Re: [Jmol-users] Jmol 14.14.1

[Pshemak Maslak]

I can confirm: the command (in bold below) generated the expected closed 
CAP surfaces in Jmol and JSmol.


Thanks Bob,

PM


On 4/20/2017 10:34 PM, Robert Hanson wrote:



On Thu, Apr 20, 2017 at 8:35 AM, Pshemak Maslak <n...@psu.edu 
<mailto:n...@psu.edu>> wrote:


Bob;

I am looking forward to exploring the new R/S and E/Z
functionality; it's a great addition.

Does this version include fix for "/*spacefill ionic;lcaocartoon
scale 1.0 CAP unitcell "cpk";spacefill off" */which freezes the
Jmol (Java) and leaves open surfaces (no "cap') on many unticell
faces in JSmol?


yes, I think so. Please test. Also the fact that sometimes caps were 
not completely closed.


Thanks,

PM




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Re: [Jmol-users] Jmol 14.14.1

[Pshemak Maslak]

Bob;

I am looking forward to exploring the new R/S and E/Z functionality; 
it's a great addition!


Does this version include fix for "/*spacefill ionic;lcaocartoon scale 
1.0 CAP unitcell "cpk";spacefill off" */which freezes the Jmol (Java) 
and leaves open surfaces (no "cap') on many unticell faces in JSmol?


Thanks,

PM


On 4/20/2017 11:47 AM, Robert Hanson wrote:
OK - this is better:  Looking for the latest version? *Download 
Jmol-14.14.1-binary.zip (69.7 MB) 
 
*


On Wed, Apr 19, 2017 at 11:35 PM, Robert Hanson > wrote:


hmm. something is missing there. I had to delete that and will
upload again.

On Wed, Apr 19, 2017 at 11:28 PM, Robert Hanson
> wrote:

Jmol.___JmolVersion="14.14.1" // released 4/19/17

new feature: CALCULATE CHIRALITY {atom set}
  -- starts with basic CIP Rule 1-2 determination of R/S and E/Z.
  -- continues with Rules 3-5, which require full-molecule
analysis.
  -- work in progress:
 -- Rules 1 and 2 complete
 -- Rule 3 (E/Z) implemented
 -- Rule 4 partially implemented
-- simple linear sequences of R/S ok
 -- Rule 5 not implemented
  -- caveates
 -- no pseudochirality
 -- not cyclitols
 -- does not distinguish rings, so inserts "Z" into ring bonds
 -- only validated on

  -- optionally limited to the given atom set (or the
currently selected atoms by default)

new feature: set jmolInJSpecView
  -- allows Jmol window to NOT be embedded in JSpecView when
JSpecView is opened in Jmol
  -- default TRUE

new feature: WRITE ISOSURFACE "t.pmesh"; WRITE ISOSURFACE "t.pmb"
  -- creates ASCII (.pmesh) or binary (.pmb) file (a
Jmol-specific file format)
  -- relatively compact format
  -- can speed up loading of meshes and contours
  -- for filled surfaces, use .jvxl instead
  -- read back into Jmol using ISOSURFACE "t.pmesh"/"t.pmb"
  -- note that binary files are NOT RECOMMENDED for JSmol
because some platforms cannot read them locally
  -- example:

  load $methane
  isosurface plane {0 0 0 1} map vdw contours 20
  write ISOSURFACE contour.pmb
  isosurface contour.pmb


bug fix: mesh capper producing gaps
bug fix: CIP chirality fixed for rule ordering; validated for
IUPAC Rules 1, 2, and 3 (though still some questions about Rule 3)
bug fix: print getProperty("cifinfo") without file name fails




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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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Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr



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




--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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

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Re: [Jmol-users] Jmol 14.14.1

[Pshemak Maslak]

Bob;

I am looking forward to exploring the new R/S and E/Z functionality; 
it's a great addition.


Does this version include fix for "/*spacefill ionic;lcaocartoon scale 
1.0 CAP unitcell "cpk";spacefill off" */which freezes the Jmol (Java) 
and leaves open surfaces (no "cap') on many unticell faces in JSmol?


Thanks,

PM



On 4/20/2017 12:29 AM, Robert Hanson wrote:
link for this release: *Download Jmol-14.14.1-binary.zip (65.0 MB) 
 
*







bug fix: mesh capper producing gaps
bug fix: CIP chirality fixed for rule ordering; validated for
IUPAC Rules 1, 2, and 3 (though still some questions about Rule 3)
bug fix: print getProperty("cifinfo") without file name fails





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[Jmol-users] atom-label tooltips

[Pshemak Maslak]

Is there a way to turn off atom-label tooltips that show on hover (above 
an atom)?

I would like to hide their identity in some totally artificial structures.

Thanks,

PM

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Re: [Jmol-users] Jmol 14.13.1

[Pshemak Maslak]

Otis and Dean,

I just tested NaCl in JSmol (JavaSript) on a rather old version 
(14.4.1). Surprise: it works as intended (no freezing).


I will do more testing.

Otis, I will send you the cif files to your address (list does not allow 
attachments).


Thanks,

PM

On 4/10/2017 1:49 PM, Otis Rothenberger wrote:

Dean and Pshemak,

First, OK I'm a believer. The command "display unitcell" is real, and 
it's neat. It cuts off all of the exterior atoms (to unit cell). 
That's good to know.


On the desktop app issue, I think I was one of the early users to say 
good-bye to Java. I'm a small molecule guy, and Bob saved me with 
JSmol. As a small molecule guy, I can get away with my no-Java approach.


Unfortunately, I can't be of much help with Java app questions.

On your final question, can you send me (point me to) the CIF file? 
I'm assuming from the context of this question that this is the JSmol 
version. Is that correct?


Otis

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Re: [Jmol-users] Jmol 14.13.1

[Pshemak Maslak]

Otis and Dean,,

Thanks for the explanation. I was indeed able to find the whole command 
(spacefill ionic;lcaocartoon scale 1.0 CAP unitcell "cpk";spacefill 
off/) / in the documentation (in the "cpk" example of lcaoCartoons).


I think I understand it better now. The "spacefill" spheres are replaced 
with "cpk" spheres" which then are SLAB-ed (CAP-ed really) using 
"unitcell" as slabbing planes.


I tried it on NaCl (cif file). It works on a cell containing one Cl-  in 
the center of the cell and one Na+  in the corner (which is properly 
CAP-ed).


However when I load {1 1 1} cell to get all ions within the cell, the 
Jmol (desktop Java app) freezes. I tried the newest version (14.13.1) an 
an older one (14.8.0) with the same results.


I tried  Na (cif)  (loading {2 2 2} and using "display unitcell" (which 
show all needed atoms), but "lcaocartoon scale 1.0 CAP unitcell 
"cpk";spacefill off"  froze Jmol as well.


Any suggestions?

Thanks for your help.

PM



On 4/10/2017 12:08 PM, Otis Rothenberger wrote:

Pshemak,

The CAP part is discussed here:

https://chemapps.stolaf.edu/jmol/docs/index.htm?=1=14.6#isosurface

Scroll down until you see CAP listing.

The spacefill 1% is just hiding the atoms leaving the lcaocartoons

Dean, the main reason I'm jumping in here is the display unitcell 
command. Is that a legal Jmol Script command? After loading a CIF 
file, I thought that you had to do something like this to get the unit 
cell:


save orientation; load "" {444 666 1}; set displayCellParameters 
false;restore orientation; unitcell on; display cell=555; center 
visible; zoom 200;


Otis

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On Apr 10, 2017, at 11:44 AM, Pshemak Maslak <p...@chem.psu.edu 
<mailto:p...@chem.psu.edu>> wrote:


Thank you Dean,

I do not understand the

lcaocartoon scale 1.0 CAP unitcell 'cpk'; spacefill 1%; 



part of the command. Is it documented 
inhttps://chemapps.stolaf.edu/jmol/docs/ ?


Thanks,

PM


On 4/10/2017 10:46 AM, Dean Johnston wrote:
Yes - I have an example at: 
http://crystals.otterbein.edu/packing/index.html


Pick structure from the left menu and then click the “Show Contents 
of One Unit Cell”. Works beautifully!


The commands are:
display unitcell; spacefill ionic 100%; lcaocartoon scale 1.0 CAP 
unitcell 'cpk'; spacefill 1%;


Dean Johnston

On April 10, 2017 at 9:00:03 AM, Pshemak Maslak (p...@chem.psu.edu 
<mailto:p...@chem.psu.edu>) wrote:




Can the "slab" command be used to produce presentations equivalent 
to the image linked below?


https://en.wikipedia.org/wiki/Atomic_packing_factor#/media/File:CCC_crystal_cell_(opaque).svg

If so, any suggestions on how to do that would be appreciated.

Thanks,

PM
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Re: [Jmol-users] Jmol 14.13.1

[Pshemak Maslak]

Thank you Dean,

I do not understand the

   lcaocartoon scale 1.0 CAP unitcell 'cpk'; spacefill 1%; 



part of the command. Is it documented in 
https://chemapps.stolaf.edu/jmol/docs/  ?


Thanks,

PM


On 4/10/2017 10:46 AM, Dean Johnston wrote:
Yes - I have an example at: 
http://crystals.otterbein.edu/packing/index.html


Pick structure from the left menu and then click the “Show Contents of 
One Unit Cell”. Works beautifully!


The commands are:
display unitcell; spacefill ionic 100%; lcaocartoon scale 1.0 CAP 
unitcell 'cpk'; spacefill 1%;


Dean Johnston

On April 10, 2017 at 9:00:03 AM, Pshemak Maslak (p...@chem.psu.edu 
<mailto:p...@chem.psu.edu>) wrote:




Can the "slab" command be used to produce presentations equivalent to 
the image linked below?


https://en.wikipedia.org/wiki/Atomic_packing_factor#/media/File:CCC_crystal_cell_(opaque).svg

If so, any suggestions on how to do that would be appreciated.

Thanks,

PM
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Re: [Jmol-users] Jmol 14.13.1

[Pshemak Maslak]

Thank you Dean,

I do not understand the

   lcaocartoon scale 1.0 CAP unitcell 'cpk'; spacefill 1%; 



part of the command. Is it documented in 
https://chemapps.stolaf.edu/jmol/docs/  ?


Thanks,

PM


On 4/10/2017 10:46 AM, Dean Johnston wrote:
Yes - I have an example at: 
http://crystals.otterbein.edu/packing/index.html


Pick structure from the left menu and then click the “Show Contents of 
One Unit Cell”. Works beautifully!


The commands are:
display unitcell; spacefill ionic 100%; lcaocartoon scale 1.0 CAP 
unitcell 'cpk'; spacefill 1%;


Dean Johnston

On April 10, 2017 at 9:00:03 AM, Pshemak Maslak (p...@chem.psu.edu 
<mailto:p...@chem.psu.edu>) wrote:




Can the "slab" command be used to produce presentations equivalent to 
the image linked below?


https://en.wikipedia.org/wiki/Atomic_packing_factor#/media/File:CCC_crystal_cell_(opaque).svg

If so, any suggestions on how to do that would be appreciated.

Thanks,

PM
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Re: [Jmol-users] Jmol 14.13.1

[Pshemak Maslak]

Can the "slab" command be used to produce presentations equivalent to 
the image linked below?


https://en.wikipedia.org/wiki/Atomic_packing_factor#/media/File:CCC_crystal_cell_(opaque).svg 



If so, any suggestions on how to do that would be appreciated.

Thanks,

PM
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Re: [Jmol-users] Spartan 16 files

[Pshemak Maslak]

The liserv does not like zipped files either.

I can provide files for inspection (outside of the list).

Thanks,

PM


On 12/22/2016 12:21 PM, Pshemak Maslak wrote:

Apparently the file is too large for attachment.

I enclose a file for H2 zipped

Thanks,

PM

On 12/22/2016 12:15 PM, Pshemak Maslak wrote:
It looks like Spartan 16 files are not read by Jmol (older version 
are read fine).


The message is:

script ERROR: No atoms found

I enclose ethane,spartan (if I can attached files)

Any suggestions?

Thanks,

PM





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Re: [Jmol-users] play_make_live image

[Pshemak Maslak]

Thanks Bob,

It works well.

A minor glitch: during loading, the icon does not disappear, but shows 
as a missing image.  It is all fine after the model loads.


I enclose a screen grab, but I do not know if it makes to the list.

Thanks,

PM


On 2/19/2016 11:31 AM, Robert Hanson wrote:
Yes, a couple of typos there. If you want to get it fixed right away, 
copy http://chemapps.stolaf.edu/jmol/zip/JSmol.min.js to your jsmol 
directory.


On Fri, Feb 19, 2016 at 9:04 AM, Pshemak Maslak <n...@psu.edu 
<mailto:n...@psu.edu>> wrote:


Jmol version from January added an option to change play_make_live
image:

Jmol.___JmolVersion="14.4.1_2016.01.15"

[...]

JSmol: adds Info.makeLiveImage  defaults to
j2s/img/play_make_live.jpg



I have a few questions:

The default image is no longer visible in version
14.2.1_2016.0115  or the most recent "14.4.3_2016.02.17" (missing
image icon is displayed instead). Is something broken?

Is this change documented somewhere?

We use:

coverImage: "images/catalase.jpg",

to display cover image (of catalase) and it works, but the
corresponding

Info.makeLiveImage :  "images/3D-1-trans.gif",

does not work.

Any help would be appreciated.

PM


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[Jmol-users] play_make_live image

[Pshemak Maslak]

Jmol version from January added an option to change play_make_live image:

   Jmol.___JmolVersion="14.4.1_2016.01.15"

   [...]

   JSmol: adds Info.makeLiveImage  defaults to j2s/img/play_make_live.jpg



I have a few questions:

The default image is no longer visible in version 14.2.1_2016.0115 or 
the most recent "14.4.3_2016.02.17" (missing image icon is displayed 
instead). Is something broken?


Is this change documented somewhere?

We use:

   coverImage: "images/catalase.jpg",

to display cover image (of catalase) and it works, but the corresponding

   Info.makeLiveImage :  "images/3D-1-trans.gif",

does not work.

Any help would be appreciated.

PM
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[Jmol-users] new DSSR

[Pshemak Maslak]

The new DSSR has base pairs and nucleotide indexed by numbers,  For 
example (the 9th base-pair):

auxiliaryinfo.models[1].dssr.pairs[9].bp"A-T"
auxiliaryinfo.models[1].dssr.pairs[9].nt1"|1|D|A|10"
auxiliaryinfo.models[1].dssr.pairs[9].nt2"|1|E|T|29"

What is the proper syntax to select any one of these"

Thanks,

PM




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[Jmol-users] Fwd: Re: new DSSR

[Pshemak Maslak]

Thanks Rolf!

