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#37527 - 06/14/19 10:13 AM How to keep residues across a specific range?
jtyang Offline
Forum Member

Registered: 05/09/17
Posts: 7
Hey guys,

What I want to do is to draw cluster structures and write them to cor files, but if I write like this,

...
imag byre sele all end xcen ?XAVE ycen ?YAVE zcen ?ZAVE
upda cutim 15
dele atom sele .byres. (.not.(ires @aimres .around. 10)) end
write coor card name ../../res-cor/@aimres/@ifr.cor
...

I will lose residues across the range 10, which is not expected.

How should I do to select?
Or can I just write them use `ires @aimres .around. 10` ?
also, the step `upda cutim 15` seems very time consuming, so are there any other ways more efficient or elegant to achieve my goal ?

Many thanks.

J.T.Yang

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#37528 - 06/14/19 10:55 AM Re: How to keep residues across a specific range? [Re: jtyang]
rmv Offline

Forum Member

Registered: 09/17/03
Posts: 8388
Loc: 39 03 48 N, 77 06 54 W
A residue with only a single atom outside the 10 sphere will be deleted, a consequence of the .BYRES. keyword. You may wish to use a larger value for the cutoff.

Note that by default, CHARMM only generates image atoms for slightly more than half of the transformations; you must use the IMALL keyword to generate atoms for all of the transformations. See the 'images' documentation.
_________________________
Rick Venable
computational chemist


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#37529 - 06/15/19 09:23 PM Re: How to keep residues across a specific range? [Re: rmv]
jtyang Offline
Forum Member

Registered: 05/09/17
Posts: 7
thanks for your reply, especially about the "imall" option,
this is what I use after recheck the doc file,
"imall" added twice because I don't know on which line it will work,
I hope there are no new problems, it looks like OK for me:
...
imag byre sele all end xcen ?XAVE ycen ?YAVE zcen ?ZAVE imall
upda cutim 15 imall
write coor sele .byres. ( ires @aimres .around. 10 ) end -
card name cluster.cor
* ?ZAVE
*
...

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