Re: [Jmol-users] Find SMILES problem

2010-09-01 Thread Robert Hanson 
On Wed, Sep 1, 2010 at 10:21 PM, Otis Rothenberger wrote:

>  Bob,
>
> There is a general aromatic problem that I'm having with find SMILES
> that's easiest to explain with a specific scenario. If I load benzene
> and run "var x={*}.find('SMILES');echo @x," I get:
>
> c1=cc=cc=c1
>
> If I use model kit mode to make 1,3-cyclohexadiene, the same "var
> x={*}.find('SMILES');echo @x" produces
>
> c1=cc=ccc1
>
>
I'll look into that. Almost certainly a bug. It should only use lower case c
if the ring is totally flat and there are no sp3 centers. I'm really
surprised it's doing that. The code is only supposed to insert lower case
"c" when:

-- the ring is flat
-- the ring has no sp3 centers

Is it possible you are sending it a flat no-hydrogen ring? When I use the
model kit, I get:


C1==C1




> I'm now stuck in lower case "c" mode on this ring no matter what I do to
> the ring. If I break a ring bond while the ring is no longer aromatic
> and reform the bond, I go back to upper case "C"
>
>
remember -- "aromatic" just means "flat and all sp2" for Jmol. We're not
going to get into multiple bonding issues. There's no "antiaromatic" here.
It doesn't matter if you have 6 carbons and all single bonds or 6 carbons
and all double bonds or 8 carbons (as in octadienyl dianion ligand). As long
as it's flat and there aren't any tetrahedrally directed substituents, Jmol
is going to use "c" instead of "C".

Bob



> There are really two issues here:
>
> 1) Jmol creates Kekule SMILES in lower case, and this does not seem to
> be standard. As long as compare is Jmol/Jmol, this is not a problem. And
> in fact, NIH Resolver which uses aromatic SMILES (c1c1), recognizes
> the Jmol lower case Kekule SMILES for benzene.
>

It's definitely incorrect. You really have all the H atoms there and it's
not planar?

2) Getting stuck in lower case mode, however, is a problem and seems to
> be a bug.
>
> I have a feeling that calculate/reset aromatic may offer one solution to
> the problem, but I'm not sure it can be used in a general sense to
> "unaromatise" an aromatic ring. If this is not a bug, an alternative is
> to use JavaScript toUpperCase() on s, c, n, and o, but that has ugly
> side affects.
>
>
See if you can find out more about what exactly the NIH server is requiring,
if that's the issue. There's also a

/noaromatic/ flag in Jmol's SMILES business that turns off aromatic
checking. That might be useful.

Help me define what the context is. Where are these being used?



> Otis
>
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[Jmol-users] Find SMILES problem

2010-09-01 Thread Otis Rothenberger 
  Bob,

There is a general aromatic problem that I'm having with find SMILES 
that's easiest to explain with a specific scenario. If I load benzene 
and run "var x={*}.find('SMILES');echo @x," I get:

c1=cc=cc=c1

If I use model kit mode to make 1,3-cyclohexadiene, the same "var 
x={*}.find('SMILES');echo @x" produces

c1=cc=ccc1

I'm now stuck in lower case "c" mode on this ring no matter what I do to 
the ring. If I break a ring bond while the ring is no longer aromatic 
and reform the bond, I go back to upper case "C"

There are really two issues here:

1) Jmol creates Kekule SMILES in lower case, and this does not seem to 
be standard. As long as compare is Jmol/Jmol, this is not a problem. And 
in fact, NIH Resolver which uses aromatic SMILES (c1c1), recognizes 
the Jmol lower case Kekule SMILES for benzene.

2) Getting stuck in lower case mode, however, is a problem and seems to 
be a bug.

I have a feeling that calculate/reset aromatic may offer one solution to 
the problem, but I'm not sure it can be used in a general sense to 
"unaromatise" an aromatic ring. If this is not a bug, an alternative is 
to use JavaScript toUpperCase() on s, c, n, and o, but that has ugly 
side affects.

