[phenixbb] reference model restraints by segid

Pavel Afonine pafonine at lbl.gov
Thu May 28 14:39:49 PDT 2015


I suspect this is a ribosome structure.. It would be great to make this 
work indeed, so if it still does not work please send us inputs so we 
can investigate.
Pavel

On 5/28/15 10:34 PM, Oleg Sobolev wrote:
> Hi,
>
> If removing of TER indices won't work in dev-2056, I will be happy to 
> investigate and find a way to make it work for everybody. To do so I 
> will need the inputs you are using (i.e. models and parameter files)
>
> Best regards,
> Oleg Sobolev.
>
> On Thu, May 28, 2015 at 2:10 PM, Nigel Moriarty <nwmoriarty at lbl.gov 
> <mailto:nwmoriarty at lbl.gov>> wrote:
>
>     The error says it doesn't like the TER cards. Remove them all and
>     retry.
>
>     Cheers
>
>     Nigel
>
>     ---
>     Nigel W. Moriarty
>     Building 64R0246B, Physical Biosciences Division
>     Lawrence Berkeley National Laboratory
>     Berkeley, CA 94720-8235
>     Phone : 510-486-5709 <tel:510-486-5709>     Email : NWMoriarty at LBL.gov
>     Fax   : 510-486-5909 <tel:510-486-5909>       Web  : CCI.LBL.gov
>     <http://CCI.LBL.gov>
>
>     On Thu, May 28, 2015 at 1:29 PM, jp d <yoyoq at yahoo.com
>     <mailto:yoyoq at yahoo.com>> wrote:
>
>         Hi,
>         I am having trouble getting phenix to used segid's in
>         reference model restraints when
>         my reference and target pdbs both don't use chain ID's.
>         phenix quits with this message:
>
>         *** Adding Reference Model Restraints ***
>         Sorry: chain ' ' in /home/path/removed/agnref2.pdb contains
>         one or more errant TER cards.
>         Please remove and try again.
>
>         my definition file looks like this:
>         refinement {
>            main {
>              reference_model_restraints = True
>            }
>            reference_model {
>              file = two.pdb
>            }
>         }
>
>         refinement.reference_model.reference_group {
>          reference = segid A16S
>          selection = segid A16S
>         }
>         (above about 50 more times)
>
>         this was on versions 1.9-1692 , dev-2016 and dev-2056
>
>         any suggestions ?
>         thanks
>         jpd
>
>
>
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