Re: [Jmol-users] how export in fractional coordinates
apparently is the 2nd option a Jmol bug because by typing :
print {1.1}.length = 10
print {1.2}.length = 20
print {1.1 and 1.2}.length = 10
I sent you the file too.
Thanks, Piero
Bob, I sent the file to you
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---
From: Robert Hanson [hans...@stolaf.edu]
Sent: Thursday, September 02, 2010 8:00 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] how export in fractional coordinates
Piero, on the first issue, I have a feeling this is a bug in the Crystal file
reader, because there's no way Jmol is combining 1.1 atoms into 1.2 atoms. Just
can't happen. Do the following:
print {1.1}.length
print {1.2}.length
print {1.1 and 1.2}.length
I have a hunch the reader is copying the atoms multiple times and you are going
to see something like this:
10
20
0
(Crystal file reader bug)
But you might also get
10
20
10
(Jmol select bug)
Which is it? Please send me that file (again).
Bob
On Thu, Sep 2, 2010 at 12:57 PM, P.Canepa
pc...@kent.ac.ukmailto:pc...@kent.ac.uk wrote:
Dear all,
When I do like var xyzCoord = {1.2}.label( %16.9[xyz]); print xyzCoord i get
Fe 0.355299979 0.35539 0.35539
Fe1 0.144699976 0.14461 0.14461
Fe1 0.644700050 0.644700050 0.644700050
Fe 0.85539 0.855300069 0.855300069
O 0.555899978 0.944100022 0.25030
O 0.24970 0.555899978 0.944100022
O 0.944100022 0.25060 0.555900037
O 0.444100022 0.055900037 0.75060
O 0.75000 0.444100022 0.055900037
O 0.055899978 0.75000 0.44403
Fe 0.355299652 0.355299652 0.355299652
Fe1 0.144700378 0.144700363 0.144700378
Fe1 0.644700468 0.644700408 0.644700408
Fe 0.855299592 0.855299652 0.855299592
O 0.555843592 0.944156408 0.24940
O 0.24970 0.555843532 0.944156349
O 0.944156468 0.24881 0.555843532
O 0.444156408 0.055843621 0.74881
O 0.75000 0.444156408 0.055843621
O 0.055843592 0.74940 0.444156379
which includes the second frame but also the first. Now if I type var xyzCoord
= {1.3}.label( %16.9[xyz]); print xyzCoord
I get 1, 2 and 3 and so on .
https://lists.sourceforge.net/lists/listinfo/jmol-users
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If nature does not answer first what we want,
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Re: [Jmol-users] Jmol and crystallography: the paper
Excellent - lots of beautiful examples showing why Jmol is a killer app! Dean On Thu, Sep 2, 2010 at 3:21 PM, Robert Hanson hans...@stolaf.edu wrote: *This just in! * *J. Appl. Cryst.* (2010). *43* [ doi:10.1107/S0021889810030256http://dx.doi.org/10.1107/S0021889810030256] *Jmol* - a paradigm shift in crystallographic visualization R. M. Hansonhttp://scripts.iucr.org/cgi-bin/citedin?search_on=nameauthor_name=Hanson%2C%20R%2EM%2E *Synopsis: *Features of *Jmol* that allow new ways for students to interact with three-dimensional virtual models and explore molecular and crystallographic symmetry are described. Online 1 September 2010 -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] how export in fractional coordinates
Piero wrote:
2) I cannot find in the script guide how to get the number of atoms
of a
certain frame. For instance I have a MgO cell with 4Mg and 4O atoms
how
can I know that the structure has 4 Mg and 4O?
Maybe
{1.1 and _O}.length
or is it .size ?
