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Today's Topics:
1. Re: defined groups (Robert Hanson)
2. Re: defined groups (Robert Hanson)
3. Re: Distances between centers of aromatic rings? (Eric Martz)
4. Re: Distances between centers of aromatic rings? (Robert Hanson)
5. mmcif reading problem? (s...@publcif.co.uk)
6. mmcif reading problem? (s...@publcif.co.uk)
7. jmol-14.3.12_2015.02.24.zip (Robert Hanson)
8. GLmol not working? (Geoffrey Rowland)
9. show IMAGE - a new feature with lots of potential (Robert Hanson)
10. isosurfaces (Spinney, Richard)
11. Re: mmcif reading problem? (Robert Hanson)
12. Re: mmcif reading problem? (Robert Hanson)
13. HTTPS support (Onur Sumer)
----------------------------------------------------------------------
Message: 1
Date: Sun, 22 Feb 2015 18:22:05 -0600
From: Robert Hanson <hans...@stolaf.edu>
Subject: Re: [Jmol-users] defined groups
To: Pshemak Maslak <p...@chem.psu.edu>,
"jmol-users@lists.sourceforge.net" <jmol-users@lists.sourceforge.net>
Message-ID:
<caf_yuvwezxpmmdm72kxzqkzbd2rdqdtzf3wwrtytzeacabq...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
This is exactly what SMARTS is for:
select within(SMARTS,"O1CC1")
#or for just the O:
select within(SMARTS,"[O&r3]")
#or use { } to select specific atoms:
select within(SMARTS,"{O}1CC1")
#specifically select ether O next to a CH2:
select within(SMARTS,"C{O}[CH2]")
#or the C of the CH2 (not the Hs):
select within(SMARTS,"CO{[CH2]}")
On Sun, Feb 22, 2015 at 4:45 PM, Pshemak Maslak <n...@psu.edu> wrote:
> There is a very nice list of defined groups:
> http://chemapps.stolaf.edu/jmol/docs/misc/groups.txt.
>
> My question is about the ether group specifically:
>
> define ~etherO oxygen and connected(2,carbon) and not ~carbonylO
> define ~ROR ~etherO
>
> Is it possible to make the definition more specific?
> For example can one distinguish cyclic from acyclic ethers?
> Can one set up the one of the carbons bonded to oxygen is a -CH2 group
> (like in R-CH2-O-R)?
>
> Thanks,
> PM
>
>
> ------------------------------------------------------------------------------
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>
--
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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Message: 2
Date: Sun, 22 Feb 2015 20:05:34 -0600
From: Robert Hanson <hans...@stolaf.edu>
Subject: Re: [Jmol-users] defined groups
To: Pshemak Maslak <p...@chem.psu.edu>,
"jmol-users@lists.sourceforge.net" <jmol-users@lists.sourceforge.net>
Message-ID:
<CAF_YUvUicJ4_C2LaZkVttVqYn_ozNGV8vMS-YQSDs=jqupg...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
ps - there is information about Jmol and SMARTS here:
[1] http://chemapps.stolaf.edu/jmol/docs/?search=SMARTS#jmolsmarts/smiles
A full discussion of Jmol SMARTS notation is at
[2]
sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/src/org/jmol/smiles/package.html?format=raw
The key is that SMARTS is designed for searching substructures, while
SMILES is for distinquishing full compounds. In many ways they are
indistinguishable. For example, CCCC means "normal-butane" in SMILES and
"four consecutive aliphatic carbons" in SMARTS.
But SMARTS is far more elaborate, particularly in having wild cards and
specialized [...] notation, as well as variables.
Jmol's implementation of SMARTS a nearly complete version of Daylight
SMARTS, as described here:
http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html
Jmol's version includes several additional features, such as conformational
searches, including bond distance, angle, and dihedral ranges, more
ring-checking methods, and {...} notation to select specific atoms in a
SMARTS search result.
,
I can see I need to write this up in an article somewhere.
The Jmol documentation shows several contexts where SMARTS can be used. For
selection, the easiest thing is to use the SEARCH() function, here with
SELECT ON to highlight the atoms:
*load $THF*
*select on search("{[C&v4]}[O&r5]{[C&v4]}") # flanking carbons of an
aliphatic cyclic ether*
but because the notation evolved, you can also do this:
*load $THF; select within(SMARTS,"{[C&v4]}[O&r5]{[C&v4]}")*
and to assign a variable, you can use the FIND() function:
*x = {*}.find("SMARTS","{[C&v4]}[O&r5]{[C&v4]}")print x*
({0 3})
#which, like all variables, can be used in a select command:
*select x*
Overall, the SMARTS searching in Jmol is very powerful and definitely the
way to go for anything remotely complex.
