VMD-L Mailing List

From: _at_huji.ac.il
Date: Wed Jan 24 2007 - 04:37:40 CST

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
>>
>>
>>
>
>