PM

Forwarded per Rolf's request

On 01/28/2016 07:08 PM, Pshemak Maslak wrote:
>
> The new DSSR has base pairs and nucleotide indexed by numbers,  For
> example (the 9th base-pair):
>
> auxiliaryinfo.models[1].dssr.pairs[9].bp"A-T"
> auxiliaryinfo.models[1].dssr.pairs[9].nt1"|1|D|A|10"
> auxiliaryinfo.models[1].dssr.pairs[9].nt2"|1|E|T|29"
>
> What is the proper syntax to select any one of these"
>
 From the example I showed in the previous thread regarding the DSSR
change I would suspect that the first base would be residue "A" number
"10" from chain "D". And I would suspect the "1" being the model number.
But because it wasn't included in the former residue selection
expression I am not really sure.

The syntax for the selection expression is the same as before:
   select [A]10:D
   select [T]29:E

Or if you would add the (suspected) model number it would look like this:
   select [A]10:D/1
   select [T]29:E/1

You can split the 'nt1' and 'nt2' strings by "|" into an array and then
build the selection expression as a string:

- Jmol commands --
nt1 = auxiliaryinfo.models[1].dssr.pairs[9].nt1.split("|");
nt2 = auxiliaryinfo.models[1].dssr.pairs[9].nt2.split("|");

res_nt1 = "[" + nt1[4] + "]" + nt1[5] + ":" + nt1[3] + "/" + nt1[2];
res_nt2 = "[" + nt2[4] + "]" + nt2[5] + ":" + nt2[3] + "/" + nt2[2];

select @res_nt1;
select @res_nt2;
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the list so that others can also see it.

Regards,
Rolf
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Re: [Jmol-users] a bug or changes in code?

[Pshemak Maslak]

On 1/20/2016 5:27 PM, Robert Hanson wrote:
> That sounds right. We get our DSSR analysis from Columbia University, 
> and that format did recently change. It was a beta version previously; 
> it should be stable now. Sorry for the trouble.
>
> Bob​

Which file of the JSmol distribution contains the DSSR code?  I am 
thinking about a temporary fix by replacing the file with one from an 
older JSmol version if that is feasible.

Thanks,

PM

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[Jmol-users] a bug or changes in code?

[Pshemak Maslak]

I have noticed that a script that worked with a version that was current 
in March 2015 (14.2.13_2015.03.23) does not work with the latest two (or 
more) versions.


Briefly, I have a short DNA fragment in a png file that loads with the 
following commands:


load DNAH-2.png;
set showHydrogens TRUE;
moveto 1.0 { -289 956 53 43.88}  100.0 0.0 0.0;
calculate STRUCTURE DSSR;
pairsCG = getProperty("auxiliaryinfo.models[1].dssr.basepairs[select 
res1,res2 where bp='C-G' or bp='G-C']");
pairsAT = getProperty("auxiliaryinfo.models[1].dssr.basepairs[select 
res1,res2 where bp='A-T' or bp='T-A']");


The load script does not generate any visible errors (in Java script in 
a browser or in Java on the desktop) and the structure loads fine.


and then I have a script that "hides" base pairs, leaving just one that 
is "zoomed into" user view and centered.


select @{pairsCG[1].res1},@{pairsCG[1].res2}; color translucent 9;
select @{pairsCG[12].res1},@{pairsCG[12].res2}; color translucent 9;
select @{pairsCG[11].res1},@{pairsCG[11].res2}; color translucent 9; 
delay 0.1;

 select @{pairsCG[2].res1},@{pairsCG[2].res2}; color translucent 9;
 select @{pairsCG[10].res1},@{pairsCG[10].res2}; color translucent 9;
 select @{pairsAT[5].res1},@{pairsAT[5].res2}; color translucent 9; 
delay 0.1;

 select @{pairsCG[3].res1},@{pairsCG[3].res2}; color translucent 9;
 select @{pairsCG[9].res1},@{pairsCG[9].res2}; color translucent 9;
 select @{pairsCG[8].res1},@{pairsCG[8].res2}; color translucent 9; 
delay 0.1;

 select @{pairsAT[1].res1},@{pairsAT[1].res2}; color translucent 9;
 select @{pairsAT[4].res1},@{pairsAT[4].res2}; color translucent 9; 
delay 0.1;

 select @{pairsCG[4].res1},@{pairsCG[4].res2}; color translucent 9;
  select @{pairsCG[7].res1},@{pairsCG[7].res2}; color translucent 9; 
delay 0.1;

  select @{pairsCG[5].res1},@{pairsCG[5].res2}; color translucent 9;
  select @{pairsAT[3].res1},@{pairsAT[3].res2}; color translucent 9; 
delay 0.1;

  select @{pairsCG[6].res1},@{pairsCG[6].res2}; color translucent 9;
  select @{pairsAT[2].res1},@{pairsAT[2].res2};
  moveto 1.0 { 944 144 296 71.87}  300.24 0.0 0.0  {31.878408 48.3921 
30.248789} 38.85318;
  center@989; hbonds calculate; hbonds 0.2; hbonds 0.2; color hbonds 
yellow;


That script worked fine with the old JSmol,, but it fails on the first 
line with the newer versions.  The error happens in the first line:


script ERROR: unexpected end of script command

 select { @ { pairsCG [ 1 ] . res1 } << or @ { pairsCG [ 1 ] . 
res2 } }


Any help is solving that puzzle would be appreciated (DNAH-2.png is 
available upon request).


PM


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Re: [Jmol-users] a bug or changes in code?

[Pshemak Maslak]

Thanks Rolf.  That helps.

PM

On 1/20/2016 2:51 PM, Rolf Huehne wrote:
> On 01/20/2016 07:37 PM, Pshemak Maslak wrote:
>> I have noticed that a script that worked with a version that was current
>> in March 2015 (14.2.13_2015.03.23) does not work with the latest two (or
>> more) versions.
>>
>> Briefly, I have a short DNA fragment in a png file that loads with the
>> following commands:
>>
>> load DNAH-2.png;
>> set showHydrogens TRUE;
>> moveto 1.0 { -289 956 53 43.88}  100.0 0.0 0.0;
>> calculate STRUCTURE DSSR;
>> pairsCG = getProperty("auxiliaryinfo.models[1].dssr.basepairs[select
>> res1,res2 where bp='C-G' or bp='G-C']");
>> pairsAT = getProperty("auxiliaryinfo.models[1].dssr.basepairs[select
>> res1,res2 where bp='A-T' or bp='T-A']");
>>
>> The load script does not generate any visible errors (in Java script in
>> a browser or in Java on the desktop) and the structure loads fine.
>>
>> and then I have a script that "hides" base pairs, leaving just one that
>> is "zoomed into" user view and centered.
>>
>> select @{pairsCG[1].res1},@{pairsCG[1].res2}; color translucent 9;
>> select @{pairsCG[12].res1},@{pairsCG[12].res2}; color translucent 9;
>> select @{pairsCG[11].res1},@{pairsCG[11].res2}; color translucent 9;
>> delay 0.1;
>>select @{pairsCG[2].res1},@{pairsCG[2].res2}; color translucent 9;
>>select @{pairsCG[10].res1},@{pairsCG[10].res2}; color translucent 9;
>>select @{pairsAT[5].res1},@{pairsAT[5].res2}; color translucent 9;
>> delay 0.1;
>>select @{pairsCG[3].res1},@{pairsCG[3].res2}; color translucent 9;
>>select @{pairsCG[9].res1},@{pairsCG[9].res2}; color translucent 9;
>>select @{pairsCG[8].res1},@{pairsCG[8].res2}; color translucent 9;
>> delay 0.1;
>>select @{pairsAT[1].res1},@{pairsAT[1].res2}; color translucent 9;
>>select @{pairsAT[4].res1},@{pairsAT[4].res2}; color translucent 9;
>> delay 0.1;
>>select @{pairsCG[4].res1},@{pairsCG[4].res2}; color translucent 9;
>> select @{pairsCG[7].res1},@{pairsCG[7].res2}; color translucent 9;
>> delay 0.1;
>> select @{pairsCG[5].res1},@{pairsCG[5].res2}; color translucent 9;
>> select @{pairsAT[3].res1},@{pairsAT[3].res2}; color translucent 9;
>> delay 0.1;
>> select @{pairsCG[6].res1},@{pairsCG[6].res2}; color translucent 9;
>> select @{pairsAT[2].res1},@{pairsAT[2].res2};
>> moveto 1.0 { 944 144 296 71.87}  300.24 0.0 0.0  {31.878408 48.3921
>> 30.248789} 38.85318;
>> center@989; hbonds calculate; hbonds 0.2; hbonds 0.2; color hbonds
>> yellow;
>>
>> That script worked fine with the old JSmol,, but it fails on the first
>> line with the newer versions.  The error happens in the first line:
>>
>> script ERROR: unexpected end of script command
>> 
>>select { @ { pairsCG [ 1 ] . res1 } << or @ { pairsCG [ 1 ] .
>> res2 } }
>>
>> Any help is solving that puzzle would be appreciated (DNAH-2.png is
>> available upon request).
>>
> The data structure below 'dssr' has changed (at least in my example
> below), shown by printing the hash keys:
>
>  Example -
> load =3cro;
> calculate STRUCTURE DSSR;
> x=getProperty("auxiliaryinfo");
> y=x.models[1].dssr;
> print y.keys;
>
> - Output in Jmol 14.2.9 -
> basePairs
> dbn
> hBonds
> helices
> seq
> singleStranded
> stems
> summary
>
> - Output in Jmol 14.4.1 -
> counts
> dbn
> hbonds
> helices
> metadata
> nts
> num_hbonds
> num_helices
> num_nts
> num_pairs
> num_ssSegments
> num_stacks
> num_stems
> pairs
> paths
> ssSegments
> stacks
> stems
> -
>
> The 'basePairs' substructure from Jmol 14.2.9 might be resembled by the
> 'pairs' substructure from Jmol 14.4.1 but the 'res1' and 'res2'
> properties are missing:
>
> - 'basePairs' entry -
> {
>   DSSR  :  "cW-W"
>   LW  :  "cWW"
>   Saenger  :  20
>   bp  :  "A-T"
>   bpBuckle  :  -11.52
>   bpChi1  :  -101.6
>   bpChi2  :  -99.1
>   bpDistC1C1  :  10.51
>   bpDistC6C8  :  9.22
>   bpDistNN  :  8.56
>   bpLambda1  :  53.1
>   bpLambda2  :  43.6
>   bpOpening  :  -13.25
>   bpPropeller  :  -5.68
>   bpShear  :  0.68
>   bpStagger  :  0.3298
>   bpStretch  :  -0.68
>   bpTorCNNC  :  -12.0
>   g1  :  "A"
>   g2  :  "T"

Re: [Jmol-users] play_make_live icon

[Pshemak Maslak]

I second that request. An option to (easily) specify an alternative icon 
(residing in a directory outside of Jmol directories) would be great.


Thanks,

PM


On 1/13/2016 11:29 AM, Geoffrey Rowland wrote:

Hi folks

A minor 'cosmetic' suggestion.

I'm increasingly using PNGJ files with the bundled image used as a 
cover image, deferring loading of JSmol 'til the user clicks the cover 
image.


By default, the cover image is shown with the play_make_live.jpg icon 
which only really looks good with a white background.


Could this be changed to be a transparent-background .png (or, 
perhaps, .svg) icon?


I have done this myself. A mid-grey (#99) reload arrow from 
http://www.flaticon.com/packs/font-awesome/4 (note terms-of-use) 
renamed to play_make_live.png suited my purposes. Works well with 
white, light grey or black backgrounds  - though there are obviously 
many possible variations. Perhaps 'JSmol blue'.


However, it would be nice not to have to do a global search/replace 
for play_make_live.jpg/play_make_live.png whenever I update JSmol ;-)


Thanks

Geoff


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[Jmol-users] deferred applet

[Pshemak Maslak]

The deferred applet uses a small image (light blue circular arrow) to 
indicate that the model needs to be activated. That image 
(play_make_live.jpg) resides in j2s/img subdirectory.  It has a tooltip 
(activate 3D model) associated with it.

Can that image be replaced with another and its opacity controlled 
programmatically?  I could not find any functions listed on 
http://wiki.jmol.org/index.php/Jmol_JavaScript_Object/Info that relates 
to that icon.

Thanks,

PM



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[Jmol-users] stopping scripts

[Pshemak Maslak]

It looks like my previous post got lost:

To showcase a crystal structure we have a longish tour script composed of 
several moveto, rotate, adding and removing labels, changing translucency 
(stepwise), etc. Our Tour button starts the cript and toggles to Stop.  
Unfortunately we are not able to stop the tour.

With set waitForMoveTo False, moveto Stop does work (stops in the middle of 
moveto), but only if the moveto is the last command in the script (no other 
commands after it).

Rotate (for example rotate 360 -6) does not stop as implied 
inhttp://chemapps.stolaf.edu/jmol/docs/?ver=14.2#rotate   (under x.x y.y).
A separate spin off seems to be needed, Again, it works if moveto/rotate are 
at the end of the script.

However, if there are other commands after moveto or rotate (for example 
adjusting translucency or adding labels) the script does not stop, it continues 
till the end, even if quit or exit are included.

Additionally, when we use !exit or !quit we are getting:  script compiler 
ERROR: command expected (version 14.3.14_2015.06.10c) when the script is 
finished running.

Any suggestions on how to effectively stop unfinished scripts would be 
appreciated,

PM


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[Jmol-users] stopping moveto and rotate

[Pshemak Maslak]

We have tour scripts that use several moveto and rotate commands 
during the script execution that take a few seconds each.  We would like 
to add a STOP button that once clicked would terminate the execution of 
the tour script, even if it is in the middle of one of the moveto or 
rotate steps.


We have tried various combinations of set waitForMoveTo, moveto STOP, 
quit, exit without success.  What is the proper protocol to accomplish a 
complete stop?


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[Jmol-users] jsmol.php

[Pshemak Maslak]

Bob,

We use Jmol/JSmol within Drupal and behind an access wall controlled 
by a university-wide system called  Web Access.  We had a problem with 
accessing JSmol instances using Chrome (it worked in Firefox). The issue 
coincided with the introduction of the new jsmol.php file (in March).  
Since I have zero programming knowledge, I asked a student-programmer 
who works with us to investigate.  His report is cited below.   His 
fix works for us.


I would like to check with you, if that is a valid fix;  I do not know 
if it creates any problems (security or otherwise). If it is a valid 
fix, would it be possible and worthwhile to make it a permanent part 
of jsmol.php in JSmol distributions?  (i.e make it a global fix, not 
just a local one).


