[3dem] Documentation on Difference Map tools

[Agnel Praveen Joseph - UKRI STFC]

Dear André,

The method for generating difference maps implemented in CCP-EM (and discussed in the paper you referred to) works by scaling the maps based on resolution dependent amplitude fall-offs before calculating difference. 

Latest version of CCP-EM software suite is available here (https://urldefense.com/v3/__https://www.ccpem.ac.uk/download.php__;!!Mih3wA!QHnA8ySGBEQKuH-n0cj7gdfbDQj7OiotKLlLlwvT2GcJHbLIdYkDxvm3T6UunGYXCA$ ), please use the nightly for recent updates. 

The difference map task can be accessed through the TEMPy:Diffmap tool in the CCP-EM GUI. Either two maps or a map and a model can be used as input. Scaling can be done globally (global mode, default) or in local windows (local mode). The local mode is slower but useful when there is variable local resolution. The output difference maps are saved in the job folder under the project that you are working on. The results page has the output maps which are linked to Chimera for visualisation. 
Additionally, fractional difference maps are also generated, which are simple fraction of difference w.r.t initial scaled map values. These will assist in locating areas of major differences.  
Optionally, the input page has option to post-process with a dust filter that removes smaller isolated densities (and associated with relatively minor differences). 

I am working on a tutorial/documentation which will be available soon. Meanwhile, please get back in touch if you have any questions.

Cheers,
Agnel 
 

> On 28 Jul 2020, at 18:28, André Graça <andre.graca at umu.se> wrote:
> 
> Dear community,
> 
> I am struggling to find good resources and documentation about appropriate tools to generate and help to interpret difference maps.
> 
> I have only found a paper (J. Chem. Inf. Model. 2020, 60, 2552−2560) about the tool integrated in CCP-EM software suite, but I wish to find more information. It is generally something I miss from the courses or tutorials I participated in. 
> 
> Can anyone recommend any literature? 
> 
> Keep enjoy the Summer!
> André Graça
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