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Re: [Jmol-users] camera dependent slab setting
Hi Bob, I set up a web page to clarify what I mean: http://weirdbyte.de/jmol-test/html/nav.html There are three applet, showing a protein in the same orientation. The first applet shows the protein in the normal - non navigation - mode and has some atom obscuring most of the rest. The second applet is in navigation mode and has the default visualRange = 5 setting. According to the documentation this results in any object in a plane that is less than 5.0 Angstroms across will be clipped automatically. And it works, giving a beautiful clear view, this is what I would like for the non navigation mode, too!. Applet 3 then is also in navigation mode but with visualRange set to 1 so that the notorious atom is not clipped automatically and obscures the view again, the reflection is nice though. I hope this makes my intention clear. Best Alexander ps: congrats for your jmol related publication! - Ursprüngliche Mail - Von: Robert Hanson hans...@stolaf.edu An: jmol-users@lists.sourceforge.net Gesendet: Mittwoch, 25. August 2010 15:58:20 Betreff: Re: [Jmol-users] camera dependent slab setting I thought that was what you meant -- the equivalent of visualRange but for standard mode. On Wed, Aug 25, 2010 at 7:57 AM, Alexander Rose alexander.r...@weirdbyte.de wrote: Hi, I tried rotationRadius, but it has not the effect visualRange has. In fact I do not really understand the effect, apart from somehow setting the zoom and the possible zoom range. That is with 12.0.8. Alex - Ursprüngliche Mail - Von: Robert Hanson hans...@stolaf.edu An: jmol-users@lists.sourceforge.net Gesendet: Dienstag, 24. August 2010 22:24:17 Betreff: Re: [Jmol-users] camera dependent slab setting Indeed! set rotationRadius (Angstroms) Sets the nominal rotation radius for the model effectively setting the size of the model at zoom 100 . Normally set to the radius that will contain within the screen the entire model when rotated relative to the default rotation center. :) Bob On Mon, Aug 23, 2010 at 5:16 AM, Alexander Rose alexander.r...@weirdbyte.de wrote: Because its such a different experience I came to think that something like visualRange would be useful for the non nav mode?! Best Alexander -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Sell apps to millions through the Intel(R) Atom(Tm) Developer Program Be part of this innovative community and reach millions of netbook users worldwide. Take advantage of special opportunities to increase revenue and speed time-to-market. Join now, and jumpstart your future. http://p.sf.net/sfu/intel-atom-d2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Sell apps to millions through the Intel(R) Atom(Tm) Developer Program Be part of this innovative community and reach millions of netbook users worldwide. Take advantage of special opportunities to increase revenue and speed time-to-market. Join now, and jumpstart your future. http://p.sf.net/sfu/intel-atom-d2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Sell apps to millions through the Intel(R) Atom(Tm) Developer Program Be part of this innovative community and reach millions of netbook users worldwide. Take advantage of special opportunities to increase revenue and speed time-to-market. Join now, and jumpstart your future. http://p.sf.net/sfu/intel-atom-d2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd
Re: [Jmol-users] how export in fractional coordinates
I found it. THIRD possibility: It was file reading bug that only affected
the CrystalReader, but not a CrystalReader bug.
Bob
2010/9/3 Angel Herráez angel.herr...@uah.es
Piero wrote:
2) I cannot find in the script guide how to get the number of atoms
of a
certain frame. For instance I have a MgO cell with 4Mg and 4O atoms
how
can I know that the structure has 4 Mg and 4O?
Maybe
{1.1 and _O}.length
or is it .size ?
--
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St. Olaf College
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Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [Jmol-users] camera dependent slab setting
It seems to me that is what the standard SLAB command is for. Right? If you use slab on slab 60 # or whatever set slabByAtom it might be very close to what you are talking about. Bob On Fri, Sep 3, 2010 at 9:36 AM, Alexander Rose alexander.r...@weirdbyte.dewrote: Hi Bob, I set up a web page to clarify what I mean: http://weirdbyte.de/jmol-test/html/nav.html There are three applet, showing a protein in the same orientation. The first applet shows the protein in the normal - non navigation - mode and has some atom obscuring most of the rest. The second applet is in navigation mode and has the default visualRange = 5 setting. According to the documentation this results in any object in a plane that is less than 5.0 Angstroms across will be clipped automatically. And it works, giving a beautiful clear view, this is what I would like for the non navigation mode, too!. Applet 3 then is also in navigation mode but with visualRange set to 1 so that the notorious atom is not clipped automatically and obscures the view again, the reflection is nice though. I hope this makes my intention clear. Best Alexander ps: congrats for your jmol related publication! - Ursprüngliche Mail - Von: Robert Hanson hans...