[ccp4bb] השב: [ccp4bb] LSQKAB with trajectory files

[Boaz Shaanan]

Hi Charlie, one possible way of doing this is through UCSF-Chimera. It'll read each of the models into a different slot, then you can apply the transformation you choose to each of the models. I think I'm right. The Chimera support team may help you figure out how to do this in one go.

Best regards,

 Boaz

-------- הודעה מקורית --------
מאת "Carter, Charlie" <car...@med.unc.edu>
תאריך: 03/11/2013 20:24 (GMT+02:00)
אל CCP4BB@JISCMAIL.AC.UK
נושא [ccp4bb] LSQKAB with trajectory files

I've just tried to use LSQKAB to transform an entire trajectory file that is a pdb file with ENDMDL cards between models to a new orientation for the purpose of making use of work with the new orientation.

LSQKAB returns with an error:

 *** RWBROOK error: point code unit    function
 ***                    1  -41    1    MMDB_F_Open
 *** file   : Cat_3state_traj.pdb
 *** reason : MMDB's error in structuring models
 ***          at input line #2665:
 ATOM      1  N   MET     1      19.334   0.098  11.397                         
 *** continue running, may crash ...
 
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 LSQKAB:   XYZOPEN: Error opening logical name XYZINM
 LSQKAB:   XYZOPEN: Error opening logical name XYZINM

This suggests that xyzfit cannot repeat a transformation on each model and then output a rotated pdb file for the trajectory.

Can anyone suggest an alternative, either involving lsqkab or another superposition program?

Many thanks,

Charlie