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Re: [modeller_usage] template quality selection criteria

You can also have a look at the electron density map of your template(s). It would eventually be deposited in the EDS server (http://eds.bmc.uu.se/eds/); that is the one I know, there may be others.

After that, you can visualize the PDB and de ED map together with a proper tool (such as CCP4 or PyMOL), and see if there are regions with poor or without electron density (where you won't be able to trust your template). Besides that, you will have many statistics about the quality of the crystallographic structure itself.

Hope this helps.

Best regards,

2010/4/28 Stéphane Téletchéa <stephane.teletchea AT univ-nantes.fr>
Thomas Evangelidis a écrit :

Apart from sequence similarity to the target sequence and crystallographic resolution, someone told me I should also look to the electron density map info. Yet his english is not good and I haven't found yet the parameter he's referring to. Can anyone clarify what other parameters I should look to in order to select the best templates for modelling?

thanks,
Tom

I assume he was referring to the 'temperature' factor in the pdb file.
Using a lot of viewers, you can color atoms by this "temperature" factor and have a qualitative indication of where your template is "rigid" (low temperature factor), or is more flexible (higher temperature factor).

If you target needs a "hot" section of your template, you'll probably need to pay more attention to the modeling process, since the coordinates from these regions are prone to larger deviations.

Cheers,

Stéphane

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