@stolaf.edu An: jmol-users@lists.sourceforge.net Gesendet: Mittwoch, 25. August 2010 15:58:20 Betreff: Re: [Jmol-users] camera dependent slab setting I thought that was what you meant -- the equivalent of visualRange but for standard mode. On Wed, Aug 25, 2010 at 7:57 AM, Alexander Rose alexander.r...@weirdbyte.de wrote: Hi, I tried rotationRadius, but it has not the effect visualRange has. In fact I do not really understand the effect, apart from somehow setting the zoom and the possible zoom range. That is with 12.0.8. Alex - Ursprüngliche Mail - Von: Robert Hanson hans...@stolaf.edu An: jmol-users@lists.sourceforge.net Gesendet: Dienstag, 24. August 2010 22:24:17 Betreff: Re: [Jmol-users] camera dependent slab setting Indeed! set rotationRadius (Angstroms) Sets the nominal rotation radius for the model effectively setting the size of the model at zoom 100 . Normally set to the radius that will contain within the screen the entire model when rotated relative to the default rotation center. :) Bob On Mon, Aug 23, 2010 at 5:16 AM, Alexander Rose alexander.r...@weirdbyte.de wrote: Because its such a different experience I came to think that something like visualRange would be useful for the non nav mode?! Best Alexander -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Sell apps to millions through the Intel(R) Atom(Tm) Developer Program Be part of this innovative community and reach millions of netbook users worldwide. Take advantage of special opportunities to increase revenue and speed time-to-market. Join now, and jumpstart your future. http://p.sf.net/sfu/intel-atom-d2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Sell apps to millions through the Intel(R) Atom(Tm) Developer Program Be part of this innovative community and reach millions of netbook users worldwide. Take advantage of special opportunities to increase revenue and speed time-to-market. Join now, and jumpstart your future. http://p.sf.net/sfu/intel-atom-d2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Sell apps to millions through the Intel(R) Atom(Tm) Developer Program Be part of this innovative community and reach millions of netbook users worldwide. Take advantage of special opportunities to increase revenue and speed time-to-market. Join now, and jumpstart your future. http://p.sf.net/sfu/intel-atom-d2d
Re: [Jmol-users] More on NIH Resolver
Ho, ho, HO! No kidding! Wow... 3D to 2D! I suppose you want this as a built-in Jmol option now... On Thu, Sep 2, 2010 at 9:24 PM, Otis Rothenberger osrot...@chemagic.comwrote: The NIH Resolver will generate a gif image of the Lewis line structure of a submitted SMILES. I ignored this feature because I thought it was just another pretty little picture. Boy was I wrong! A JavaScript construct of the following form: var tempStr = img width=' + sz + ' height=' + sz + ' src='http://cactus.nci.nih.gov/chemical/structure/; + escape(jmolSmiles) + /image' /; sz = desired gif size jmolSmiles = an evolving model kit mode model. When rendered the above gif not only has appropriate bond wedges. The chiral carbons are conveniently labeled R or S If you want to see a quick demo of this, go to http://chemagic.com/web_molecules/script_page_large.aspx The default model will be just fine. Click The Molecular Editor Link; click the Image link, click the NIH 2D Capture link. We edit models using our own Edit screen interface rather than the Jmol native interface. Play with editing, and you'll see that Resolver gets it right. You need to click the image capture link each time. There are some problems with complex aromatics (e.g. taxol), but I'm working on this problem. Otis -- Otis Rothenberger chemagic.com -- This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Find SMILES problem
got it -- a SMILES generator bug.
On Thu, Sep 2, 2010 at 2:50 PM, Otis Rothenberger osrot...@chemagic.comwrote:
Bob,
The ring is flat, but it has two sp3 carbons (CH2's). To make sure this was
not associated with my post model change processing, I reproduced the effect
by building benzene from methane followed by 1,3-cyclohexadiene formation
at:
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
I get the same results.
My issue is fairly localized to one problem, and I'd be hesitant to change
Jmol in a way that might create more problems down the road for this one
problem. At this point, the only thing this issue is fouling is using NIH
Resolver as a minimization tool. It keeps returning benzene on some
modified benzene queries - most notably 1,3-cyclohexadiene.
I'm experimenting with
escape(jmolSmile.replace(/c/ig, 'C'))
on this type of query only - i.e. NIH Resolver minimize.
I'm not sure that I'd even call this a work around since there is nothing
wrong with Jmol smiles. Playing around with benzene and pyridine indicates
that this approach is working. Even though I do not change n in the
2,3-dihydropyridine query, the Resolver reads in correctly and returns the
correct SMILES and model.
The lower case Kekule aromatic SMILES will play havoc with asymmetric
compares - JME/Jmol NIH/Jmol. But I'm not sure these asymmetric
compares are an issue, just a nuisance in constructing an internal data
base. In this latter case, one has to hand convert JME SMILES (for example)
to lower case aromatic.