Bob
?
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Message: 3
Date: Mon, 23 Feb 2015 09:23:17 -0500
From: Eric Martz <ema...@microbio.umass.edu>
Subject: Re: [Jmol-users] Distances between centers of aromatic rings?
To: jmol-users@lists.sourceforge.net
Message-ID: <54eb37d5.9080...@microbio.umass.edu>
Content-Type: text/plain; charset="utf-8"
Thanks so much, Bob! This seems to be working perfectly.
The only change I had to make is that rings.length is an array of zeros.
So I used rings.lines.count.
I was able to get His rings with
ringsh = {*}.find("SMARTS","c1cncn1", true)
and then make a single array
ringsall = rings + ringsh
Jmol continues to amaze and delight me!
Eric
On 2/10/15 5:47 PM, Robert Hanson wrote:
> This is what SMARTS searching does.
>
> rings = {*}.find("SMARTS","c1ccccc1", true) // an array of atom sets
> centers = rings.xyz // centers of those atom sets; still an array
> print centers[1]
> print centers[2]
> ...
>
>
> On Tue, Feb 10, 2015 at 3:59 PM, Eric Martz <ema...@microbio.umass.edu
> <mailto:ema...@microbio.umass.edu>> wrote:
>
> I would like to generate a list of distances between the centers of
> aromatic rings, identifying the pair of residues that each distance
> represents.
>
> I believe the following reports the center of the 6-carbon ring of
> Tyr3
> in 1pgb:
>
>
> $ load =1pgb
> IMMUNOGLOBULIN BINDING PROTEIN 23-NOV-93 1PGB
> TWO CRYSTAL STRUCTURES OF THE B1 IMMUNOGLOBULIN-BINDING
> DOMAIN OF STREPTOCCOCAL PROTEIN G AND COMPARISON WITH NMR
> found biomolecule 1: A
>
> // all rings:
>
> $ rings = {*}.find("SMARTS","c1ccccc1", true)
> $ print rings.xyz
> {13.123668 14.505501 26.274666}
> {7.7295 15.019166 20.959}
> {1.7821666 16.910334 17.072166}
> {7.07 8.775001 16.5255}
> {15.482834 9.6655 22.505835}
> {11.408334 10.879166 21.280832}
>
> // just tyr
>
> $ rings = {tyr}.find("SMARTS","c1ccccc1", true)
> $ print rings.xyz
> {13.123668 14.505501 26.274666}
> {1.7821666 16.910334 17.072166}
> {15.482834 9.6655 22.505835}
>
> // with labels
>
> for (var i = 1; i <= rings.length; i++) {
> print (rings[i])[1].label("%n%r") + " " + rings[i].xyz
> }
>
> TYR3 {13.123668 14.505501 26.274666}
> TYR33 {1.7821666 16.910334 17.072166}
> TYR45 {15.482834 9.6655 22.505835}
>
> If I had such lists, how would I generate a list of distances between
>
> the ring-centers, being able to identify the two residues for each
> distance?
>
>
> // use .xyz.distance (average position...distance....)
>
> for (var i = 1; i <= rings.length; i++) {
> for (var j = i + 1; j <= rings.length; j++) {
> print (rings[i])[1].label("%n%r") + "\t" +
> (rings[j])[1].label("%n%r") + "\t" +
> rings[i].xyz.distance(rings[j].xyz).format("%6.3f")
> }
> }
>
> TYR3 TYR33 14.802
> TYR3 TYR45 6.572
> TYR33 TYR45 16.423
>
>
> :)
>
>
>
> ------------------------------------------------------------------------------
> Dive into the World of Parallel Programming. The Go Parallel Website,
> sponsored by Intel and developed in partnership with Slashdot Media, is your
> hub for all things parallel software development, from weekly thought
> leadership blogs to news, videos, case studies, tutorials and more. Take a
> look and join the conversation now. http://goparallel.sourceforge.net/
>
>
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
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Message: 4
Date: Mon, 23 Feb 2015 12:00:05 -0600
From: Robert Hanson <hans...@stolaf.edu>
Subject: Re: [Jmol-users] Distances between centers of aromatic rings?
