from:"Kubasik, Matthew A."

Re: [Jmol-users] SMARTS question

2017-06-29 Thread Kubasik, Matthew A.

Eric,

I’ve not used SMARTS before, so I tried your commands below:

> rings6 = {*}.find("SMARTS","c1c1", true)
select rings6

and
> ringsh = {*}.find("SMARTS","c1cncn1", true)
select ringsh

Running the Jmol application, v. 14.8.0, and loading tryptophan via “load 
$tryptophan”, your selections do, indeed, identify tryptophan rings.

Not much help, but it seems to work in the app.

Matt




> On Jun 29, 2017, at 1:28 PM, Eric Martz  wrote:
> 
> This selects the aromatic ring carbons of Phe and Tyr:
> 
> rings6 = {*}.find("SMARTS","c1c1", true)
> 
> It does not select the 6-atom ring of Trp.
> 
> This selects the ring of His:
> 
> ringsh = {*}.find("SMARTS","c1cncn1", true)
> 
> How do I select the 5 and 6 atom rings of Trp?
> 
> Thanks, Eric
> 
> 
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Re: [Jmol-users] Followup to "Re: vibrate.htm for Gaussian output?"

2017-04-03 Thread Kubasik, Matthew A.

Hi, Pascal,

A revised version is here:

http://faculty.fairfield.edu/mkubasik/GaussianReaders/GaussianOutput.2017.html

As you know, the original distribution comes with “vibrate.html”.  My page is 
based heavily on that one, shown here:

http://faculty.fairfield.edu/mkubasik/jmol148/jsmol/vibrate.htm

Matt

On Apr 3, 2017, at 4:08 PM, Robert Hanson 
> wrote:

Can't help you, sorry. But any of the applications at 
https://chemapps.stolaf.edu/jmol/jsmol can do that. Take a look at 
https://chemapps.stolaf.edu/jmol/jsmol/vibrate.htm.  It is a Spartan file by 
default, but you should be able to drag drop a Gaussian output file into it 
(although it may or may not automatically show vibration info). Unfortunately I 
do not seem to have any Gaussian files that have IR data.

On Mon, Apr 3, 2017 at 1:24 PM, PASCAL Andrew 
> wrote:
Hi

I was looking into making a jsmol applet to read a Gaussian log file, and 
animate the vibrations it contains. I came across this old mailing list thread, 
but I don't know how to get it to my Email client to reply to it! (I'm 
newly-subscribed to the list):

https://sourceforge.net/p/jmol/mailman/message/31853145/

Would Matt Kubasik (or anyone else who may have done this) be prepared to share 
this jsmolvib.html? (Its no longer on the server referred to.)

Thanks...

andy pascal (andrew.pas...@cea.fr)

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Re: [Jmol-users] use of select bonds

2017-01-13 Thread Kubasik, Matthew A.

Angel,

I am unfamiliar with the syntax you are using.

However, placing the bonds into a variable has worked for me, as in:

select {oxygen and connected(1) and connected(carbon)} or {carbon and 
(connected(oxygen))}
x1={selected}.bonds
select x1
bondorder 2
select none

I use the above code to make carbonyl bonds “double”. Works for my small 
peptides, but will give odd bonding structures to things like carboxylates.

Matt

> On Jan 13, 2017, at 11:51 AM, Angel Herráez  wrote:
> 
> Hi all
> 
> I am not familiar with the use of "select bonds" command, so I am asking 
> here.
> 
> We have somewhat old state scripts (saved in Proteopedia scenes)  that 
> were generated by an older version of Jmol (# Jmol state version 11.8.24  
> 2010-04-26 08:00;).
> 
> Right now, Jmol 14.6.0 fails to select the bonds and render their thickness 
> and color.
> The commands in state are of this type:
> 
> select BONDS ({5 16 27});
> 
> Q: Has this syntax changed, or is it broken?
> 
> I've just tried Jmol app 14.6.4 and don't know how to select bonds, my 
> simple test is failing
> 
> load $caffeine
> select bonds ({2 3})
> 
> Should that work as such?
> 
> ·
> Dr. Angel Herráez
> Biochemistry and Molecular Biology,
> Dept. of Systems Biology, University of Alcalá
> E-28871 Alcalá de Henares  (Madrid), Spain
> 
> 
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Re: [Jmol-users] Running Jmol in Linux command line

2016-12-19 Thread Kubasik, Matthew A.

Huan,

You can add a line to your .profile or your .bashrc to recognize an alias to 
run Jmol.

For example, on my mac, I have edited my .profile to include:

alias jmol144="java -jar /Applications/jmol-14.4.0_2015.12.02/Jmol.jar”

This line means that typing jmol144 opens Jmol.

Note that if you are processing a lot of files, you may want JmolData.jar 
instead, which will run your scripts without graphical overhead.

Matt

On Dec 19, 2016, at 10:37 AM, Huan Wang 
> wrote:

Dear Jmol developers and users,

I am a newbie to Jmol and I have a question on running Jmol in Linux command 
line.

Previously, when I prepared Ramachandran plot, I used Jmol interface to open 
PDB file and typed command in Jmol console as:
write ramachandran "OUTPUT_FILE_NAME"

That was very low efficient especially when dealing with large amount of PDB 
files. If Jmol could run in command line in Linux system with Bash Shell 
script, that would be perfect.

Actually, I found a very brief introduction in Jmol Wiki website, where listed 
some commands for loading PDB file and running script in command line. However, 
I did not see any command for saving data.
http://wiki.jmol.org/index.php/Jmol_Application

I tried to use
Jmol -n PDB_FILE -J ramachandran "OUT_PUT_FILE_NAME" -x
Howeve, it does not save data.

