[phenixbb] Help for pdb deposition

qiang liu qiangliuscu at gmail.com
Mon Feb 14 04:29:32 PST 2011


Hi,Fred,

Thank you very much.I will try to upload the mtz file after scala.

Qiang

2011/2/14 Vellieux Frederic <Frederic.Vellieux at ibs.fr>

> Hi,
>
> the mtz file you are trying to deposit is the mtz file obtained after
> refinement, which contains the map calculation coefficients. This is not
> what the PDB requires, they require the input mtz file for refinement (which
> should contain H K L FP SIGFP FreeRFlag). Simple as that... This mtz file is
> the mtz file obtained after data processing (either MOSFLM, XDS, D*TREK....)
> and generation of the Free Rfactor test set.
>
> Fred.
>
> qiang liu wrote:
>
>>  Hi,Dear all,
>>  Maybe it's a simple question for you,because I am a beginner in
>> crystallography. Recently I deposited a structure in the pdb and got a reply
>> bellow.
>> "The deposited structure factor file is incomplete. We failed convert the
>> deposited mtz file to cif format. Please send me the correct SF file
>> including h, k, l, F, SigmaF (and/or I and SigmaI)and test flags as an
>> attachment."
>>  The mtz file I uploaded is map_coeffs.mtz after refinement.The column
>> lables are listed.
>>
>>  type    column lable
>>  H             H
>>  H             K
>>  H             L
>>  F             2FOFCWT
>>  P             PH2FOFCWT
>>  F             2FOFCWT_no_fill
>>  P             PH2FOFCWT_no_fill
>>  F             FOFCWT
>>  P             PHFOFCWT
>>
>>  So how can I get the parameters for deposition in PHENIX?  Any
>> suggestions will be appreciated! Thank you very much.
>>
>> Qiang Liu
>> ------------------------------------------------------------------------
>>
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>
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