Previous Thread
Next Thread
Print Thread
How to keep residues across a specific range?
#37527 06/14/19 02:13 PM
Joined: May 2017
Posts: 7
J
jtyang Offline OP
Forum Member
OP Offline
Forum Member
J
Joined: May 2017
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

Re: How to keep residues across a specific range?
jtyang #37528 06/14/19 02:55 PM
Joined: Sep 2003
Posts: 8,424
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,424
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

Re: How to keep residues across a specific range?
rmv #37529 06/16/19 01:23 AM
Joined: May 2017
Posts: 7
J
jtyang Offline OP
Forum Member
OP Offline
Forum Member
J
Joined: May 2017
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
*
...


Moderated by  John Legato, lennart 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.4
(Release build 20200307)
Responsive Width:

PHP: 5.6.33-0+deb8u1 Page Time: 0.008s Queries: 20 (0.003s) Memory: 0.9020 MB (Peak: 0.9757 MB) Data Comp: Off Server Time: 2020-04-08 04:31:26 UTC
Valid HTML 5 and Valid CSS