I also tried
Jmol -n PDB_FILE -J ramachandran -w "OUT_PUT_FILE_NAME" -x
It saved the image file, not data.

other trials were:
Jmol -n PDB_FILE -J ramachandran > "OUT_PUT_FILE_NAME" -x
Jmol -n PDB_FILE -J write -j ramachandran "OUT_PUT_FILE_NAME" -x

However, none of them worked as I expected...

It would be greatly appreciated if anyone could help me.

Thank you very much.

Best wishes,
Huan
.


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Re: [Jmol-users] Best way to access getproperty with JSmol

2016-10-23 Thread Kubasik, Matthew A.

Bob,

Thanks to you and the team, for your ongoing development of JSmol!

I think Mark’s initial approach was consistent with an orientation in the 
bioinformatics world of “grab-everything-and-sort-later.”  It makes sense to do 
that…sometimes!

Best,

Matt




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Re: [Jmol-users] Best way to access getproperty with JSmol

2016-10-22 Thread Kubasik, Matthew A.

Mark,

One other thing.  You wrote that "when you load the model it prints all the 
vibrational energies out”. 

But here’s the thing…I think that, technically, the “names” of the models 
containing vibrations are printed, i.e., what you would get from 
x = getproperty("modelinfo.models.name”)

The file reader seems to be set up to name the models containing vibrational 
modes according to the energy of the vibration.

To get vibrational energies in cm^-1, use 
getproperty(“modelinfo.models.modelproperties.Frequency”)

To get only the value of the energy, use 
getproperty(“modelinfo.models.modelproperties.FreqValue”)

The Gaussian file reader seems to be coded to print model numbers with the 
model name/frequency value, while the GAMESS reader seems not to.  These seem 
to be arbitrary decisions of the authors of the file reading code.  

Matt Kubasik




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Re: [Jmol-users] Best way to access getproperty with JSmol

2016-10-22 Thread Kubasik, Matthew A.

Dear Mark and Bob,

Perhaps getting a large quantity of “auxiliarydata” is slowing things down?

Maybe, Mark, you could drill down a bit to get the specific auxiliary data that 
you want.  So, for example, maybe instead of

var x = Jmol.getPropertyAsArray(jmolApplet0,"auxiliaryInfo");

You could use

var x = Jmol.getPropertyAsArray(jmolApplet0, 
“auxiliaryinfo.models[1].modata.mos.coefficients”)  // where [1] is the model # 
with the mo data

I’m not sure exactly what properties of the mos that you want, and I am not 
familiar with GAMESS.  However, the above line might get you a 2D array 
containing mo coefficients.  So, for example, the coefficients of the first mo 
would be in (x[1])[1], the second set of coefficients would be in (x[1])[2], 
etc.

Also, the frequencies can be obtained from

x=Jmol.getPropertyAsArray(jmolApplet0, 
"modelinfo.models.modelproperties.frequency”)

That’s how I understand it, but I’m not 100% sure this will work.

Matt Kubasik

On Oct 22, 2016, at 8:30 AM, Robert Hanson 
> wrote:

If you are interested in just getting one model's auxiliary info, you can use _M

$ load c:/temp/t.gamess
7 models
46 molecular orbitals in model 1.2
17 molecular orbitals in model 1.7

$ frame 1.7
$ print _M.keys
Energy
EnergyString
dipole
fileName
fileType
initialAtomCount
initialBondCount
moData
modelFileNumber
modelName
modelNumber
modelNumberDotted
modelProperties

From JavaScript you would use:

info = Jmol.evaluateVar(jmolApplet0, "_M")

Should be relatively efficient.

Alternatively, if you want instantaneous direct access to that Java object you 
can use

info = 
jmolApplet0._applet.viewer.ms.am[0].auxiliaryInfo

But two caveats:

1) You are bypassing the interfaces and tapping in to officially "nonpublic" 
objects. Sometimes those underlying objects get name changes or are otherwise 
refactored.

2) You are working with a transpiled Java Object. In this case, 
java.util.Hashtable. You  have to use .get(key) to access its information:

jmolApplet0._applet.viewer.ms.getAuxiliaryInfo(6).__CLASS_NAME__
"java.util.Hashtable"

modata = jmolApplet0._applet.viewer.getAuxiliaryInfo(6).get("moData")
modata.__CLASS_NAME__
"java.util.Hashtable"

and deal with all of those values appropriately as well.

On Fri, Oct 21, 2016 at 7:54 PM, Mark Perri 
> wrote:

Dear users list,

I'm trying to get MO energies and vibrational frequencies from a GAMESS output 
file that I read into JSmol.  Right now I use:

var x = Jmol.getPropertyAsArray(jmolApplet0,"auxiliaryInfo");

Then I iterate over every frame and look at x.models[i].moData.mos and 
x.models[i].modelProperties.Frequency

But for a large file the getPropertyAsArray takes > 10 seconds and freezes 
Firefox while it's loading.  Reading the manual it seems that I can use 
getProperty asynchronously, but I don't understand how to use it properly.

I set a message callback function to handle getProperty, but I'm not sure how 
to actually read in the moData.  It appears to be in arguments[1], but 
everything I try is undefined.  Here's an example of what I've tried.

Thanks,

Mark

var Info = {
width: 450,
height: 450,
debug: false,
color: "white",
addSelectionOptions: false,
serverURL: "http://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php;,
use: "HTML5",
j2sPath: "/jsmol/j2s",
readyFunction: jmol_isReady,
script: script,
loadStructCallback: "onJSmolLoad",
messageCallback: "processFrames",
disableInitialConsole: true
}

function processFrames()
{

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Re: [Jmol-users] Potential bug in reading xyz files

2016-09-26 Thread Kubasik, Matthew A.

Peter,

On my editor, your “broken” file has an additional text (the letter “a’) on the 
first line.

Could that be the problem?