Thanks,

PM

   The issue occurs because of our configuration (since jsmol usually
   produces absolute urls while we convert absolute urls pointing to
   the same site to relative urls). The problem is that when it calls
   getRawDataFromDatabase it checks for :// at the beginning of the
   string with strpos($query, '://') == 0 which is a protocol
   relative url. However, in php when you use == both 0 and FALSE are
   treated as the same, so the condition also evaluates to true when
   the query doesn't contain :// which is the case for relative urls
   (our case). You can fix this by using === (which is what I did),
   but it's possible that the behavior with == was intended
 (probably not, but it's very ambiguous).

   It is our bug but it's uncertain whether the bug was intentional
   or not and could potentially be fixed. There isn't a way for us to
   work around it without modifying the file (unless we authenticate
   with webaccess somehow). It might be worth submitting a bug report
   to see if it was intended (probably unintentional).

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[Jmol-users] fetching cif files while loading pdb files

[Pshemak Maslak]

Using the Jmol Java applet (desktop) I have noticed that when I load a 
pdb file (for example 1EHZ.pdb) using load 1EHZ.pdb, some additional 
files are fetched.  For example (a partial list for 1EHZ):


   fetching http://www.rcsb.org/pdb/files/ligand/2MG.cif
   2N-METHYLGUANOSINE-5'-MONOPHOSPHATE
   fetching http://www.rcsb.org/pdb/files/ligand/H2U.cif
   5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
   fetching http://www.rcsb.org/pdb/files/ligand/M2G.cif
   N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE

When I drag the same pdb file directly into the applet, no fetching 
takes place.


What is the role of the fetched files?
Where are the fetching instructions coming from?
What happens when the server of www.rcsb.org is not accessible?

Thanks,

PM
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[Jmol-users] refining selection using within

[Pshemak Maslak]

I can select GC base pairs within a DNA stretch using: 
within(BASEPAIR,GC). Let's say I have 10 such pairs.  Is there a way 
to select any specific pair from that set?


Thanks,

PM
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[Jmol-users] defined groups

[Pshemak Maslak]

There is a very nice list of defined groups: 
http://chemapps.stolaf.edu/jmol/docs/misc/groups.txt.


My question is about the ether group specifically:

   define ~etherO oxygen and connected(2,carbon) and not ~carbonylO
   define ~ROR ~etherO

Is it possible to make the definition more specific?
For example can one distinguish cyclic from acyclic ethers?
Can one set up the one of the carbons bonded to oxygen is a -CH2 group 
(like in R-CH2-O-R)?


Thanks,
PM
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Re: [Jmol-users] molecular dipoles

[Pshemak Maslak]

Let me start by repeating the original question:  is there a way to get 
a numerical value of the dipole moment calculated by Jmol based on the 
partial charges in the file?



Now back to spartan files (see below).  If the spartan file is generated 
by double calculations the charge information in the file is not 
readable by Jmol.


By double calculations I mean (1). a full-optimization using one method 
(density functional for example) that is saved under a different file 
name on which file (2) a point (energy) calculation is performed with 
another method (HF for example). If the geometry from the first 
calculation is saved as xyz (for example) and then the point 
calculations are carried on that geometry, the partial charge 
information can be read by Jmol.


PM








On 9/10/2014 2:03 PM, Pshemak Maslak wrote:
The puzzle is partially solved.  It looks like the problem with 
dipoles originates in (some) spartan files that were saved as mol2 
files with partial charge information included.  I am still trying to 
figure out what the problem is with these spartan files (they 
definitely have charge information, but also do not display dipoles in 
Jmol).


I would still appreciate help with getting the numerical values of 
dipole moments out of Jmol.


What is the command to print (view) the numerical value of the 
dipole moment calculated by Jmol?


Thanks,

PM




On 9/9/2014 11:55 AM, Pshemak Maslak wrote:
I have run into an issue with displaying molecular dipoles (and 
finding their values).


mol2 file (with Mulliken partial charges) will not display (or 
calculate)  the molecular dipole.


/dipole molecular/  or /dipole calculate molecular/ do nothing (no 
error, no display of any kind)


The MEP is generated as expected so I assume that partial charges are 
read.


Is the mol2 (Sybyl) file a wrong format for displaying dipoles?

PM






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Re: [Jmol-users] molecular dipoles

[Pshemak Maslak]

Thank you.

This was very educational! In the Interactive Script Documentation 
getProperty shapeInfo lists dipoles, but  shapeInfo.txt example 
(http://chemapps.stolaf.edu/jmol/docs/misc/shapeInfo.txt) has no listing 
for dipoles, which confused me (I was looking for .dipole.obj[1] or 
equivalent with no luck)  Now, I have discovered that just typing  
getProperty shapeinfo lists the included properties in the console, (but 
only if that property has been previously calculated).  Make sense of 
course.


PM


On 9/11/2014 7:17 PM, Robert Hanson wrote:

Sorry -- deep-sixed this one.

On Thu, Sep 11, 2014 at 1:43 PM, Pshemak Maslak n...@psu.edu 
mailto:n...@psu.edu wrote:


Let me start by repeating the original  question: is there a way
to get a numerical value of the dipole moment calculated by Jmol
based on the partial charges in the file?


dipole molecular
d = getProperty(shapeInfo.Dipoles[1].vector)
x = sqrt(d*d)



On 9/10/2014 2:03 PM, Pshemak Maslak wrote:


Is the mol2 (Sybyl) file a wrong format for displaying dipoles?




mol2 should be fine - provided the partial charges are there.


PM








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[Jmol-users] molecular dipoles

[Pshemak Maslak]

I have run into an issue with displaying molecular dipoles (and finding 
their values).


mol2 file (with Mulliken partial charges) will not display (or 
calculate)  the molecular dipole.


/dipole molecular/  or /dipole calculate molecular/ do nothing (no 
error, no display of any kind)


The MEP is generated as expected so I assume that partial charges are read.

Is the mol2 (Sybyl) file a wrong format for displaying dipoles?

PM


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[Jmol-users] problems with zip and jvxl files in JSmol

[Pshemak Maslak]

I have encountered a problem working with jvxl and zip files.

I have a big spartan file of cholesterol (cholesterol.spartan) with all 
MOs calculated. For a web application, I need just charges (for dipole 
vector and MEP) and the HOMO and LUMO surfaces.

In Jmol (Java) app I have written separate HOMO.jvxl and LUMO.jvxl file 
using

 mo HOMO  (with spartan file loaded)
 write  MO HOMO.jvxl

and the analogous file for the LUMO.

I have saved the spartan file as cholesterol.mol2 (to preserve partial 
charge info).

I have zipped the three files into a zipped folder cholesterol.zip

I have tested it in the Java app,  for example:

load cholesterol.zip|cholesterol.mol2;
dipole molecular

or

load cholesterol.zip|HOMO.jvxl;
isosurface cholesterol.zip|HOMO.jvxl; isosurface mesh nofill

It worked as expected.

None of the files (zipped folder or jvxl files are read by JSmol (including 
here: http://chemapps.stolaf.edu/jmol/jsmol/test2.htm)

I am doing something wrong?

Thanks,

PM

P.S. I did not include zipped folder (to avoid issues with the list server), 
but I can e-mail it if needed for inspection






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Re: [Jmol-users] IF for multiple frames

[Pshemak Maslak]

Thanks Angel,

I have missed that in the manual, that is much simpler.

PM





On 8/14/2014 6:35 AM, Angel Herráez wrote:
 Hello  Pshemak!
 if structures are not hard, at least if you have some experience e.g. with
 Javascript.
 But for your problem you don't need that; the connect command will set the
 bond type based on distance, very easily, for all frames at a time.

 Let's say I have some boundary conditions (in angstroms, totally arbitrary 
 for the purpose of this
 example):
  C-O 1.44 and less is single, more than 1.44 but less than 1.55 is 
 partial,
  and more than 1.55 is no bond
  C-Br 1.92 and less is single, more than 1.92 but less than 2.07 is 
 partial and
  more than 2.07 is no bond
 select all;
 connect (_C) (_O) delete;
 connect 1.441 1.55 (_C) (_O) partial;
 connect 1.44 (_C) (_O) single;

 connect (_C) (_Br) delete;
 connect 1.921 2.07 (_C) (_Br) partial;
 connect 1.92 (_C) (_Br) single;
   
 I am not sure about wether the given limits will be taken as less than or
 less or equal than.


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[Jmol-users] IF for multiple frames

[Pshemak Maslak]

I am just starting to explore if/else and related constructs.  I would 
like to apply it to animations containing multiple frames (=20).


Since I am learning, I will start with a simple example: an animation of 
the SN2 reaction between hydroxide and methyl bromide.


I have two parameters of interest O-C and C-Br separation lengths, 
Depending on the specific value of these two distances in each frame, I 
would like to display their bonds as no bond partial bond, or 
single bond.


Let's say I have some boundary  conditions (in angstroms, totally 
arbitrary for the purpose of this example):


 C-O   1.44 and less is single, more than 1.44 but less than 1.55
   is partial, and more than 1.55 is no bond
 C-Br   1.92 and less is single,  more than 1.92 but less than 2.07
   is partial and more than 2.07 is no bond


How can I write the if/else statement(s) to work (i.e. display properly) 
in all frames?


An illustration would be especially appreciated (as I have no 
programming experience).


Thanks,

PM


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Re: [Jmol-users] contact

[Pshemak Maslak]

Thank you for clarification and the fix of the problem.

PM





On 8/5/2014 8:37 AM, Robert Hanson wrote:

It's a bug. Three issues there.

First, the CONTACT command has a bug that makes it only work on the 
first model.


Second, you probably should be issuing

mySet1={1.6  _H}; mySet2={1.6  _H}; contact*model 1.6 *150% {mySet1} 
{mySet2}


to display the contact in the proper model.

Third, CONTACT was not set up for allowing model 1.6 as an option.

That's corrected.

Hope to get that uploaded soon.

Bob





On Mon, Aug 4, 2014 at 11:03 PM, Pshemak Maslak n...@psu.edu 
mailto:n...@psu.edu wrote:


I still have problems with contact when using butane file
containing 20 models (rotamers around the central C-C bond).
Separately, one frame (say gauche) shows contacts fine: contact
100% {_H} {_H},  (net volume 0.14 A^3),  but when that frame is a
part (frame 6) of the collection,
something like the following does not work: mySet1={1.6  _H};
mySet2={1.6  _H}; contact 100% {mySet1} {mySet2} (net volume 0).

What am I doing wrong?

Thanks,

PM





On 5/6/2014 5:42 PM, Robert Hanson wrote:

Oh, sure. But it's generally designed to ignore intramolecular
contacts.

contact {atomset1} {atomset2}

and if {atomset2} is not present, then same model and not
atomset1 is the default.

You can do intramolecular clashes by specifying two distinct
intramolecular atom sets.

For example:

$ load caffeine.xyz
$ contact {_O} {_H}



On Tue, May 6, 2014 at 9:43 AM, Pshemak Maslak n...@psu.edu
mailto:n...@psu.edu wrote:
Can contact command be used to visualize clashes in small
molecules
(such as eclipsed CH3/CH3 in butane, for example)?

What would the full command look like?

Thanks,




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Re: [Jmol-users] Allow access to the following application

[Pshemak Maslak]

You may try the following:

1. uninstall all Java
2. delete all Java directories (I do not know where they are on OS X, 
but on Win they are within AppData and within users) with Oracle and Sun 
in the name (does OS X has a good search utility?)

3, reinstall Java

These are probably desperation moves, but it MAY work on OS X too.

PM



On 8/5/2014 12:50 PM, Rzepa, Henry S wrote:

Can anyone help with this mystery.

If  I open a web page using a properly signed  Java applet (from Bob), I get a 
dialog (OS X Mavericks, Safari, Java 7.67) which says

Web site: http://www.ch.ic.ac.uk
Application: UNKNOWN   (why unknown, its properly signed!)
Publisher: UNKOWNN  (no they are not!
Check box Do not show this again for this app and web site is checked

The trouble is that this check box is entirely ignored.  Next time the app 
loads, up pops this dialog again.
If you want to see if this can be replicated, try it at  
http://www.ch.ic.ac.uk/rzepa/cub2jvxl/

(PS using 14.0.1 for the above.  14.2.4 does not work with the file dialog 
request to load a cube file from a local disk).

By the way if I accidentally press  Do not allow instead of allow the site 
is entirely disabled permanently on that computer,  and I cannot get it to  ever work again 
(despite browser cache purges, restarts, etc. ).  If only  I knew where the file was which 
remembers this (accidentally entered) information,  I could delete it, but try as I might  I cannot 
find it!  Nor does editing the  Exception site list help either.

Java, to quote  Steve Jobs, is a bag of hurt, and hurting more and more.  But I 
need it to eg generate isosurfaces from (often  500 Mbyte) cube files.


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Re: [Jmol-users] Allow access to the following application

[Pshemak Maslak]

On 8/5/2014 1:06 PM, Rzepa, Henry S wrote:

On 5 Aug 2014, at 18:01, Pshemak Maslak n...@psu.edu wrote:


You may try the following:

1. uninstall all Java
2. delete all Java directories (I do not know where they are on OS X, but on 
Win they are within AppData and within users) with Oracle and Sun in the name 
(does OS X has a good search utility?)

Non trivial.  Despite the  deceptively simple uninstall instructions on  
Oracle’s page, there are  Java caches all over the place. And OS X does not 
search system files, only user files.  I have tried doing this, but it has not 
yet worked for me.



3, reinstall Java

These are probably desperation moves, but it MAY work on OS X too.

PM



Now I know why I do not like Mac's.

You probably seen this already, but just in case:

https://developer.apple.com/library/mac/qa/qa1170/_index.html

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Re: [Jmol-users] contact

[Pshemak Maslak]

I still have problems with contact when using butane file containing 
20 models (rotamers around the central C-C bond).
Separately, one frame (say gauche) shows contacts fine: contact 100% 
{_H} {_H},  (net volume 0.14 A^3),  but when that frame is a part (frame 
6) of the collection,
something like the following does not work: mySet1={1.6  _H}; 
mySet2={1.6  _H}; contact 100% {mySet1} {mySet2} (net volume 0).


What am I doing wrong?

Thanks,

PM





On 5/6/2014 5:42 PM, Robert Hanson wrote:

Oh, sure. But it's generally designed to ignore intramolecular contacts.

contact {atomset1} {atomset2}

and if {atomset2} is not present, then same model and not atomset1 
is the default.


You can do intramolecular clashes by specifying two distinct 
intramolecular atom sets.


For example:

$ load caffeine.xyz
$ contact {_O} {_H}



On Tue, May 6, 2014 at 9:43 AM, Pshemak Maslak n...@psu.edu 
mailto:n...@psu.edu wrote:

Can contact command be used to visualize clashes in small molecules
(such as eclipsed CH3/CH3 in butane, for example)?

