VMD-L Mailing List

From: Monika Madhavi (monikamadhavi_at_gmail.com)
Date: Mon Mar 09 2015 - 05:26:18 CDT

Thanks Norman, your answer is exactly what I wanted. Is it possible to loop
this around each frame also. Can I write the pdb entries for my
atomselection ($sel here) for each frame in the same pdb?

Regards,
Monika

On Mon, Mar 9, 2015 at 3:12 PM, Norman Geist <norman.geist_at_uni-greifswald.de
> wrote:

> This is not the way it should be done. It is much easier and faster to
> just collect the resids you need 1st and write out the coordinates
> afterwards. You can easily collect the list of resids with “lappend”.
>
>
>
> example:
>
>
>
> set myresids {}
>
> for {whatever} {
>
> if {whatever} {
>
> lappend myresids $resid
>
> }
>
> }
>
> set residlist [lrange $myresids 0 end]
>
> set sel [atomselect top “resid $residlist”]
>
> $sel writepdb my.pdb
>
> $sel delete
>
>
>
> Norman Geist.
>
>
>
> *From:* owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] *On
> Behalf Of *Monika Madhavi
> *Sent:* Monday, March 09, 2015 7:24 AM
> *To:* Joaquim Rui de Castro Rodrigues
> *Cc:* vmd-l_at_ks.uiuc.edu
> *Subject:* Re: vmd-l: How to write coordinates to a pdb without replacing
> existing entries
>
>
>
> Thanks Rui,
> Actually I can select the residue ids I want to select but they are
> selected in a random manner and the number is large. Therefore I am
> wondering whether I can write coordinates of the selected molecule at the
> time it is selected without giving the whole list of ids at the end.
>
> Regards,
> Monika
>
> Monika Madhavi
> Department of Physics
> University of Colombo
>
> On Mar 8, 2015 11:03 PM, "Monika Madhavi" <monikamadhavi_at_gmail.com> wrote:
>
> I want to achieve the result I would get if I write this command while
> looping around without writing line 2 as it is.
>
> set residlist {1 2 3 4 5}
>
> set sel [atomselect top "resid 1 2 3 4 5"]
>
> $sel writepdb out.pdb
>
> $sel delete
>
> Regards,
>
> Monik
>
>
>
>
>
> On Sun, Mar 8, 2015 at 10:47 PM, Monika Madhavi <monikamadhavi_at_gmail.com>
> wrote:
>
> Thanks Joaquim. Actually i set N outside the loop. What i want is to write
> all the coordinates in a single pdb file. As an example, something like
>
> If my molecule is water,
>
> Resid atomname coordinates
> 1 H1 .........
> 1 H2 ........
> 1 OH .........
> 2 H1 .........
> 2 H1 ..........
> 2 OH .........
> .
> .
> .
>
> Regards,
> Monika
>
> Monika Madhavi
> Department of Physics
> University of Colombo
>
> On Mar 8, 2015 10:11 PM, "Joaquim Rui de Castro Rodrigues" <
> joaquim.rodrigues_at_ipleiria.pt> wrote:
>
> Dear Monika,
>
> I don't quite get what you are trying to achieve... Do you want to get
> separate PDB files for each resid?
> Anyhow, I see a few problems with your script:
> - the for loop contains a strange comparison: $i<N. I just tested this and
> it results in an infinite loop. You must set N outside of the loop.
> - you're looping over resid's, but always writing to same the same file
> (out.pdb)
> - you're building atomselections at each iterations without deleting them--001a11c3294cf8cee50510d876aa--