Matt Kubasik

On Sep 26, 2016, at 6:46 AM, Peter Brommer 
> wrote:

Hi,

This concerns Jmol Version: 14.6.1_2016.08.11  2016-08-11 22:11.

There is an issue with reading/recognising xyz files. On the wiki page 
http://wiki.jmol.org/index.php/File_formats/Formats/XYZ those are described as 
having two header lines per step in a multi-step format, the first of which 
states "the number of atoms in that step. This integer may be preceded by 
whitespace; anything on the line after the integer is ignored.”

However, if there is anything after the integer, the xyz file is no longer 
recognised and the load command gives up with “script ERROR: unrecognised file 
format for file broken.xyz". I attach two files which only differ by a 
supposedly ignored character after the number of atoms, and both fulfil the 
standard given in the wiki.

So, at the moment there is a discord between documentation and code. I’d prefer 
this was fixed in the code, so I don’t have to change a bunch of xyz files.

Cheers,

Peter

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Re: [Jmol-users] Use of variable in a call to getProperty

2016-07-08 Thread Kubasik, Matthew A.

How about here?
http://wiki.jmol.org/index.php/Scripting/GetProperty


On Jul 8, 2016, at 11:46 AM, Angel Herráez 
> wrote:

Sure!
The question is... where to locate it?

Goes to the to-do list. Suggestions or actual page edition are welcome



On 8 Jul 2016 at 9:59, Robert Hanson wrote:

Might be a nice addition to the Wiki.


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Re: [Jmol-users] Use of variable in a call to getProperty

2016-07-07 Thread Kubasik, Matthew A.

Thanks, Angel.  I'm never sure about these things.  Sometimes in my scripts I 
get "TRUE" when I'm expecting a numerical result.  This makes me think I'm 
mixing types.  Maybe I'm just mis-using built in functions.  But that's for 
another thread!

From: Herráez Sánchez Ángel [angel.herr...@uah.es]
Sent: Thursday, July 07, 2016 11:50 AM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Use of variable in a call to getProperty

Yes, Matt

it will be corrrect and safe. Jmol scripting does not care about variable 
types, as far as I know

You are right this is a string issue and concatenation is the right approach.

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Re: [Jmol-users] Use of variable in a call to getProperty

2016-07-07 Thread Kubasik, Matthew A.

Hi, Max,

Yes, I think the stuff inside the parentheses is literally a string, so,if you 
want to vary the string, you need to reconstruct the string in your loop with 
the + signs.  Although it "works", I think the line sums two different types 
(string and integer), so, I am not certain the syntax is strictly correct.

Best,

Matt

From: Latévi Max LAWSON DAKU [max.law...@unige.ch]
Sent: Thursday, July 07, 2016 11:15 AM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Use of variable in a call to getProperty

On 07. 07. 16 17:04, Kubasik, Matthew A. wrote:
> Max,
>

Hi Matt,

Thanks for your suggestions.

> Two suggestions.
>
> First, something like:
>
> freqvalues = getproperty('modelInfo.models.modelProperties.FreqValue')
>
> will look for frequency values of all models and put them in the array 
> "freqvalues".
>
> Unfortunately, this array will have empty entries for models lacking 
> frequency values.
>
> Second, if you know the range of models that contain freq values (say, models 
> 300 to 370), you can use something like:
>
> for (var i=300; i<370;i+=1){
> print getproperty('modelInfo.models['+i+'].modelProperties.FreqValue')
> }

I tried this latter and it works !! :D

Thanks again!

Best,
Max


>
> Perhaps more skilled coders on the list could suggest improvements to these 
> clunky lines!
>
> Matt
>
>
>
>
> 
> From: Latévi Max LAWSON DAKU [max.law...@unige.ch]
> Sent: Thursday, July 07, 2016 10:38 AM
> To: jmol-users@lists.sourceforge.net
> Subject: [Jmol-users] Use of variable in a call to getProperty
>
> Dear Jmol users/developers,
>
> I would like to be able to use a variable in a call to getProperty.
> So far, the following command works.
>
>  $ print getproperty('modelInfo.models[7].modelProperties.FreqValue')
>  129.529358
>
> But I rwould like to use a variable as follows
>
>  $ i=7
>  $ print getproperty('modelInfo.models[i].modelProperties.FreqValue')
>
> But this doesn't work. I also tried to use @{i}, with no success as
> well. I'm not comfortable with dereferencing a variable in Jmol.
>
> The reason for trying to do so us that I'ld like to iterate through the
> frames and use the variable i hold the index of the frame.
>
>
> I thank you in advance for your help.
>
> Best regards,
> Max
>
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Re: [Jmol-users] Use of variable in a call to getProperty

2016-07-07 Thread Kubasik, Matthew A.

Max,

Two suggestions.

First, something like:

freqvalues = getproperty('modelInfo.models.modelProperties.FreqValue')

will look for frequency values of all models and put them in the array 
"freqvalues".  

Unfortunately, this array will have empty entries for models lacking frequency 
values. 

Second, if you know the range of models that contain freq values (say, models 
300 to 370), you can use something like:

for (var i=300; i<370;i+=1){
print getproperty('modelInfo.models['+i+'].modelProperties.FreqValue')
}

Perhaps more skilled coders on the list could suggest improvements to these 
clunky lines!

Matt





From: Latévi Max LAWSON DAKU [max.law...@unige.ch]
Sent: Thursday, July 07, 2016 10:38 AM
To: jmol-users@lists.sourceforge.net
Subject: [Jmol-users] Use of variable in a call to getProperty

Dear Jmol users/developers,

I would like to be able to use a variable in a call to getProperty.
So far, the following command works.

 $ print getproperty('modelInfo.models[7].modelProperties.FreqValue')
 129.529358

But I rwould like to use a variable as follows

 $ i=7
 $ print getproperty('modelInfo.models[i].modelProperties.FreqValue')

But this doesn't work. I also tried to use @{i}, with no success as
well. I'm not comfortable with dereferencing a variable in Jmol.

