That's fair enough.
Thanks for clarifying the situation.
Cheers
Simon
Quoting Robert Hanson :
> The difference is that the mmCIF reader was split off from the CIF reader.
> In the past, the CIF reader included all the macromolecule code, and
> somewhere along the way of reading it all Jmol de
Sorry - I was looking at the script console.
Indeed Jmol 14.3.12 and Jmol 13.3.7 both 'think Cif'
Console output is below for both:
1) From Jmol 14.3.12_2015.02.25c:
cacheGet file:/srv/www/htdocs/publcryst/cifmoldb/gui/tests/4QQS.cif false
FileManager opening 1
file:/srv/www/htdocs/publcryst
Using Jmol application I dont get any 'resolver' messages in the console,
and using the Jmol application to open a file via the menus you dont get an
option to say 'this is an mmcif'.
Fair enough I can pre-process the CIF or script Jmol to make sure it
will be recognized by Jmol (application or
Thanks for the info -
the original problem was the second example I gave -
I only added the blank lines in order to try and figure out what the problem
was.
In the case of the second example, Jmol-13.3.7 had no problem with
reading the CIF, while Jmol 14+ doesnt offer cartoons as an option etc.,
b
I'm afraid I'm still having some problems:
If I add 13 blank lines after the start of a data block,
Jmol seems to not handle the secondary structure again, e.g.
data_UNNAMED
#
loop_
_atom_site.group_PDB ...
Furthermore, its not just blank lines, e.g.
data_
_atom_sites.entry_
Thanks for this, and fixing the problem. For info, this mmCIF is the sort of
thing that may be available to an author before the full pdb mmCIF is
generated/available, so its great that Jmol can handle such things.
On an unrelated matter, its also great that JSmol can produce animated gifs
from
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/wo
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/wo
I use gifsicle to reduce the size of Jmol's animated gifs
see http://www.lcdf.org/gifsicle/
Quoting GABRIEL PONS IRAZAZABAL :
>
> Good Morning,
> I have two qüestions:
> 1. The animated gif Works very well in the last version of jmol.
> However, In my hands the size of the file is too big an
Do you mean this sort of thing:
http://cif.publcryst.co.uk/cifmoldb/gui/cifjmol.php?fetch=https://dl.dropboxusercontent.com/u/71197105/eg3122.cif
(its a service that the IUCr are considering)
If so, I too would be interested if there are any sites out there that
provide such services... i.e. fe
Thanks Bob - I'll certainly change the description.
Cheers
Simon
PS - I think I used Jmol defaults in generating the gifs - I'll check...
Quoting Robert Hanson :
> Fantastic, Simon. This will go a long way to informing people. I would like
> to suggest some more explicit explanation in:
>
>
>
For anyone interested in modulated structures and especially
Jmol's visulaization - see http://publcif.iucr.org/cifmoldb/mscif/
Not a fully 'public' page yet - will probably add some of Bob's links...
Quoting Robert Hanson :
> [Sorry for the blog-like nature of this message. I'm not ready to
Just for info, I've tested the animated gif creation with 60+ msCIF
structures in the IUCr archive and am extremely pleased to report that
both representation of the modulation and gif creation worked very nicely
in all cases.
Anyone interested in modulated structures might like to take a look at
Just for info, I've found JAVA detection can not be relied upon
as even if the browser reports that JAVA is present, it may not
actually be enabled (browser blocks it).
I used to work around this by trying to run a simple jmolscript on a
timeout after I'd initialized the jmol applet and 'catching
This msCIF stuff is excellent.
However, the scaling and vibration dont seem to be working in
the jsmol version?
Cheers
Simon
Quoting Robert Hanson :
> some major improvements on the code. See
> http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.1_2013.12.11b.zip and
> http://chemapps.stolaf.edu/jm
Thanks Bob - all is well
Quoting Robert Hanson :
> select symop=1555 is fixed.