To: "jmol-users@lists.sourceforge.net"
<jmol-users@lists.sourceforge.net>
Message-ID:
<CAF_YUvVRiHBv=sxnhxd6mxxljkhqrgbv1zzf6xpmh9n6-j+...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
?Good to see you are having fun, Eric. I'm happy to see that people are
discovering the use of Jmol's SMARTS implementation.
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Message: 5
Date: Tue, 24 Feb 2015 14:46:39 +0000
From: s...@publcif.co.uk
Subject: [Jmol-users] mmcif reading problem?
To: "jmol-users@lists.sourceforge.net"
<jmol-users@lists.sourceforge.net>
Message-ID: <20150224144639.68915shyxaiam...@webmail.publcif.co.uk>
Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
format="flowed"
Jmol doesnt appear to be recognizing/calculating secondary structure
for some mmcifs - i.e. no cartoons etc.
example cif is at http://cif.publcryst.co.uk/cifmoldb/gui/tests/noname.mcf
This problem seems to apply to Jmol 14.2 onwards (i.e. works as expected with
earlier versions).
Any fix/help/workaround would be much appreciated
Cheers
Simon
------------------------------
Message: 6
Date: Tue, 24 Feb 2015 19:59:07 +0000
From: s...@publcif.co.uk
Subject: [Jmol-users] mmcif reading problem?
To: jmol-users@lists.sourceforge.net
Message-ID: <20150224195907.126246fbn0ohh...@webmail.publcif.co.uk>
Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
format="flowed"
Jmol doesnt appear to be recognizing/calculating secondary structure
for some mmcifs - i.e. no cartoons etc.
example cif is at http://cif.publcryst.co.uk/cifmoldb/gui/tests/noname.mcf
This problem seems to apply to Jmol 14.2 onwards (i.e. works as expected with
earlier versions).
Any fix/help/workaround would be much appreciated
Cheers
Simon
------------------------------
Message: 7
Date: Tue, 24 Feb 2015 22:13:23 -0600
From: Robert Hanson <hans...@stolaf.edu>
Subject: [Jmol-users] jmol-14.3.12_2015.02.24.zip
To: "jmol-users@lists.sourceforge.net"
<jmol-users@lists.sourceforge.net>
Message-ID:
<CAF_YUvUVSpWU93su5fSJnsJF-vPygdbXHyswDfnwbdvTR=b...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.12_2015.02.24.zip
this version adds the capability to very easily pop up a div (HTML5) or
window (Java) displaying a 2D image such as the current view, a chemical
drawing, or a standard Ramachandran plot. Anything that can be obtained as
one of the file formats Jmol reads (PNG, JPG, GIF, BMP)
Jmol.___JmolVersion="14.3.12_2015.02.24"
new feature: show IMAGE
-- pops up a frame with the current image
-- allows "Save As..."
new feature: show IMAGE "filename"
-- pops up a frame with the image loaded from a file
-- allows "Save As..."
new feature: show image 300 400 # adjustable size
new feature: show image NONE # closes all image panels
new feature: show image CLOSE # "all" presumed
new feature: show image CLOSE "" # the model image
new feature: show image CLOSE "c:/temp/t.bmp" # the image for this file
new feature: write IMAGE
-- same as SHOW IMAGE
new feature: write IMAGE 500 500
-- same as SHOW IMAGE 500 500; allows customization of width and height
new feature: Windows BMP image reading
-- reads 24-bit (full color) as well as 16-, 8-, 4-, 2-, and 1-bit color
palette modes
-- 14-byte and 40-byte headers only
-- does not read compressed modes
bug fix: restriction against getting SMILES string for biomolecule lifted
bug fix: end-on bonds may appear to disappear
bug fix: JavaScript -2.format("%8.3") gives 2.000 not -2.000
bug fix: minimizer treats hydrogen bonds as covalent single bonds
--
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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Message: 8
Date: Wed, 25 Feb 2015 16:07:27 +0000
From: Geoffrey Rowland <rowland.ge...@gmail.com>
Subject: [Jmol-users] GLmol not working?
To: jmol-users@lists.sourceforge.net
Message-ID:
<CAH7S2GUoYwLiJxonmggup8kT0BvLnbHDE0e0=-ntanan1ks...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Just noticed that the WebGL display is not working (blank, no structure
loaded) in recent stable releases of JSmol.
In my hands, the last working version was 14.2.9_2014.11.23.
Something broken, or am I doing something daft?