The reason for trying to do so us that I'ld like to iterate through the
frames and use the variable i hold the index of the frame.


I thank you in advance for your help.

Best regards,
Max

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Re: [Jmol-users] Wildcard for atom properties

2016-06-22 Thread Kubasik, Matthew A.

Thank you for your help, Rolf.  I am not always sure what properties are 
available, or even how they are named.  The full output is useful.

Matt


From: Rolf Huehne [rolf.hue...@leibniz-fli.de]
Sent: Wednesday, June 22, 2016 3:30 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Wildcard for atom properties

On 06/22/2016 09:02 PM, Kubasik, Matthew A. wrote:
> Rolf,
>
> Sorry, I switched conventions, which is confusing everything.
>
> So, yes, "print {atomno=3}.a?"  works to print atom properties with names 
> beginning with "a", but I thought "print {atomno=3}.?" would give ALL atom 
> properties.
>
> Same as, "print @3.a?"  works, but I thought "print @3.?" would print all 
> atom properties.
>
> Am I wrong about this?  Perhaps I am.
>
It seems like the shortcut notations for getting all properties at once
are broken (or the documentation is wrong). But the longer versions
still work for me:

   print getProperty("atomInfo",{atomno=3});
   print getProperty("atomInfo",{@3});

Regards,
Rolf

> Matt
>
> 
> From: Rolf Huehne [rolf.hue...@leibniz-fli.de]
> Sent: Wednesday, June 22, 2016 2:53 PM
> To: jmol-users@lists.sourceforge.net
> Subject: Re: [Jmol-users] Wildcard for atom properties
>
> On 06/22/2016 08:25 PM, Kubasik, Matthew A. wrote:
>> Bob and List,
>>
>> Using the stand alone app on a Mac (10.11.5), I cannot seem to get the 
>> wildcard for atom properties to work as I would expect from
>>
>> http://chemapps.stolaf.edu/jmol/docs/index.htm?ver=14.6.0_2016.06.14#atomproperties.
>>
>> The doc says print {atomno=3}.a?  will give the atom properties that begin 
>> with "a".  This works.
>>
>> The doc also says print @3.?  will give all atom properties.  But print @3.? 
>> gives  "0.0".
>>
> Matt, it looks like typo for me. I guess the 'a' got lost and it should
> be 'print @3.a?', which works for me.
>
> Regards,
> Rolf
>
> --
>
> Rolf Huehne
> Postdoc
>
> Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)
> Beutenbergstrasse 11
> 07745 Jena, Germany
>
> Phone:   +49 3641 65 6205
> Fax: +49 3641 65 6210
> E-Mail:  rolf.hue...@leibniz-fli.de
> Website: http://www.leibniz-fli.de
>
> Scientific Director: Prof. Dr. K. Lenhard Rudolph
>  Head of Administration: Dr. Daniele Barthel
> Chairman of Board of Trustees: Burkhard Zinner
>
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> Register of Associations: No. 230296, Amtsgericht Jena
> Tax Number: 162/141/08228
>
>
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Postdoc

Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)
Beutenbergstrasse 11
07745 Jena, Germany

Phone:   +49 3641 65 6205
Fax: +49 3641 65 6210
E-Mail:  rolf.hue...@leibniz-fli.de
Website: http://www.leibniz-fli.de

   Scientific Director: Prof. Dr. K. Lenhard Rudolph
Head of Administration: Dr. Daniele Barthel
Chairman of Board of Trustees: Burkhard Zinner

VAT No: DE 153 925 464
Register of Associations: No. 230296, Amtsgericht Jena
Tax Number: 162/141/08228


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Re: [Jmol-users] Wildcard for atom properties

2016-06-22 Thread Kubasik, Matthew A.

Rolf,

Sorry, I switched conventions, which is confusing everything.

So, yes, "print {atomno=3}.a?"  works to print atom properties with names 
beginning with "a", but I thought "print {atomno=3}.?" would give ALL atom 
properties.  

Same as, "print @3.a?"  works, but I thought "print @3.?" would print all atom 
properties.

Am I wrong about this?  Perhaps I am.

Matt


From: Rolf Huehne [rolf.hue...@leibniz-fli.de]
Sent: Wednesday, June 22, 2016 2:53 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Wildcard for atom properties

On 06/22/2016 08:25 PM, Kubasik, Matthew A. wrote:
> Bob and List,
>
> Using the stand alone app on a Mac (10.11.5), I cannot seem to get the 
> wildcard for atom properties to work as I would expect from
>
> http://chemapps.stolaf.edu/jmol/docs/index.htm?ver=14.6.0_2016.06.14#atomproperties.
>
> The doc says print {atomno=3}.a?  will give the atom properties that begin 
> with "a".  This works.
>
> The doc also says print @3.?  will give all atom properties.  But print @3.? 
> gives  "0.0".
>
Matt, it looks like typo for me. I guess the 'a' got lost and it should
be 'print @3.a?', which works for me.

Regards,
Rolf

--

Rolf Huehne
Postdoc

Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)
Beutenbergstrasse 11
07745 Jena, Germany

Phone:   +49 3641 65 6205
Fax: +49 3641 65 6210
E-Mail:  rolf.hue...@leibniz-fli.de
Website: http://www.leibniz-fli.de

   Scientific Director: Prof. Dr. K. Lenhard Rudolph
Head of Administration: Dr. Daniele Barthel
Chairman of Board of Trustees: Burkhard Zinner

VAT No: DE 153 925 464
Register of Associations: No. 230296, Amtsgericht Jena
Tax Number: 162/141/08228


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[Jmol-users] Wildcard for atom properties

2016-06-22 Thread Kubasik, Matthew A.

