> >> 19
> print {visible}.resno.max;
> >> 501
> print {visible}.length;
> >> 8603
> print {visible}.resno;
> >> 2259973
>
that's a bug. How odd -- summing! That's fixed for Jmol 12.1.41 and 12.0.38.
See http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
[ It was a problem with integer properties such as resno, atomno,
modelindex, etc. These were summing instead of averaging. ]
> print {visible}[1];
> >> ({0})
> I understand the first 3 values: min and max of resno are 19 and 501,
> respectively; There are 8603 atoms.
> But I don't understand the 4th value 2259973. What I want is to see a list
> of residue numbers.
> I don't understand the 5th value either. I thought this should return the
> first visible atom. I guess what I don't understand here is {} inside ().
>
> 2. This question is not related to the above.
> load file1.pdb; load APPEND file2.pdb
> If after loading two files, I somehow decide to "unload" file2.pdb, how
> should I do it?
>
delete file=2
>
> Thanks for your patience.
>
>
You are asking great questions -- and look -- you found a bug! Thank you!
> Yingjie
>
> ------------------------------
>
>
> Message: 2
>
> Date: Wed, 23 Mar 2011 19:31:25 +0100
>
> From: " Angel Herr?ez " <[email protected]>
>
> Subject: Re: [Jmol-users] one label per residue
>
> To: [email protected]
>
> Message-ID: <[email protected]>
>
> Content-Type: text/plain; charset=US-ASCII
>
>
> Hello Yingjie
>
>
> You can probably use the atoms array, and either use their geometric
>
> center (not for a label, but an echo) or the first atom in the array.
>
> The result will probably not look very nice.
>
>
> I cannot give you the exact syntax, but check the doc under "atom
>
> expressions". It will be something like
>
>
> select {resno=3}[0]; label %r
>
>
> Good luck!
>
>
>
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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