Re: [PyMOL] Polar interactions within selection
Thanks, Thomas!
Your script works fine. I've tested in one pdb structure and it finds all
polar and salt-bridges perfectly.
As I've understood this script also is usefull for examination of the
ensemble of pdb structures in NMR-like format ( each pdb structure as the
individual state in pymol) isn't it?
So now I must find a way to save my trajectories in this NMR-like pattern
by means of vmd software. I have found only possibility to save individual
snapshots as the individual pdb files or as the set pdb in one pdb in one
state ( i think this is not very usefull). Do you know how any python
modules for working with and extracting snapshots from big trr files from
gromacs runs ?
Thanks again
James
16 апреля 2012 г. 19:18 пользователь Thomas Holder <
spel...@users.sourceforge.net> написал:
> Hi James,
>
> maybe something like this could help. It finds contacts between charged
> sidechains and prints the number of contacts in each state (requires
> get_raw_distances from [1] or [2]).
>
> --**--
> # region of interest
> select roi, chain A
>
> # charged residues
> select positive, resn ARG+LYS and not name N+O
> select negative, resn GLU+ASP and not name N+O
>
> # increase cutoff
> set h_bond_cutoff_center, 5.0
> set h_bond_cutoff_edge , 5.0
>
> # find polar contacts
> delete saltbridges
> distance saltbridges, roi and negative, roi and positive, mode=2
> hide label
>
> # count contacts in each state
> python
> try:
>get_raw_distances
> except NameError:
>from psico.querying import get_raw_distances
>
> for state in range(1, cmd.count_states()+1):
>sb = get_raw_distances('**saltbridges', state)
>print ' %2d charged contacts in state %d' % (len(sb), state)
> python end
> --**
>
> [1]
> http://pymolwiki.org/index.**php/Get_raw_distances
> [2]
> http://pymolwiki.org/index.**php/Psico
>
> Cheers,
> Thomas
>
>
>
> On 04/16/2012 03:22 PM, James Starlight wrote:
>
>> Hi Thomas!
>>
>> Yes I'd like find possible way for quick examining of the polar
>> interactions ( nor only h-bonds but mainly salt-bridges) within
>> selection. As the consequence I'd like to examine the ensemble of the
>> pdb fies obtained as the different snapshots from MD trajectory for the
>> evolution of the new salt-bridges occuring during simulation.
>>
>> James
>>
>> 16 апреля 2012 г. 15:58 пользователь Thomas Holder
>> > > >>
>>
>> написал:
>>
>>Hi James,
>>
>>I just noticed that this question is without any answer on the
>>mailing list. Do you still need help on this topic?
>>
>>Cheers,
>> Thomas
>>
>>
>>On 04/04/2012 09:26 AM, James Starlight wrote:
>>
>>Dear PyMol users!
>>
>>I'm analysing polar interactions occured during MD simulation of my
>>protein. In particular I have PDB file obtained from such
>> trajectory
>>where I'd like to check new polar contacts ( salt bridges first
>>of all)
>>within selection region. I've tried to select specified region
>>and use
>>Find polar contact- > within selection as well as other options
>> from
>>this context meny but results was blank and I have not seen any
>>polar
>>contacts despite some charged residues were presented in the
>>adjacent
>>interface positions in the selected region.
>>
>>IS there any else way to study dynamics of the salt-bridges
>>formation
>>based on the selected regions in the snapshots ?