Bob and List,

Using the stand alone app on a Mac (10.11.5), I cannot seem to get the wildcard 
for atom properties to work as I would expect from

http://chemapps.stolaf.edu/jmol/docs/index.htm?ver=14.6.0_2016.06.14#atomproperties.

The doc says print {atomno=3}.a?  will give the atom properties that begin with 
"a".  This works.

The doc also says print @3.?  will give all atom properties.  But print @3.? 
gives  "0.0".

Any hints?

Matt Kubasik







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[Jmol-users] Energies of "color hbonds energy"?

2016-01-23 Thread Kubasik, Matthew A.

Bob and list,

Are the energies used to color the hydrogen bonds, using the command “color 
hbonds energy”, available, say, in an array?

Are the hbonds themselves indexed or arrayed in some way?

Are atom properties, e.g., atomno, of atoms identified as participating in 
h-bonding available as in a variable or as an array?

Matt Kubasik
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Re: [Jmol-users] Energies of "color hbonds energy"?

2016-01-23 Thread Kubasik, Matthew A.

Already answered:

http://ehc.ac/p/jmol/mailman/message/31977259/

Thanks, Bob!

Apologies to the list,

MK

On Jan 23, 2016, at 11:53 AM, Kubasik, Matthew A. 
<mkuba...@fairfield.edu<mailto:mkuba...@fairfield.edu>> wrote:

Oops…sorry, I see this was asked and answered six years ago!

http://ehc.ac/p/jmol/mailman/message/25694185/

I guess my question is about printing the “connect_atoms” data below, from the 
current state?

function _setModelState() {
data "connect_atoms"
44 16 4096 1.0 -2.41 hbond;
57 29 4096 1.0 -1.358 hbond;
70 42 4096 1.0 -1.674 hbond;
83 55 4096 1.0 -1.798 hbond;
end "connect_atoms";

Matt


On Jan 23, 2016, at 11:31 AM, Kubasik, Matthew A. 
<mkuba...@fairfield.edu<mailto:mkuba...@fairfield.edu>> wrote:

Bob and list,

Are the energies used to color the hydrogen bonds, using the command “color 
hbonds energy”, available, say, in an array?

Are the hbonds themselves indexed or arrayed in some way?

Are atom properties, e.g., atomno, of atoms identified as participating in 
h-bonding available as in a variable or as an array?

Matt Kubasik
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Re: [Jmol-users] Energies of "color hbonds energy"?

2016-01-23 Thread Kubasik, Matthew A.

Oops…sorry, I see this was asked and answered six years ago!

http://ehc.ac/p/jmol/mailman/message/25694185/

I guess my question is about printing the “connect_atoms” data below, from the 
current state?

function _setModelState() {
data "connect_atoms"
44 16 4096 1.0 -2.41 hbond;
57 29 4096 1.0 -1.358 hbond;
70 42 4096 1.0 -1.674 hbond;
83 55 4096 1.0 -1.798 hbond;
end "connect_atoms";

Matt


On Jan 23, 2016, at 11:31 AM, Kubasik, Matthew A. 
<mkuba...@fairfield.edu<mailto:mkuba...@fairfield.edu>> wrote:

Bob and list,

Are the energies used to color the hydrogen bonds, using the command “color 
hbonds energy”, available, say, in an array?

Are the hbonds themselves indexed or arrayed in some way?

Are atom properties, e.g., atomno, of atoms identified as participating in 
h-bonding available as in a variable or as an array?

Matt Kubasik
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Re: [Jmol-users] Jmol scripting speed in JSmol/HTML5

2015-12-17 Thread Kubasik, Matthew A.

Bob,

Could you expand on your comment that “Jmol uses typed arrays when possible"?

I am in the habit of initializing arrays with a line like:

a=array()

Should I be doing something else?  Does the array get “typed” after I add an 
entry?

Matt

On Dec 16, 2015, at 3:48 PM, Robert Hanson 
> wrote:

Jmol uses typed arrays when possible. Parsing of scripts is relatively slow. 
Rolf, if you want to give me something to try, I will be happy to play with it 
and see what I can learn.

On Wed, Dec 16, 2015 at 12:30 PM, Paul PILLOT 
> wrote:
Hi Rolf,
my experience in this area is not JSmol related, but when I had to deal with 
big tables in javascript (for a multiple sequence alignment script, aligning 2 
sequences of 5000 signs, requires at least 1 table of 5000 rows and 5000 
columns), I noticed that :
- using integers only tables is fastest
- opting for one dimensional array instead of two dimensional didn’t make a 
noticeable difference
- using typed arrays in some cases improved significantly the performance ( see 
https://developer.mozilla.org/en/docs/Web/JavaScript/Typed_arrays ). This was 2 
years ago, and the browsers’ engine landscape can be quickly moving...
When you parse your data from your TSV file, are the fields stored as text ?

My 2 cents,
Paul

Le 16-12-2015 à 13:12, Rolf Huehne 
> a écrit :

Hi all,

I am looking for some speedup tips for Jmol scripting in JSmol/HTML5.

The speed difference between JSmol/Java and JSmol/HTML5 for graphical
operations like rotation and zooming seems to be about 10 times or less
in Firefox and Chrome (if you don't consider the recent rotation speed
problems in Chrome).

Unfortunately the difference for Jmol scripting seems to be much higher
in my experience: about 50-70 times.

If I load for example 3 TSV (tab separated value) format files with
overall about 34,000 lines, JSmol/Java needs about 26 seconds for
laoding and parsing the data and putting it into a multi-level hash
structure. JSmol/HTML5 needs about 1700 seconds instead.

I already tried to write the final data structure into a file with
'write VAR ...' and read it in again as a script (after adding a proper
variable assignment) but this already took in Java endlessly (I stopped
waiting after more than an hour...).

Q: Does anyone have any other ideas that might speed up this process?