What would the full command look like?

Thanks,


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[Jmol-users] mirror sync

[Pshemak Maslak]

There is a very nice command to sync the applets (sync).  Is there a 
relatively simple way to do mirror sync?


I imagine that the two models (say enantiomers) would be first manually 
oriented to give mirror orientation of each other and locked to give 
the synced pair.


Perhaps some fine tuning of the original manually-set positions could be 
done programmatically (using compare?) before locking?


Thanks,

PM
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[Jmol-users] measure labels

[Pshemak Maslak]

How can control measure labels (position and font)?

How does  set defaultDistanceLabel format work?

What is format in this case?

Thanks,

PM

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Re: [Jmol-users] Java Update 65 Causing Issues?

[Pshemak Maslak]

I had similar problems (I reported them some time ago).  They were 
limited to one Windows machine (Win 7, Firefox, Chrome, IE) of 3 tried 
(Win 7 and Win 8).

My problem was with the update procedure.  It was insufficient to 
uninstall the old version, I had to delete (after uninstalling) all Java 
directories (hiding under Oracle and even Sun Systems names in Users 
directories).

After clean up, it works fine.

One curiosity: I have tested multiple Java applets (not just Jmol) and 
only Jmol did not work for me (it never fully loaded to get to the 
permission window, no error messages).

Please report back if it work for you too.

PM




On 7/25/2014 7:26 PM, Eric Martz wrote:
 In Windows 7, my tests indicate that Java 7 update 65 does not work
 with the current Jmol_S, or recent 14.0.17 Jmol_S. However, update 60
 does work.

 Do others confirm this?

 Previous emails indicate that Java 7 update 65 runs Jmol applet in
 Windows 8 (Angel H), and that Java 8 runs Jmol applet (Henry R, OS
 not specified?).

 However, on Windows 7, when I upgraded Java 7 from 60 to 65 today, I
 could not get the current Jmol_S applet to work in IE 11, Firefox 31,
 or Chrome (current).

 I tested Jmol 14.2.3
 http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=SIGNED
 and Jmol_S 14.0.17
 http://bioinformatics.org/firstglance/fgij/fg.htm?mol=1d66JAVA

 Curiously, a very old old unsigned applet (11.4.RC3) worked in
 Firefox and Chrome (but not in IE).
 http://www.umass.edu/molvis/tutorials/dna/dnapairs.htm

 All the above test sites work fine with Java 7 update 65 on OS X
 (Mavericks) with Safari or Firefox.

 All the above test sites work fine with Java 7 update 65 on Windows
 XP in Firefox 31 or Internet Explorer 8.

 I then uninstalled Java from my Windows 7, downloaded and installed
 Java 7 update 60
 (x86 version).
 http://www.oracle.com/technetwork/java/javase/downloads/java-archive-downloads-javase7-521261.html
 Everything worked again.

 Eric


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[Jmol-users] Java Update 65 Causing Issues

[Pshemak Maslak]

Jmol (v14.1.16) is not agreeing with Java 7.65 update (both Windows and 
OS X, several browsers).

The test page: http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm 
JSmol/Java link works with Java 7.51, it does not load with Java 7.65 
(no error messages, see below).

Does  ___JmolVersion=14.2.3_2014.07.12  works with Java 7.65? Where 
can this version be downloaded?

Thanks,

PM







On 7/16/2014 2:19 AM, Rzepa, Henry S wrote:
 On 16 Jul 2014, at 04:45, Pshemak Maslak n...@psu.edu wrote:

 I can confirm that observations. All my (remaining) Jmol (Java) instances 
 show as gray squares. There are no error messages in the Java console (in 
 fact, loading of the page with the app does not trigger opening of the 
 console even if it is set up to open).

 Other java applets on the same site work fine (and the Java console opens 
 when they load).

 PM

 I would also point out that there is Java 8 on the very near horizon,

 http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html

 I have been running  Java 8u5 for some months now (with no particular 
 problems on OS X, but 8u11 has just been released which  I have not tested), 
 but we should start testing both  7 AND 8 from now on.

 It is certainly true that as Oracle tightened the security sandbox for  Java, 
 we have had a period of significant instability (not least coping with all 
 those sites running  Java that have not replaced their unsigned  Jar’s with 
 signed ones).

 There are still a few functions of  Jmol that simply run too slowly in  JSmol 
 for  Java-Jmol to be phased out just yet (generating  .jvxl surfaces from 
 large cube files for example)  but  I suspect that day is going to have to 
 come. It might be useful to us all for a list of functions such as .jvxl 
 surface generation which simply cannot map to  JSmol to be created?

 Has anyone got any other suggestions for operations that really require  Jmol?


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Re: [Jmol-users] Java Update 65 Causing Issues?

[Pshemak Maslak]

I can confirm that observations. All my (remaining) Jmol (Java) 
instances show as gray squares. There are no error messages in the 
Java console (in fact, loading of the page with the app does not trigger 
opening of the console even if it is set up to open).


Other java applets on the same site work fine (and the Java console 
opens when they load).


PM



On 7/15/2014 8:03 PM, David Hibbitts wrote:

After updating Java today, I've been unable to run jmol on my webpage:

http://atlas.che.virginia.edu/mm/dim.php?user=ddh9rjobid=82043struct=Dimer_Mode.res

or any others that i've tried, including:

http://jmol.sourceforge.net/demo/atoms/

Java itself, however, seems to work as expected on

http://java.com/en/download/installed.jsp

and

http://javatester.org/version.html

Turning on the console in the Java control panel shows that the 
console doesn't run at all when on jmol pages, but does run on the 
testing pages. Is anyone else noticing this issue?


(Testing a different pc with an older version of Java (Update 55) 
confirms that all pages above work as expected).


Thanks,

David Hibbitts


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Re: [Jmol-users] is there a way to undisplay Jmol_S on the applet?

[Pshemak Maslak]

On 6/18/2014 7:20 AM, Ravi Raja Merugu wrote:
Thanks Angel, Thats what I thought .  But unfortunately I cant import 
files from RCSB server if I use unsigned applets right !! and how to 
fix that !!, and recently JAVA applets are being blocked for security 
issues, if they are unsigned by almost all the Operating systems. Any 
quick fix for this issue ?






Unsigned Java applets can be viewed by setting a security exception (for 
a page or a whole site) in the Java panel (security tab).


PM








On 18 June 2014 16:40, Angel Herráez angel.herr...@uah.es 
mailto:angel.herr...@uah.es wrote:


To clarify:

  set frank off
is the way to do it,  but DOES NOT APPLY to signed Jmol/Java applet
from a web server. I understand this is for security reasons, being a
signed applet it is a reminder of what is being displayed there.

The documentation says so:
http://chemapps.stolaf.edu/jmol/docs/#frank

set frank off
works for JSmol and for unsigned Jmol/Java



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[Jmol-users] contact

[Pshemak Maslak]

Can contact command be used to visualize clashes in small molecules 
(such as eclipsed CH3/CH3 in butane, for example)?

What would the full command look like?

Thanks,

PM





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[Jmol-users] ionic radii

[Pshemak Maslak]

On 4/18/2014 5:47 AM, Angel Herráez wrote:

Hi Pshemak

try this:

spacefill ionic;
print {*}.radius.all;

  If you want the full list of original values used, you probably need to check
the source code. The Scripting Doc page has a link to an Excel table (it may
be not up to date, I know there was a recent change in something related to
bonding radii) at
http://chemapps.stolaf.edu/jmol/docs/misc/radii.xls





Thanks!  That helps..  It looks like there are some unusual 
discrepancies.  For example:


Br(-1)  1.96 A on the xls list  and 1.21 A in Jmol when read from 
KBr,cif file
Cl(-1)  1.81 A on the xls list and 0.99 A in Jmol when read from 
CsCl.cif file   (it shows correctly at 1.81 A from NaCl.cif file)


Any idea of what is happening?

PM

PS. (Can I enclose the cif files with the email?).
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[Jmol-users] ionic radii

[Pshemak Maslak]

Is it possible to print out ionic radii used by Jmol?

PM

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Re: [Jmol-users] Problem with Test2.htm CONFIRMATION

[Pshemak Maslak]

I can confirm these observations:

At http://chemapps.stolaf.edu/jmol/jsmol/test2.htm caffeine disappear 
when rotated with the mouse on Mac (OS X, 10.9.2) in Firefox (28) and in 
Safari (7.0.3)


The same site/molecule works fin in Firefox(28)/Win 7.

PM





On 4/13/2014 10:09 PM, Philip Bays wrote:
I see the same issue on my iMac running 10.9.2, Safari 7.0.3 or 
Firefox 27.0.1 and JSmol 4.10 running locally or over the network. 
   Have not tried other browsers.  It's as if something is going on in 
the background.  For me the manipulation of the structure is quite 
jerky, freezes, then is jerky, and finally disappears.


I am having a different issue with Safari as well.  I run a local 
network at home.  All browsers work fine using [network 
name].local/~[account name]/  except for Safari.   I get a cannot 
connect to server error.  I am required to use the ip address 
approach as the URL.  This arose with OSX 9.2. All other browsers are 
fine using the local network name, and I can access it with a PC or my 
iPad using the network name.



On Apr 13, 2014, at 9:56 PM, Otis Rothenberger osrot...@chemagic.com 
mailto:osrot...@chemagic.com wrote:


I'm running 14.1.12_2014.3.21 and it's OK Mac Safari, Chrome, and 
Firefox. This is OS 10.9.2 Mavericks.


I've been keeping a close eye on iPad, and this version of JSmol runs 
really well on iPad Air and iPad 2.


Otis
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On Apr 13, 2014, at 8:05 PM, Eric Martz ema...@microbio.umass.edu 
mailto:ema...@microbio.umass.edu wrote:



From the online URL http://chemapps.stolaf.edu/jmol/jsmol/test2.htm

In addition to Firefox, I also see the disappearance with slight
rotation in Safari and Chrome (again, on Mac OS 10.9.1 Mavericks).

Those browsers will not run test2.htm from local files (network error
is reported), so I can only test them from the server.

Eric


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[Jmol-users] NMR predictions

[Pshemak Maslak]

http://chemapps.stolaf.edu/jmol/jsmol/jsv_jme.htm
http://chemapps.stolaf.edu/jmol/jsmol/jsv_predict2.htm

do not work with the newst Jmol version. .  Error message:

JSV.exception.JSVException: Error reading data: 
java.lang.NullPointerException

Is it Jmol or any of the other servers?

BTW: does the spectra-simulation algorithm takes into account 
diastereoscopic protons?


PM



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Re: [Jmol-users] last chance before Jmol 14.1.11; JJSME/JSpecView

[Pshemak Maslak]

On 3/6/2014 11:23 PM, Robert Hanson wrote:
 Do let me know if there are any bugs I've forgotten to fix before 
 tomorrow afternoon for 14.0.11 and 14.1.11 (will be identical)

 Also, some significant success this week in the JSME/JSpecView area 
 with NMR prediction AND hand-annotated files created using ACD/Labs 
 ACD/Spectrus 2012 v 14.01

 See http://chemapps.stolaf.edu/jmol/jsmol/jsv_jme.htm and
 http://chemapps.stolaf.edu/jmol/jsmol/jsv_predict2.htm

 -- 
This is a bit dated response but:

None of the above generates a spectrum. The first does not give any 
error message, the second shows 3D model but does not generate a 
spectrum. It gives a series of error messages starting with 
JSV.exception.JSVException: Error reading data: 
java.lang.NullPointerException

Tested in Firefox (Windows).

PM



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[Jmol-users] MEP questions

[Pshemak Maslak]

I have visualized MEP for NaCl (molecule) in Spartan and in Jmol). In 
Spartan, I see MEP mapped on a density surface that correspond to the 
expectation of ionic sizes (Na+ small, Cl- big).  In Jmol, MEP is mapped 
on what appears to be a molecular surface matching atomic sizes (Na big, 
Cl small).

1. Can I reproduce the Spartan surface in Jmol?  If so, how?

2. can I read the surface from the spartan file?  If so, how?

Thanks,

PM

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Re: [Jmol-users] alertNoBinary

[Pshemak Maslak]

On 1/10/2014 7:13 PM, Robert Hanson wrote:
Let's track this down. I've seen this on iPads, and it seems to me it 
should not be happening.


I believe that happens only in Chrome on windows or in Safari on apple 
OS (which apparently use the same browser engine).


PM






On Fri, Jan 10, 2014 at 2:55 PM, Spinney, Richard 
rspin...@chemistry.ohio-state.edu 
mailto:rspin...@chemistry.ohio-state.edu wrote:


I can help you with #1. The following makes it go away:

script type=text/javascript

Jmol._alertNoBinary = false;

jmolApplet0 =
Jmol.getApplet(jmolApplet0, Info);

/script

Otis


4 tel:%28614%29%C2%A0292%20-%201685
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[Jmol-users] lcaoCartoons translucent

[Pshemak Maslak]

It looks like translucent is broken in v 14 for lcaoCartoons.

For example, on 
http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?USE=HTML5 and loading 
water (load data/water.xyz.gz javascript:Jmol.script(jmolApplet0,'load 
data/water.xyz.gz'))


select @3
lcaoCartoon scale 1.3 color  [97 173 62]  translucent
lcaoCartoon create sp3c  sp3d

or

select @3
lcaoCartoon scale 1.3  color [97 173 62]
lcaoCartoon  translucent
lcaoCartoon create sp3c  sp3d

Create desired lobes but they are nit translucent.

Did something change or is it a bug?

PM


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[Jmol-users] an error in chrome?

[Pshemak Maslak]

I am referring to: http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?USE=HTML5

Loading spartan (load data/square_planar.spartan) or xyx.gz files (load 
data/water.xyz.gz)in Chrome (but not in Firefox) gives an error popup:


JmolCore.js: synchronous binary file transfer is requested but not
   available

The models load as expected when the message is dismissed (OK).

1. Is this related to: 
http://wiki.jmol.org/index.php/Jmol_JavaScript_Object#Reading_binary_files?


2. Is that expected behavior?  Can that popup be removed?

PM




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[Jmol-users] map on pointillist broken?

[Pshemak Maslak]

Bob,

It appears that mapping on pointillist representation of atomic orbitals 
is broken.


It works in v, 12,2 but not in v 13 on 14 of Jmol.

For example:

   isosurface atomicOrbital 1 0 0 1 points 5000 2 map atomicOrbital 1 0
   0 1

does not work (no errors in script console).