>>
>>Thanks for help,
>>
>>James
>>
>
> --
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
>
--
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[PyMOL] Using cmd.png with ray=False still ray traces the image
Hello all, I'm using Pymol v1.5 (from fink, so open source version) to trace large scene that I have. To that end, I'm avoiding having PyMOL open and I wrote a small python script to do the rendering for me. All goes well, except this last part (don't mind the obvious variable names): cmd.ray(width, height, renderer=2) > cmd.png(default_name+'.png', dpi=300, ray=False) This actually renders my scene *twice. *I've tried cmd.do and it does the same.. am I missing something or is this not supposed to happen? Thanks and cheers, João [...] Rodrigues http://nmr.chem.uu.nl/~joao -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev___ 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
Re: [PyMOL] Using cmd.png with ray=False still ray traces the image
Hi João, What about cmd.png(default_name+'.png', dpi=300, ray=0) Cheers, -- Jason On Tue, Apr 17, 2012 at 11:18 AM, João Rodrigues wrote: > Hello all, > > I'm using Pymol v1.5 (from fink, so open source version) to trace large > scene that I have. To that end, I'm avoiding having PyMOL open and I wrote a > small python script to do the rendering for me. All goes well, except this > last part (don't mind the obvious variable names): > >> cmd.ray(width, height, renderer=2) >> cmd.png(default_name+'.png', dpi=300, ray=False) > > > This actually renders my scene twice. I've tried cmd.do and it does the > same.. am I missing something or is this not supposed to happen? > > Thanks and cheers, > > João [...] Rodrigues > http://nmr.chem.uu.nl/~joao > > > -- > Better than sec? Nothing is better than sec when it comes to > monitoring Big Data applications. Try Boundary one-second > resolution app monitoring today. Free. > http://p.sf.net/sfu/Boundary-dev2dev > ___ > 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev ___ 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
Re: [PyMOL] Using cmd.png with ray=False still ray traces the image
Same result Jason, i also tried =false... No dia 17 de Abr de 2012 20:45, "Jason Vertrees" < jason.vertr...@schrodinger.com> escreveu: > Hi João, > > What about > > cmd.png(default_name+'.png', dpi=300, ray=0) > > Cheers, > > -- Jason > > > On Tue, Apr 17, 2012 at 11:18 AM, João Rodrigues > wrote: > > Hello all, > > > > I'm using Pymol v1.5 (from fink, so open source version) to trace large > > scene that I have. To that end, I'm avoiding having PyMOL open and I > wrote a > > small python script to do the rendering for me. All goes well, except > this > > last part (don't mind the obvious variable names): > > > >> cmd.ray(width, height, renderer=2) > >> cmd.png(default_name+'.png', dpi=300, ray=False) > > > > > > This actually renders my scene twice. I've tried cmd.do and it does the > > same.. am I missing something or is this not supposed to happen? > > > > Thanks and cheers, > > > > João [...] Rodrigues > > http://nmr.chem.uu.nl/~joao > > > > > > > -- > > Better than sec? Nothing is better than sec when it comes to > > monitoring Big Data applications. Try Boundary one-second > > resolution app monitoring today. Free. > > http://p.sf.net/sfu/Boundary-dev2dev > > ___ > > 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 > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrödinger, LLC > > (e) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 > -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev___ 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
Re: [PyMOL] Using cmd.png with ray=False still ray traces the image
João,
I'm not sure why this is giving you problems. Why do you have
renderer=2? Why not the default? Are you counting primitives? If so, I
suggest:
cmd.set("ray_default_renderer", 2)
# snapshot
cmd.png(myFile, width=w, height=h, dpi=d, ray=0)
# this will ray trace
cmd.png(myFile, width=w, height=h, dpi=d, ray=1)
Cheers,
-- Jason
On Tue, Apr 17, 2012 at 1:21 PM, João Rodrigues wrote:
> Same result Jason, i also tried =false...
>
> No dia 17 de Abr de 2012 20:45, "Jason Vertrees"
> escreveu:
>
>> Hi João,
>>
>> What about
>>
>> cmd.png(default_name+'.png', dpi=300, ray=0)
>>
>> Cheers,
>>
>> -- Jason
>>
>>
>> On Tue, Apr 17, 2012 at 11:18 AM, João Rodrigues
>> wrote:
>> > Hello all,
>> >
>> > I'm using Pymol v1.5 (from fink, so open source version) to trace large
>> > scene that I have. To that end, I'm avoiding having PyMOL open and I
>> > wrote a
>> > small python script to do the rendering for me. All goes well, except
>> > this
>> > last part (don't mind the obvious variable names):
>> >
>> >> cmd.ray(width, height, renderer=2)
>> >> cmd.png(default_name+'.png', dpi=300, ray=False)
>> >
>> >
>> > This actually renders my scene twice. I've tried cmd.do and it does the
>> > same.. am I missing something or is this not supposed to happen?