Otis
Otis Rothenbergerchemagic.com
On 9/2/2010 3:09 PM, Robert Hanson wrote:
On Thu, Sep 2, 2010 at 9:17 AM, Otis Rothenberger
osrot...@chemagic.comwrote:
Bob,
Thanks. Your explanation of what aromatic means is the key here. I see now
why this is happening. If I start with benzene and make 1,3-cyclohexadiene,
then it ends up in flat energy minimum that minimize does not change. I
always get the lower case smiles. If I use drag to pull it out of shape,
then I get upper case. If I make cyclohexene from benzene, minimize
eventually get it and twists a bit. Once it twists, I get upper case.
One thing here is that it looks like the statement aromatic just means
flat and all sp2 for Jmol is not quite correct. Flat seems to be a
sufficient condition.
then there's a bug. You sure you have a tetrahedral center? -- not just
square planar but distorted square planar?
The context here may seem strange, but we are working on student model kit
exercises, and we want the Jmol model kit to allow the same kind on tactile
playing that a ball and stick model kit allows - e.g. take a double bond out
of benzene. To be sure, I do not see the problem if I make
1,3-cyclohexadiene from cyclohexane. That should have been a clue that the
flatness was the issue!
Re NIH, for all of the following, the Resolver returns benzene (no
explicit hydrogens in submitted SMILES):
Jmol lower case benzene
Jmol lowercase cyclohexadiene
Jmol lower case cylohexene
Jmol lower case cyclohexane, which is, of course synonymous with aromatic
SMILES for benzene.
Evidently, the Resolver is just ignoring = in this lower case context.
that makes sense. What do you propose? There could be an aromatic option
that requires explicit hydrogens:
/explicitaromatic/
--- flat ring
--- tricoordinate carbon
--- all substituents in plane of ring
/aromatic/ (default)
-- flat ring
-- all substituents in plane of ring
I hate to think what implications it might have for heterocycles, though.
That's what I was trying to avoid.
Bob
Otis
Otis Rothenbergerchemagic.com
On 9/2/2010 1:52 AM, Robert Hanson wrote:
On Wed, Sep 1, 2010 at 10:21 PM, Otis Rothenberger osrot...@chemagic.com
wrote:
Bob,
There is a general aromatic problem that I'm having with find SMILES
that's easiest to explain with a specific scenario. If I load benzene
and run var x={*}.find('SMILES');echo @x, I get:
c1=cc=cc=c1
If I use model kit mode to make 1,3-cyclohexadiene, the same var
x={*}.find('SMILES');echo @x produces
c1=cc=ccc1
I'll look into that. Almost certainly a bug. It should only use lower case
c if the ring is totally flat and there are no sp3 centers. I'm really
surprised it's doing that. The code is only supposed to insert lower case
c when:
-- the ring is flat
-- the ring has no sp3 centers
Is it possible you are sending it a flat no-hydrogen ring? When I use the
model kit, I get:
C1==C1
I'm now stuck in lower case c mode on this ring no matter what I do to
the ring. If I break a ring bond while the ring is no longer aromatic
and reform the bond, I go back to upper case C
remember -- aromatic just means flat and all sp2 for Jmol. We're not
going to get into multiple bonding issues. There's no antiaromatic here.
