[phenixbb] depositing pdb files
mengbinc at sas.upenn.edu
Tue May 21 13:29:21 PDT 2013
Got it, thanks Phil!
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
> 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
> *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
> Thanks again,
> 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
>> Thank you in advance,
>> Mengbin Chen
>> Department of Chemistry
>> University of Pennsylvania
>> 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
>> phenixbb mailing list
>> phenixbb at phenix-online.org
> Mengbin Chen
> Department of Chemistry
> University of Pennsylvania
> phenixbb mailing list
> phenixbb at phenix-online.org
Department of Chemistry
University of Pennsylvania
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