PM





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Re: [Jmol-users] proposed restyling of JSmol pop-up menu

[Pshemak Maslak]

On 8/30/2013 9:00 AM, Angel Herráez wrote:
 Dear JSmolers,

 As a result of a recent post, I've been playing with the look and feel of the
 pop-up menu in JSmol/HTML5

 I'd like to share a CSS-customised variation for your comments, individual
 adoption or implementation into default JSmol code.

 Please see the example at
 http://biomodel.uah.es/Jmol/pop-up_menu/test_popupmenu.htm
 There is a live demo, an image for comparison and you may look at the page
 source code to see the customisation (only CSS is changed)



Angel,

Those menu options look nice.

Are these versions (1, 2, and 3 on your site) part of the JSmol or do 
you need to install them individually?

Could you, please, explain in a bit more detail where I can find the 
relevant css changes and how to implement them?

Thanks,

PM

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Re: [Jmol-users] proposed restyling of JSmol pop-up menu

[Pshemak Maslak]

On 10/2/2013 11:58 AM, Robert Hanson wrote:

This is included in both JSmol 13.3.7 and 13.2.7



Bob and Angel:  Thanks!

PM








On Wed, Oct 2, 2013 at 10:10 AM, Angel Herráez angel.herr...@uah.es 
mailto:angel.herr...@uah.es wrote:


Hello Pshemak

I'm happy you are interested

 Are these versions (1, 2, and 3 on your site) part of the JSmol
or do
 you need to install them individually?

Those are the evolution steps of my testing. Only the last one is to
be considered (in fact, nr. 4 which may not be linked yet and needs a
later JSmol version). Yes, it is made with local changes, not yet in
JSmol files.


 Could you, please, explain in a bit more detail where I can find the
 relevant css changes and how to implement them?

Please see the page source code.
I have already sent the files to Bob and they should be included as
default in an upcoming release of JSmol.

If you are in a hurry, email me privately and I can sort out which
files or changes you need. Please let me know what your JSmol version
number is, to be safe.




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Re: [Jmol-users] replacement by a picture

[Pshemak Maslak]

On 8/18/2013 6:18 AM, Angel Herráez wrote:

 I'm not sure I understand the css/printing business.

Me either, but Pshemak said he wanted a substitute image for the 
printed version, and seemed to imply that the regular model does not 
print.


What I am seeing is indeed that the browser prints the HTML5 version 
all fine. For the Java applet it just gives an empty box. My trick 
allows to print an image in that place in both the Java and HTML5 
versions (there may a way to make it java-only).


Pshemak, please tell us where it was that you wanted the image to be 
printed.



It is a bit more complicated in my case.
I have two goals:
replace Jmol/JSmol with images on devices that do not support them, 
in the best way possible (I know it is impossible to cover all 
permutations of device/browser)

replace Jmol/JSmol with images in printed documents

For the second case, I know that Firefox and Chrome print Jmol, and 
JSmol, but I also use wkhtmltopdf on our server to produce well 
organized pdf booklets. The  wkhtmltopdf mechanism of printing relies 
on capturing the page image (html/css equivalent) produced by the 
server.  Apparently the Jmol/JSmol components are generated too slowly 
to be captured effectively.  We are trying to resolve that issue, but 
till then, image substitution seems like a good patch.


Thanks for all your help,

PM












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[Jmol-users] replacement by a picture

[Pshemak Maslak]

What are the best strategies to have  Jmol or JSmol instances replaced 
with a static picture when the browser does not have Java or java script 
enabled or is on a device that is not capable of handling Jmol/Jsmol?

How can one do the same for for printing browser pages?

Thanks,

PM





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Re: [Jmol-users] replacement by a picture

[Pshemak Maslak]

Thanks, these are examples of how to hide Jmol/JSmol before (or 
during) the loading of the app.


I am after a situation where Jmol/JSmol is normally displayed on page 
load for all of those who have Java/JS on their device, but a substitute 
picture is displayed for those who do no not, or when the page is 
printed (from the browser).


Thanks,

PM


On 8/15/2013 6:10 PM, Robert Hanson wrote:

Pschemak,

You can see this in operation at 
http://ispcsrv.weizmann.ac.il/a2jmolb/browse. Just click on one of the 
JSmol icons




Or go here:

http://ispcsrv.weizmann.ac.il/a2jmolb/browse?ip=824e0a1df426f51eed2a5873a5b1978b;set=testSet;jsmolUSE=HTML5

for a single example. This works by setting a few flags in the Info 
array. In this case we are showing the same file as a PNG as we are 
loading, because it is a PNGJ file.


coverImage: /a2jmolb/browse?sn=testSet/1bna_surface/jmol.png,
coverCommand: ,
coverTitle: Loading ... Please wait.,  // tip that is displayed before model 
starts to load
deferApplet: false, // true == the model should not be loaded until the image 
is clicked
deferUncover: true, // true == the image should remain until command execution 
is complete
script: load /a2jmolb/browse?sn=testSet/1bna_surface/jmol.png,








On Thu, Aug 15, 2013 at 1:24 PM, Pshemak Maslak p...@chem.psu.edu 
mailto:p...@chem.psu.edu wrote:


What are the best strategies to have  Jmol or JSmol instances replaced
with a static picture when the browser does not have Java or java
script
enabled or is on a device that is not capable of handling Jmol/Jsmol?

How can one do the same for for printing browser pages?

Thanks,

PM






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Re: [Jmol-users] MEP units

[Pshemak Maslak]

On 5/30/2013 9:22 AM, Robert Hanson wrote:

It's whatever units come from this calculation:


  public float valueFor(float x0, float d2, int distanceMode) {
switch (distanceMode) {
case ONE_OVER_D:
  return (d2 == 0 ? x0 * Float.POSITIVE_INFINITY : x0 / (float) 
Math.sqrt(d2));

case ONE_OVER_ONE_PLUS_D:
  return  x0 / (1 + (float) Math.sqrt(d2));
case E_MINUS_D_OVER_2:
  return x0 * (float) Math.exp(-Math.sqrt(d2) / 2);
case E_MINUS_D:
  return x0 * (float) Math.exp(-Math.sqrt(d2));
}
return x0;
  }

  public MepCalculation() {
rangeBohrOrAngstroms = 8; // Angstroms
distanceMode = ONE_OVER_D;
unitFactor = 1;
  }

d would be in angstroms, I think. Charge would be whatever you get 
that from; different programs will be different.


The only think I can read from that is that you do prefer positive 
infinity when you divide by zero.-:)


PM













On Wed, May 29, 2013 at 11:17 AM, Pshemak Maslak p...@chem.psu.edu 
mailto:p...@chem.psu.edu wrote:


I know I have asked this before, but I still cannot figure it out:

What are  the MEP units when the rainbow range is set?

I have tried eV, hartrees, but these do not match pictures usually
shown
with the range of -25/+25 kcal/mol or -50/+ 50 kcal/mol.

If they are not energy, what are they?

Thanks,

PM


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Re: [Jmol-users] MEP units

[Pshemak Maslak]

On 5/31/2013 2:02 PM, Pshemak Maslak wrote:

On 5/30/2013 9:22 AM, Robert Hanson wrote:

It's whatever units come from this calculation:


  public float valueFor(float x0, float d2, int distanceMode) {
switch (distanceMode) {
case ONE_OVER_D:
  return (d2 == 0 ? x0 * Float.POSITIVE_INFINITY : x0 / (float) 
Math.sqrt(d2));

case ONE_OVER_ONE_PLUS_D:
  return  x0 / (1 + (float) Math.sqrt(d2));
case E_MINUS_D_OVER_2:
  return x0 * (float) Math.exp(-Math.sqrt(d2) / 2);
case E_MINUS_D:
  return x0 * (float) Math.exp(-Math.sqrt(d2));
}
return x0;
  }

  public MepCalculation() {
rangeBohrOrAngstroms = 8; // Angstroms
distanceMode = ONE_OVER_D;
unitFactor = 1;
  }

d would be in angstroms, I think. Charge would be whatever you get 
that from; different programs will be different.


The only think I can read from that is that you do prefer positive 
infinity when you divide by zero.-:)


PM



If the charges in the file are in atomic units (multiple of electron 
charge) and the distances are measured in angstroms the Jmol calculated 
values of electrostatic potential can be converted into kcal/mol by 
multiplying by 332.


I think that is what Jmol does with Spartan files.

PM
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[Jmol-users] MEP units

[Pshemak Maslak]

I know I have asked this before, but I still cannot figure it out:

What are  the MEP units when the rainbow range is set?

I have tried eV, hartrees, but these do not match pictures usually shown 
with the range of -25/+25 kcal/mol or -50/+ 50 kcal/mol.

If they are not energy, what are they?

Thanks,

PM

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Re: [Jmol-users] select WITHIN(...)

[Pshemak Maslak]

On 5/24/2013 10:49 AM, Robert Hanson wrote:




On Fri, May 24, 2013 at 9:54 AM, Angel Herráez angel.herr...@uah.es 
mailto:angel.herr...@uah.es wrote:


Hello Pshemak

 Finally, can the selected groups of atom (ions) be given a name
(ID) so
 they could be referred to without repeating the selection criteria?

Yes, two ways: using the define command or using a JmolScript
variable

e.g.
define myAtomSet  _Cl and within(6.0, atomNo=6);
then
select myAtomSet;

I'm never sure with the variables, but something like
var myAtomSet = _Cl and within(6.0, atomNo=6);


Need braces there on that one since it is not a legacy Jmol command.


myAtomSet = {_Cl and within(6, @6)}

for example. var would localize that definition to a given {...} 
enclosure.


load nacl.mol
myAtomSet = {_Cl and within(6, @6)}
print myatomset
({0 1 3:5 7 10 15 19 21:23})
color {myatomset} blue
color @myatomset green




Thanks Angel and Bob.  That clarifies a lot.

PM
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Re: [Jmol-users] Jmol menu surface : scripting

[Pshemak Maslak]

On 5/19/2013 12:25 PM, Otis Rothenberger wrote:

Chen,

The menu command is:

isosurface delete resolution 0 molecular map MEP translucent

This hides an important issue that I don't fully understand because of 
seemingly inconsistent charge units in various files. The issue is the 
charge range of painted colors. The above uses a default range that I 
don't know. Angel, do you know the default? By trial and error, I 
settled on the following:


isosurface resolution 0 molecular color range -.07 .07 map mep translucent


Otis



BTW: what are the units for MEP?  What is  -0.07 in the example 
above?  Is that number for potential energy?   Or just Q/distance? (Q in 
what units, distance in what units)? Or something else?


PM








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On May 19, 2013, at 11:49 AM, Angel Herráez wrote:


Hello Chen

You can try enetering this in the script console just after you use 
the menu option:


show isosurface

amongst the long text displayed, there is a section entitled
jvxlIsosurfaceState
which has the script that will render the isosurface you have.

As for getting a color, you can include the color definition in your 
isosurface script, but sometimes that is a little tricky, and it is 
always safe and easy to apply color in a second command, like e.g.


isosurface mysurf1 molecular;
color $mysurf1 translucent** green;

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[Jmol-users] closing non-java options

[Pshemak Maslak]

I am referring to the deferred-applet mode where an initial image is 
displayed and with a click on that image the 3D canvas/model is 
activated (whether preloaded or not).

I have not tried anything like that yet, just trying to figure out what 
the limitations are.

Let's say I have a number of such images (as described above) on one 
webpage, and some have been activated.

How many such activated instances would a typical browser be able to 
handle?

Is there a way to close the once activated instance so it returns to 
the starting image (and releases any computer/browser resources that it 
utilized when it was active)?

Thanks,

PM


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[Jmol-users] floating window

[Pshemak Maslak]

Can JSmol instance be displayed (and be functional) in a floating window 
(pop-up window)?

I do not know the correct terminology, I do not mean a new browser 
window, but one than can only float within the browser, like those 
generated, for example by HighSlide (http://highslide.com/)





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Re: [Jmol-users] JSmol error

[Pshemak Maslak]

On 4/19/2013 6:05 PM, Robert Hanson wrote:

right -- don't use Chrome for local file access. See the wiki.

This is not a local file, it is on the server.

The same thing happens in FireFox (except I do not have firebug installed).

PM




On Fri, Apr 19, 2013 at 9:38 AM, Pshemak Maslak p...@chem.psu.edu 
mailto:p...@chem.psu.edu wrote:


I am practicing with JSmol:

I have a simple script that loads dna.pdb file and executes a
couple of
simple commands.

It works well in Java Jmol, but in JSmol in Chrome JS console throws 
XMLHttpRequest.responseType cannot be changed for synchronous HTTP(S)
requests made from the window context. on line 209 of JSmol.min.js.


If I remove that load line, the error goes away, but obviously the DNA
molecule isn't loaded then.

Is there a problem in JSmol?

Thanks,

PM

zap;
load

/courses/chem110_master/sites/edu.courses.chem110_master/files/molecules/dna-pwz.pdb;

moveto 0.01 { 945 -209 -251 85.33 tel:209%20-251%2085.33} 28.43
0.0 0.0 {31.317 41.607502
28.2905} 33.063145 {0.0 0.0 0.0} -7.721215 -15.052243 0.0;
delay 1.0
moveto 3.0 { -300 -935 -190 27.93} 100.0 0.0 0.0  {31.317 41.607502
28.2905} 33.063145 {0.0 0.0 0.0} -27.401278 63.2362 0.0;
delay 1.0;
rotate y 360 90;
delay 4.0
moveto 6.0 { -505 295 -811 178.2}  404.56 0.0 0.0  {31.317 41.607502
28.2905} 33.063145 {0.0 0.0 0.0} 15.9948635 -310.97995 0.0;
delay 1.0
cartoon on; color group;
delay 1.0
moveto 4.0 { 409 -49 911 172.45} 86.96 0.0 0.0  {31.317 41.607502
28.2905} 33.063145 {0.0 0.0 0.0} 7.332866 -53.193756 0.0;
rotate y 720 90;
delay 3.0
cartoon off;
delay 3.0
color cpk
delay 2.0
set spiny 90; spin on;




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[Jmol-users] JSmol error

[Pshemak Maslak]

I am practicing with JSmol:

I have a simple script that loads dna.pdb file and executes a couple of 
simple commands.

It works well in Java Jmol, but in JSmol in Chrome JS console throws  
XMLHttpRequest.responseType cannot be changed for synchronous HTTP(S) 
requests made from the window context. on line 209 of JSmol.min.js.


If I remove that load line, the error goes away, but obviously the DNA 
molecule isn't loaded then.

Is there a problem in JSmol?

