VMD-L Mailing List

From: Nicolas Sapay (nsapay_at_ucalgary.ca)
Date: Fri Sep 21 2007 - 15:14:23 CDT

Thanks for the fast answer,

I have tried the selection text "residue $res" as you have suggested but
the problem was still there. So, I have re-rechecked my pdb file.
Apparently, a bond between the O1 and the P1 of the 200the lipid is not
recognized by VMD. Lipid 200 is thus considered as 2 different residues.
Same thing probably happened to 3 other lipids. That would explain why I
have 4 more residues that expected. The problem is probably solvable if
I find a way to modify the VMD criteria that define bonds.

Nicolas

Axel Kohlmeyer wrote:
> On Fri, 21 Sep 2007, Nicolas Sapay wrote:
>
>
> nicolas,
>
>
> NS> 5 set sel [ atomselect $molid "$seltext" ]
> NS> 6 # Retrieve the 'residue' number of the selection
> NS> 7 set reslist [ lsort -integer -unique [ $sel get residue ] ]
> NS> 8
> NS> 9 # Assign a new 'resid' to each residue of the selection
> NS> 10 foreach res $reslist {
> NS> 11 # Do a temporary selection
> NS> 12 set tmpsel [ atomselect $molid "$seltext and residue
> NS> $res" ]
>
> please note, that in this case you overwrite only the resids
> of those atoms that are in the selection, so parts of the same
> residue may have different resids after the procedure.
> if you want to overwrite the resid of all atoms in a given residue,
> just use the selection text of "residue $res".
>
> NS> 13 $tmpsel set resid $start
> NS> 14 $tmpsel delete
> NS> 15 # Increment the new resid
> NS> 16 incr start
> NS> 17 }
> NS> 18 $sel delete
> NS> 19 return
> NS> 20}
> NS> #======================================
> NS> However, the proc doesn't work with a simple system of 214 identical
> NS> residues (it's a membrane bilayer). When I use the 'residue' keyword at
> NS> line 7, I obtain a list of 218 'residue' which is wrong. But when I do
> NS> the same thing using the 'resid' keyworkd, I obtain a correct list of
> NS> 214 'resid'. Why do the 'residue' keyword give me 4 more residues? (When
> NS> I do the renumbering, the resids start to be wrong at 200)
>
> please check, whether those resids have been actually overwritten.
> see above.
>
> cheers,
> axel.
>
> NS>
> NS> Thanks for your help. I hope I'm not too confusing with all this
> NS> 'residue' and 'resid'
> NS>
> NS>
> NS>
> NS> Nicolas
> NS>
> NS>
>
>