VMD-L Mailing List

From: Monika Madhavi (monikamadhavi_at_gmail.com)
Date: Thu Mar 12 2015 - 03:51:49 CDT

Thanks Norman, it works perfectly!!!

Monika

On Mon, Mar 9, 2015 at 7:00 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> Hi Monika,
>
> It is possible to write out a "trajectory pdb". I think, based on the
> documentation for the animate command (http://www.ks.uiuc.edu/
> Research/vmd/current/ug/node121.html), that it would be something like
> this:
>
> animate write pdb output.pdb beg 0 end 0 sel $sel
>
> The $sel writepdb version of file writing I believe can only handle one
> frame at a time. Also, does it need to be a pdb output? A binary format is
> going to be much smaller.
>
> -Josh Vermaas
>
> On 03/09/2015 05:26 AM, Monika Madhavi wrote:
>
>> Thanks Norman, your answer is exactly what I wanted. Is it possible to
>> loop
>> this around each frame also. Can I write the pdb entries for my
>> atomselection ($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
>>>
>>
> 

-- 
W.A.Monika Madhavi
Lecturer (Probation),
Department of Physics,
University of Colombo.