Re: [Jmol-users] Jmol 14.4.4_2016.03.21

[Andreas Prlic]

Hi,

The Safari problem has been resolved. Again apologies for the
inconvenience. Please let me know if anything else does not work as
expected.

Andreas

On Mon, Mar 21, 2016 at 4:58 PM, Otis Rothenberger 
wrote:

> Andreas,
>
> Sorry about the letter transposition in the RCSB acronym. My brain is not
> dyslexic, but the two fingers that I use to type sure are!
>
> Earlier today, the last XML post was not responding on my iPad. It’s
> working now, however.
>
> Just tried again. I see the problem. On the iPad the button needs two
> taps. The first tap is being detected as a “hover."
>
> Otis - AKA Oits ;>)
>
> --
> Otis Rothenberger
> o...@chemagic.org
> http://chemagic.org
>
> On Mar 21, 2016, at 7:23 PM, Andreas Prlic  wrote:
>
> I confirm, there is a problem with access from Safari.
>
> We (RCSB) already know how to fix it, but we'll need a few hours (prob
> until tomorrow morning US west coast time) to implement the fix.
>
> The problem has to do with a recent infrastructure change (and CORS). All
> file downloads now get redirected to files.rcsb.org, which is a more
> scaleable infrastructure than the old location. In the process of this,
> support for the "accept gzip encoding" HTTP header has a bug and breaks
> Safari right now.  Apologies for the inconvenience. We'll roll out a fix
> for this ASAP.
>
> Regarding the problem with http://www.rcsb.org/pdb/software/rest.do .
> There has been not change here in a while. I just tested this and it worked
> fine for me. Which URL did you query?
>
> Andreas
>
>
>
>
> On Mon, Mar 21, 2016 at 3:24 PM, Otis Rothenberger 
> wrote:
>
>> Something weird is going on that’s not related to today’s release.
>>
>> On the Mac side, RSCB is broken here:
>>
>> http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
>>
>> unless I set Safari to Disable Cross-Origin Restrictions - Develop Menu.
>>
>> RSCB is broken on my model kit app (JSmol 14.4.3) no matter what the
>> browser setting. Also, on the RSCB REST site:
>>
>> http://www.rcsb.org/pdb/software/rest.do
>>
>> Their local REST test on that page was up and down for me on Sarai during
>> several tests today.
>>
>> Otis
>>
>> --
>> Otis Rothenberger
>> o...@chemagic.org
>> http://chemagic.org
>>
>> On Mar 21, 2016, at 5:55 PM, Andreas Prlic  wrote:
>>
>> Hi,
>>
>> RCSB is up and running. http://status.rcsb.org/
>>
>> I also tested from http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm and
>> all seems be running fine from there.
>>
>> Can you access the RCSB web site in your browser? Perhaps there is a
>> networking issue. Also: do you see a stacktrace in your javascript console?
>>
>> Andreas
>>
>>
>>
>>
>>
>> On Mon, Mar 21, 2016 at 2:34 PM, Philip Bays 
>> wrote:
>>
>>> And I am seeing on the campus website using the 0228 release.
>>>
>>> Possible that RCSB is down??
>>>
>>>
>>> > On Mar 21, 2016, at 5:13 PM, Robert Hanson  wrote:
>>> >
>>> > I am not seeing that. Others?
>>> > ​
>>>
>>>
> --
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>
>
>
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>
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Re: [Jmol-users] Jmol 14.4.4_2016.03.21

[Andreas Prlic]

I confirm, there is a problem with access from Safari.

We (RCSB) already know how to fix it, but we'll need a few hours (prob
until tomorrow morning US west coast time) to implement the fix.

The problem has to do with a recent infrastructure change (and CORS). All
file downloads now get redirected to files.rcsb.org, which is a more
scaleable infrastructure than the old location. In the process of this,
support for the "accept gzip encoding" HTTP header has a bug and breaks
Safari right now.  Apologies for the inconvenience. We'll roll out a fix
for this ASAP.

Regarding the problem with http://www.rcsb.org/pdb/software/rest.do . There
has been not change here in a while. I just tested this and it worked fine
for me. Which URL did you query?

