Hi,
it's nice to see that an other translation of the documentation is being
done :)
From: "Daniel Leidert" <[EMAIL PROTECTED]>
> Hello,
>
> I found some issues in the documentation. JmolDevelopersGuide.docbok.xml
> does not contain valid xml[1]. I fixed this. But: I use tabs (the
> current sourc
Miguel wrote:
> > Hello,
> >
> > I found some issues in the documentation. JmolDevelopersGuide.docbok.xml
> > does not contain valid xml[1]. I fixed this. But: I use tabs (the
> > current source is mix of tabs and spacings) for indent and I don't use
> > linewrap after 80 chars for a better look.
>
I don't remember who worked on the Gamess Reader ... may have been me.
It currently is looking for the text 'GAMESS' to identify a gamess file.
Tamas submitted a file that has the following header
$CONTRL SCFTYP=RHF RUNTYP=OPTIMIZE COORD=ZMT ICHARG=-2 MULT=1
NPRINT=-2 MAXIT=200 $END
$BASIS GB
> Hello,
>
> I found some issues in the documentation. JmolDevelopersGuide.docbok.xml
> does not contain valid xml[1]. I fixed this. But: I use tabs (the
> current source is mix of tabs and spacings) for indent and I don't use
> linewrap after 80 chars for a better look.
>
> Q: Does anyone run int
Hello,
I found some issues in the documentation. JmolDevelopersGuide.docbok.xml
does not contain valid xml[1]. I fixed this. But: I use tabs (the
current source is mix of tabs and spacings) for indent and I don't use
linewrap after 80 chars for a better look.
Q: Does anyone run into problems with
Based on information at
http://ndbserver.rutgers.edu/NDB/mmcif/index.html
and
http://ndbserver.rutgers.edu/mmcif/examples/index.html
I'd say mmCIF is a subset of CIF and has to still follow the same basic rules.
All the descriptions at
http://ndbserver.rutgers.edu/mmcif/dictionaries/html/cif_mm.dic
Tamas wrote:
> Miguel,
>
> CIF and mmCIF are too different formats. mmCIF is for macromolecular CIF,
> the extension of the original CIF format to proteins etc.
> Cf.: http://www.ccp4.ac.uk/dist/html/mmcifformat.html
Tamas,
I am not familiar with the details ...
I thought that mmCIF was basical
Miguel,
CIF and mmCIF are too different formats. mmCIF is for macromolecular CIF,
the extension of the original CIF format to proteins etc.
Cf.: http://www.ccp4.ac.uk/dist/html/mmcifformat.html
Tamas
Dr. Tamas E. Gunda
Dept. of Pharmaceutical Chemistry
University of Debrecen
POBox 36
H-4010 Deb
I agree with what you have said before, Miguel, that if you start reading
"bogus" CIF files, you are starting down into a deep dark hole.
I vote to not support invalid CIF files.
Some documentation on our site that we could point users to in defense of this
position would be a nice compromise. I
> I think
>
> http://www.iucr.org/iucr-top/cif/spec/version1.1/cifsyntax.html#syntax
>
> is pretty clear on this (data_ required):
Q: What should our stance be on the support of invalid .cif files?
Q: The iucr wants people to refuse to read them in order to encourage
companies to be compliant ...
I think
http://www.iucr.org/iucr-top/cif/spec/version1.1/cifsyntax.html#syntax
is pretty clear on this (data_ required):
4. A CIF consists of data names (tags) and associated values organized into data
blocks. A data block may contain data items (associated data names and data
values) and/or it m
Rene,
We have received some output from Gaussian 98 that is crashing the
GaussianReader. It is dying with the following stack backtrace:
FileManager.openFile(/home/mth/jmol/tamas/G98.out)
SmarterJmolAdapter:The Resolver thinks:Gaussian
java.lang.ArrayIndexOutOfBoundsException: 2
at
org.jm
My question is about the validity of a CIF file ...
I have received a file which claims to be a CIF file. The first few lines
look like:
##
# mmCIF file created by CS Chem3D
##
###
Rajarshi,
Someone has reported a problem with a HIN file.
The file is not being recognized as a HIN file because there is additional
information at the beginning of the file ... so Resolver.java is not
finding any indentifying information in the first 4 lines of the file.
Currently the Resolver
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