Regards,
Rolf

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Phone:   +49 3641 65 6205
Fax: +49 3641 65 6210
E-Mail:  rhue...@leibniz-fli.de
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Re: [Jmol-users] Plotting molecular orbitals with jmol from a molden input file: Problem with symmetry

2015-09-08 Thread Kubasik, Matthew A.

Daniel,

Could it be the MO settings in your second file?   The MO’s may be there, just 
hard to see.   You may need to adjust the Jmol’s MO parameters in your second 
model that isn’t showing MO’s.

MO documentation is here:
http://chemapps.stolaf.edu/jmol/docs/index.htm?command=mo=14.3.16_2015.08.21

Specifically, try the CUTOFF parameter:

mo CUTOFF (decimal)
Sets the cutoff value for the isosurface that defines the orbital. This number 
may be dependent upon the computational package used to generate the orbitals. 
Values in the range 0.005 - 0.05 may need to be experimented with in order to 
get the best display. Values closer to zero lead to surfaces further from the 
atoms (larger orbitals). Both positive and negative cutoffs are allowed. A 
positive number indicates to use both positive and negative cutoffs. Adding an 
explicit "+" sign before the number indicates that only the positive part of 
the surface is desired.


Matt



On Sep 8, 2015, at 5:47 AM, Friese Daniel Henrik 
> wrote:

Dear jmol users and developers,

Yesterday I was really happy when I found out that I can plot molecular 
orbitals in JMOL by just loading a molden input file which is generated 
automatically by the Dalton program. Today I tried this for another molecule 
and it turned out to be that it did not work. The major difference between the 
molecules is that the one I tried yesterday had no point group symmetry while 
the one I tried today has it. If I request plotting for e.g. orbital 80 by 
typing "mo 80" in the console nothing happens. There is neither an error 
message nor a result. Do I do anything wrong there or is it a bug? I am using 
version 13.2.7

Thanks to everybody who takes the time to answer.

Best regards,
Daniel



__
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Centre for Theoretical and Computational Chemistry
Universitetet i Tromsø - Norges Arktiske Universitet
Norway

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Re: [Jmol-users] Plotting molecular orbitals with jmol from a molden input file: Problem with symmetry

2015-09-08 Thread Kubasik, Matthew A.

Daniel,

By “second file” I only meant the file that is not working.

Like Angel, I’m no expert on MO visualization, either.  In version 14.3.16 of 
the Jmol app, the console shows (when reading Gaussian files) which model has 
the mo’s.

For example, the console reads, upon loading a gaussian log file:

24 models
26 molecular orbitals in model 1.2
26 molecular orbitals in model 1.10
26 molecular orbitals in model 1.12

$ model 1.12
$ mo 1

So, you may want to download a more recent version to have a console confirm 
for you that mo’s exist in your file.

Gaussian performs a population analysis before and after geometry optimization, 
so you get MO’s in model 1.2 and model 1.10.  I must confess I do not know 
what, exactly, is the difference between mo’s in model 1.10 vs model 1.12.  
They look identical to me.  Subsequent models hold the normal mode information.)

(File read by Jmol was generated by g09,  using a route section of # HF/6-31G 
opt freq pop=full gfprint)

Matt

On Sep 8
, 2015, at 8:02 AM, Friese Daniel Henrik 
<daniel.h.fri...@uit.no<mailto:daniel.h.fri...@uit.no>> wrote:

Dear Matthew,

Thank you for your reply. I do not use a second file. The command I am typing is

$ jmol jmol ecd_camb3lyp_6hel.molden

Then I get a jmol window with the structure. For a file for a molecule with 
similar size but without symmetry I can easily get the mos by typing e.g.

$ mo 80

in the jmol console. Then it takes some time to render the orbital. What 
happens in this case is that the calculation time is way shorter (although the 
molecule is of the same size) and nothing happens after it is through 
(indicated by a movement of the mouse indicator in the jmol window). I have 
also already compared the entries in the molden input files for the different 
molecules and the only difference I found is that for certain orbitals there is 
another indicator for the point group. Without point group symmetry the 
indicator is always A, in my case (C2 symmetry) it is either A or B. Also 
playing around with the cutoff values does not have any influence. When I open 
the console the number of orbitals is recognized properly, however I should 
mention that the order is not in energy order but in in energy order within the 
irreducible representation. The molden input file has been generated by the 
Dalton program by the way.

I already had a look at the manual page but I did not find any solution for the 
problem. Do I maybe have to tell jmol that the orbitals contain symmetry?


Best regards,
Daniel


__
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Centre for Theoretical and Computational Chemistry
Universitetet i Tromsø - Norges Arktiske Universitet
Norway

Best regards also to the secret reader from the National Security Agency

____
Von: Kubasik, Matthew A. <mkuba...@fairfield.edu<mailto:mkuba...@fairfield.edu>>
Gesendet: Dienstag, 8. September 2015 13:22
An: jmol-users@lists.sourceforge.net<mailto:jmol-users@lists.sourceforge.net>
Betreff: Re: [Jmol-users] Plotting molecular orbitals with jmol from a molden 
input file: Problem with symmetry

Daniel,

Could it be the MO settings in your second file?   The MO’s may be there, just 
hard to see.   You may need to adjust the Jmol’s MO parameters in your second 
model that isn’t showing MO’s.

MO documentation is here:
http://chemapps.stolaf.edu/jmol/docs/index.htm?command=mo=14.3.16_2015.08.21

Specifically, try the CUTOFF parameter:

mo CUTOFF (decimal)
Sets the cutoff value for the isosurface that defines the orbital. This number 
may be dependent upon the computational package used to generate the orbitals. 
Values in the range 0.005 - 0.05 may need to be experimented with in order to 
get the best display. Values closer to zero lead to surfaces further from the 
atoms (larger orbitals). Both positive and negative cutoffs are allowed. A 
positive number indicates to use both positive and negative cutoffs. Adding an 
explicit "+" sign before the number indicates that only the positive part of 
the surface is desired.


