Also, a related aesthetic issue: try loading both maps with 'fill
translucent 0.3' and with the same colour.them compare how they look
separately. There's a difference: the 'outside' of the EDS map looks like
the 'inside' of the other map, and the other way around. So it looks like
the surface from my problematic ccp4 file is reversed inside-out.
Regards,
Adrià
2013/3/12 Adrià Cereto Massagué <[email protected]>
> 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
>>>
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>>
>
------------------------------------------------------------------------------
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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