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Message: 9
Date: Wed, 25 Feb 2015 06:58:51 -0600
From: Robert Hanson <hans...@stolaf.edu>
Subject: [Jmol-users] show IMAGE - a new feature with lots of
potential
To: "jmol-users@lists.sourceforge.net"
<jmol-users@lists.sourceforge.net>
Message-ID:
<CAF_YUvVbTUFJZiAgdr5c6O+58MCxykfABbm=4kkr3pcw6bt...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
I thought I would point out what I think will be a hugely valuable new
feature of Jmol, both Java and JavaScript (hereafter referred to as
J(S)mol). This is hot off the press, and in fact is being compiled into
JavaScript and uploaded as I write. For sure it needs testing.
see http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.12_2015.02.25.zip
J(S)mol can now pop up 2D images on call that appear in separate frames,
either as floating divs on a web page (HTML5) or in a stand-alone frame
(Java). These can be static images such as
*show IMAGE "whatever.gif"*
*select 1.1; show chemical drawing*
or they can be dynamic:
*show IMAGE 500 500*
Thus, if you have static resources, you can now pop them up (and close
them) at will. More interesting, though, is that one could send dynamic
information to a server and retrieve an image. I am just starting to think
about the possibilities -- RNA loop diagrams, 2D binding site layouts,
custom Ramachandran plots, MO diagrams, spectra -- what else?
I'm hoping this message initiates some brainstorming and experimentation
among this group. Right now J(S)mol taps into the NCI Resolver for
structure drawings. For example, displaying
http://cactus.nci.nih.gov/chemical/structure/taxol/image for
*load $taxol*
*show drawing*
Q: What other resources are out there that could be pulled up with an ID or
SMILES string?
Bob
--
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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Message: 10
Date: Wed, 25 Feb 2015 15:56:04 +0000
From: "Spinney, Richard" <rspin...@chemistry.ohio-state.edu>
Subject: [Jmol-users] isosurfaces
To: "jmol-users@lists.sourceforge.net"
<jmol-users@lists.sourceforge.net>
Message-ID:
<f3ad8b5537452542bb84ab715e4f3815621ca...@cio-krc-d1mbx05.osuad.osu.edu>
Content-Type: text/plain; charset="us-ascii"
Isosurfaces seem to be broken in jmol 14.3.12 2015.2.22. Mapped surfaces are
appearing mono-colored rather than multi-colored, i.e. see
https://undergrad-ed.chemistry.ohio-state.edu/bonding/polar-covalent.html
Thanks, Rick
--------------------------------------
Dr. Richard Spinney
Department of Chemistry and Biochemistry
The Ohio State University
120A Celeste Laboratory
120 West 18th Ave
Columbus, Ohio 43210
email:
rspin...@chemistry.ohio-state.edu<mailto:rspin...@chemistry.ohio-state.edu>
Phone: (614) 247 - 6847
Fax: (614) 292 - 1685
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Message: 11
Date: Wed, 25 Feb 2015 14:18:35 -0600
From: Robert Hanson <hans...@stolaf.edu>
Subject: Re: [Jmol-users] mmcif reading problem?
To: "jmol-users@lists.sourceforge.net"
<jmol-users@lists.sourceforge.net>
Message-ID:
<caf_yuvxqxdhhfgqf61ryqj3wun9jrvupjahjwk2goquyuff...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.12_2015.02.25c.zip
Jmol.___JmolVersion="14.3.12_2015.02.25c"
bug fix: Jmol 14.1.2_2013.12.13 disabled some mmCIF file reading for
non-wwPDB mmCIF files
On Tue, Feb 24, 2015 at 8:46 AM, <s...@publcif.co.uk> wrote:
> Jmol doesnt appear to be recognizing/calculating secondary structure
> for some mmcifs - i.e. no cartoons etc.
>
> example cif is at http://cif.publcryst.co.uk/cifmoldb/gui/tests/noname.mcf
>
> This problem seems to apply to Jmol 14.2 onwards (i.e. works as expected
> with
> earlier versions).
>
> Any fix/help/workaround would be much appreciated
>
> Cheers
>
> Simon
>
>
>
>
> ------------------------------------------------------------------------------
> Dive into the World of Parallel Programming The Go Parallel Website,
> sponsored
> by Intel and developed in partnership with Slashdot Media, is your hub for
> all
> things parallel software development, from weekly thought leadership blogs
> to
> news, videos, case studies, tutorials and more. Take a look and join the
> conversation now. http://goparallel.sourceforge.net/
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
--
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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Message: 12
Date: Wed, 25 Feb 2015 14:45:53 -0600
From: Robert Hanson <hans...@stolaf.edu>
Subject: Re: [Jmol-users] mmcif reading problem?
