[phenixbb] one or more errant TER cards

jp d yoyoq at yahoo.com
Wed Mar 20 08:58:53 PDT 2013


hi,
the work directory is here

http://musso.ucsc.edu/phenix/refine_andrei/

the last script i tried is here
http://musso.ucsc.edu/phenix/refine_andrei/refref.csh

the chain is empty for everything.
it is all identified by segid
should i assign chains to everything ?

thanks
jpd



--- On Tue, 3/19/13, Jeff Headd <jjheadd at lbl.gov> wrote:

From: Jeff Headd <jjheadd at lbl.gov>
Subject: Re: [phenixbb] one or more errant TER cards
To: "PHENIX user mailing list" <phenixbb at phenix-online.org>
Date: Tuesday, March 19, 2013, 6:03 PM

If you've removed all of the TER cards then that error shouldn't still be showing up. If it is, then that's a bug.
Do all of your chains have the same chain ID, but different segid's? That could be problem, though that should work.


Would you be willing to send me the input files (off list)? It will be easier to diagnose what is going on if I can have a look at exactly what is going on.
Jeff



On Tue, Mar 19, 2013 at 8:42 PM, jp d <yoyoq at yahoo.com> wrote:


hi,

i am trying to refine using a reference model

and keep getting this error



*** Adding Reference Model Restraints ***

Sorry: chain ' ' in start.pdb contains one or more errant TER cards.

Please remove and try again



i've tried various things including removing all the TER lines

my models (reference and working) has many chains identified by segid's

any suggestions ?



thanks

jpd





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