Thanks,

PM

zap;
load 
/courses/chem110_master/sites/edu.courses.chem110_master/files/molecules/dna-pwz.pdb;
 

moveto 0.01 { 945 -209 -251 85.33} 28.43 0.0 0.0 {31.317 41.607502 
28.2905} 33.063145 {0.0 0.0 0.0} -7.721215 -15.052243 0.0;
delay 1.0
moveto 3.0 { -300 -935 -190 27.93} 100.0 0.0 0.0  {31.317 41.607502 
28.2905} 33.063145 {0.0 0.0 0.0} -27.401278 63.2362 0.0;
delay 1.0;
rotate y 360 90;
delay 4.0
moveto 6.0 { -505 295 -811 178.2}  404.56 0.0 0.0  {31.317 41.607502 
28.2905} 33.063145 {0.0 0.0 0.0} 15.9948635 -310.97995 0.0;
delay 1.0
cartoon on; color group;
delay 1.0
moveto 4.0 { 409 -49 911 172.45} 86.96 0.0 0.0  {31.317 41.607502 
28.2905} 33.063145 {0.0 0.0 0.0} 7.332866 -53.193756 0.0;
rotate y 720 90;
delay 3.0
cartoon off;
delay 3.0
color cpk
delay 2.0
set spiny 90; spin on;



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[Jmol-users] hex colors in JSmol

[Pshemak Maslak]

Is there a bug in JSmol where it ignores background colors in hex?

In the Jmol info JS array, the color property is ignored if the color is 
in hex (specifying it as black, or white works though), whereas in 
the (Java) Jmol, the color is set properly.  (13.1.15_dev from 2013-04-01).

Thanks,

PM



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Re: [Jmol-users] hex colors in JSmol

[Pshemak Maslak]

On 4/18/2013 1:40 PM, Robert Hanson wrote:

define hex.



Hexadecimal, for example [xF0F0F0]  for gray

PM





On Thu, Apr 18, 2013 at 11:57 AM, Pshemak Maslak p...@chem.psu.edu 
mailto:p...@chem.psu.edu wrote:



Is there a bug in JSmol where it ignores background colors in hex?

In the Jmol info JS array, the color property is ignored if the
color is
in hex (specifying it as black, or white works though), whereas in
the (Java) Jmol, the color is set properly.  (13.1.15_dev from
2013-04-01).

Thanks,

PM




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Re: [Jmol-users] Jmol | lcaocartoon

[Pshemak Maslak]

On 3/11/2013 2:18 PM, Robert Hanson wrote:

Since when are they sp2 ? ;)


Since freshman chemistry covered hybridization?

I am guessing that there is no simple fix...

PM






On Mon, Mar 11, 2013 at 12:40 PM, Pshemak Maslak p...@chem.psu.edu 
mailto:p...@chem.psu.edu wrote:


On 3/11/2013 12:58 PM, Robert Hanson wrote:

Good catch, Michael. Yes, it's specifically a problem with
-sp3d -- easily fixed.

See http://chemapps.stolaf.edu/jmol/Jmol-13.zip and
http://chemapps.stolaf.edu/jmol/jsmol.zip


Bob


I have lcaocartoon-related questions. For CO2 (for example) the
sp2 lone pair lobes are shown as the sp lobes instead.  Similar
outcome is observed for other linear molecules. Is that a general
limitation?

I know that the cartoons lobes can be drawn and oriented (per
demand) using isosurface command, but the lonepair dots are much
harder if one wants them to keep up with molecular rotations and
not eclipse each other at some orientations.

Is there a simple way to deal with these issues?

Thanks,

PM








On Sun, Mar 10, 2013 at 2:19 PM, Michael Evans
evan...@illinois.edu mailto:evan...@illinois.edu wrote:

Jmol'ers,
I am having trouble using lcaocartoon in a very specific
case. If you look on this page, the antibonding orbitals
render fine:

http://butane.chem.illinois.edu/jsmoore/Experimental/DFE.html

However, on this updated version of the same page using
either JSmol or Jmol 13.0.12, the last antibonding orbitals
(C3-H6 and C2-H8) fail to render properly.


http://www.metallacycle.com/lec/chem332/jmolpages/difluoroethane/?use=java

Those last antibonding orbitals use the -sp3d lobe, which
appears not to render properly no matter what I try. I even
tried back here with no success:

http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm

An sp3d lobe renders fine, but nothing happens when I try
lcaocartoon create -sp3d. Am I missing something?

Cheers, Mike

---
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it is better to take what answer we get.

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Re: [Jmol-users] Jmol | lcaocartoon

[Pshemak Maslak]

On 3/15/2013 1:42 PM, Simone Sturniolo wrote:

I think the point here is that CO2 has simple sp hybridization, not sp2...


We are talking about lone pairs on oxygens (not about carbon hybridization).

PM



2013/3/15 Pshemak Maslak p...@chem.psu.edu mailto:p...@chem.psu.edu

On 3/11/2013 2:18 PM, Robert Hanson wrote:

Since when are they sp2 ? ;)


Since freshman chemistry covered hybridization?

I am guessing that there is no simple fix...

PM







On Mon, Mar 11, 2013 at 12:40 PM, Pshemak Maslak p...@chem.psu.edu
mailto:p...@chem.psu.edu wrote:

On 3/11/2013 12:58 PM, Robert Hanson wrote:

Good catch, Michael. Yes, it's specifically a problem with
-sp3d -- easily fixed.

See http://chemapps.stolaf.edu/jmol/Jmol-13.zip and
http://chemapps.stolaf.edu/jmol/jsmol.zip


Bob


I have lcaocartoon-related questions. For CO2 (for example)
the sp2 lone pair lobes are shown as the sp lobes instead. 
Similar outcome is observed for other linear molecules. Is

that a general limitation?

I know that the cartoons lobes can be drawn and oriented 
(per demand) using isosurface command, but the lonepair

dots are much harder if one wants them to keep up with
molecular rotations and not eclipse each other at some
orientations.

Is there a simple way to deal with these issues?

Thanks,

PM








On Sun, Mar 10, 2013 at 2:19 PM, Michael Evans
evan...@illinois.edu mailto:evan...@illinois.edu wrote:

Jmol'ers,
I am having trouble using lcaocartoon in a very specific
case. If you look on this page, the antibonding orbitals
render fine:

http://butane.chem.illinois.edu/jsmoore/Experimental/DFE.html

However, on this updated version of the same page using
either JSmol or Jmol 13.0.12, the last antibonding
orbitals (C3-H6 and C2-H8) fail to render properly.


http://www.metallacycle.com/lec/chem332/jmolpages/difluoroethane/?use=java

Those last antibonding orbitals use the -sp3d lobe,
which appears not to render properly no matter what I
try. I even tried back here with no success:

http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm

An sp3d lobe renders fine, but nothing happens when I
try lcaocartoon create -sp3d. Am I missing something?

Cheers, Mike

---
Michael Evans
Department of Chemistry
University of Illinois, Urbana-Champaign


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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 | lcaocartoon

[Pshemak Maslak]

On 3/15/2013 2:11 PM, Michael Evans wrote:
There seems to be a philosophical and technological debate brewing 
here. Rigorously, the lone pairs of CO2 are not sp2-hybridized; a 
canonical calculation of the MOs reveals that.

I do not think that CARTOON orbitals inspire a philosophical debate; :-)
I am strictly after the technical aspects.



But on another note, how would Jmol even know where to put the sp2 
hybridized lone pairs? The two ends of CO2 would have to know 
something about each other, since the lone pairs ought to be at right 
angles (I hope we can agree on that...). It seems a technological 
impossibility to lay down sp2 or even px and py lobes on the oxygens.
That is part of my question: is there a simple way (within lcaoCartoon) 
to draw sp2 lobes on oxygens and to do it in the correct relative 
orientation. As is, Jmol draws  sp lobes on oxygens. (There is a similar 
limitation for other linear molecules and other hybridization types).


p orbitals can be draw correctly by manually selecting their 
orientation  (px, py, or pz). Would it be possible to similarly define 
planes for lone pair lobes?


PM




Sounds like independent isosurfaces are the way to go.

On Friday, March 15, 2013, Pshemak Maslak wrote:

On 3/15/2013 1:42 PM, Simone Sturniolo wrote:

I think the point here is that CO2 has simple sp hybridization,
not sp2...


We are talking about lone pairs on oxygens (not about carbon
hybridization).

PM



2013/3/15 Pshemak Maslak p...@chem.psu.edu

On 3/11/2013 2:18 PM, Robert Hanson wrote:

Since when are they sp2 ? ;)


Since freshman chemistry covered hybridization?

I am guessing that there is no simple fix...

PM







On Mon, Mar 11, 2013 at 12:40 PM, Pshemak Maslak
p...@chem.psu.edu wrote:

On 3/11/2013 12:58 PM, Robert Hanson wrote:

Good catch, Michael. Yes, it's specifically a problem
with -sp3d -- easily fixed.

See http://chemapps.stolaf.edu/jmol/Jmol-13.zip and
http://chemapps.stolaf.edu/jmol/jsmol.zip


Bob


I have lcaocartoon-related questions. For CO2 (for
example) the sp2 lone pair lobes are shown as the sp
lobes instead.  Similar outcome is observed for other
linear molecules. Is that a general limitation?

I know that the cartoons lobes can be drawn and
oriented  (per demand) using isosurface command, but
the lonepair dots are much harder if one wants them to
keep up with molecular rotations and not eclipse each
other at some orientations.

Is there a simple way to deal with these issues?

Thanks,

PM








On Sun, Mar 10, 2013 at 2:19 PM, Michael Evans
evan...@illinois.edu wrote:

Jmol'ers,




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Re: [Jmol-users] Jmol | lcaocartoon

[Pshemak Maslak]

On 3/15/2013 2:21 PM, Robert Hanson wrote:
But I would argue that CO2 is sp hybridized, and the six left-over p 
orbitals form two orthogonal three-orbital pi sets. Isn't that 
necessary from symmetry considerations?


Bob



In the MO-sense, yes, but I am thinking about simple (freshman-level) 
hybridization scheme.



PM






On Fri, Mar 15, 2013 at 12:32 PM, Pshemak Maslak p...@chem.psu.edu 
mailto:p...@chem.psu.edu wrote:


On 3/11/2013 2:18 PM, Robert Hanson wrote:

Since when are they sp2 ? ;)


Since freshman chemistry covered hybridization?

I am guessing that there is no simple fix...

PM







On Mon, Mar 11, 2013 at 12:40 PM, Pshemak Maslak p...@chem.psu.edu
mailto:p...@chem.psu.edu wrote:

On 3/11/2013 12:58 PM, Robert Hanson wrote:

Good catch, Michael. Yes, it's specifically a problem with
-sp3d -- easily fixed.

See http://chemapps.stolaf.edu/jmol/Jmol-13.zip and
http://chemapps.stolaf.edu/jmol/jsmol.zip


Bob


I have lcaocartoon-related questions. For CO2 (for example)
the sp2 lone pair lobes are shown as the sp lobes instead. 
Similar outcome is observed for other linear molecules. Is

that a general limitation?

I know that the cartoons lobes can be drawn and oriented 
(per demand) using isosurface command, but the lonepair

dots are much harder if one wants them to keep up with
molecular rotations and not eclipse each other at some
orientations.

Is there a simple way to deal with these issues?

Thanks,

PM








On Sun, Mar 10, 2013 at 2:19 PM, Michael Evans
evan...@illinois.edu mailto:evan...@illinois.edu wrote:

Jmol'ers,
I am having trouble using lcaocartoon in a very specific
case. If you look on this page, the antibonding orbitals
render fine:

http://butane.chem.illinois.edu/jsmoore/Experimental/DFE.html

However, on this updated version of the same page using
either JSmol or Jmol 13.0.12, the last antibonding
orbitals (C3-H6 and C2-H8) fail to render properly.


http://www.metallacycle.com/lec/chem332/jmolpages/difluoroethane/?use=java

Those last antibonding orbitals use the -sp3d lobe,
which appears not to render properly no matter what I
try. I even tried back here with no success:

http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm

An sp3d lobe renders fine, but nothing happens when I
try lcaocartoon create -sp3d. Am I missing something?

Cheers, Mike

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Re: [Jmol-users] Jmol | lcaocartoon

[Pshemak Maslak]

On 3/15/2013 4:38 PM, Robert Hanson wrote:
  lcaocartoon ID lp1 center {_O}[1] lobe {0 -0.866 -0.5  0.7}

 looks to me to be a decent sp2 orbital for which the associated p 
 orbital is along x.

 The first three numbers are the axis direction; the last one is the 
 ratio of width to length.

 Will that do, Pshemak?

 Bob


Thanks Bob!  It works great.

I did essentially the same with the isosurface (lobe) command.

Can this be extended to LONEPAIR to get two electron dots that do not 
eclipse each other in some positions upon model rotations (i.e. 
reproduce the dots from lcaoCartoon LONEPAIR)?

PM

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Re: [Jmol-users] Jmol | lcaocartoon

[Pshemak Maslak]

On 3/11/2013 12:58 PM, Robert Hanson wrote:
Good catch, Michael. Yes, it's specifically a problem with -sp3d -- 
easily fixed.


See http://chemapps.stolaf.edu/jmol/Jmol-13.zip and 
http://chemapps.stolaf.edu/jmol/jsmol.zip



Bob


I have lcaocartoon-related questions. For CO2 (for example) the sp2 lone 
pair lobes are shown as the sp lobes instead.  Similar outcome is 
observed for other linear molecules. Is that a general limitation?


I know that the cartoons lobes can be drawn and oriented  (per demand) 
using isosurface command, but the lonepair dots are much harder if one 
wants them to keep up with molecular rotations and not eclipse each 
other at some orientations.


Is there a simple way to deal with these issues?

Thanks,

PM








On Sun, Mar 10, 2013 at 2:19 PM, Michael Evans evan...@illinois.edu 
mailto:evan...@illinois.edu wrote:


Jmol'ers,
I am having trouble using lcaocartoon in a very specific case. If
you look on this page, the antibonding orbitals render fine:

http://butane.chem.illinois.edu/jsmoore/Experimental/DFE.html

However, on this updated version of the same page using either
JSmol or Jmol 13.0.12, the last antibonding orbitals (C3-H6 and
C2-H8) fail to render properly.

http://www.metallacycle.com/lec/chem332/jmolpages/difluoroethane/?use=java

Those last antibonding orbitals use the -sp3d lobe, which
appears not to render properly no matter what I try. I even tried
back here with no success:

http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm

An sp3d lobe renders fine, but nothing happens when I try
lcaocartoon create -sp3d. Am I missing something?

Cheers, Mike

---
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Department of Chemistry
University of Illinois, Urbana-Champaign


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it is better to take what answer we get.

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Re: [Jmol-users] lcaoCartoon for CO2

[Pshemak Maslak]

I have figured out how to use isosurface with lobe  commands to 
generate and orient the cartoon orbital lobes.