To: "jmol-users@lists.sourceforge.net"
<jmol-users@lists.sourceforge.net>
Message-ID:
<CAF_YUvWfK-++XFfc6sWE-uT-pPTwsfPC4-bCPve=6pu9cfs...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Nice, simple mmCIF file. This would be a good template for us to use for
writing from Jmol.
I note that the following three fields in that sample file are ignored by
Jmol:
_atom_site.label_atom_id
(This data item is a pointer to _chem_comp_atom.atom_id in the
CHEM_COMP_ATOM category.)
_atom_site.label_comp_id
(This data item is a pointer to _chem_comp.id in the CHEM_COMP category.)
_atom_site.pdbx_auth_comp_id
(Author's residue name.)
Instead, Jmol uses:
_atom_site.auth_atom_id
(An alternative identifier for _atom_site.label_atom_id that may be
provided by an author in order to match the identification used in the
publication that describes the structure.)
_atom_site.auth_comp_id
(An alternative identifier for _atom_site.label_comp_id that may be
provided by an author in order to match the identification used in the
publication that describes the structure.)
I realize that these are listed as "alternative" identifiers; still, this
is what Jmol uses.
In contrast, Jmol requires these:
_atom_site.auth_asym_id (chain ID provided by author)
_atom_site.auth_seq_id (residue number provided by author)
but also reads these for special purposes:
_atom_site.label_asym_id (chain ID used in BIOMOLECULE definition, in
_pdbx_struct_assembly_gen)
_atom_site.label_seq_id (residue number used in validation and sequence
annotation references)
Bob
On Wed, Feb 25, 2015 at 2:18 PM, Robert Hanson <hans...@stolaf.edu> wrote:
> http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.12_2015.02.25c.zip
>
> Jmol.___JmolVersion="14.3.12_2015.02.25c"
>
> bug fix: Jmol 14.1.2_2013.12.13 disabled some mmCIF file reading for
> non-wwPDB mmCIF files
>
>
>
>
> On Tue, Feb 24, 2015 at 8:46 AM, <s...@publcif.co.uk> wrote:
>
>> Jmol doesnt appear to be recognizing/calculating secondary structure
>> for some mmcifs - i.e. no cartoons etc.
>>
>> example cif is at
>> http://cif.publcryst.co.uk/cifmoldb/gui/tests/noname.mcf
>>
>> This problem seems to apply to Jmol 14.2 onwards (i.e. works as expected
>> with
>> earlier versions).
>>
>> Any fix/help/workaround would be much appreciated
>>
>> Cheers
>>
>> Simon
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Dive into the World of Parallel Programming The Go Parallel Website,
>> sponsored
>> by Intel and developed in partnership with Slashdot Media, is your hub
>> for all
>> things parallel software development, from weekly thought leadership
>> blogs to
>> news, videos, case studies, tutorials and more. Take a look and join the
>> conversation now. http://goparallel.sourceforge.net/
>> _______________________________________________
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>
>
>
> --
> 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
>
>
--
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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Message: 13
Date: Wed, 25 Feb 2015 16:18:57 -0500
From: Onur Sumer <s.onur.su...@gmail.com>
Subject: [Jmol-users] HTTPS support
To: jmol-users@lists.sourceforge.net
Cc: Jianjiong Gao <j...@cbio.mskcc.org>
Message-ID:
<CA+49tJF5_4eDfTjCLioM-ApwK1=fftsbgyabs8eh9emc8mr...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hello,
We are using JSmol for the cBioPortal <http://www.cbioportal.org/> project.
We have encountered a problem with the HTTPS version of our web
application. Looks like JSmol cannot retrieve data from PDB when we host
our application through HTTPS.
This is the error message that I get in the console:
Mixed Content: The page at '
https://cbioportal.mskcc.org/index.do?tab_index=tab_visualize&cancer_study_?CA1+BRCA2&gene_set_choice=user-defined-list&Action=Submit#mutation_details'
was loaded over HTTPS, but requested an insecure XMLHttpRequest endpoint '
http://www.rcsb.org/pdb/files/3pxe.pdb'. This request has been blocked; the
content must be served over HTTPS.
And, here is the error message shown within the JSmol viewer:
[image: Inline image 1]
We also tried changing the *serverURL* parameter of the *Info* variable,
but looks like it doesn't work for PDB files.
Do you know if there is an easy way to allow loading the PDB files through
an HTTPS connection?
Thanks,
Onur
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