>> >
>> > Thanks and cheers,
>> >
>> > João [...] Rodrigues
>> > http://nmr.chem.uu.nl/~joao
>> >
>> >
>> >
>> > --
>> > Better than sec? Nothing is better than sec when it comes to
>> > monitoring Big Data applications. Try Boundary one-second
>> > resolution app monitoring today. Free.
>> > http://p.sf.net/sfu/Boundary-dev2dev
>> > ___
>> > 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
>>
>>
>>
>> --
>> Jason Vertrees, PhD
>> PyMOL Product Manager
>> Schrödinger, LLC
>>
>> (e) jason.vertr...@schrodinger.com
>> (o) +1 (603) 374-7120
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
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Re: [PyMOL] Using cmd.png with ray=False still ray traces the image
Hi Jason,
I've tried a lot of stuff, thus the renderer=2.. (i installed povray and
tried to use it). With the default option the result is the same.
cmd.png(default_name+'.png', width, height, dpi, ray=0)
Doing what you wrote still causes the renderer to kick in.. I'm a bit out
of ideas..
Cheers,
João [...] Rodrigues
http://nmr.chem.uu.nl/~joao
No dia 17 de Abril de 2012 22:33, Jason Vertrees <
jason.vertr...@schrodinger.com> escreveu:
> João,
>
> I'm not sure why this is giving you problems. Why do you have
> renderer=2? Why not the default? Are you counting primitives? If so, I
> suggest:
>
> cmd.set("ray_default_renderer", 2)
>
> # snapshot
>
> cmd.png(myFile, width=w, height=h, dpi=d, ray=0)
>
> # this will ray trace
>
> cmd.png(myFile, width=w, height=h, dpi=d, ray=1)
>
> Cheers,
>
> -- Jason
>
>
> On Tue, Apr 17, 2012 at 1:21 PM, João Rodrigues wrote:
> > Same result Jason, i also tried =false...
> >
> > No dia 17 de Abr de 2012 20:45, "Jason Vertrees"
> > escreveu:
> >
> >> Hi João,
> >>
> >> What about
> >>
> >> cmd.png(default_name+'.png', dpi=300, ray=0)
> >>
> >> Cheers,
> >>
> >> -- Jason
> >>
> >>
> >> On Tue, Apr 17, 2012 at 11:18 AM, João Rodrigues
> >> wrote:
> >> > Hello all,
> >> >
> >> > I'm using Pymol v1.5 (from fink, so open source version) to trace
> large
> >> > scene that I have. To that end, I'm avoiding having PyMOL open and I
> >> > wrote a
> >> > small python script to do the rendering for me. All goes well, except
> >> > this
> >> > last part (don't mind the obvious variable names):
> >> >
> >> >> cmd.ray(width, height, renderer=2)
> >> >> cmd.png(default_name+'.png', dpi=300, ray=False)
> >> >
> >> >
> >> > This actually renders my scene twice. I've tried cmd.do and it does
> the
> >> > same.. am I missing something or is this not supposed to happen?
> >> >
> >> > Thanks and cheers,
> >> >
> >> > João [...] Rodrigues
> >> > http://nmr.chem.uu.nl/~joao
> >> >
> >> >
> >> >
> >> >
> --
> >> > Better than sec? Nothing is better than sec when it comes to
> >> > monitoring Big Data applications. Try Boundary one-second
> >> > resolution app monitoring today. Free.