>
> http://chemapps.stolaf.edu/jmol/zip/jmol-14.0.1_2013.12.09.zip (uploading
> now)
>
>
> On Mon, Dec 9, 2013 at 12:28 PM, Robert Hanson wrote:
>
>> should be a fixable bug.
>>
>>
>> On Mon, Dec 9, 2013 at 4:56 AM,
Hi - some of my scripts no longer work with Jmol14
In the first instance I've narrowed this down to
select symop=1555
This selects nothing even though I'm working with CIFs that
have the symmetry information.
symop=1 works OK but symops with the 'ijk' translation part fail.
Has something been
Excellent - it works!
Thanks very much
Simon
Quoting Robert Hanson :
> please try
>
> http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.25c.zip
>
> Not only was there an issue with the applet, Jmol was not filtering the
> atoms correctly, either. These look MUCH better!
>
>
>
> On Mon, No
Good to see that the Java certification issue seems to be sorted.
With respect to bug-fix requests, I'm still experiencing the following
problem:
calling:
load =3fsx.cif filter "ASSEMBLY 1"
works in the Java application *only*. That is, it
causes the Java Applet to 'hang' and produces the fol
I have been in touch with an organization that is prepared to
sponsor the certification - i.e. they will donate the money -
but it is unlikely that they would want the certificate in their name,
partly because of the legal considerations and partly because they
feel strongly that such sponsorship
Although Jsmol is impressive, far too often I get 'script taking too long'
messages from the browser, so although I believe the future of Jmol
lies in Jsmol, I woul not like to lose the java applet at this time
simply because of
supposed security threats...
Cheers
Simon
Quoting "Rzepa, Henr
Assuming the $500 certificate ensures that the signed Jmol java applet
will not be blocked (?), I suspect there are a number of organizations that
would be prepared to become sponsors...
Quoting Robert Hanson :
> I direct the discussion to
>
> https://blogs.oracle.com/java-platform-group/entry/
Tried this and the latest release and I'm afraid there's still a problem.
I've experimented quite a bit and it looks like an assembly that is
generated by using *only* the identity operation is causing the problem.
e.g. in the cae of 3fsx:
loop_
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_
Thanks, but I now get the error:
File Error:ERROR creating model: TypeError: c.get(...).get(...) is null
script ERROR: ERROR creating model: TypeError: c.get(...).get(...) is null
when calling load =3fsx.cif filter "ASSEMBLY 1"
However, I am also unable to use the java applets at all
(I'm gettin
Calling:
load =3fsx.cif filter "ASSEMBLY 1"
gives the following error:
for file http://www.rcsb.org/pdb/files/3fsx.cif
type MMCIF_PDBX
script ERROR: Error reading file at line 14991:
2 1,2,3 D,Q,R,S,T,U,DA
null
Am I doing something wrong, or is Jmol (version 13.3.4), or perhaps the PDB?
Cheers
Me too
Quoting Naomi Fox :
> I just updated to the latest stable version of jsmol from the Jmol 13.2.7
> full download.
>
> When I loaded the jmol viewer in my web page, I got the following error:
>
>
> Jmol applet jmol_object__004228470381349__ ready
> call loadScript ..\..\js\J\viewer\Sc
For multiple applets, I've been storing references to the applets in an array:
var newapp=Jmol.getApplet('jmolApplet'+modelno, Info);
myapplets[modelno]=newapp;
But I haven't updated to latest Jmol yet.
Quoting Otis Rothenberger :
> I'm having an erratic display issue with multiple applets.
OK CIF reader seems to be coming along nicely (it emulates
Jmol's {ijk i'j'k' 0} load and reduces to a 'molecular' view)...
so will hopefully have a demo available within the week (assuming
I don't eat too many chocolate bunnies in the meantime :-)
Cheers
Simon
Quoting Bob Hanson :
> Ps. If
Yes, a CIF reader is on its way (actually part of something else I'm
working on). That said, I'd prefer to use one app ('jmol') so will
certainly have a look
at JSmolTM...
