Well, now this gets weirder.
Not it *sometimes* loads as before. Here's the result:
http://dl.dropbox.com/u/41040783/weird2.png (this is a PNGJ file too).
If you open it with Jmol (it uses the same files as before), the result
will not be like the image: the blue and yellow isosurfaces will be
superposed, which is the expected result.
I cannot reproduce it neither from a PNGJ nor from a .jmol file (like this
one http://dl.dropbox.com/u/41040783/weird2.jmol). Also, for some reason,
from the 3 isusurfaces I make out of the same file, it only happens to one
of them (the cyan one). I cannot even reproduce it consistently.
This is with Jmol 13.0.12. I couldn't find 13.0.14 for download.
2013/3/12 Adrià Cereto Massagué <[email protected]>
> Indeed, with Jmol 13.0.12 it works as it should.
>
> Thank you for your help.
>
>
> 2013/3/12 Robert Hanson <[email protected]>
>
>> I opened that with Jmol 13.0.14 with no problem. See
>> http://chemapps.stolaf.edu/jmol/temp/toadria.png
>> (This is a PNGJ file -- you should be able open it in Jmol.)
>>
>> So I think you just need to upgrade.
>>
>>
>> On Tue, Mar 12, 2013 at 5:38 AM, Adrià Cereto Massagué <
>> [email protected]> wrote:
>>
>>> Hi,
>>>
>>> I'm having a strange problem with a CCP4 and Jmol 13.0.6.
>>> I load a model from a pdb file, and then load the CCP4 file. When I do
>>> this in PyMol or Coot, the model fits inside the electron density at 1
>>> sigma. However, in Jmol, nothing fits. It looks like the electron density
>>> is offset or something like that. If I load a CCP4 file from the EDS it
>>> 'fits' as it should.
>>>
>>> If I couldn't get the expected result in Pymol or Coot without doing
>>> anything special, I would blame the CCP4 file, but that's not the case.
>>> Am I missing something?
>>> Here's a link to a zip archive with all the files needed to reproduce it
>>> (the PDB file, the 2 CCP4 files and a text file containing the script I use
>>> to load them): http://dl.dropbox.com/u/41040783/weird_edm.zip
>>>
>>> Any help woulb be appreciated.
>>>
>>> Regards,
>>>
>>> Adrià
>>>
>>> --
>>> *Adrià Cereto Massagué*
>>> Ph.D Student
>>> Nutrigenomics Research Group
>>> Biochemistry and Biotechnology Department
>>> Building N4, Campus Sescelades
>>> Universitat Rovira i Virgili
>>> Tarragona, Catalonia
>>>
>>> Languages: Català, Español, English, Français, Deutsch, Português
>>>
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>>>
>>>
>>> ------------------------------------------------------------------------------
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>>
>>
>> --
>> Robert M. Hanson
>> Larson-Anderson Professor of Chemistry
>> Chair, Chemistry Department
>> St. Olaf College
>> Northfield, MN
>> http://www.stolaf.edu/people/hansonr
>>
>>
>> If nature does not answer first what we want,
>> it is better to take what answer we get.
>>
>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester
>> Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the
>> endpoint security space. For insight on selecting the right partner to
>> tackle endpoint security challenges, access the full report.
>> http://p.sf.net/sfu/symantec-dev2dev
>>
>> _______________________________________________
>> Jmol-users mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
------------------------------------------------------------------------------
Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester
Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the
endpoint security space. For insight on selecting the right partner to
tackle endpoint security challenges, access the full report.
http://p.sf.net/sfu/symantec-dev2dev
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