It may be the case that the R-factors calculated by the refinement program
are based on anisotropic B-factor parameterisation (as seems to be the case
for 1sjw) or TLS-type refinements. The R-factor calculation performed by the
EDS may not take these into account, hence the discrepancies.
Not sure how to get round it though, other than emailing Gerard to change
the script, or do-it-yourself.
Martin
On 26/11/07 10:15, "Andreas Förster" <[log in to unmask]> wrote:
> Hey all,
>
> can I take this thread in an unforeseen direction? I've come across the
> same problem lately, the EDS's "automatic script failed to produce an
> electron density map" for a structure I'm analyzing. Besides being
> amazed that the EDS uses automatic scripts - I thought Gerard would type
> one for every submission - I'm wondering how to proceed.
>
> With all due respect to the original poster, do I assume the structure
> is rubbish? Or is it DVD's script? Should I completely reanalyze?
> Where does the problem likely lie? And how to get around it?
>
> Thanks.
>
>
> Andreas
>
>
>
> William Scott wrote:
>> Here is the problem:
>>
>> http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode=1sjw
>>
>> EDS won't make a map because it thinks your R-factor is too low compared
>> to the one it calculates.
>>
>> So it isn't coot's fault at least.
>>
>>
>>
>> William Scott wrote:
>>> I tried 1sjw and it failed in the way you described.
>>>
>>> I then tried one of mine (2goz) and it worked fine.
>>>
>>> Presumably this could happen if there is no 1sjw or the data are not
>>> available...
>>>
>>>
>>> Azmiri Sultana wrote:
>>>> Hi,I am using the coot version 0.4 pre 1 on my OSX leopard. Now, I can
>>>> not
>>>> use the options 'Get PDB and map from EDS' or 'get PDB
>>>> using accession code'. I get some mtz and ent files in the
>>>> coot-download
>>>> directory if I use the EDS server.
>>>> Here is the error message I get if I use EDS:
>>>>
>>>> "PDB Accession Code: 1sjw
>>>> read model status: #<closed: file 0>
>>>> read mtz status: #<closed: file 0>
>>>> Reading coordinate file: coot-download/pdb1sjw.ent
>>>> There was an error reading coot-download/pdb1sjw.ent.
>>>> ERROR 20 READ: Attempt to read unknown-type file.
>>>> No Spacegroup found for this PDB file
>>>> Cell: 1 1 1 90 90 90
>>>> There was a coordinates read error
>>>>>>>>>> CCP4 library signal mtz:File not identified as MTZ (Error)
>>>> raised in MtzGet <<<<<<
>>>> CCP4MTZfile: open_read - File missing or corrupted:
>>>> coot-download/1sjw_sigmaa.mtz
>>>> INFO:: not an mtz file: coot-download/1sjw_sigmaa.mtz
>>>> ERROR: no f_cols!
>>>> ERROR: no phi_cols!
>>>> WARNING:: label(s) not found in mtz file coot-download/1sjw_sigmaa.mtz
>>>> 2FOFCWT PH2FOFCWT
>>>>>>>>>> CCP4 library signal mtz:File not identified as MTZ (Error)
>>>> raised in MtzGet <<<<<<
>>>> CCP4MTZfile: open_read - File missing or corrupted:
>>>> coot-download/1sjw_sigmaa.mtz
>>>> INFO:: not an mtz file: coot-download/1sjw_sigmaa.mtz
>>>> ERROR: no f_cols!
>>>> ERROR: no phi_cols!
>>>> WARNING:: label(s) not found in mtz file coot-download/1sjw_sigmaa.mtz
>>>> FOFCWT PHFOFCWT
>>>> WARNING:: -1 is not a valid molecule in set_scrollable_map"
>>>>
>>>> If I use the PDB server I get the following error message:
>>>> "Reading coordinate file: coot-download/1sjw.pdb
>>>> There was an error reading coot-download/1sjw.pdb.
>>>> ERROR 41 READ: Non-existent or empty file.
>>>> No Spacegroup found for this PDB file
>>>> Cell: 1 1 1 90 90 90
>>>> There was a coordinates read error"
>>>>
>>>> This error msg is understandable because the PDB file in the coot
>>>> directory
>>>> empty. Why am I getting empty PDB file?
>>>>
>>>> Any help is greatly appreciated!!!
>>>>
>>>> Thanks,
>>>> Azmiri
>>>>
>>
---------------------------------------------------------------------
Martin R. Singleton
Macromolecular Structure and Function Laboratory
Cancer Research UK
Lincoln's Inn Fields Laboratories
44 Lincoln's Inn Fields
London WC2A 3PX
Phone: +44 (0) 207 269 3148
Fax: +44 (0) 207 269 3258
Email: [log in to unmask]
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