Cheers
Simon
Quoting Robert Hanson :
> It would be nice to have a CIF reader; createRadialGradient() is great.
> I'll l
Thanks for this - useful to know.
Simon
Quoting Robert Hanson :
> The original question was related to jsmol - does jsmol add some
>>> properties to the javascript array object?
>>>
>>
>
> Yes it does. Most importantly, it implements several types in ALL browsers:
> Float64Array and Int32Array
Just found this while looking for the answer to another unrelated question
(see below). Coincidentally I've been working on much the same sort of thing -
i.e. a quick 'first view' with the option to load the full Jsmol on demand,
for use on the IUCr's 3d view pages. Its based on GLmol as a model -
Might be of interest:
"Jana2000 can export modulated structure
into a user defined three-dimensional area as a standard structure
with one large cell
of symmetry P1 and call an external viewer to plot it"
See: http://jana.fzu.cz/doc/manual2000_part1.pdf
A year or so ago, there was some discus
I recently encountered problems with FF on linux -
1) the linux distro didnt come with sun java
2) even after installing sun java, FF still had an icedtea java plugin -
I had to remove this to get applets to work properly.
This may not be relevant to your problem, but might be worth noting anyw
Thanks for fixing this
Cheers
Simon
Quoting Robert Hanson :
> sure enough. CIF reader (specifically) not reading D or T.
> You should be able to find the fixed version here in a few minutes:
> http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/Jmol-12.zip
>
> On Sat, Sep 3, 2011 at 7:15 AM
Seems the problem is with
_atom_site_type_symbol being set as D for deuterium
If I change it to H, the CIF loads OK.
Cheers
Simon
Quoting s...@publcif.co.uk:
>
> Dear Jmol team
>
> The attached CIF will not load in Jmol 12.1 unless I remove the bond loops.
> I get an "unexpected end of fil
Dear Jmol team
The attached CIF will not load in Jmol 12.1 unless I remove the bond loops.
I get an "unexpected end of file after line..." error message.
The CIF looks fine, and opened in an older version of Jmol, so I
suspect this is
a bug in the release candidates. Please forgive if this isn
One last quick question related to this:
Once Jmol has loaded a molecular view, is there any way of knowing whether the
model is polymeric? I've looked at the modelinfo properties etc but cant
see anything obvious (please forgive me if I missed something though).
The reason I ask is because for o
This works fine now - thanks very much.
Cheers
Simon
Quoting Robert Hanson :
> You should be able to get the correct molecular view even without any {xxx
> xxx xxx}, but maybe only if you use the latest build. Would you please try
> that? http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol
Quoting Dean Johnston :
Thanks for this Dean - both scripts work nicely
I hadnt tried the extended load {333 777 1} before -
starting with it, I can now produce a correct 'molecular view' also.
Cheers
Simon
>
> Simon,
>
> Here's what I've used. It obviously only works for molecular systems an
Quoting r...@ellerbach.com:
> On [2011-Jul-14] Robert Hanson wrote:
>> OK, I got it. In generating models, Jmol was not establishing this
> connection:
>>
>> C4 C6 2_855 1.393(3)
>>
>
> [snip]
>
>> I'll take a look at this and get back to you. I'm a bit surprised that
> Jmol can't handle it
The model should contain a
2,2'-(p-Phenylene)bis(4,5-dihydro-1H-imidazol-3-ium)
molecule, but just displays half of it (the imidazol plus half the phenylene -
the remainder being related by symmetry). For a better picture, see
http://journals.iucr.org/e/issues/2011/02/00/ds2078/index.html
or uplo
I'm having trouble obtaining a 'molecular view' from a CIF (attached) -
seems very difficult to obtain a connected molecule for one of the moities
(as well as jmols 'molecular load', I've tried various unit-cell loads
coupled with scripts to find and display the connected molecules).
Any help or
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