Otis

-- 
Otis Rothenberger
chemagic.com




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Re: [Jmol-users] Bug in Jmol 12.0.11_dev

2010-09-01 Thread Robert Hanson 
heh,heh, not THERE's an obscure bug:

# bug fix: color label none when already none and after rendering for
multi-line labels or with antialiasdisplay crashes Jmol

Here's the test:

label "x|x"
color labels none
refresh
color labels none


Bob

On Wed, Sep 1, 2010 at 3:46 PM, Eric Martz wrote:

> Dear Bob,
>
> I downloaded Jmol-12.0.11_dev today 9/1 about 10 AM.
>
> The VERY good news: It works fine in both my under-development
> tutorial on MHC in the JTAT shell, and in FirstGlance in Jmol
> (limited testing).
>
> -
>
> I found 1 Bug. This bug has been present since 11.6.RC12. I was
> hoping this version would not have it. I can run many script files
> just fine, but, on the SECOND attempt to run one particular script
> named labelm1.spt, it reproducibly crashes Jmol:
>
> FileManager opening file:/Volumes/JTAT/mhc/chapter04/labelm1.spt
> Exception in thread "QueueThread0" java.lang.NullPointerException
> at org.jmol.shape.Labels.setColix(Unknown Source)
> at org.jmol.shape.Labels.setProperty(Unknown Source)
> at org.jmol.shape.Shape.setShapeProperty(Unknown Source)
> at org.jmol.viewer.ShapeManager.setShapeProperty(Unknown Source)
> at org.jmol.script.ScriptEvaluator.setShapeProperty(Unknown Source)
> at org.jmol.script.ScriptEvaluator.colorShape(Unknown Source)
> at org.jmol.script.ScriptEvaluator.color(Unknown Source)
> at
> org.jmol.script.ScriptEvaluator.instructionDispatchLoop(Unknown Source)
> at org.jmol.script.ScriptEvaluator.script(Unknown Source)
> at
> org.jmol.script.ScriptEvaluator.instructionDispatchLoop(Unknown Source)
> at
> org.jmol.script.ScriptEvaluator.evaluateCompiledScript(Unknown Source)
> at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source)
> at
> org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runScript(Unknown Source)
> at
> org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runNextScript(Unknown
> Source)
> at
> org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(Unknown Source)
> at java.lang.Thread.run(Thread.java:613)
>
> I have narrowed it down to this.
>
> Start Jmol.jar.
>
> In the console, enter "set antialiasdisplay"
>
> Load any PDB file (it must contain an atom with the number specified,
> e.g. 3053 below, which occurs in 2vaa or 2hu4; for 1d66, use e.g. 1549).
>
> Now execute the following script TWICE:
>
> select all
> set fontsize 16
> set labelfront
> color labels none
> select atomno=3053
> label Beta-2 Mic.
>
> On the second execution, Jmol will crash.
>
> It does not seem to be a single command, but perhaps two. I haven't
> narrowed it down further.
>
> The antialiasdisplay can be entered before or after loading the molecule.
>
> -Eric
>
>
>
> At 8/31/10, Robert Hanson wrote:
> >I would appreciate those recently requesting bug fixes to take a
> >look at this version prior to our releasing it. The changes I made
> >were rather involved, and I'm not sure I have all the files here to
> >test it. I would appreciate your testing both 12.1.9 and 12.0.11
> >(and especially 12.0.11).
> >
> >Thank you.
> >
> >12.1.9
> >
> http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
> >12.0.11 http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12_0.zip
>
>
>
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St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [Jmol-users] [Jmol-developers] feature request: complexer hybrid orbitals

2010-09-01 Thread Robert Hanson 
done. I retro-added it to 12.0, just because.
Jmol 12.1.9 and 12.0.11 will have sp3d and sp3d2 hybridizations. See
documentation for details.

