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From: Andreas T. <atr...@gm...> - 2012-07-24 16:39:02
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Hi,
when I use the following code snippet:
"color _H TRANSLUCENT 0.00 [255,51,0];"
then following error appears:
eval ERROR: a colour or palette name (Jmol, Rasmol) is required
----
color _h >> translucent << 0.0 [ 255 , 0 , 0 ]
But when first a SELECT _H; COLOR ATOMS..... is executed the script
works fine. Unfortunately, if a new model is loaded the setting gets lost.
Is this an intended behaviour?
Kind regards,
Andreas
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From: A. H. <ang...@ua...> - 2012-07-24 16:54:58
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Hi Andreas Yes, it seems that translucency cannot be permanently assigned to an element. I don't think this is too bad an idea. Element color is identity, but translucency is just cosmetic (like ball size). But you can assign the color permanently, then apply translucency per case: color _H [255,51,0]; load $caffeine; select _H; color translucent 0.5; select all; load $tylenol; select _H; color translucent 0.5; select all; On the other hand, if you say TRANSLUCENT 0.00 that's opaque, so what's the point? |
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From: Andreas T. <atr...@gm...> - 2012-07-24 17:23:00
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Am 24.07.2012 18:54, schrieb Angel Herráez: > On the other hand, if you say > TRANSLUCENT 0.00 > that's opaque, so what's the point? Ok, the example was stupid.. But anyway thanks for the response. Andreas |
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From: Martin H. <ma...@bl...> - 2012-07-25 09:55:53
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Dear Jmol Users For the Jmol function "jmolGetPropertyAsArray", what are valid "sKey"s? Where are they listed? Thank you for hints Martin |
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From: Robert H. <ha...@st...> - 2012-07-25 19:50:20
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Should be in the documentation, but also you can enter this at the console
and get the whole list
getproperty
If you to inspect one, try:
print getProperty("xxxx").keys
or, if that gives nothing, use [0].keys:
$ print getProperty("atominfo")[0].keys
_ipt
atomIndex
atomno
bondCount
clickabilityFlags
colix
color
coord
element
elemno
formalCharge
info
model
partialCharge
radius
shape
spacefill
sym
visibilityFlags
visible
x
y
z
On Wed, Jul 25, 2012 at 4:55 AM, Martin Hediger <ma...@bl...> wrote:
> Dear Jmol Users
> For the Jmol function "jmolGetPropertyAsArray", what are valid "sKey"s?
> Where are they listed?
>
> Thank you for hints
> Martin
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Jmol-users mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
--
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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From: Martin H. <ma...@bl...> - 2012-07-26 11:14:30
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Hi Bob,
I think what I was trying to figure out is, what are possible
properties, meaning "xxxx" in your example below, or put differently,
what else, besides "atominfo" can be used as an argument to 'getProperty'?
Thanks for your support
Martin
On 25.07.12 21:19, Robert Hanson wrote:
> Should be in the documentation, but also you can enter this at the
> console and get the whole list
>
> getproperty
>
> If you to inspect one, try:
>
> print getProperty("xxxx").keys
>
> or, if that gives nothing, use [0].keys:
>
> $ print getProperty("atominfo")[0].keys
> _ipt
> atomIndex
> atomno
> bondCount
> clickabilityFlags
> colix
> color
> coord
> element
> elemno
> formalCharge
> info
> model
> partialCharge
> radius
> shape
> spacefill
> sym
> visibilityFlags
> visible
> x
> y
> z
>
>
> On Wed, Jul 25, 2012 at 4:55 AM, Martin Hediger <ma...@bl...
> <mailto:ma...@bl...>> wrote:
>
> Dear Jmol Users
> For the Jmol function "jmolGetPropertyAsArray", what are valid
> "sKey"s?
> Where are they listed?
>
> Thank you for hints
> Martin
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond.
> Discussions
> will include endpoint security, mobile security and the latest in
> malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Jmol-users mailing list
> Jmo...@li...