For example: isosurface sp2a color  [97 173 62] center (atomno=2)  lobe 
{1 1 -1 0.8}; color $sp2a translucent 4 on;


I can even add electron pair dots using draw circle and place them 
within the lobe.


For example:

draw dot1 circle {@2} {z} scale 0.03 color black offset {0.77 0.60 -0.6}
draw dot2 circle {@2} {z} scale 0.03 color black offset {0.60 0.60 -0.6}

My dots are rigidly positioned, and in some orientations of the model 
they eclipse each other.


However,  the lcaoCartoo lonepair generated dots always stay the same 
distance apart (adjust their relative position) as the model is 
manipulated.


How can I reproduce that lonepair behavior?

Thanks,

PM


On 12/5/2012 2:47 PM, Pshemak Maslak wrote:

The lcaoCartoon command run on CO2 structure (spartan):

select @2
lcaoCartoon scale 2.0 color  [97 173 62]  translucent
lcaoCartoon create sp2b


creates a lobe that is collinear with the O-C-O axis (rather than 
about 120 degrees from it).  lonepair creates similarly positioned 
pair of dots.


Is there a way to adjust that position to its proper angle?  I 
presume that the problem is common to all linear molecules. The sp3 
lobes (or lone pairs) are created essentially in one plane (for 
example for fluorines in XeF2).


Any suggestions would be appreciated,

PM


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[Jmol-users] lcaoCartoon for CO2

[Pshemak Maslak]

The lcaoCartoon command run on CO2 structure (spartan):

select @2
lcaoCartoon scale 2.0 color  [97 173 62]  translucent
lcaoCartoon create sp2b


creates a lobe that is collinear with the O-C-O axis (rather than about 
120 degrees from it).  lonepair creates similarly positioned pair of dots.

Is there a way to adjust that position to its proper angle?  I presume 
that the problem is common to all linear molecules. The sp3 lobes (or 
lone pairs) are created essentially in one plane (for example for 
fluorines in XeF2).

Any suggestions would be appreciated,

PM

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Re: [Jmol-users] radio buttons

[Pshemak Maslak]

  On 10/6/2012 4:43 PM, Robert Hanson wrote:
 Oops. Clearly I never tested radio buttons with JmolJSO. Attached is a 
 new JmolControls.js

 Bob

Thanks, but we still cannot make it work.

Now, the call to

c._getRadio()


in Jmol.jmolRadioGroup in JmolApi.js is returning null causing only 
the first radio to be rendered on the page. However, that radio button 
does work.

PM



our code

var radios = new Array();
radios[0] = [set background [xF0F0F0], light, true];
radios[1] = [set background black, black];
Jmol.jmolRadioGroup(jmol5, radios);





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[Jmol-users] radio buttons

[Pshemak Maslak]

  I need help with a couple of radio buttons:


The current code I'm using is:

var radios = new Array();
radios[0] = [set background [xF0F0F0], light bckg, true];
radios[1] = [set background black, black bckg];
Jmol.jmolRadioGroup(jmol5, radios);


And the error I keep getting is:

Uncaught TypeError: Cannot call method '_script' of undefined

on line 60 of JmolApi.js


Any suggestions of what is wrong?

Thanks,

PM



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[Jmol-users] ion sizes

[Pshemak Maslak]

Displaying NaCl (from a cif file) shows Na+  sphere bigger than that of 
Cl-.  I am assuming that atomic radii are use. Is there ionic radii info 
in Jmol? If so, how can one display it?

PM




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Re: [Jmol-users] Draw polyhedra without central atom

[Pshemak Maslak]

On 9/13/2012 12:16 PM, Robert Hanson wrote:

Isn't the latest version 13.1.5?


I am confused. Where can I find  13.1.5?

The bleeding edge ( http://chemapps.stolaf.edu/jmol/) is 13.1.4 HOLD 2012.

PM




On Tue, Sep 11, 2012 at 7:29 PM, Pshemak Maslak p...@chem.psu.edu 
mailto:p...@chem.psu.edu wrote:


On 9/11/2012 8:09 PM, Robert Hanson wrote:

working OK for me. Is this app or applet? What script commands
are you giving Jmol to request select atoms with the mouse?


Tested on the *desktop only* 13.1.4 HOLD (2012-9-8) with .spartan
files

The atom labels do not show on hover.


Yes, I think I fixed that, though. They are there, but one line too high.


The files cannot be dragged into Jmol (they do load with script 
load). on XP, files with space in their name cannot be dragged

on win 7

Ah. Interesting.

PM.









On Tue, Sep 11, 2012 at 2:41 PM, Nikolay Bogdanov
nikol.bogda...@gmail.com mailto:nikol.bogda...@gmail.com wrote:

It is unable to select atoms using mouse, and there is no
hint with atom ID and  number when cursor hangs at atom.
Rotation with left click, and right click menu work. Same on
both mac os and linux.

2012/9/11 Robert Hanson hans...@stolaf.edu
mailto:hans...@stolaf.edu

details?


On Tue, Sep 11, 2012 at 11:36 AM, Nikolay Bogdanov
nikol.bogda...@gmail.com
mailto:nikol.bogda...@gmail.com wrote:

One more thing is that atom picking is broken in the
modified Jmol version. 





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

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1900




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it is better to take what answer we get.

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Re: [Jmol-users] Draw polyhedra without central atom

[Pshemak Maslak]

 On 9/11/2012 8:09 PM, Robert Hanson wrote:
working OK for me. Is this app or applet? What script commands are you 
giving Jmol to request select atoms with the mouse?


Tested on the *desktop only* 13.1.4 HOLD (2012-9-8) with .spartan files

The atom labels do not show on hover.

The files cannot be dragged into Jmol (they do load with script  
load). on XP, files with space in their name cannot be dragged on win 7


PM.








On Tue, Sep 11, 2012 at 2:41 PM, Nikolay Bogdanov 
nikol.bogda...@gmail.com mailto:nikol.bogda...@gmail.com wrote:


It is unable to select atoms using mouse, and there is no hint
with atom ID and  number when cursor hangs at atom. Rotation with
left click, and right click menu work. Same on both mac os and linux.

2012/9/11 Robert Hanson hans...@stolaf.edu
mailto:hans...@stolaf.edu

details?


On Tue, Sep 11, 2012 at 11:36 AM, Nikolay Bogdanov
nikol.bogda...@gmail.com mailto:nikol.bogda...@gmail.com
wrote:

One more thing is that atom picking is broken in the
modified Jmol version. 





-- 
Robert M. Hanson

Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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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it is better to take what answer we get.

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Re: [Jmol-users] Draw polyhedra without central atom

[Pshemak Maslak]

On 9/7/2012 1:03 PM, Robert Hanson wrote:
The polyhedron needs a central atom. But you can add that yourself. 
The command appears to be undocumented --


assign {attachmentAtom} Symbol {x y z}

For example:

assign atom {atomno=14} Cl {2 3 4}

That position {2 3 4} could also be an average position of a number of 
atoms:


assign atom {atomno=14} Cl {2 3 4} {atomno=14 or atomno=13 or 
atomno=12 or atomno=11}


then you would also need to do the connections before creating the 
polyhedra.


HOWEVER, with a bit of a tweak of Jmol, I can make this possible 
without connecting the atoms. You  will still need a central atom, 
though. Let me get back to you on this.


Bob



Could the tweak include the option of drawing polyhedra if not all 
vertices are present? Such as a tetrahedron for ammonia or water?


Something that would draw a polyhedron when the central atom and a 
number of vertices is specified with the size equal the specified bond 
(something like O1 4 O1-H 1 for water)..


I know I am asking too much, but if you are tweaking it...

Thanks

PM








On Fri, Sep 7, 2012 at 8:16 AM, Nikolay Bogdanov 
nikol.bogda...@gmail.com mailto:nikol.bogda...@gmail.com wrote:


I'm trying to make a figure showing the coordination of metal ions
in crystal - they form network of tetrahedra. I can do this with
bonds, but the
figure looks confusing. It would be much more clear with opaque
tetrahedrons.

As I understand Jmol builds polyhedra around some central atoms,
which are missing in my case. So I wonder is there a way to build
the polyhedra just
from bonds.

Thanks,
Nikolay


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[Jmol-users] polyhedra

[Pshemak Maslak]

Is there a way to draw idealized polyhedra for molecules with missing 
vertex atoms, for example a tetrahedron for water or ammonia?

PM

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Re: [Jmol-users] lcaoCartoons

[Pshemak Maslak]

On 7/2/2012 11:55 AM, Robert Hanson wrote:

add the keyword MOLECULAR and you should have it:

lcaocartoon CREATE pz MOLECULAR

/Creates a new LCAO cartoon of the given type using the molecular axes 
system as reference. Applicable only for px, py, pz, -px, 
-py, and -pz. /




 I did not see it  :-(

Thanks!

PM










On Sun, Jul 1, 2012 at 10:34 PM, Pshemak Maslak p...@chem.psu.edu 
mailto:p...@chem.psu.edu wrote:


I have encountered a problem with displaying p orbital cartoons
with matching colors on all atoms of SO2 molecule.

select all
lcaoCartoon create pz


creates one p orbital with opposite color lobes to the other two.

I can individually add p lobes to all three atoms (and adjust the
phase):

select atomno=1
lcaoCartoon create pz
select atomno=2
lcaoCartoon create -pz
select atomno=3
lcaoCartoon create pz


but I do not know if the phase color problem is a bug (Jmol
12.3.32 6/23/2012), or is there some design reason for this behavior.

Any suggestions?

PM



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[Jmol-users] lcaoCartoons

[Pshemak Maslak]

I have encountered a problem with displaying p orbital cartoons with 
matching colors on all atoms of SO2 molecule.


   select all
   lcaoCartoon create pz


creates one p orbital with opposite color lobes to the other two.

I can individually add p lobes to all three atoms (and adjust the phase):

   select atomno=1
   lcaoCartoon create pz
   select atomno=2
   lcaoCartoon create -pz
   select atomno=3
   lcaoCartoon create pz


but I do not know if the phase color problem is a bug  (Jmol 12.3.32 
6/23/2012), or is there some design reason for this behavior.


Any suggestions?

PM

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[Jmol-users] spartan file issue

[Pshemak Maslak]

  Did anybody noticed problems with Jmol reading Spartan 10  .spartan 
files?

  I have observed that the current version of Spartan  (10) produces 
files that cannot be read by Jmol. The error message reads: no atoms 
found.  The file opens correctly in Spartan.

The old version files produced by Spartan 08 displays correctly.

Any help would be appreciated.

PM

PS. The files are too large to be attached to this e-mail..



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Re: [Jmol-users] Changing the phase of a signed surface?

[Pshemak Maslak]

  On 10/10/2011 2:46 PM, Rzepa Henry wrote:
 I am loading two  MO surfaces thus

 load HHa_mo15.xyz;isosurface HHa_mo15.jvxl translucent;isosurface append 
 HHa_mo17.jvxl translucent;

 I want to show the overlap between two  MOs.  It is of course a  50% 
 probability that the phases will match to show the effect I want.  Can anyone 
 offer a solution to inverting the phase of one of the  MOs if it turns out 
 wrong (i.e. change red to blue and vice versa for just one of the surfaces?)

I believe specific listing of colors will do the trick: phase color red 
blue vs phase color blue red.


 And this is pushing it rather!  If the two surfaces do overlap with the same 
 phase,  does any code exist to tell me the overlapping volume  (or if the 
 phase differs, the negative overlap volume?)


I am not sure if that is what you have in mind, but there is linear 
combination of MOs possible (in the manual under mo, example 48 at 
http://chemapps.stolaf.edu/jmol/docs/examples-12/new2.htm  ).

Regards,

PM


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Re: [Jmol-users] Electron density maps - dots

[Pshemak Maslak]

 On 6/22/2011 2:23 PM, Greeves, Nick wrote:
I use Jmol to display atomic and molecular orbitals and it works well. 
I would like to be able to render simple atomic orbitals 1s, 2s, 2p as 
electron density maps made up of dots.
Is this currently possible and if so what sort of input file would 
work best?


Something like this 
http://ursula.chem.yale.edu/~chem125/125/answ/a198/Image69.gif 
http://ursula.chem.yale.edu/%7Echem125/125/answ/a198/Image69.gif but 
better. Taken from 
http://ursula.chem.yale.edu/~chem125/125/answ/a198/a198.html 
http://ursula.chem.yale.edu/%7Echem125/125/answ/a198/a198.html

Best regards
Nick
--



You can do much better than what is on these pictures!  In the newest 
Jmol try for example: isosurface color yellow atomicOrbital 4 2 -2 4.0 
POINTS  5000;


See Bob Hanson pages with the most recent examples for full explanation.

PM
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[Jmol-users] multiple structures in cif files

[Pshemak Maslak]

  I have attempted to combine cif files of graphite, diamond and c60 
into one file. The new file shows all three models (separately) as 
desired. However, each model is displayed off center, and is off 
rotation center when manipulated with a mouse,

Is it possible to do the above (combining files without any additional 
action) to get the desired display with center of rotation within the 
models preserved?

Any suggestions would be appreciated,

PM

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[Jmol-users] baby-steps in crystal structures

[Pshemak Maslak]

  I am just beginning to learn and explore display of crystal structures 
in Jmol.

For now, I  am just looking at elements and their basic crystal lattices.

I have started with excellent Jmol Crystal Symmetry Explorer 
(http://chemapps.stolaf.edu/jmol/docs/examples-11/jcse/explore.htm)   
[Thank you Bob!]

I looked at cif file of gold:

data_global
_chemical_name 'Diamond'
_chemical_formula_sum 'Au'
_cell_length_a 4.0786
_cell_length_b 4.0786
_cell_length_c 4.0786
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
_cell_volume 67.85
_symmetry_space_group_name_H-M 'f m -3 m'
loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Au   0.0   0.0   0.0

My questions:

Where is the connectivity information in that file? The Jmol shows the 
nice tetrahedron subunits {1,1,1} with bonds between atoms. Is that 
based on proximity of these atoms?

[please excuse my imprecise terminology, but I just started learning the 
subject]

Could I manually generate a cif file for, let's say, manganese by doing 
the following:

data_global
_chemical_name 'Manganese'
_chemical_formula_sum 'Mn'
_cell_length_a 8.9125
_cell_length_b 8.9125
_cell_length_c 8.9125
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
_cell_volume 707.94
_symmetry_space_group_name_H-M 'I -4 3 m'
loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Au   0.0   0.0   0.0


In other words, can I generate correct displays for any element if I 
just know the cell parameters (a, b, c, alpha, beta, gamma) and the 
space group?