Matt



On Sep 8, 2015, at 5:47 AM, Friese Daniel Henrik 
<daniel.h.fri...@uit.no<mailto:daniel.h.fri...@uit.no>> wrote:

Dear jmol users and developers,

Yesterday I was really happy when I found out that I can plot molecular 
orbitals in JMOL by just loading a molden input file which is generated 
automatically by the Dalton program. Today I tried this for another molecule 
and it turned out to be that it did not work. The major difference between the 
molecules is that the one I tried yesterday had no point group symmetry while 
the one I tried today has it. If I request plotting for e.g. orbital 80 by 
typing "mo 80" in the console nothing happens. There is neither an error 
message nor a result. Do I do anything wrong there or is it a bug? I am using 
version 13.2.7

Thanks to

[Jmol-users] WebMO and Jmol Application

2015-08-31 Thread Kubasik, Matthew A.

Bob and list,

Like many others, I’ve been using WebMO to facilitate student access to 
computational engines on a server.  Unfortunately, WebMO (on a desktop browser) 
still uses Java.  

Fortunately, WebMO easily facilitates running input files uploaded from a 
desktop.  

So, the plan is, create g09 input files using Jmol Application>Tool>Gaussian, 
then upload and submit jobs to the computational server using WebMO.  

Here’s the hitch, I think:  Gaussian input file needs to terminate in an 
“empty” line.  When I upload the file, the “empty line” that I put in seems to 
get stripped, and the job fails.

Here are my questions:  Can the Gaussian tool be configured, by default, to add 
an empty line?  What is the best way to do this?  

I have found that terminating the file created by the Jmol app with:

[blank line]
! 

creates a g09 input files that run to completion.  ! is a comment, of course, 
and text in [blank line ] should be empty.

I’m interested in hearing other strategies, of course.  “Why aren’t you using 
X?” is welcome.  (E.g., why aren’t you using the iOS version of WebMO?)  For 
the time being, though, I like the WebMO interface for keeping track of 
jobs/job failures of newbie quantum chemists!   (We of course could add the 
[blank line] \r ! to each file, but it’d be nice to have something that’s 
automatic.)

Matt Kubasik
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Re: [Jmol-users] WebMO and Jmol Application

2015-08-31 Thread Kubasik, Matthew A.

Thank you, Bob, for your rapid fix.

As to your question:  yes, I am learning that there is almost nothing that Jmol 
cannot do!

I’m not exactly sure what WebMO is doing, as installed on a computational 
server, so that it can receive/upload gaussian input files and run gaussian 
computations.  If you are suggesting that there has to be something that could 
be installed on a server/web page, serving up the Jmol applet, that could 
execute gaussian jobs, I am certain that you are right.  It’s what WebMO does, 
right?

For anyone who wants to check out WebMO, which supports Gaussian, GAMESS, and 
eight(!) other computational engines, visit the demo server at 
http://www.webmo.net/demo/index.html.

So, I agree that the “bit of extra interface” you mention is certainly do-able, 
but I’m not really sure how it’s done!

Matt


On Aug 31, 2015, at 8:06 PM, Robert Hanson 
> wrote:

It was a missing character at the end of the line just as the file was saved. 
Very easy fix.

http://chemapps.stolaf.edu/jmol/zip/Jmol.jar

fixes that.

Question: Could you just use JSmol and a bit of extra interface to do this on 
the web? Obviously there's a lot more to WebMO than that -- scheduling and 
monitoring jobs, for instance. But still...

Bob



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[Jmol-users] Feature Request: HPModes for Gaussian File Reader

2015-08-26 Thread Kubasik, Matthew A.

Dear Bob,

Could you and the Jmol development community consider adding the reading of 
“High Precision” modes (g09 option freq(HPModes)) to Jmol’s Gaussian file 
reader?

Additionally, if the displacement vectors could be added to atom properties, 
that would be great!

Currently, Jmol will reads this section of a Gaussian output file:

  1  2  3
  A  A  A
 Frequencies -- 11.138112.490815.3386
 Red. masses --  4.5657 4.9034 5.4670
 Frc consts  --  0.0003 0.0005 0.0008
 IR Inten--  0.2569 0.0415 0.0019
  Atom  AN  X  Y  ZX  Y  ZX  Y  Z
 1   6 0.01   0.01   0.01 0.04   0.02   0.10 0.09  -0.05  -0.01
 2   6 0.01   0.01  -0.02 0.00  -0.01   0.15 0.10  -0.03   0.01
 3   1 0.03   0.00  -0.03-0.02   0.00   0.17 0.08  -0.02   0.02
 4   6 0.00   0.02  -0.03 0.00  -0.04   0.19 0.15  -0.02   0.01
 5   1 0.01   0.02  -0.05-0.03  -0.06   0.23 0.16   0.00   0.02
 6   6-0.02   0.03  -0.02 0.03  -0.05   0.17 0.18  -0.03  -0.01
…

This provides atomic displacement properties, such as  {model=m and 
atomno=n}.vxyz, as well as vX, vY, and VZ.

The Gaussian formatting for HPModes is like this:

   1 2 3 4 5
   A A A A A
   Frequencies ---11.1381   12.4908   15.3386   18.8667   21.7801
Reduced masses --- 4.56574.90345.46704.72614.7314
   Force constants --- 0.00030.00050.00080.00100.0013
IR Intensities --- 0.25690.04150.00190.08090.0278
 Coord Atom Element:
   1 1 6  0.00808   0.03641   0.08901  -0.04609   0.03999
   2 1 6  0.00694   0.02030  -0.05281   0.01034   0.03379
   3 1 6  0.01135   0.09711  -0.01221  -0.02791  -0.04076
   1 2 6  0.01455   0.00394   0.10466  -0.01421   0.00668
   2 2 6  0.00958  -0.00739  -0.03172   0.03848   0.01153
   3 2 6 -0.01679   0.15117   0.00826  -0.07526   0.05221
…

Perhaps these data could be put into atomic properties of vHPxyz, vHPx, vHPy, 
and vHPz?

