VMD-L Mailing List
From: Sourav Ray (souravray90_at_gmail.com)
Date: Tue Feb 17 2015 - 11:22:12 CST
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- Maybe in reply to: Maxim Belkin: "Re: Extracting coordinates from DCD file to a single PDB file"
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Finally figured it out! Load the molecule (psf and dcd files), isolate the
protein segment using the Graphical Representation and Selection area. Go
to save coordinates and select protein from the drop-down menu (default
format is pdb only) and hit save, you are done!
On Tue, Feb 17, 2015 at 1:27 PM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:
> You need to use the correct molecule id for the atomselection, if the
> molecule isn't top. You find the id in the VMD Main window on the left.
>
>
>
> set molid 1
>
> set a [atomselect $molid "resid 1 to 10"]
>
>
>
> If the molecule has frames, than this should output the correct number:
>
>
>
> molinfo $molid get numframes
>
>
>
> So this command should output all the frames then:
>
>
>
> animate write pdb myframes.pdb beg 0 end [molinfo $molid get numframes]
> sel $a
>
>
>
> Norman Geist.
>
>
>
> *From:* Sourav Ray [mailto:souravray90_at_gmail.com]
> *Sent:* Tuesday, February 17, 2015 8:20 AM
> *To:* Norman Geist
> *Cc:* VMD Mailing List
>
> *Subject:* Re: vmd-l: Extracting coordinates from DCD file to a single
> PDB file
>
>
>
> Hello
>
> It writes one frame only. Can you please suggest some modification?
>
> Regards
>
> Sourav
>
>
>
> On Mon, Feb 16, 2015 at 6:03 PM, Norman Geist <
> norman.geist_at_uni-greifswald.de> wrote:
>
> From the help it wasn't clear, but you need to do:
>
>
>
> set a [atomselect top "resid 1 to 10"]
>
> animate write pdb myframes.pdb beg 0 end [molinfo top get numframes] sel $a
>
>
>
> Norman Geist.
>
>
>
> *From:* Sourav Ray [mailto:souravray90_at_gmail.com]
> *Sent:* Monday, February 16, 2015 11:53 AM
> *To:* Maxim Belkin
> *Cc:* Norman Geist; VMD Mailing List
>
>
> *Subject:* Re: vmd-l: Extracting coordinates from DCD file to a single
> PDB file
>
>
>
> Hi Maxim
>
> I got 1 2 .. 12 13 after executing the last line.
>
> Regards
>
> Sourav
>
>
>
> On Mon, Feb 16, 2015 at 4:13 PM, Maxim Belkin <mbelkin_at_ks.uiuc.edu> wrote:
>
> Can you share with us the result of the following two commands?
>
>
>
> set sel [atomselect top "protein"]
>
> puts "[lsort -unique -integer [$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
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
- Next message: Tristan Croll: "Re: MDFF plugin calculating ccc"
- Previous message: Ryan McGreevy: "Re: MDFF plugin calculating ccc"
- Maybe in reply to: Maxim Belkin: "Re: Extracting coordinates from DCD file to a single PDB file"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]