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From: Marius R. <mar...@gm...> - 2008-06-27 11:16:53
|
Hi All, I'm using pymol to select (by residue) all the atoms around 10 angstroms from a certain atom. Now I would like to write the residue id's of my selection to an external file, so that I can integrated in the ndx file from Gromacs. Do you have any idea how I could do that? Thanks, Marius Retegan |
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From: Tsjerk W. <ts...@gm...> - 2008-06-27 11:35:54
|
Hi,
This should've gone to the list... (isn't there an option "send
replies to list rather than to poster" to the mailing list?)
Tsjerk
On Fri, Jun 27, 2008 at 1:34 PM, Tsjerk Wassenaar <ts...@gm...> wrote:
> Hi Marius,
>
> You want iterate.
> You do have to make sure though that the numbering of your atoms in
> the structure file is correct. Than you can do:
>
> ndx=open("index.ndx","w")
> ndx.write("[ MyIndex ]\n")
> iterate selection, ndx.write("%d\n" % ID)
> ndx.close()
>
> I did make the assumption that you wanted the atom id's rather than
> the residue id's, since the latter are of no use to Gromacs.
>
> Hope it helps,
>
> Tsjerk
>
> On Fri, Jun 27, 2008 at 1:17 PM, Marius Retegan
> <mar...@gm...> wrote:
>> Hi All,
>> I'm using pymol to select (by residue) all the atoms around 10 angstroms
>> from a certain atom. Now I would like to write the residue id's of my
>> selection to an external file, so that I can integrated in the ndx file from
>> Gromacs. Do you have any idea how I could do that?
>>
>> Thanks,
>>
>> Marius Retegan
>>
>> -------------------------------------------------------------------------
>> Check out the new SourceForge.net Marketplace.
>> It's the best place to buy or sell services for
>> just about anything Open Source.
>> http://sourceforge.net/services/buy/index.php
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
>
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
|
|
From: Justin L. <j.l...@fz...> - 2008-06-27 11:54:56
Attachments:
signature.asc
|
Tsjerk Wassenaar schrieb: > Hi, > > This should've gone to the list... (isn't there an option "send > replies to list rather than to poster" to the mailing list?) > > Tsjerk > > Depends on the list, but there is a nifty addon for thunderbird http://alumnit.ca/wiki/index.php?page=ReplyToListThunderbirdExtension Justin -- Justin Lecher Institute for Neuroscience and Biophysics INB 2 - Molecular Biophysics II Research centre Juelich GmbH, 52425 Juelich,Germany phone: +49 2461 61 5385 |
|
From: Marius R. <mar...@gm...> - 2008-06-27 16:00:54
|
Hi,
It seems that I run into a little problem. When I try to write a large
selection I get only a partial list of ID. If for example I print ID after
the iterate command, all the list is printed into pymol window. Do you have
any idea why?
I run Pymol 1.1pre5 under Fedora 8.
On Fri, Jun 27, 2008 at 1:36 PM, Tsjerk Wassenaar <ts...@gm...> wrote:
> Hi,
>
> This should've gone to the list... (isn't there an option "send
> replies to list rather than to poster" to the mailing list?)
>
> Tsjerk
>
> On Fri, Jun 27, 2008 at 1:34 PM, Tsjerk Wassenaar <ts...@gm...>
> wrote:
> > Hi Marius,
> >
> > You want iterate.
> > You do have to make sure though that the numbering of your atoms in
> > the structure file is correct. Than you can do:
> >
> > ndx=open("index.ndx","w")
> > ndx.write("[ MyIndex ]\n")
> > iterate selection, ndx.write("%d\n" % ID)
> > ndx.close()
> >
> > I did make the assumption that you wanted the atom id's rather than
> > the residue id's, since the latter are of no use to Gromacs.