Andreas




On Mon, Mar 21, 2016 at 3:24 PM, Otis Rothenberger 
wrote:

> Something weird is going on that’s not related to today’s release.
>
> On the Mac side, RSCB is broken here:
>
> http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
>
> unless I set Safari to Disable Cross-Origin Restrictions - Develop Menu.
>
> RSCB is broken on my model kit app (JSmol 14.4.3) no matter what the
> browser setting. Also, on the RSCB REST site:
>
> http://www.rcsb.org/pdb/software/rest.do
>
> Their local REST test on that page was up and down for me on Sarai during
> several tests today.
>
> Otis
>
> --
> Otis Rothenberger
> o...@chemagic.org
> http://chemagic.org
>
> On Mar 21, 2016, at 5:55 PM, Andreas Prlic  wrote:
>
> Hi,
>
> RCSB is up and running. http://status.rcsb.org/
>
> I also tested from http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm and
> all seems be running fine from there.
>
> Can you access the RCSB web site in your browser? Perhaps there is a
> networking issue. Also: do you see a stacktrace in your javascript console?
>
> Andreas
>
>
>
>
>
> On Mon, Mar 21, 2016 at 2:34 PM, Philip Bays  wrote:
>
>> And I am seeing on the campus website using the 0228 release.
>>
>> Possible that RCSB is down??
>>
>>
>> > On Mar 21, 2016, at 5:13 PM, Robert Hanson  wrote:
>> >
>> > I am not seeing that. Others?
>> > ​
>>
>>
--
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Re: [Jmol-users] Jmol 14.4.4_2016.03.21

[Otis Rothenberger]

Something weird is going on that’s not related to today’s release.

On the Mac side, RSCB is broken here:

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

unless I set Safari to Disable Cross-Origin Restrictions - Develop Menu.

RSCB is broken on my model kit app (JSmol 14.4.3) no matter what the browser 
setting. Also, on the RSCB REST site:

http://www.rcsb.org/pdb/software/rest.do

Their local REST test on that page was up and down for me on Sarai during 
several tests today.

Otis

--
Otis Rothenberger
o...@chemagic.org
http://chemagic.org

> On Mar 21, 2016, at 5:55 PM, Andreas Prlic  wrote:
> 
> Hi,
> 
> RCSB is up and running. http://status.rcsb.org/ 
> 
> I also tested from http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm 
>  and all seems be running 
> fine from there.
> 
> Can you access the RCSB web site in your browser? Perhaps there is a 
> networking issue. Also: do you see a stacktrace in your javascript console? 
> 
> Andreas
> 
> 
> 
> 
> 
> On Mon, Mar 21, 2016 at 2:34 PM, Philip Bays  > wrote:
> And I am seeing on the campus website using the 0228 release.
> 
> Possible that RCSB is down??
> 
> 
> > On Mar 21, 2016, at 5:13 PM, Robert Hanson  > > wrote:
> >
> > I am not seeing that. Others?
> > ​
> > --
> > Transform Data into Opportunity.
> > Accelerate data analysis in your applications with
> > Intel Data Analytics Acceleration Library.
> > Click to learn more.
> > http://pubads.g.doubleclick.net/gampad/clk?id=278785351=/4140___
> >  
> > 
> > Jmol-users mailing list
> > Jmol-users@lists.sourceforge.net 
> > https://lists.sourceforge.net/lists/listinfo/jmol-users 
> > 
> 
> Philip Bays
> Emeritus Professor of Chemistry
> Saint Mary's College
> Notre Dame, IN 46556
> pb...@saintmarys.edu 
> 
> 
> 
> --
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
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> 
> ___
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> https://lists.sourceforge.net/lists/listinfo/jmol-users 
> 
> 
> 
> 
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Re: [Jmol-users] Jmol 14.4.4_2016.03.21

[Hoelzer, Mark]

Hmm - I've also been seeing this same error for a number of our pages over the 
past week or two (for example, see the email below that I just received from a 
teacher).  It looks like if I host the PDB file on our site, it loads just 
fine. But if I try to use the "load=" command to grab it directly from the 
RCSB, it throws this "unrecognized file format" error.

Doesn't seem to be consistent across browsers either - works on some but not 
others.  I'll try to run some more tests and figure out what the "load=" 
command is and isn't working on here.

