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 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 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

On Thu, May 28, 2015 at 1:29 PM, jp d 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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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 mailto:[email protected]> 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 : [email protected] 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 mailto:[email protected]> 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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_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected] mailto:[email protected]

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