Thank you so much Tsejrk and Seera for your kind help!!
Thomas replied. He said that I can load the .gro files too by giving a
command on the terminal.
PyMOL> cd your/working/directory
PyMOL> load file.gro
It worked!!
Thank you so much, once again. I'm sharing his reply here so that in case
anybody else faces the same problem, they can view this in the archive.
On Tue, Sep 22, 2015 at 8:24 PM, <pymol-users-requ...@lists.sourceforge.net>
wrote:
> Send PyMOL-users mailing list submissions to
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> Today's Topics:
>
> 1. Re: Ploting coordinates (Tsjerk Wassenaar)
> 2. Re: Ploting coordinates (Thomas Holder)
> 3. Re: Ploting coordinates (Suzanne Scott)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 22 Sep 2015 11:34:26 +0200
> From: Tsjerk Wassenaar <tsje...@gmail.com>
> Subject: Re: [PyMOL] Ploting coordinates
> To: Suzanne Scott <suzanne.sc...@merton.ox.ac.uk>
> Cc: "pymol-users@lists.sourceforge.net"
> <pymol-users@lists.sourceforge.net>
> Message-ID:
> <
> cabze1sg0xkcegpqxwe7gadnynb5p2az3o2j3gwd5fbfg5dq...@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Suzanne,
>
> I'll make the guess that it's position and color. Are there any lines to be
> ignored? Probably this will work anyway... Save this in a script called
> holecgo.py:
>
>
> def holecgo(filename,radius=0.1,name="hole"):
> data = [ i.split() for i in open(filename) ]
> data = [ [ float(i) for i in k[:6] ] if len(k) == 7 and
> k[6].startswith("#") ]
> cmd.load_cgo([u for x,y,z,r,g,b in data for u in
> [6.0,r,g,b,7.0,x,y,z,radius]],name)
>
>
> Then in Pymol, do:
>
> run holecgo.py
> holecgo("yourfilename")
>
> You can add radius=0.25 or something else to make the spheres larger.
>
> Hope it helps,
>
> Tsjerk
>
>
>
> On Mon, Sep 21, 2015 at 9:06 PM, Suzanne Scott <
> suzanne.sc...@merton.ox.ac.uk> wrote:
>
> > Hi everyone,
> >
> > I hope this isn?t a silly question, but I?m not sure how to do it: I want
> > to plot some coordinates in PyMOL. Not atoms, just coordinates - they?re
> > the output of HOLE implemented in Coot, and have the following format:
> >
> > 145.32307 113.91329 116.36907 0.44800 0.47168 0.80000
> > #7278cc
> > 147.35472 113.65778 116.36907 0.44800 0.47168 0.80000
> > #7278cc
> > 149.39126 113.87088 116.36907 0.44800 0.47168 0.80000
> > #7278cc
> > 141.61303 115.28156 115.56962 0.44800 0.47168 0.80000
> > #7278cc
> >
> > Where the first three columns are the x, y and z coordinates, the next
> > three are the size of the object, and the last is the colour (which isn?t
> > so important - neither is the size, really). I can?t work out how to
> > import them into PyMOL. If anybody has any ideas, I?d be really
> grateful!
> >
> > Thanks,
> > Suzanne
> >
> >
> ------------------------------------------------------------------------------
> > _______________________________________________
> > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 2
> Date: Tue, 22 Sep 2015 10:40:33 -0400
> From: Thomas Holder <thomas.hol...@schrodinger.com>
> Subject: Re: [PyMOL] Ploting coordinates
> To: Suzanne Scott <suzanne.sc...@merton.ox.ac.uk>, Tsjerk Wassenaar
> <tsje...@gmail.com>
> Cc: "pymol-users@lists.sourceforge.net"
> <pymol-users@lists.sourceforge.net>
> Message-ID: <c6753897-d540-4525-871e-bbfdbc934...@schrodinger.com>
> Content-Type: text/plain; charset=windows-1252
>
> Hi Suzanne & Tsjerk,
>
> To get those points in as pseudoatoms, you could also simply place a CIF
> atom site header above the data and load it as a .cif file.
>
> data_foo
> loop_
> _atom_site.Cartn_x
> _atom_site.Cartn_y
> _atom_site.Cartn_z
> _atom_site.ignore_size_a
> _atom_site.ignore_size_b
> _atom_site.ignore_size_c
> 145.32307 113.91329 116.36907 0.44800 0.47168 0.80000
> #7278cc
> 147.35472 113.65778 116.36907 0.44800 0.47168 0.80000
> #7278cc
> 149.39126 113.87088 116.36907 0.44800 0.47168 0.80000
> #7278cc
> 141.61303 115.28156 115.56962 0.44800 0.47168 0.80000
> #7278cc
>
> The color will be ignored because # is the comment delimiter.
>
> The only issue is that all atoms will have the same (empty) identifiers,
> so in order to select individual atoms, run something like this:
>
> PyMOL> alter all, resi=index
>
> Cheers,
> Thomas
>
> On 22 Sep 2015, at 05:34, Tsjerk Wassenaar <tsje...@gmail.com> wrote:
>
> > Hi Suzanne,
> >
> > I'll make the guess that it's position and color. Are there any lines to
> be ignored? Probably this will work anyway... Save this in a script called
> holecgo.py:
> >
> >
> > def holecgo(filename,radius=0.1,name="hole"):
> > data = [ i.split() for i in open(filename) ]
> > data = [ [ float(i) for i in k[:6] ] if len(k) == 7 and
> k[6].startswith("#") ]
> > cmd.load_cgo([u for x,y,z,r,g,b in data for u in
> [6.0,r,g,b,7.0,x,y,z,radius]],name)
> >
> >
> > Then in Pymol, do:
> >
> > run holecgo.py
> > holecgo("yourfilename")
> >
> > You can add radius=0.25 or something else to make the spheres larger.
