Re: [phenixbb] generate_cif_for_NT_MPD

On Tue, Mar 6, 2012 at 3:05 AM, Xue-Yuan Pei wrote:

Yes, I did try to import both cif files (for nucleic acid and MPD individually) into phenix.refine, but with no luck. any suggestion?

Can you please send us the .eff file and log file for a representative run? You can email them to [email protected] if you don't want the entire list to see. thanks, Nat

Regards, Xue

On Mon, 5 Mar 2012, Kelly Daughtry wrote:

...

Maybe I'm missing something here, but don't you just import both cif files (for nucleic acid, and MPD individually) into phenix.refine? Did you try that?Kelly Daughtry

******************************************************* Kelly Daughtry, Ph.D. Post-Doctoral Fellow, Raetz Lab Biochemistry Department Duke University Alex H. Sands, Jr. Building 303 Research Drive RM 250 Durham, NC 27710 P: 919-684-5178 *******************************************************

On Mon, Mar 5, 2012 at 12:29 PM, Xue-Yuan Pei wrote:      Dear All:      I am using phenix-1.7.2 to refine my structure. Now i am facing a problem with .cif file. I could not generate       cif files for a modified nucleic acid and MPD at same time with phenix.elbow or phenix.ready_set. If I use      phenix.elbow to generate cif file for modefied nucleic acid only, phenix .refine complains about MPD cif not      found, same for MPD. If I combine two cif files together, phenix.refine also complains. Is there better to      generate cif file containing both modified nucleic acid and MPD?      Many thanks for your help,      Xue

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