It doesn't matter if you have 6 carbons and all single bonds or 6 carbons
and all double bonds or 8 carbons (as in
Re: [Jmol-users] odd results (12.0.11 and 12.1.9)
When you have multiple layers of translucent objects, it is possible to get some odd effects. On Thu, Sep 2, 2010 at 8:01 AM, Pshemak Maslak 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 -- This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] More on NIH Resolver
Bob, Yeah, it's amazing how fast this is done. It's not a database look-up. It's being done on the fly from SMILES. But here's the big thing. The Resolver molfile has stereo information. I checked this out because on the Web site their embedded JME will translate the word taxol (or any SMILES) into a complete stereo drawing in JME. When I checked their code, I discovered that they are actually loading JME files (not molfies) into JME. Some how they are generating JME files from SMILES. Before I bother Markus again, I'm going to try to load their molfiles into JME to see if the stereo drawing renders. JME does not read files from server. You have to feed it a string. Further the molfile string needs to be line break tweaked. I'm just now looking into this. Otis Otis Rothenberger chemagic.com On 9/3/2010 10:50 AM, Robert Hanson wrote: Ho, ho, HO! No kidding! Wow... 3D to 2D! I suppose you want this as a built-in Jmol option now... On Thu, Sep 2, 2010 at 9:24 PM, Otis Rothenberger osrot...@chemagic.com mailto:osrot...@chemagic.com wrote: The NIH Resolver will generate a gif image of the Lewis line structure of a submitted SMILES. I ignored this feature because I thought it was just another pretty little picture. Boy was I wrong! A JavaScript construct of the following form: var tempStr = img width=' + sz + ' height=' + sz + ' src='http://cactus.nci.nih.gov/chemical/structure/; + escape(jmolSmiles) + /image' /; sz = desired gif size jmolSmiles = an evolving model kit mode model. When rendered the above gif not only has appropriate bond wedges. The chiral carbons are conveniently labeled R or S If you want to see a quick demo of this, go to http://chemagic.com/web_molecules/script_page_large.aspx The default model will be just fine. Click The Molecular Editor Link; click the Image link, click the NIH 2D Capture link. We edit models using our own Edit screen interface rather than the Jmol native interface. Play with editing, and you'll see that Resolver gets it right. You need to click the image capture link each time. There are some problems with complex aromatics (e.g. taxol), but I'm working on this problem. Otis -- Otis Rothenberger chemagic.com http://chemagic.com -- This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net mailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] More on NIH Resolver
Oh my, it's this simple! http://cactus.nci.nih.gov/chemical/structure/CCC%28C%29CC/file?format=jme OR http://cactus.nci.nih.gov/chemical/structure/CCC(C)CC/file?format=jme Otis Otis Rothenberger chemagic.com On 9/3/2010 11:26 AM, Otis Rothenberger wrote: Bob, Yeah, it's amazing how fast this is done. It's not a database look-up. It's being done on the fly from SMILES. But here's the big thing. The Resolver molfile has stereo information. I checked this out because on the Web site their embedded JME will translate the word taxol (or any SMILES) into a complete stereo drawing in JME. When I checked their code, I discovered that they are actually loading JME files (not molfies) into JME. Some how they are generating JME files from SMILES. Before I bother Markus again, I'm going to try to load their molfiles into JME to see if the stereo drawing renders. JME does not read files from server. You have to feed it a string. Further the molfile string needs to be line break tweaked. I'm just now looking into this. Otis Otis Rothenberger chemagic.com On 9/3/2010 10:50 AM, Robert Hanson wrote: Ho, ho, HO! No kidding! Wow... 3D to 2D! I suppose you want this as a built-in Jmol option now... On Thu, Sep 2, 2010 at 9:24 PM, Otis Rothenberger osrot...@chemagic.com mailto:osrot...