Thank you for your help

PM




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Re: [Jmol-users] baby-steps in crystal structures

[Pshemak Maslak]

 On 4/1/2011 1:13 PM, Robert Hanson wrote:



It does, and it doesn't always work properly for all metals. So you 
may have to do some


connect

commands for a given specific case to get it exactly the way you want it.

I like the brevity of that file format. Is there a good source of
cif files for (crystalline) elements somewhere?


I like the American Mineralogist site at 
http://rruff.geo.arizona.edu/AMS/amcsd.php



Thank you. Info and the link are of great help.

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Re: [Jmol-users] baby-steps in crystal structures

[Pshemak Maslak]

  On 4/1/2011 1:24 PM, Paul Pillot wrote:
 The Cristallography Open Database is a good open resource for cif files :
 http://www.crystallography.net/
 -Paul

Thank you: a very good source of cif files, indeed.

PM

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Re: [Jmol-users] new web page displays orbitals

[Pshemak Maslak]

  On 3/24/2011 9:43 AM, Robert Hanson wrote:
 I have put up a new web page that uses some very recent capabilities 
 of Jmol 12.1.41.

 http://chemapps.stolaf.edu/jmol/docs/examples-12/motest/

 Specifically, you can:

 -- drag/drop any Spartan file or QM output into the applet from your 
 computer.
 -- select and display a molecular orbital from a drop-down list
 -- select and display a linear combination of MOs
 -- create a vertical list of MO images that can be clicked on to 
 activate in Jmol or to save

 New features utilized:

  -- MO [] linear combination option
  -- better control over refreshing and image creation (locks out mouse 
 and system refreshing)
  -- jmolGetPropertyAsString(image,height=... width=...)  
 height/width  option

 Bob

Wow! Very impressive. Great illustration tool.

PM




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Re: [Jmol-users] drawing cones

[Pshemak Maslak]

 On 10/7/2010 9:11 AM, Robert Hanson wrote:
Well, it's symmetry axis is along Z, so just shorten or lengthen Z to 
change the opening angle. Or change X and Y distances. Right?


Yes, it works.  Changing the z value (I presume) in vector type 2 
changes the opening angle by moving the apex of the cone away from the 
origin along the z axis. So if I want to bring the apex back to the 
origin, I need to adjust the z value (I presume) of the origin from 
-5.0 to ?. My question is what is the relationship between these numbers.


Thanks for your help and your patience.

PM

PS. [I do not (obviously) understand how the cone was constructed and 
what are the meanings of the volume vectors and how is the origin 
defined, so it is all by trial and error].


On Wed, Oct 6, 2010 at 12:30 PM, Pshemak Maslak p...@chem.psu.edu 
mailto:p...@chem.psu.edu wrote:


On 10/4/2010 1:14 PM, Robert Hanson wrote:

yes, I think so. Just adjust the vector parameters to make it any
size you want.


The top of the jvxl file with the cone:
[...]
functionXY
curveAsStringXY
-2 -5.0 -5.0 -5.0 ANGSTROMS
/jvxlFileTitle
jvxlVolumeData origin={-5.0 -5.0 -5.0}  changing these
changes origin
jvxlVolumeVector type=0 count=51 vector={0.2 0.0
0.0}/jvxlVolumeVector  changing these changes size
jvxlVolumeVector type=1 count=51 vector={0.0 0.2
0.0}/jvxlVolumeVector  changing these changes size
jvxlVolumeVector type=2 count=51 vector={0.0 0.0
0.2}/jvxlVolumeVector  changing these changes size
[]

I can change the origin, or size or make it elliptic (if the
vectors are not the same), but I do not know how to change the
opening angle.


Thanks for your help,

PM



On Mon, Oct 4, 2010 at 11:08 AM, Pshemak Maslak p...@chem.psu.edu
mailto:p...@chem.psu.edu wrote:


On 10/1/2010 11:04 PM, Robert Hanson wrote:

 I lied. OK, see the JVXL file at


http://stolaf.edu/people/hansonr/chemapps/jmol/docs/misc/cone.jvxl

 for a the surface z = sqrt(x^2 + y^2). Because it is a JVXL
file, you
 can go in and change the axes, change the scaling, change
the origin,
 etc., and have any cone you want. Even elliptical cones.

Thank you very much for creating this nice cone. Can I change its
opening angle directly in the jvxl file?



 This was created at



http://chemapps.stolaf.edu/jmol/docs/examples-11/isosurface.htm?USSIGNEDAPPLETtopic=14

http://chemapps.stolaf.edu/jmol/docs/examples-11/isosurface.htm?USSIGNEDAPPLETtopic=14


http://chemapps.stolaf.edu/jmol/docs/examples-11/isosurface.htm?USSIGNEDAPPLETtopic=14

http://chemapps.stolaf.edu/jmol/docs/examples-11/isosurface.htm?USSIGNEDAPPLETtopic=14

 by entering

 Math.sqrt(x^2 + y^2) into the input box, clicking the link
discussed
 there to set the function and then issuing the following
on the
 command line:

 javascript x0=-5;y0=-5;dx=.2;dy=.2;isosurface functionXY
 curveAsStringXY {-5 -5 -5} {-51 0.2 0 0} {51 0 0.2 0} {51
0 0 0.2};

 followed by

 write isosurface cone.jvxl

I tried that (under item 14, after zapping the preloaded
model). I
entered Math.sqrt(x^2 + y^2) into the box and clicked the
click here
to set the function link (confirmed by the message window).
After
entering the script (above) on the command line I am getting
a very
complicated egg-box shape.

If I do not click on the click here to set the function
link I get a
half of an ellipsoid (a cone with parabolic cross-sections)
with the
above script..

I am sure I am doing something wrong.

All below is above my head (I speak no programming language
:-(). And
that is my problem.

Thanks for your help,

PM




 That instructs Jmol to get the Z coordinate of the function
from the
 JavaScript function curveAsStringXY, which reads:

 function curveAsStringXY(app, nX, nY) {
   var i1 = Math.abs(parseInt(+nX));
   var i2 = Math.abs(0.0 + parseInt(+nY));
   var s = 
   for (var i = 0; i  i1; i++)
 for (var j = 0; j  i2; j++) {
   s+= curveXY(,i, j) + \n;
 }
   return s;

 }


 x0 = 0
 y0 = 0
 dx = 1
 dy = 1
 x = 0
 y = 0

 function curveXY(app, ix, iy) {
  setXY(ix, iy)
  return eval(myfunction);
 }

 function setXY(ix, iy) {
  x = ix * dx + x0
  y = iy * dy + y0
 }


 function

[Jmol-users] orbital isosurface default cutoff values

[Pshemak Maslak]

  I have a general question:

What are the default cutoff values for atomic and molecular orbitals 
isosurfaces generated by Jmol. Are they listed somewhere?

Thanks,

PM

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Re: [Jmol-users] orbital isosurface default cutoff values

[Pshemak Maslak]

 On 10/6/2010 9:24 AM, Robert Hanson wrote:

The Java console reports the cutoff. I think it's 0.05.


I found:

MOs   0.05
atomic orbitals 0.14

Is there a graphical rationale for selecting certain values?

Are these wavefunction values in atomic units?

Thanks,

PM







On Wed, Oct 6, 2010 at 8:12 AM, Pshemak Maslak p...@chem.psu.edu 
mailto:p...@chem.psu.edu wrote:


 I have a general question:

What are the default cutoff values for atomic and molecular orbitals
isosurfaces generated by Jmol. Are they listed somewhere?

Thanks,

PM



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Re: [Jmol-users] orbital isosurface default cutoff values

[Pshemak Maslak]

 On 10/6/2010 11:20 AM, Robert Hanson wrote:
just looked good. It's a cutoff for the psi function. I believe that's 
unitless.


What I meant is that I assumed that values of r (in bohr) and Z (in 
electron-charge units) are used to calculate psi. Is that correct?


Thanks,

PM

(for example 1s = (1/sqrt(pi))*Z^(3/2)*exp(-Zr)




On Wed, Oct 6, 2010 at 8:57 AM, Pshemak Maslak p...@chem.psu.edu 
mailto:p...@chem.psu.edu wrote:


On 10/6/2010 9:24 AM, Robert Hanson wrote:

The Java console reports the cutoff. I think it's 0.05.


I found:

MOs   0.05
atomic orbitals 0.14

Is there a graphical rationale for selecting certain values?

Are these wavefunction values in atomic units?

Thanks,

PM








On Wed, Oct 6, 2010 at 8:12 AM, Pshemak Maslak p...@chem.psu.edu
mailto:p...@chem.psu.edu wrote:

 I have a general question:

What are the default cutoff values for atomic and molecular
orbitals
isosurfaces generated by Jmol. Are they listed somewhere?

Thanks,

PM





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Re: [Jmol-users] drawing cones

[Pshemak Maslak]

 On 10/4/2010 1:14 PM, Robert Hanson wrote:
yes, I think so. Just adjust the vector parameters to make it any size 
you want.


The top of the jvxl file with the cone:
[...]
functionXY
curveAsStringXY
-2 -5.0 -5.0 -5.0 ANGSTROMS
/jvxlFileTitle
jvxlVolumeData origin={-5.0 -5.0 -5.0}  changing these changes 
origin
jvxlVolumeVector type=0 count=51 vector={0.2 0.0 
0.0}/jvxlVolumeVector  changing these changes size
jvxlVolumeVector type=1 count=51 vector={0.0 0.2 
0.0}/jvxlVolumeVector  changing these changes size
jvxlVolumeVector type=2 count=51 vector={0.0 0.0 
0.2}/jvxlVolumeVector  changing these changes size

[]

I can change the origin, or size or make it elliptic (if the vectors are 
not the same), but I do not know how to change the opening angle.


Thanks for your help,

PM


On Mon, Oct 4, 2010 at 11:08 AM, Pshemak Maslak p...@chem.psu.edu 
mailto:p...@chem.psu.edu wrote:



On 10/1/2010 11:04 PM, Robert Hanson wrote:

 I lied. OK, see the JVXL file at

 http://stolaf.edu/people/hansonr/chemapps/jmol/docs/misc/cone.jvxl

 for a the surface z = sqrt(x^2 + y^2). Because it is a JVXL
file, you
 can go in and change the axes, change the scaling, change the
origin,
 etc., and have any cone you want. Even elliptical cones.

Thank you very much for creating this nice cone. Can I change its
opening angle directly in the jvxl file?



 This was created at



http://chemapps.stolaf.edu/jmol/docs/examples-11/isosurface.htm?USSIGNEDAPPLETtopic=14

http://chemapps.stolaf.edu/jmol/docs/examples-11/isosurface.htm?USSIGNEDAPPLETtopic=14


http://chemapps.stolaf.edu/jmol/docs/examples-11/isosurface.htm?USSIGNEDAPPLETtopic=14

http://chemapps.stolaf.edu/jmol/docs/examples-11/isosurface.htm?USSIGNEDAPPLETtopic=14

 by entering

 Math.sqrt(x^2 + y^2) into the input box, clicking the link discussed
 there to set the function and then issuing the following on the
 command line:

 javascript x0=-5;y0=-5;dx=.2;dy=.2;isosurface functionXY
 curveAsStringXY {-5 -5 -5} {-51 0.2 0 0} {51 0 0.2 0} {51 0 0
0.2};

 followed by

 write isosurface cone.jvxl

I tried that (under item 14, after zapping the preloaded model). I
entered Math.sqrt(x^2 + y^2) into the box and clicked the click
here
to set the function link (confirmed by the message window). After
entering the script (above) on the command line I am getting a very
complicated egg-box shape.

If I do not click on the click here to set the function link I get a
half of an ellipsoid (a cone with parabolic cross-sections) with the
above script..

I am sure I am doing something wrong.

All below is above my head (I speak no programming language :-(). And
that is my problem.

Thanks for your help,

PM




 That instructs Jmol to get the Z coordinate of the function from the
 JavaScript function curveAsStringXY, which reads:

 function curveAsStringXY(app, nX, nY) {
   var i1 = Math.abs(parseInt(+nX));
   var i2 = Math.abs(0.0 + parseInt(+nY));
   var s = 
   for (var i = 0; i  i1; i++)
 for (var j = 0; j  i2; j++) {
   s+= curveXY(,i, j) + \n;
 }
   return s;

 }


 x0 = 0
 y0 = 0
 dx = 1
 dy = 1
 x = 0
 y = 0

 function curveXY(app, ix, iy) {
  setXY(ix, iy)
  return eval(myfunction);
 }

 function setXY(ix, iy) {
  x = ix * dx + x0
  y = iy * dy + y0
 }


 function setFunction(f,isSilent){
   myfunction =
 (arguments.length1?document.getElementById(fOfXY).value:f)
   var x=1
   var y=1
   var z=NaN
   try{eval(z=+myfunction)}catch(e){alert(e)}
   if(isNaN(z)){
 alert(Your function is invalid)
 myfunction = (x*x+y*y)
   }
   try{curveXY(,1,1)}catch(e){alert(e);return}
   if (!isSilent)alert(The function Jmol will use is now z= +
 myfunction)
 }

 myfunction = (x*x + y*y)/3
 setFunction(myfunction,1)





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

[Jmol-users] drawing cones

[Pshemak Maslak]

  How can I draw open right cones in Jmole?

For example, how can draw the double cone for nodal surface of 3d(z^2) 
orbital?

Thanks, for your help.

PM

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Re: [Jmol-users] odd results (12.0.11 and 12.1.9)

[Pshemak Maslak]

 On 9/3/2010 11:06 AM, Robert Hanson wrote:
When you have multiple layers of translucent objects, it is possible 
to get some odd effects.


I am not surprised by that, but by the fact that they are different in 
the three Jmol versions.


PM

PS. Congrats on your crystallography paper. I have to try some Jmol 
displays in that category (too many toys, not enough time :-))





On Thu, Sep 2, 2010 at 8:01 AM, Pshemak Maslak p...@chem.psu.edu 
mailto:p...@chem.psu.edu wrote:


 A case of odd outcome.

I have run the following in 12.0.11 and 12.1.9 (and compared to 12.0,8
which I happen to have on my website)::

  isosurface cutoff 0.09 resolution 5 phase color
translucent 7 atomicOrbital 2 0 0 1.0

One would expect three concentric isosurface spheres, the big
outside
one (red) and two small inner ones with the bigger of the two
also red
and the smallest blue; with all partially translucent.

That is indeed what is observed for 12.0.8, 12.011 and 12.1.9.

However rotation of the object leads to partial (12.0.11) or almost
complete (12.1.9) occlusion of the most inner sphere as if the
middle
sphere had lost transparency of one of its halves.

It is difficult to describe, but clearly visible if the above
script is
executed in all three Jmol versions, side by side.

Not a big issue, but

PM



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