From: Sourav Ray (souravray90_at_gmail.com)
Date: Mon Feb 16 2015 - 04:53:02 CST

Hi Maxim

I got 1 2 .. 12 13 after executing the last line.

Regards
Sourav

On Mon, Feb 16, 2015 at 4:13 PM, Maxim Belkin <mbelkin_at_ks.uiuc.edu> wrote:

> Can you share with us the result of the following two commands?
>
> set sel [atomselect top "protein"]
> puts "[lsort -unique -integer [$sel get resid]]"
>
>
> On Feb 16, 2015, at 04:36, Sourav Ray <souravray90_at_gmail.com> wrote:
>
> It doesn't work, I substituted "protein" instead of "resid 1 to 10", it
> failed to recognize the selection in both the cases.
>
> On Mon, Feb 16, 2015 at 1:22 PM, Norman Geist <
> norman.geist_at_uni-greifswald.de> wrote:
>
>> animate write pdb myframes.pdb beg 0 end [molinfo top get numframes]
>> sel "resid 1 to 10"
>>
>>
>>
>> Norman Geist.
>>
>> *From:* owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] *On
>> Behalf Of *Sourav Ray
>> *Sent:* Monday, February 16, 2015 7:32 AM
>> *To:* Maxim Belkin
>> *Cc:* vmd-l_at_ks.uiuc.edu
>> *Subject:* Re: vmd-l: Extracting coordinates from DCD file to a single
>> PDB file
>>
>>
>>
>> .psf file for defining the topology and .dcd file for the coordinates. it
>> would be convenient to get all the frames in a single pdb file as
>> processing will be much easier.
>>
>> regards
>>
>> Sourav
>>
>>
>>
>> On Mon, Feb 16, 2015 at 11:21 AM, Maxim Belkin <mbelkin_at_ks.uiuc.edu>
>> wrote:
>>
>> What do you have as input (file format and content)?
>>
>>
>>
>> On Feb 15, 2015, at 23:21, Sourav Ray <souravray90_at_gmail.com> wrote:
>>
>>
>>
>> I guess there is some misunderstanding, I would like all the frames in a
>> single .pdb file, that too sequentially (frame 1, frame 2...). Is it
>> possible somehow?
>>
>>
>>
>> On Fri, Feb 13, 2015 at 5:03 PM, Maxim Belkin <mbelkin_at_ks.uiuc.edu>
>> wrote:
>>
>> set nf [molinfo top get numframes]
>> set sel [atomselect top "protein"]
>> for {set i 0} {$i < $nf} {incr i} {
>> $sel frame $i
>> $sel writepdb "protein-$i.pdb"
>> }
>> $sel delete
>> mol delete top
>>
>> If there are multiple proteins use more specific selection text, e.g. use
>> resids or something else.
>>
>> Maxim
>>
>> > On Feb 13, 2015, at 04:09, Sourav Ray <souravray90_at_gmail.com> wrote:
>> >
>> > Hello
>> >
>> > I have been trying to extract all the frames of a protein into a single
>> PDB file. There is a code available currently in a thread here for
>> extracting each frame in different PDB files:
>> >
>> > set nf [molinfo top get numframes]
>> >
>> > for { set i 0 } {$i < $nf } { incr i } {
>> > set sel [atomselect top protein frame $i]
>> > $sel writepdb $i.pdb
>> > }
>> >
>> > Can someone please suggest a modification that works? Also, what if
>> there are multiple proteins? Can we extract each one separately?
>> >
>> > Regards
>> > Sourav
>>
>>
>>
>>
>>
>>
>>
>
>
>