[phenixbb] depositing pdb files

[Mengbin Chen]

Got it, thanks Phil!

Mengbin Chen


On Tue, May 21, 2013 at 4:22 PM, Jeffrey, Philip D.
<pjeffrey at princeton.edu>wrote:

>  In the section that looks like this in the header of the PDB file out of
> phenix.refine:
> REMARK   3  DEVIATIONS FROM IDEAL VALUES.
> REMARK   3                 RMSD     MAX  COUNT
> REMARK   3   BOND      :  0.002   0.058   6768
> REMARK   3   ANGLE     :  0.634   9.630   9127
> REMARK   3   CHIRALITY :  0.046   0.300   1037
> REMARK   3   PLANARITY :  0.003   0.040   1182
> REMARK   3   DIHEDRAL  : 13.422  88.272   2558
>
>  The bottom line is that the PDB file out of refinement contains much of
> the info you will need for the refinement section of PDB deposition.
>
>  Phil Jeffrey
> Princeton
>  ------------------------------
> *From:* phenixbb-bounces at phenix-online.org [
> phenixbb-bounces at phenix-online.org] on behalf of Mengbin Chen [
> mengbinc at sas.upenn.edu]
> *Sent:* Tuesday, May 21, 2013 4:15 PM
> *To:* PHENIX user mailing list
> *Subject:* Re: [phenixbb] depositing pdb files
>
>   I see, thanks a lot! Also, where can I get the rmsd dihedral angle
> value?
>
>  Thanks again,
> Mengbin
>
>
> On Tue, May 21, 2013 at 3:56 PM, Ed Pozharski <epozh001 at umaryland.edu>wrote:
>
>>  Just do not report luzzati errors, they are essentially meaningless.
>> PDB is not going to reject your deposition because of that.
>>
>>
>> On 05/21/2013 03:15 PM, Mengbin Chen wrote:
>>
>>  Hi Phenix Users,
>>
>>  I am going to deposit some pdb files into RCSB, which requires Luzzati
>> plots and a bunch of other things. I don't know how to get these results
>> from Phenix (actually the main problem is luzzati errors, Phenix does not
>> seem to provide them), although SFcheck from CCP4i provides only some of
>> them. I know CNS can do this by model_stats.inp, but that's too much
>> trouble since I have complicated ligands bound.  Any suggestions would be
>> appreciated!
>>
>>  Thank you in advance,
>> Mengbin
>>
>>  --
>> Mengbin Chen
>> Department of Chemistry
>> University of Pennsylvania
>>
>>
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>> phenixbb mailing listphenixbb at phenix-online.orghttp://phenix-online.org/mailman/listinfo/phenixbb
>>
>>
>>
>> --
>> Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
>>                                                 Julian, King of Lemurs
>>
>>
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>
>
>  --
> Mengbin Chen
> Department of Chemistry
> University of Pennsylvania
>
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>


-- 
Mengbin Chen
Department of Chemistry
University of Pennsylvania
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