Hi,
Miguel wrote:
Nico & Egon,
My ISP seems to be having some kind of email problem and I am currently
unable to post this to [EMAIL PROTECTED] ... I tried twice but
the messages bounced.
Miguel
---------------------------- Mensaje original ----------------------------
Asunto: Re: Testing of jmol 10.00.12
De: "Miguel" <[EMAIL PROTECTED]>
Fecha: Jue, 2 de Junio de 2005, 21:46
Para: "Victor Manuel Rosas-Garcia" <[EMAIL PROTECTED]>
Cc: [email protected]
--------------------------------------------------------------------------
Hi Miguel,
I did some testing of jmol versions 10.00.11 and 10.00.12 using the
sample files from jmol version 9. Please find the results in the
attached text file
have a nice day!
Victor,
Thank you *very* much for taking the time to do this.
Egon & Nico, there are some questions in here about file formats that you
may be able to help answer.
----
File 10.00.11 10.00.12
1CRN.cif.gz GOOD GOOD
...
test2.g03.out GOOD GOOD
Miguel: At least we have some that are GOOD :-)
4-cyanophenylnitrene-Benzazirine-TS.g94.out GOOD (Does
not animate vibrations)
...
phenol-without-para-H.g98.out GOOD
(Does
not animate vibrations)
Miguel: Support for has gone through several changes. I believe that these
do work properly. However, it may be confusing because the first model in
the file is now the *input*, not one of the output frequencies. I suggest
that you take a look at Tools->AtomChooser => Frequencies.
I actually did not think that there were changes in this area between
10.00.11 and 10.00.12 ...
Q: Nico, what changes were made in this area between 10.00.11 and 10.00.12?
I too didn't think that there were changes there.
crystal.cml GOOD
GOOD
buckyball.cml no protocol:cml.dtd
no
protocol:cml.dtd
...
unchemical.cml no protocol:cml.dtd
no
protocol:cml.dtd
estron.cml No atoms in file
No
atoms in file
glycine-crystal.cml No atoms in file
No
atoms in file
methanol3.cml No atoms in file
No
atoms in file
Miguel: I believe that all these CML problems are there because Jmol 10
supports CML2, not the CML1 that was supported in Jmol 9.
Q: Egon, can you confirm this?
benzene.hin unrecognized file format
unrecognized file format
molecule2.hin unrecognized file format
unrecognized file format
molecule3.hin unrecognized file format
unrecognized file format
multiple.hin unrecognized file format
unrecognized file format
Miguel: I do not know. There are a few sample .hin files in the Jmol v10
repository and they work OK.
Q: Do we think that these .hin files from Jmol 9 should be valid and
should be readable by Jmol 10?
bulk_Si.in No atoms in file
No
atoms in file
HfO2_mol_opt.in unrecognized file format
unrecognized file format
HfO2_on_Si_relax.in unrecognized file format
unrecognized file format
t54.in unrecognized file format
unrecognized file format
ammonia.adf.out unrecognized file format
unrecognized file format
LiMoS2_optimisation_ISIF3.vasp unrecognized file format
unrecognized file format
Si_eband.out unrecognized file format
unrecognized file format
slab_7Si_3Vac_2x.in unrecognized file format
unrecognized file format
slab_7Si_3Vac_2x_relax_2x1.out unrecognized file format
unrecognized file format
t01.out.abinit.v3.x.x unrecognized file format
unrecognized file format
t01.out.abinit.v4.x.x unrecognized file format
unrecognized file format
t12.abinit.out unrecognized file format
unrecognized file format
t13.abinit.out unrecognized file format
unrecognized file format
ch4-opt.out No atoms in file
No
atoms in file
h2o_b3lyp_IR.out No atoms in file
No
atoms in file
zeolite_AFI.out unrecognized file format
unrecognized file format
Miguel: I do not know about these. Egon, do you know the status of them?
tms.log OutOfBoundsException:5
OutOfBoundsException:5
phenylnitrene.g92.out OutOfBoundsException:5
OutOfBoundsException:5
ch3oh_ace.out NoSuchElementException
NoSuchElementException
ch3oh_gam.out (Blank screen)
(Blank
screen)
Cl2O.log (Blank screen)
(Blank
screen)
Bug 1155968 Confuses Ca with C and
Correctly identifies Ca,
oxygen with Xx
confuses oxygen with Xx
Bug 1204598 Misses a beta strand
Misses
a beta strand with
rockets
and
ribbons,
but not
with
cartoons
Miguel: I will look at these.
New bug -------
"color
rockets structure"
yields
uniform
pink
molecule.
Same
thing
with
ribbons
and
cartoons
Miguel: These are bugs that I introduced with the recent changes to
colors. Thank you for pointing them out. I will fix them.
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