@chemagic.com wrote: The NIH Resolver will generate a gif image of the Lewis line structure of a submitted SMILES. I ignored this feature because I thought it was just another pretty little picture. Boy was I wrong! A JavaScript construct of the following form: var tempStr = img width=' + sz + ' height=' + sz + ' src='http://cactus.nci.nih.gov/chemical/structure/; + escape(jmolSmiles) + /image' /; sz = desired gif size jmolSmiles = an evolving model kit mode model. When rendered the above gif not only has appropriate bond wedges. The chiral carbons are conveniently labeled R or S If you want to see a quick demo of this, go to http://chemagic.com/web_molecules/script_page_large.aspx The default model will be just fine. Click The Molecular Editor Link; click the Image link, click the NIH 2D Capture link. We edit models using our own Edit screen interface rather than the Jmol native interface. Play with editing, and you'll see that Resolver gets it right. You need to click the image capture link each time. There are some problems with complex aromatics (e.g. taxol), but I'm working on this problem. Otis -- Otis Rothenberger chemagic.com http://chemagic.com -- This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net mailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] camera dependent slab setting
Hi, - Ursprüngliche Mail - Von: Robert Hanson hans...@stolaf.edu An: jmol-users@lists.sourceforge.net Gesendet: Freitag, 3. September 2010 16:46:50 Betreff: Re: [Jmol-users] camera dependent slab setting It seems to me that is what the standard SLAB command is for. Right? In a way, but it's static, the slab is not dependent on the zoom. So when I zoom in more deeply, I would have to adjust the slab setting to show less, and when I zoom out to show more again. This fine when creating images or focusing on one area, but when exploring a larger part of a protein it becomes annoying and I miss such a feature as it is available in other viewers. Best Alexander If you use slab on slab 60 # or whatever set slabByAtom it might be very close to what you are talking about. Bob On Fri, Sep 3, 2010 at 9:36 AM, Alexander Rose alexander.r...@weirdbyte.de wrote: Hi Bob, I set up a web page to clarify what I mean: http://weirdbyte.de/jmol-test/html/nav.html There are three applet, showing a protein in the same orientation. The first applet shows the protein in the normal - non navigation - mode and has some atom obscuring most of the rest. The second applet is in navigation mode and has the default visualRange = 5 setting. According to the documentation this results in any object in a plane that is less than 5.0 Angstroms across will be clipped automatically. And it works, giving a beautiful clear view, this is what I would like for the non navigation mode, too!. Applet 3 then is also in navigation mode but with visualRange set to 1 so that the notorious atom is not clipped automatically and obscures the view again, the reflection is nice though. I hope this makes my intention clear. Best Alexander ps: congrats for your jmol related publication! - Ursprüngliche Mail - Von: Robert Hanson hans...@stolaf.edu An: jmol-users@lists.sourceforge.net Gesendet: Mittwoch, 25. August 2010 15:58:20 Betreff: Re: [Jmol-users] camera dependent slab setting I thought that was what you meant -- the equivalent of visualRange but for standard mode. On Wed, Aug 25, 2010 at 7:57 AM, Alexander Rose alexander.r...@weirdbyte.de wrote: Hi, I tried rotationRadius, but it has not the effect visualRange has. In fact I do not really understand the effect, apart from somehow setting the zoom and the possible zoom range. That is with 12.0.8. Alex - Ursprüngliche Mail - Von: Robert Hanson hans...@stolaf.edu An: jmol-users@lists.sourceforge.net Gesendet: Dienstag, 24. August 2010 22:24:17 Betreff: Re: [Jmol-users] camera dependent slab setting Indeed! set rotationRadius (Angstroms) Sets the nominal rotation radius for the model effectively setting the size of the model at zoom 100 . Normally set to the radius that will contain within the screen the entire model when rotated relative to the default rotation center. :) Bob On Mon, Aug 23, 2010 at 5:16 AM, Alexander Rose alexander.r...@weirdbyte.de wrote: Because its such a different experience I came to think that something like visualRange would be useful for the non nav mode?! Best Alexander -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Sell apps to millions through the Intel(R) Atom(Tm) Developer Program Be part of this innovative community and reach millions of netbook users worldwide. Take advantage of special opportunities to increase revenue and speed time-to-market. Join now, and jumpstart your future. http://p.sf.net/sfu/intel-atom-d2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Sell apps to millions through the Intel(R) Atom(Tm) Developer Program Be part of this innovative community and reach millions of netbook users worldwide. Take advantage of special opportunities to increase revenue and speed time-to-market. Join now, and jumpstart your future. http://p.sf.net/sfu/intel-atom-d2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave.
