[Chimera-users] Issue with Comparative Modeling Tutorial

Elaine Meng meng at cgl.ucsf.edu
Sat May 31 09:50:30 PDT 2014

Hi Janan Zhu,
You are correct, I see that the behavior has changed since the tutorial was created: the scores that are already there don't get updated.

I didn't know about this change until you mentioned it.  I'll open a bug report about it, but in the meanwhile you would just have to use the scores that were assigned after the deletion.

Another possibility is to use the SaliLab Model Evaluation Server directly, but that's more work since you would have to save the sequence alignment as Aligned NBRF/PIR format and the models as PDB files from Chimera and then upload them to the server:

Thanks for letting us know,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On May 30, 2014, at 9:03 PM, Janan Zhu wrote:

> Hi,
> I'm new to Chimera and I've been trying to learn about the various features of the program through the tutorials. 
> I've been having issues with the Comparative Modeling Tutorial from the User Guide (link here) - for some reason, when I try to get updated zDOPE scores after deleting the unaligned termini of the target sequence, the zDOPE scores fail to update, and I only get new RMSD and overlap values. If I try calculating the scores again, I get a message that all models already have scores assigned.
> I've tried this both with the tutorial structure and some of my own structures and I get the same result. Could anyone possibly provide any assistance with this?
> Thank you,
> Janan Zhu

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