> >> > http://p.sf.net/sfu/Boundary-dev2dev
> >> > ___
> >> > 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
> >>
> >>
> >>
> >> --
> >> Jason Vertrees, PhD
> >> PyMOL Product Manager
> >> Schrödinger, LLC
> >>
> >> (e) jason.vertr...@schrodinger.com
> >> (o) +1 (603) 374-7120
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrödinger, LLC
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
>
--
Better than sec? Nothing is better than sec when it comes to
monitoring Big Data applications. Try Boundary one-second
resolution app monitoring today. Free.
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Re: [PyMOL] Using cmd.png with ray=False still ray traces the image
It may be worth trying pymol 1.4 (instead of 1.5) - although this
shouldn't make a difference, it might provide some more information (you
also mentioned that you've got a large scene - depending on composition
1.4 may use less memory than 1.5).
You may also want to try using a pml script vs python (start pymol with
"-q -c your_raytrace_script.pml" arguments) and see if that helps, or at
least breaks in different ways.
Pete
João Rodrigues wrote:
> Hi Jason,
>
> I've tried a lot of stuff, thus the renderer=2.. (i installed povray and
> tried to use it). With the default option the result is the same.
>
> cmd.png(default_name+'.png', width, height, dpi, ray=0)
>
> Doing what you wrote still causes the renderer to kick in.. I'm a bit out of
> ideas..
>
> Cheers,
>
> João [...] Rodrigues
> http://nmr.chem.uu.nl/~joao
>
>
>
> No dia 17 de Abril de 2012 22:33, Jason Vertrees
> mailto:jason.vertr...@schrodinger.com>>
> escreveu:
> João,
>
> I'm not sure why this is giving you problems. Why do you have
> renderer=2? Why not the default? Are you counting primitives? If so, I
> suggest:
>
> cmd.set("ray_default_renderer", 2)
>
> # snapshot
>
> cmd.png(myFile, width=w, height=h, dpi=d, ray=0)
>
> # this will ray trace
>
> cmd.png(myFile, width=w, height=h, dpi=d, ray=1)
>
> Cheers,
>
> -- Jason
>
>
> On Tue, Apr 17, 2012 at 1:21 PM, João Rodrigues
> mailto:anar...@gmail.com>> wrote:
>> Same result Jason, i also tried =false...
>>
>> No dia 17 de Abr de 2012 20:45, "Jason Vertrees"
>> mailto:jason.vertr...@schrodinger.com>>
>> escreveu:
>>
>>> Hi João,
>>>
>>> What about
>>>
>>> cmd.png(default_name+'.png', dpi=300, ray=0)
>>>
>>> Cheers,
>>>
>>> -- Jason
>>>
>>>
>>> On Tue, Apr 17, 2012 at 11:18 AM, João Rodrigues
>>> mailto:anar...@gmail.com>>
>>> wrote:
Hello all,
I'm using Pymol v1.5 (from fink, so open source version) to trace large
scene that I have. To that end, I'm avoiding having PyMOL open and I
wrote a
small python script to do the rendering for me. All goes well, except
this
last part (don't mind the obvious variable names):
> cmd.ray(width, height, renderer=2)
> cmd.png(default_name+'.png', dpi=300, ray=False)
This actually renders my scene twice. I've tried cmd.do and it does the
same.. am I missing something or is this not supposed to happen?
Thanks and cheers,
João [...] Rodrigues
http://nmr.chem.uu.nl/~joao
--
Better than sec? Nothing is better than sec when it comes to
monitoring Big Data applications. Try Boundary one-second
resolution app monitoring today. Free.
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___
PyMOL-users mailing list
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>>>
>>>
>>> --
>>> Jason Vertrees, PhD
>>> PyMOL Product Manager
>>> Schrödinger, LLC
>>>
>>> (e) jason.vertr...@schrodinger.com
>>> (o) +1 (603) 374-7120
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrödinger, LLC
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
>
--
Better than sec? Nothing is better than sec when it comes to
monitoring Big Data applications. Try Boundary one-second
resolution app monitoring today. Free.
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