Re: [Jmol-users] odd results (12.0.11 and 12.1.9)
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 -- This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] camera dependent slab setting
So I think we could set some slab option to be dependent upon zoom. For example: slab 5.0 a decimal here would indicate that at whatever zoom level you are at, the slab would be set to be wherever the visual range is 5.0 Angstroms. Something like that? On Fri, Sep 3, 2010 at 11:10 AM, Alexander Rose alexander.r...@weirdbyte.de wrote: Hi, - Ursprüngliche Mail - Von: Robert Hanson hans...@stolaf.edu An: jmol-users@lists.sourceforge.net Gesendet: Freitag, 3. September 2010 16:46:50 Betreff: Re: [Jmol-users] camera dependent slab setting It seems to me that is what the standard SLAB command is for. Right? In a way, but it's static, the slab is not dependent on the zoom. So when I zoom in more deeply, I would have to adjust the slab setting to show less, and when I zoom out to show more again. This fine when creating images or focusing on one area, but when exploring a larger part of a protein it becomes annoying and I miss such a feature as it is available in other viewers. Best Alexander If you use slab on slab 60 # or whatever set slabByAtom it might be very close to what you are talking about. Bob On Fri, Sep 3, 2010 at 9:36 AM, Alexander Rose alexander.r...@weirdbyte.de wrote: Hi Bob, I set up a web page to clarify what I mean: http://weirdbyte.de/jmol-test/html/nav.html There are three applet, showing a protein in the same orientation. The first applet shows the protein in the normal - non navigation - mode and has some atom obscuring most of the rest. The second applet is in navigation mode and has the default visualRange = 5 setting. According to the documentation this results in any object in a plane that is less than 5.0 Angstroms across will be clipped automatically. And it works, giving a beautiful clear view, this is what I would like for the non navigation mode, too!. Applet 3 then is also in navigation mode but with visualRange set to 1 so that the notorious atom is not clipped automatically and obscures the view again, the reflection is nice though. I hope this makes my intention clear. Best Alexander ps: congrats for your jmol related publication! - Ursprüngliche Mail - Von: Robert Hanson hans...@stolaf.edu An: jmol-users@lists.sourceforge.net Gesendet: Mittwoch, 25. August 2010 15:58:20 Betreff: Re: [Jmol-users] camera dependent slab setting I thought that was what you meant -- the equivalent of visualRange but for standard mode. On Wed, Aug 25, 2010 at 7:57 AM, Alexander Rose alexander.r...@weirdbyte.de wrote: Hi, I tried rotationRadius, but it has not the effect visualRange has. In fact I do not really understand the effect, apart from somehow setting the zoom and the possible zoom range. That is with 12.0.8. Alex - Ursprüngliche Mail - Von: Robert Hanson hans...@stolaf.edu An: jmol-users@lists.sourceforge.net Gesendet: Dienstag, 24. August 2010 22:24:17 Betreff: Re: [Jmol-users] camera dependent slab setting Indeed! set rotationRadius (Angstroms) Sets the nominal rotation radius for the model effectively setting the size of the model at zoom 100 . Normally set to the radius that will contain within the screen the entire model when rotated relative to the default rotation center. :) Bob On Mon, Aug 23, 2010 at 5:16 AM, Alexander Rose alexander.r...@weirdbyte.de wrote: Because its such a different experience I came to think that something like visualRange would be useful for the non nav mode?! Best Alexander -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Sell apps to millions through the Intel(R) Atom(Tm) Developer Program Be part of this innovative community and reach millions of netbook users worldwide. Take advantage of special opportunities to increase revenue and speed time-to-market. Join now, and jumpstart your future. http://p.sf.net/sfu/intel-atom-d2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Sell apps to millions through the Intel(R) Atom(Tm) Developer Program Be part of this innovative community and
[Jmol-users] True Jmol Depict Jmol to JME
This is an outgrowth of the gif image note, but its a new subject. So new chain... Here's a true Jmol depict - i.e. Jmol model kit mode 3D -- JME stereo 2D http://chemagic.com/web_molecules/script_page_large.aspx Click The Molecular Editor link; Click the Draw link. Click the Depict link; The appropriate query to NIH Resolver is: http://cactus.nci.nih.gov/chemical/structure/CCC(C)CC/file?format=jme http://cactus.nci.nih.gov/chemical/structure/CCC%28C%29CC/file?format=jme Bob, is this one worth building into Jmol like the Resolver molfile load? If it's built into Jmol, them users embedding JME should be able to use it with the signed Jmol applet sans server side programming. Unless JME has a signed applet version, I don't think you can pass the Resolver data directly to JME. If the JME file comes into a Jmol/JME combined page via Jmol, my guess is that it's legal for the signed Jmol applet to pass the data to JME via JavaScript??? Otis -- Otis Rothenberger chemagic.com -- This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] how export in fractional coordinates
ok Thanks a lot huh!
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Pieremanuele Canepa
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Functional Material Group
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mobile: +44 (0) 7772-9756456
---
From: Robert Hanson [hans...@stolaf.edu]
Sent: Friday, September 03, 2010 3:39 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] how export in fractional coordinates
I found it. THIRD possibility: It was file reading bug that only affected the
CrystalReader, but not a CrystalReader bug.
Bob
2010/9/3 Angel Herráez angel.herr...@uah.esmailto:angel.herr...@uah.es
Piero wrote:
2) I cannot find in the script guide how to get the number of atoms
of a
certain frame. For instance I have a MgO cell with 4Mg and 4O atoms
how
can I know that the structure has 4 Mg and 4O?
Maybe
{1.1 and _O}.length
or is it .size ?
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phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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