[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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