Bob


On Fri, Aug 27, 2010 at 6:45 AM, Egon Willighagen <
egon.willigha...@gmail.com> wrote:

> Hi Bob,
>
> I'm writing up a short tutorial on orbital drawing, as I want to
> visualize the kind of thing I represent in my ODK project [0]... Up to
> sp3 everything is fine, but I was hoping you could also add sp3d and
> sp3d2 hybridizations, see the nice slides at [1], and slides 21-22 in
> particular. Please consider it as feature request :)
>
> Grtz from Boston,
>
> Egon
>
> 0.
> http://chem-bla-ics.blogspot.com/2010/08/third-acsboston-talk-orbital.html
> 1.http://www.slideshare.net/chem.dummy/valence-bond-theory-pptx
>
> --
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St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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[Jmol-users] Bug in Jmol 12.0.11_dev

2010-09-01 Thread Eric Martz 
Dear Bob,

I downloaded Jmol-12.0.11_dev today 9/1 about 10 AM.

The VERY good news: It works fine in both my under-development 
tutorial on MHC in the JTAT shell, and in FirstGlance in Jmol 
(limited testing).

-

I found 1 Bug. This bug has been present since 11.6.RC12. I was 
hoping this version would not have it. I can run many script files 
just fine, but, on the SECOND attempt to run one particular script 
named labelm1.spt, it reproducibly crashes Jmol:

FileManager opening file:/Volumes/JTAT/mhc/chapter04/labelm1.spt
Exception in thread "QueueThread0" java.lang.NullPointerException
 at org.jmol.shape.Labels.setColix(Unknown Source)
 at org.jmol.shape.Labels.setProperty(Unknown Source)
 at org.jmol.shape.Shape.setShapeProperty(Unknown Source)
 at org.jmol.viewer.ShapeManager.setShapeProperty(Unknown Source)
 at org.jmol.script.ScriptEvaluator.setShapeProperty(Unknown Source)
 at org.jmol.script.ScriptEvaluator.colorShape(Unknown Source)
 at org.jmol.script.ScriptEvaluator.color(Unknown Source)
 at 
org.jmol.script.ScriptEvaluator.instructionDispatchLoop(Unknown Source)
 at org.jmol.script.ScriptEvaluator.script(Unknown Source)
 at 
org.jmol.script.ScriptEvaluator.instructionDispatchLoop(Unknown Source)
 at 
org.jmol.script.ScriptEvaluator.evaluateCompiledScript(Unknown Source)
 at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source)
 at 
org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runScript(Unknown Source)
 at 
org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runNextScript(Unknown Source)
 at 
org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(Unknown Source)
 at java.lang.Thread.run(Thread.java:613)

I have narrowed it down to this.

Start Jmol.jar.

In the console, enter "set antialiasdisplay"

Load any PDB file (it must contain an atom with the number specified, 
e.g. 3053 below, which occurs in 2vaa or 2hu4; for 1d66, use e.g. 1549).

Now execute the following script TWICE:

select all
set fontsize 16
set labelfront
color labels none
select atomno=3053
label Beta-2 Mic.

On the second execution, Jmol will crash.

It does not seem to be a single command, but perhaps two. I haven't 
narrowed it down further.

The antialiasdisplay can be entered before or after loading the molecule.

-Eric



At 8/31/10, Robert Hanson wrote:
>I would appreciate those recently requesting bug fixes to take a 
>look at this version prior to our releasing it. The changes I made 
>were rather involved, and I'm not sure I have all the files here to 
>test it. I would appreciate your testing both 12.1.9 and 12.0.11 
>(and especially 12.0.11).
>
>Thank you.
>
>12.1.9 
>http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
>12.0.11 http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12_0.zip


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Re: [Jmol-users] Jmol 12.011 and 12.1.9 testing

2010-09-01 Thread Robert Hanson 
The hole in the center is always going to be a hole in the center unless you
use the FULLPLANE option. Jmol has no idea what to do with the data in the
hole, as there is no data there! If you don't want the hole, increase the
resolution of the plane.

ISSQUARED is fixed now. I'll upload that later today.