> <mailto:Jmo...@li...>
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
>
> --
> 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
>
>
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>
>
> _______________________________________________
> Jmol-users mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-users
|
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From: Robert H. <ha...@st...> - 2012-07-29 01:10:12
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just type getProperty in the console and you will get a full list. Sorry, I guess that wasn't clear. also, at the bottom of the left-hand scrolling region of http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm there is a list of clickable getproperty commands that shows what they all report. Bob On Thu, Jul 26, 2012 at 6:14 AM, Martin Hediger <ma...@bl...> wrote: > Hi Bob, > I think what I was trying to figure out is, what are possible properties, > meaning "xxxx" in your example below, or put differently, what else, > besides "atominfo" can be used as an argument to 'getProperty'? > > Thanks for your support > Martin > > > > > > On 25.07.12 21:19, Robert Hanson wrote: > > Should be in the documentation, but also you can enter this at the console > and get the whole list > > getproperty > > If you to inspect one, try: > > print getProperty("xxxx").keys > > or, if that gives nothing, use [0].keys: > > $ print getProperty("atominfo")[0].keys > _ipt > atomIndex > atomno > bondCount > clickabilityFlags > colix > color > coord > element > elemno > formalCharge > info > model > partialCharge > radius > shape > spacefill > sym > visibilityFlags > visible > x > y > z > > > On Wed, Jul 25, 2012 at 4:55 AM, Martin Hediger <ma...@bl...> wrote: > >> Dear Jmol Users >> For the Jmol function "jmolGetPropertyAsArray", what are valid "sKey"s? >> Where are they listed? >> >> Thank you for hints >> Martin >> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> > > > > -- > 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 > > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > > > > _______________________________________________ > Jmol-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- 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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From: Martin H. <ma...@bl...> - 2012-07-26 12:06:06
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Dear Jmol Users If I load a PDB structure into the Jmol application (not the Jmol applet) and use getProperty "atomInfo", "1.1" I receive the output atomInfo *List[0] in bold blue font. However, when I just use getProperty "atomInfo" the application crashes. I have two questions: 1) In the Jmol application, how can I assign the *List[0] content to a variable and access its elements? Whats the Jmol syntax for this? 2) What do the '*' and the [0] mean in this context? Thanks for help. Martin |
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From: Robert H. <ha...@st...> - 2012-07-29 01:17:24
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I don't see the crashing. What's the error report?
x = getProperty("atomInfo")
gets that into a model.
$ load $caffeine
print getProperty("atomInfo")[3]
$
_ipt : 2
atomIndex : 2
atomno : 3
bondCount : 3
clickabilityFlags : 12
colix : -32762
color : [x909090]
coord : {1.7906001 0.2081 0.0010}
element : carbon
elemno : 6
formalCharge : 0
info : C3 #3
model : 1
partialCharge : 0.0
radius : 0.80833334
shape : trigonal planar
spacefill : 0.391
sym : C
visibilityFlags : 13
visible : true
x : 1.7906001
y : 0.2081
z : 0.0010
$ print getProperty("atomInfo")[3]["atomno"]
3
It's more efficient, if you only want one value, to put it all in the
quotes:
$ print getProperty("atomInfo[3][color]")
[x909090]
and if you skip the [3], you get a list over all the atoms (in this case)
$ print getProperty("atomInfo[color]")
[x3050f8]
[x909090]
[x909090]
[xff0d0d]
...
Bob
On Thu, Jul 26, 2012 at 7:05 AM, Martin Hediger <ma...@bl...> wrote:
> Dear Jmol Users
> If I load a PDB structure into the Jmol application (not the Jmol
> applet) and use
>
> getProperty "atomInfo", "1.1"
>
> I receive the output
>
> atomInfo *List[0]
>
> in bold blue font. However, when I just use
>
> getProperty "atomInfo"
>
> the application crashes.
>
> I have two questions:
> 1) In the Jmol application, how can I assign the *List[0] content to a
> variable and access its elements? Whats the Jmol syntax for this?
> 2) What do the '*' and the [0] mean in this context?
>
> Thanks for help.
> Martin
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Jmol-users mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
--
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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