- Mark


MSOE Center for BioMolecular Modeling - http://cbm.msoe.edu
3D Molecular Designs - www.3dmoleculardesigns.com
hoel...@msoe.edu
office: 414-277-4554
cell: 414-640-8668


-

Afternoon Mark,

I am wondering if you can help me.  The page at 
http://www.3dmoleculardesigns.com/jmol/aask/zincfinger.html is not loading. my 
class was able to use it 2 weeks ago, but now it has this message "unrecogized 
file format"

-




From: Philip Bays <pb...@saintmarys.edu>
Sent: Monday, March 21, 2016 4:34 PM
To: Jmol Jmol
Subject: Re: [Jmol-users] Jmol 14.4.4_2016.03.21

And I am seeing on the campus website using the 0228 release.

Possible that RCSB is down??


> On Mar 21, 2016, at 5:13 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
> I am not seeing that. Others?
> ​
> --
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785351=/4140___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Notre Dame, IN 46556
pb...@saintmarys.edu



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Re: [Jmol-users] Jmol 14.4.4_2016.03.21

[Andreas Prlic]

Hi,

RCSB is up and running. http://status.rcsb.org/

I also tested from http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm and all
seems be running fine from there.

Can you access the RCSB web site in your browser? Perhaps there is a
networking issue. Also: do you see a stacktrace in your javascript console?

Andreas





On Mon, Mar 21, 2016 at 2:34 PM, Philip Bays  wrote:

> And I am seeing on the campus website using the 0228 release.
>
> Possible that RCSB is down??
>
>
> > On Mar 21, 2016, at 5:13 PM, Robert Hanson  wrote:
> >
> > I am not seeing that. Others?
> > ​
> >
> --
> > Transform Data into Opportunity.
> > Accelerate data analysis in your applications with
> > Intel Data Analytics Acceleration Library.
> > Click to learn more.
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=278785351=/4140___
> > Jmol-users mailing list
> > Jmol-users@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/jmol-users
>
> Philip Bays
> Emeritus Professor of Chemistry
> Saint Mary's College
> Notre Dame, IN 46556
> pb...@saintmarys.edu
>
>
>
>
> --
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
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> ___
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>
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Re: [Jmol-users] Jmol 14.4.4_2016.03.21

[Philip Bays]

And I am seeing on the campus website using the 0228 release.

Possible that RCSB is down??


> On Mar 21, 2016, at 5:13 PM, Robert Hanson  wrote:
> 
> I am not seeing that. Others?
> ​
> --
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785351=/4140___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Notre Dame, IN 46556
pb...@saintmarys.edu



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Re: [Jmol-users] Jmol 14.4.4_2016.03.21

[J. Bays]

OK.  I have looked at it again.  PubChem works but I am getting the invalid 
message from RCSB.  I am running on Mac OS X the latest version (before today). 
  I have it on my home server and accessing it as a localhost file or from my 
laptop on the local network.  I have cleared cache.  But I am also seeing this 
on the release of the 13th.  so I am not sure that it the software or me.




> On Mar 21, 2016, at 5:13 PM, Robert Hanson  wrote:
> 
> I am not seeing that. Others?
> ​
> --
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785351=/4140___
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> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users


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Re: [Jmol-users] Jmol 14.4.4_2016.03.21

[Robert Hanson]

I am not seeing that. Others?
​
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Re: [Jmol-users] Jmol 14.4.4_2016.03.21

[Philip Bays]

Bob:
I am seeing “unrecognized file format” errors in this release for both PubChem 
and RCSB.


