Quoting Miguel <[EMAIL PROTECTED]>:
> > What is this problem ? A bug ?
>
> No, it is a fact of life.
>
> I will investigate the possibility of providing additional formatting
> control in the 'label' statement to allow numeric precision specification.
Thanks, Francois
-
> Quoting Miguel <[EMAIL PROTECTED]>:
>
>> > to be able to display _partial_ charge values
>> > as Labels in Jmol (as Atom Name Labels are displayed).
>>
>> select ;
>> label "%P"; # show partial charge as the label
>
> All works pretty good with however one problem: See
> http://www.u-picardie.
On Saturday 08 October 2005 11:30, FyD wrote:
> Quoting Egon Willighagen <[EMAIL PROTECTED]>:
> > On Saturday 08 October 2005 09:33, FyD wrote:
> > > With the corresponding CML file converted from a Tripos file:
> > > http://www.u-picardie.fr/labo/lbpd/jmol-10.00/Test/MeOH.cml
> >
> > Very good!
>
Quoting Egon Willighagen <[EMAIL PROTECTED]>:
> On Saturday 08 October 2005 09:33, FyD wrote:
> > With the corresponding CML file converted from a Tripos file:
> > http://www.u-picardie.fr/labo/lbpd/jmol-10.00/Test/MeOH.cml
>
> Very good!
>
> I'm happy to see that you took this approach. BTW, how
On Saturday 08 October 2005 09:33, FyD wrote:
> With the corresponding CML file converted from a Tripos file:
> http://www.u-picardie.fr/labo/lbpd/jmol-10.00/Test/MeOH.cml
Very good!
I'm happy to see that you took this approach. BTW, how did you convert the
file? Did you indeed make a custom scr
Quoting Miguel <[EMAIL PROTECTED]>:
> > to be able to display _partial_ charge values
> > as Labels in Jmol (as Atom Name Labels are displayed).
>
> select ;
> label "%P"; # show partial charge as the label
All works pretty good with however one problem: See
http://www.u-picardie.fr/labo/lbpd/j
Quoting Miguel <[EMAIL PROTECTED]>:
> > So it should be quite simple to write a perl script
> > to convert ".mol2 files" into "CML files"
>
> Yes.
> The task would be simple for some developers, but not simple for others :-)
OK, we will work on this...
> > to be able to display _partial_ charge
> Quoting Miguel <[EMAIL PROTECTED]>:
>
>> Jmol already supports both formal charges and partial charges.
>> Some file formats support one ... other file formats support the other.
>> CML, for example, supports both.
>
> So it should be quite simple to write a perl script
> to convert ".mol2 files
Quoting Miguel <[EMAIL PROTECTED]>:
> Jmol already supports both formal charges and partial charges.
> Some file formats support one ... other file formats support the other.
> CML, for example, supports both.
So it should be quite simple to write a perl script to convert ".mol2 files"
into "CML
On Thu, October 6, 2005 11:33 am, Miguel said:
> This is a good task for a novice who wants to contribute. It is a
> self-contained, well-defined task that would provide the opportunity to
> gain some experience with Java, CVS, open source development, and Jmol.
>
> Some possible ideas:
>
> * Fran
> We could also imagine to generate pseudo .pdb i.e .pqr
> file from Tripos files using some perl scripts and
> display the charges added in this new .pqr file in
> Jmol as an atom name or chemical element or atom number.
You could convert to .pdb (or any other supported format) as an interim
step
Quoting Miguel <[EMAIL PROTECTED]>:
> > Is there a way to display the Tripos file format (.mol2) with the atom
> > names &
> > atomic charges available in those files using Jmol...
> > My understanding is that it is not implemented.
>
> That is correct.
> There is currently no support for this fil
> Dear All,
>
> I am a new Jmol user.
>
> Is there a way to display the Tripos file format (.mol2) with the atom
> names &
> atomic charges available in those files using Jmol...
> My understanding is that it is not implemented.
That is correct.
There is currently no support for this file format
Just in case it clarifies ideas:
- atom (or element, if available) names and charges are indeed
recognized by Jmol in .pdb files.
- at least charges are also recognized in .mol files (MDL).
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Dear All,
I am a new Jmol user.
Is there a way to display the Tripos file format (.mol2) with the atom names &
atomic charges available in those files using Jmol...
My understanding is that it is not implemented. I guess if it is possible to
display the atom names of PDB files, it should be possi
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