> >
> > Hope it helps,
> >
> > Tsjerk
> >
> > On Fri, Jun 27, 2008 at 1:17 PM, Marius Retegan
> > <mar...@gm...> wrote:
> >> Hi All,
> >> I'm using pymol to select (by residue) all the atoms around 10 angstroms
> >> from a certain atom. Now I would like to write the residue id's of my
> >> selection to an external file, so that I can integrated in the ndx file
> from
> >> Gromacs. Do you have any idea how I could do that?
> >>
> >> Thanks,
> >>
> >> Marius Retegan
> >>
> >>
> -------------------------------------------------------------------------
> >> Check out the new SourceForge.net Marketplace.
> >> It's the best place to buy or sell services for
> >> just about anything Open Source.
> >> http://sourceforge.net/services/buy/index.php
> >> _______________________________________________
> >> PyMOL-users mailing list
> >> PyM...@li...
> >> https://lists.sourceforge.net/lists/listinfo/pymol-users
> >>
> >>
> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > Junior UD (post-doc)
> > Biomolecular NMR, Bijvoet Center
> > Utrecht University
> > Padualaan 8
> > 3584 CH Utrecht
> > The Netherlands
> > P: +31-30-2539931
> > F: +31-30-2537623
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
>
> -------------------------------------------------------------------------
> Check out the new SourceForge.net Marketplace.
> It's the best place to buy or sell services for
> just about anything Open Source.
> http://sourceforge.net/services/buy/index.php
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
|
|
From: DeLano S. <de...@de...> - 2008-06-27 23:30:19
|
Marius,
Hmm...are you perhaps looking at the output before the file is closed and/or
flushed? You should issue ndx.flush() or ndx.close() before attempting to
use the output file.
Cheres,
Warren
_____
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Marius
Retegan
Sent: Friday, June 27, 2008 9:01 AM
To: pymol-users
Subject: Re: [PyMOL] writing selection to a external file
Hi,
It seems that I run into a little problem. When I try to write a large
selection I get only a partial list of ID. If for example I print ID after
the iterate command, all the list is printed into pymol window. Do you have
any idea why?
I run Pymol 1.1pre5 under Fedora 8.
On Fri, Jun 27, 2008 at 1:36 PM, Tsjerk Wassenaar <ts...@gm...> wrote:
Hi,
This should've gone to the list... (isn't there an option "send
replies to list rather than to poster" to the mailing list?)
Tsjerk
On Fri, Jun 27, 2008 at 1:34 PM, Tsjerk Wassenaar <ts...@gm...> wrote:
> Hi Marius,
>
> You want iterate.
> You do have to make sure though that the numbering of your atoms in
> the structure file is correct. Than you can do:
>
> ndx=open("index.ndx","w")
> ndx.write("[ MyIndex ]\n")
> iterate selection, ndx.write("%d\n" % ID)
> ndx.close()
>
> I did make the assumption that you wanted the atom id's rather than
> the residue id's, since the latter are of no use to Gromacs.
>
> Hope it helps,
>
> Tsjerk
>
> On Fri, Jun 27, 2008 at 1:17 PM, Marius Retegan
> <mar...@gm...> wrote:
>> Hi All,
>> I'm using pymol to select (by residue) all the atoms around 10 angstroms
>> from a certain atom. Now I would like to write the residue id's of my
>> selection to an external file, so that I can integrated in the ndx file
from
>> Gromacs. Do you have any idea how I could do that?
>>
>> Thanks,
>>
>> Marius Retegan
>>
>> -------------------------------------------------------------------------
>> Check out the new SourceForge.net Marketplace.
>> It's the best place to buy or sell services for
>> just about anything Open Source.
>> http://sourceforge.net/services/buy/index.php
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
>
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
-------------------------------------------------------------------------
Check out the new SourceForge.net Marketplace.
It's the best place to buy or sell services for
just about anything Open Source.
http://sourceforge.net/services/buy/index.php
_______________________________________________
PyMOL-users mailing list
PyM...@li...
https://lists.sourceforge.net/lists/listinfo/pymol-users
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