I tried to extract HPmodes by using y.find() and y.replace and y.split() 
functions and for loops, etc, after loading the file into a variable, but I am 
confident that adding this feature to the native Gaussian file reader would be 
more elegant.

Thoughts?

Matt
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Re: [Jmol-users] Dissect PNGJ content?

2015-08-22 Thread Kubasik, Matthew A.

Thanks, Rolf.

I should start a new thread. There are two additional split functions at 
http://chemapps.stolaf.edu/jmol/docs/index.htm?ver=14.2 , as compared to the 
split function in your link, and these two contain the “true” parameter.  
However, the documentation is kind of spare about the need and use for “true” 
in these additional split functions.

I’ll play around with it and start a new thread when I get stuck.

Matt

On Aug 22, 2015, at 1:42 PM, Rolf Huehne 
rhue...@fli-leibniz.demailto:rhue...@fli-leibniz.de wrote:

Am 22.08.15 um 17:23 schrieb Kubasik, Matthew A.:
Thanks, Bob, for this.

Can you clarify the purpose of  “true”, as in:

var x = load(“filename”, TRUE)

I would like to learn when is it necessary.  Your example uses “true” for .png 
but not for .cif.   The help page shows the TRUE flag showing up elsewhere, as 
in the function
x = y.split(, TRUE)

I am uncertain of how to use “true properly.

The meaning of true as a parameter depends on the specific
command/function. You should look up the documentation for the
commands/functions you want to use.

http://jena3d.fli-leibniz.de/doc/jmol_scripting/index.htm#functions
contains for 'x = load(filename,TRUE)':

Adding a second parameter TRUE creates a binary associative array
variable x that contains the contents of the file. Data are stored as
raw bytes (but will appear as a string in the PRINT command). If the
file is a standard file, the key _DATA_ will hold the file data. If
the file is a PNGJ file, the key _IMAGE_ will hold the image data and
additional files will be keyed by file name. If the file is a zip file,
the files will be keyed by file name, but no _IMAGE_ key will be
present (presumably). Note that x = load(myfile) without TRUE loads
just the file list for PNGJ or ZIP files, not the actual data.

Regards,
Rolf

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Re: [Jmol-users] Dissect PNGJ content?

2015-08-22 Thread Kubasik, Matthew A.

Thanks, Bob, for this.

Can you clarify the purpose of  “true”, as in:

var x = load(“filename”, TRUE)

I would like to learn when is it necessary.  Your example uses “true” for .png 
but not for .cif.   The help page shows the TRUE flag showing up elsewhere, as 
in the function
x = y.split(, TRUE)

I am uncertain of how to use “true properly.

Matt

On Aug 22, 2015, at 12:51 AM, Robert Hanson 
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:

http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.3/Jmol%2014.3.16/Jmol-14.3.16_2015.08.21-binary.zip/download

Jmol.___JmolVersion=14.3.16_2015.08.21

new feature: load var x
  -- same as load @x
  -- similar in syntax to write var x t.png
  -- example:

  var x = load(quartz.cif)
  load var x {1 1 1}

bug fix: creating and running and saving binary hash from PNGJ fails
  -- allows creating an associative binary array from a PNGJ file
 then modifying it and loading that variable
 then saving it as a new PNGJ file
  -- initial PNGJ file is not necessary if binary array x is created first
  -- example:

  var x = load(test.png,true)
  load @x
  write test2.png as PNGJ

bug fix: hover callback is not supposed to be stopped with HOVER OFF
bug fix: atom.sx and atom.syhttp://atom.sy/ and atom.szhttp://atom.sz/ 
report incorrectly when antialiasing is on
bug fix: write VAR x test.png creates a ZIP file instead of a PNGJ file when 
x is from load(test.png,true)
bug fix: write test.png as PNGJ (without initial quotes) fails


comments:

OK, that wasn't so bad. Thank you, Rolf, for suggesting this. It is a nice 
complement to write var x.

This completes the capability for Jmol or JSmol to read, modify,  load, and 
save PNGJ and ZIP files.

1) Reading a PNGJ or ZIP file into a variable using TRUE to indicate binary 
file:

x = load(test.png, TRUE)
# [x is a binary associative array]
print x.keys
$_BINARY_$
JmolManifest.txt
Jmol_version_14.3.16_2015.08.21__2015-08-21_09.06
_IMAGE_
http___cactus.nci.nih.gov_chemical_structure_caffeine_file_format_sdf_get3d_True
state.spt

where $_BINARY_$ indicates that entries are byte arrays.
and _IMAGE_ is the PNG image, indicating this is from a PNGJ file

2) modifying that file if desired

# coerce to string:
s =  + x[state.spt]
# ...modify here...
# replace state.spt in PNGJ file data
x[state.spt] = s

# Or, for example, adding an image that will be used for an optional background 
image

x = load(test.png,true)
# a standard binary associative array will have just two keys, $BINARY$ and 
_DATA_
# only PNGJ has _IMAGE_

x[z.jpg] = load(z.jpg,true)._DATA_
print x.keys
write var x test3.png
sometime later...
load test3.png
background image test3.png|z.jpg


3) write to a new PNGJ file

write var x test2.png

4) optionally, load that PNGJ data directly from the variable, perhaps to see 
that the modifications are correct:

load var x

(new syntax; same as older load @x)

Note that both of these syntaxes work with standard string file data and can be 
extended with options:

x = load(quartz.cif)
load var x {1 1 1}

Bob



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