VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Jan 24 2007 - 07:55:05 CST

Please see the documentation on the animate command:
http://www.ks.uiuc.edu/Research/vmd/current/ug/node108.html

You'll note that it takes a sel option, which contains the selection to
write.

Peter

" politr"@huji.ac.il wrote:
> Thank you for your answers
> The problem is that I'm trying to append only protein from all the
> frames to the same pdb file and it doesn't work. when I'm using the
> next command:
> "animate write pdb prot_only.pdb beg $startframe end $lastframe"
> all the atoms of the frame are written (and not only protein atoms) so
> I have tried to use
> "set sel [atomselect top protein]" and after that
> "$sel animate write pdb prot_only.pdb beg $startframe end $lastframe"
> but it doesn't work.
> I have also tried to use:
> "$sel writepdb prot_only.pdb" when
> $sel is updated in my tcl program according to the frame but in this
> case the pdb file is overwritten for each frame.
> So how can I solve this problem?
> Regina
> John Stone wrote:
>> Hi,
>> If you want a very specific PDB construction, you could write a script
>> to emit the frames one at a time, and then use Tcl I/O commands to
>> concatenate them yourself, which would allow you to control what records
>> are written between structures if you like. By default, the records
>> placed between emitted structures are "END" at present. Your script
>> can tack on "MDL" while concatenating the files.
>>
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>>
>> On Tue, Jan 23, 2007 at 05:41:49PM +0200, " politr"@huji.ac.il wrote:
>>
>>> I want all the frames to be appended to the same pdb file separated by
>>> lets say "ENDMDL"
>>> Thanks
>>>
>>> -------- Original Message --------
>>> Subject: pdb from trajectory
>>> Date: Tue, 23 Jan 2007 17:16:29 +0200
>>> From: politr_at_huji.ac.il
>>> Organization: Fritz Haber Research Center
>>> To: vmd-l_at_ks.uiuc.edu
>>>
>>>
>>>
>>> Dear VMD users and developers,
>>> I have a trajectory of protein in a water box. I have loaded this
>>> trajectory in a VMD and I'm interested to create pdb file of my protein
>>> from every frame of the trajectory. What I mean is, to create tcl script
>>> that will save only my protein from every frame in a pdb format. Can
>>> someone help me with this issue? Any help is more than appreciated.
>>> Thank you very much
>>> Regina
>>>
>>>
>>>
>>
>>
>