Bob


On Wed, Sep 1, 2010 at 8:25 AM, Pshemak Maslak  wrote:

>  On 9/1/2010 9:15 AM, Robert Hanson wrote:
>
> Pshemak,
>
> I'll take that as "all works except SQUARED"
>
> Thanks very much.
>
> Bob
>
>
> Yes indeed.
>
> I understand the the "hole" (at the center of cross-section) is under
> development because of "grid issues".
>
> The "SQUARED" not working may be my ineptitude. Perhaps I placed the
> command in the wrong order, although I tried several with no error message
> in the console, but without any effect on the surfaces drawn.
>
> Thank you.
>
> PM
>
>
>
>
>
>
>
> On Wed, Sep 1, 2010 at 7:58 AM, Pshemak Maslak  wrote:
>
>> BTW: Does "squared" work? It did not have any effect on contour or
>> color-cross-sections.
>>
>>
>> --
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>
>
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> St. Olaf College
> 1520 St. Olaf Ave.
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> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
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>
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>
>
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phone: 507-786-3107


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-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [Jmol-users] Jmol 12.011 and 12.1.9 testing

2010-09-01 Thread Pshemak Maslak 

 On 9/1/2010 9:15 AM, Robert Hanson wrote:

Pshemak,

I'll take that as "all works except SQUARED"

Thanks very much.

Bob


Yes indeed.

I understand the the "hole" (at the center of cross-section) is under 
development because of "grid issues".


The "SQUARED" not working may be my ineptitude. Perhaps I placed the 
command in the wrong order, although I tried several with no error 
message in the console, but without any effect on the surfaces drawn.


Thank you.

PM







On Wed, Sep 1, 2010 at 7:58 AM, Pshemak Maslak > wrote:


BTW: Does "squared" work? It did not have any effect on contour or
color-cross-sections.


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phone: 507-786-3107


If nature does not answer first what we want,
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-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900


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Re: [Jmol-users] Jmol 12.011 and 12.1.9 testing

2010-09-01 Thread Robert Hanson 
Pshemak,

I'll take that as "all works except SQUARED"

Thanks very much.

Bob

On Wed, Sep 1, 2010 at 7:58 AM, Pshemak Maslak  wrote:

> BTW: Does "squared" work? It did not have any effect on contour or
> color-cross-sections.
>
>
> --
> This SF.net Dev2Dev email is sponsored by:
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>


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http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
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[Jmol-users] Jmol 12.011 and 12.1.9 testing

2010-09-01 Thread Pshemak Maslak 

 Here is my report.

PM*

12.0.11 and 12.1.9: no differences in performance observed

*

# bug fix: failure to read old-style JVXL files.

works fine, old file read correctly

# bug fix: isosurface contour colors, contours, and drawHover

set drawHover true; isosurface color absolute -0.01 0.9 plane xy resolution 6 
FULLPLANE atomicOrbital 1 0 0 1.0


works OK, the hole in the middle still there, but can be covered with 
FULLPLANE,

hover shows values at any point of the plane,
gorgeous effect with "isosurface scale3d 5.0", nice "volcano" without 
FULLPLANE



set drawHover true; isosurface plane xy contour 16 atomicOrbital 1 0 0 1.0

works OK, the hole in the middle still there, and there are four 
"corner" residual contour lines

hover shows values at contour lines
"isosurface scale3d 5.0" gives a "hat" with the top cut off (the hole in 
the middle)


set drawHover true; isosurface plane xy contour 17 atomicOrbital 2 1 1 1.0

works OK, there are holes in both lobes (where the highest absolute 
values are); the contours of individual lobes are not symmetrical, the 
look depends somewhat on odd vs even number of contour lines (odd looks 
better), occasional small gaps in contour lines, draw hover works as 
expected


set drawHover true; isosurface color absolute -0.3 0.3 plane xy 
resolution 6 atomicOrbital 2 1 1 1.0


works OK, but only the positive lobe (blue) has the hole, FULLPLANE 
fixes it,

beautiful effect with "isosurface scale3d 5.0"

BTW: Does "squared"  work? It did not have any effect on contour or 
color-cross-sections.


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