> On Mar 21, 2016, at 2:38 PM, Robert Hanson  wrote:
> 
> This update takes care of a few minor bugs and also introduces several 
> powerful features in relation to polyhedra, unit cells, and SMILES. 
> 
> Jmol.___JmolVersion="14.4.4_2016.03.21"
> released
> 
> new feature: moveto axis [a1-c4]
>  -- extends moveto axis a|b|c to all for corners 1|2|3|4
> where 1 is upper left, 2 is upper right, 3 is lower right, and 4 is lower 
> left
>  -- for example, MOVETO AXIS a3
>  -- defaults: a==a1, b==b1, c==c4
>  
> new feature: axes OFFSET x.x
>  -- applies offset of x.x in fractional coordinates in each axis direction
>  -- AXES OFFSET -0.1   same as   AXES CENTER {-0.1 -0.1 -0.1/1}
>  
> new feature: expanded unitcell() function
>  -- adds additional types: "A", "B", "C", "I", "F"
>  -- default is the lattice type of the model's space group
>  -- not just cubic; "BCC" is converted to "I"
>  -- for example:
>  
>  load =ams/silicon 15 packed   // Cmca
>  draw id "uc" diameter 0.1 unitcell mesh nofill color black
>  unitcell @{unitcell("primitive")}
>  color unitcell red
>  unitcell 0.1
>  axes unitcell
>  axes on
> 
> new feature: expanded UNITCELL command to include PRIMITIVE option for any 
> space group
> 
> new feature: show smiles/NCI  aka  show smiles/CACTVS  aka show 
> smiles/canonical
> 
>  -- generates nonaromatic SMILES and sends that to NCI for canonicalization
>  
> bug fix: SMILES matcher not allowing azulene to be aromatic
> 
> bug fix: OpenSMILES matcher not allowing non-chemist Hueckel 4+2 
> interpretation
> 
> bug fix: SMILES generator not adding "-" for biphenyl Ar-Ar bond
> 
> bug fix: set picking invertSTEREO  does not work on open-ring systems
> 
> bug fix: SMARTS [R] matching all atoms
>   
> bug fix: dashed lines not visible in measurements, unit cells, and axes 
> 
> bug fix: axes 0.01  produces thick 20-pixel-wide lines
>  -- solution was to drop that to 0.001 for this effect
>  
> bug fix: Polyhedra with verticies that are also centers of polyhedra for 
> atoms that were visible
>  but are no longer visible do not update screen positions properly
> 
> 
> 
> -- 
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr 
> 
> 
> If nature does not answer first what we want,
> it is better to take what answer we get. 
> 
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
> 
> --
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
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Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Notre Dame, IN 46556
pb...@saintmarys.edu


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[Jmol-users] Jmol 14.4.4_2016.03.21

[Robert Hanson]

This update takes care of a few minor bugs and also introduces several
powerful features in relation to polyhedra, unit cells, and SMILES.

Jmol.___JmolVersion="14.4.4_2016.03.21"
released

new feature: moveto axis [a1-c4]
 -- extends moveto axis a|b|c to all for corners 1|2|3|4
where 1 is upper left, 2 is upper right, 3 is lower right, and 4 is
lower left
 -- for example, MOVETO AXIS a3
 -- defaults: a==a1, b==b1, c==c4

new feature: axes OFFSET x.x
 -- applies offset of x.x in fractional coordinates in each axis direction
 -- AXES OFFSET -0.1   same as   AXES CENTER {-0.1 -0.1 -0.1/1}

new feature: expanded unitcell() function
 -- adds additional types: "A", "B", "C", "I", "F"
 -- default is the lattice type of the model's space group
 -- not just cubic; "BCC" is converted to "I"
 -- for example:

 load =ams/silicon 15 packed   // Cmca
 draw id "uc" diameter 0.1 unitcell mesh nofill color black
 unitcell @{unitcell("primitive")}
 color unitcell red
 unitcell 0.1
 axes unitcell
 axes on

new feature: expanded UNITCELL command to include PRIMITIVE option for any
space group

new feature: show smiles/NCI  aka  show smiles/CACTVS  aka show
smiles/canonical

 -- generates nonaromatic SMILES and sends that to NCI for canonicalization

bug fix: SMILES matcher not allowing azulene to be aromatic

bug fix: OpenSMILES matcher not allowing non-chemist Hueckel 4+2
interpretation

bug fix: SMILES generator not adding "-" for biphenyl Ar-Ar bond

bug fix: set picking invertSTEREO  does not work on open-ring systems

bug fix: SMARTS [R] matching all atoms

bug fix: dashed lines not visible in measurements, unit cells, and axes

bug fix: axes 0.01  produces thick 20-pixel-wide lines
 -- solution was to drop that to 0.001 for this effect

bug fix: Polyhedra with verticies that are also centers of polyhedra for
atoms that were visible
 but are no longer visible do not update screen positions properly



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


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

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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