Message: 5
Date: Thu, 2 Oct 2008 16:13:42 -0400
From: Jeff Hansen <[EMAIL PROTECTED]>
Subject: [Jmol-users] problem reading spardir file
To: [email protected]
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
Could someone with experience using Spartan files in Jmol give me
some
help? What I did in Spartan is to create a butane molecule and save
it. Then I defined a dihedral angle and did an Energy Profile
calculation varying that dihedral angle from -180 to 180 with 24
steps. The results of that calculation were then saved separately.
The first is called nbutane.spardir. The second is called
butane.spardir. In Jmol the simpler nbutane.spardir file is
displayed
as expected. The second, butane.spardir, is not displayed and
instead
gives the following error message:
Error reading file at line 7:
BEGIN Directory Entry file:/Users/jeffhans/Sites/Jmol/jmol/models/
butane.spardir/M0001/proparc
9
for file file:/Users/jeffhans/Sites/Jmol/jmol/models/butane.spardir
type spartan directory
Does anyone know what I'm doing wrong and how to fix it so I can see
this molecule in Jmol? What I'm looking to see is a file loaded that
has multiple models so I can see each conformer.
Thanks for any help you can provide.
***********************************************
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
[EMAIL PROTECTED]
***********************************************
------------------------------
Message: 6
Date: Thu, 02 Oct 2008 23:26:23 +0200
From: [EMAIL PROTECTED]
Subject: Re: [Jmol-users] Jmol 11.6 release -- delayed
To: [email protected]
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
format="flowed"
Quoting Robert Hanson <[EMAIL PROTECTED]>:
Rolf,
First, realize that it's an unusual situation that you are in,
accessing
files through an absolute path on your web server. Most of us use
relative
paths.
This is not a bug. The problem is that that now that the signed
applet can
read from the hard drive, if you just say:
/xxx/xxx/xxx
Jmol has to assume that's from the hard drive, because it doesn't
have a URL
associated with it. (This was fixed recently for people on Macs
and Unix
boxes, where there is no X: prefix.)
Whether or not the applet is signed doesn't make a difference --
we really
don't want the signed and unsigned applet accessing different
files. So you
can no longer use
load "/xxx/xxx"
with no HTTP:// in front of it with the applet -- signed or
unsigned -- to
access root files on the web server. I suppose you could argue
that we
should allow "/" to mean "root on the web server" for the unsigned
applet,
but that would mean that the signed applet and unsigned applet
would have
two different interpretations, and I at least suggest that's not a
good
idea.
Jmol now has to read that as a local file. Instead, use your full
URL call,
or set the default directory to
http://[EMAIL PROTECTED]/
and then just use the load command without the initial slash.
Will that work for you?
Disabling server absolute paths is a severe change that at least
should be announced very clearly. There might be other sites that
will
also be broken by this change. From the discussion about this topic
on
this list about 3 years ago (when the Jmol.js library popped up an
alert when a server absolute path was used) I remember that there
were
also other people who voted for allowing server absolute paths.
It is of course not always easy to maintain backward compatibility.
But since the abilities of the signed applet are new features it
might
be better to disable server absolute paths by a switch instead of
enabling them by a switch (or some other way) or disabling them
totally.
Q: What do others think about this?
Q: Are there other Jmol sites that use server absolute paths?
Regards,
Rolf
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------------------------------
Message: 7
Date: Thu, 2 Oct 2008 14:28:41 -0700
From: "Dean Johnston" <[EMAIL PROTECTED]>
Subject: [Jmol-users] Creation / representation of aromatic bonds
To: [email protected]
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"
I don't know if this is a bug or a feature, but my script to
display a model
of benzene ends up with all double bonds. Here is a snippet of the
script
(the structure is defined via an inline data file):
set autobond false;
data "model benzene" | ... (atom coordinates here) ... |end "model
benzene";
show data;
connect (atomno=1) (atomno=2) AROMATIC create;
connect (atomno=2) (atomno=3) AROMATIC create;
connect (atomno=3) (atomno=4) AROMATIC create;
connect (atomno=4) (atomno=5) AROMATIC create;
connect (atomno=5) (atomno=6) AROMATIC create;
connect (atomno=6) (atomno=1) AROMATIC create;
This produces all double bonds. When I play around with the
console, the
only way I can get what I want (and expect) is to say:
connect;
connect (atomno=1) (atomno=2) AROMATIC modify;
...etc. for all the remaining bonds
I've attached a state file.
Dean
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