> >
> > Hope it helps,
> >
> > Tsjerk
> >
> >
> >
> > On Mon, Sep 21, 2015 at 9:06 PM, Suzanne Scott <
> suzanne.sc...@merton.ox.ac.uk> wrote:
> > Hi everyone,
> >
> > I hope this isn?t a silly question, but I?m not sure how to do it: I
> want to plot some coordinates in PyMOL. Not atoms, just coordinates -
> they?re the output of HOLE implemented in Coot, and have the following
> format:
> >
> > 145.32307 113.91329 116.36907 0.44800 0.47168
> 0.80000 #7278cc
> > 147.35472 113.65778 116.36907 0.44800 0.47168
> 0.80000 #7278cc
> > 149.39126 113.87088 116.36907 0.44800 0.47168
> 0.80000 #7278cc
> > 141.61303 115.28156 115.56962 0.44800 0.47168
> 0.80000 #7278cc
> >
> > Where the first three columns are the x, y and z coordinates, the next
> three are the size of the object, and the last is the colour (which isn?t
> so important - neither is the size, really). I can?t work out how to
> import them into PyMOL. If anybody has any ideas, I?d be really grateful!
> >
> > Thanks,
> > Suzanne
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schr?dinger, Inc.
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 22 Sep 2015 14:54:18 +0000
> From: Suzanne Scott <suzanne.sc...@merton.ox.ac.uk>
> Subject: Re: [PyMOL] Ploting coordinates
> To: Thomas Holder <thomas.hol...@schrodinger.com>
> Cc: Tsjerk Wassenaar <tsje...@gmail.com>,
> "pymol-users@lists.sourceforge.net"
> <pymol-users@lists.sourceforge.net>
> Message-ID: <5641961b-6e64-43d3-ad75-912d88787...@merton.ox.ac.uk>
> Content-Type: text/plain; charset="windows-1252"
>
> The code threw up a syntax error for me and I don?t know enough python to
> figure out why, but the CIF approach worked well, thanks very much!
>
>
> On 22 Sep 2015, at 15:40, Thomas Holder <thomas.hol...@schrodinger.com
> <mailto:thomas.hol...@schrodinger.com>> wrote:
>
> Hi Suzanne & Tsjerk,
>
> To get those points in as pseudoatoms, you could also simply place a CIF
> atom site header above the data and load it as a .cif file.
>
> data_foo
> loop_
> _atom_site.Cartn_x
> _atom_site.Cartn_y
> _atom_site.Cartn_z
> _atom_site.ignore_size_a
> _atom_site.ignore_size_b
> _atom_site.ignore_size_c
> 145.32307 113.91329 116.36907 0.44800 0.47168 0.80000
> #7278cc
> 147.35472 113.65778 116.36907 0.44800 0.47168 0.80000
> #7278cc
> 149.39126 113.87088 116.36907 0.44800 0.47168 0.80000
> #7278cc
> 141.61303 115.28156 115.56962 0.44800 0.47168 0.80000
> #7278cc
>
> The color will be ignored because # is the comment delimiter.
>
> The only issue is that all atoms will have the same (empty) identifiers,
> so in order to select individual atoms, run something like this:
>
> PyMOL> alter all, resi=index
>
> Cheers,
> Thomas
>
> On 22 Sep 2015, at 05:34, Tsjerk Wassenaar <tsje...@gmail.com<mailto:
> tsje...@gmail.com>> wrote:
>
> Hi Suzanne,
>
> I'll make the guess that it's position and color. Are there any lines to
> be ignored? Probably this will work anyway... Save this in a script called
> holecgo.py:
>
>
> def holecgo(filename,radius=0.1,name="hole"):
> data = [ i.split() for i in open(filename) ]
> data = [ [ float(i) for i in k[:6] ] if len(k) == 7 and
> k[6].startswith("#") ]
> cmd.load_cgo([u for x,y,z,r,g,b in data for u in
> [6.0,r,g,b,7.0,x,y,z,radius]],name)
>
>
> Then in Pymol, do:
>
> run holecgo.py
> holecgo("yourfilename")
>
> You can add radius=0.25 or something else to make the spheres larger.
>
> Hope it helps,
>
> Tsjerk
>
>
>
> On Mon, Sep 21, 2015 at 9:06 PM, Suzanne Scott <
> suzanne.sc...@merton.ox.ac.uk<mailto:suzanne.sc...@merton.ox.ac.uk>>
> wrote:
> Hi everyone,
>
> I hope this isn?t a silly question, but I?m not sure how to do it: I want
> to plot some coordinates in PyMOL. Not atoms, just coordinates - they?re
> the output of HOLE implemented in Coot, and have the following format:
>
> 145.32307 113.91329 116.36907 0.44800 0.47168 0.80000
> #7278cc
> 147.35472 113.65778 116.36907 0.44800 0.47168 0.80000
> #7278cc
> 149.39126 113.87088 116.36907 0.44800 0.47168 0.80000
> #7278cc
> 141.61303 115.28156 115.56962 0.44800 0.47168 0.80000
> #7278cc
>
> Where the first three columns are the x, y and z coordinates, the next
> three are the size of the object, and the last is the colour (which isn?t
> so important - neither is the size, really). I can?t work out how to
> import them into PyMOL. If anybody has any ideas, I?d be really grateful!
>
> Thanks,
> Suzanne
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schr?dinger, Inc.
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
>
> ------------------------------------------------------------------------------
>
>
> ------------------------------
>
> _______________________________________________
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
> End of PyMOL-users Digest, Vol 112, Issue 8
> *******************************************
>
--
Regards,
Raag
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