[phenixbb] how to generate an isomorphous difference map

[Philip Kiser]

Good points. But also, the traditional isomorphous difference map is not as
susceptible to model bias issues compared to a real space difference map
(or a "vector" isomorphous difference map).

On Tue, May 12, 2015 at 11:37 AM, Edward A. Berry <BerryE at upstate.edu>
wrote:

>
>
> On 05/12/2015 09:46 AM, Philip Kiser wrote:
>
>> crystallogrphy,
>>
>> If you did everything correctly, you should be able to directly calculate
>> the difference map in Coot from the MTZ file generated by PHENIX. You would
>> need to open it with "Open MTZ" rather than "Auto open MTZ" and then select
>> the appropriate map coefficients. Note that what Tim described (a real
>> space difference map) is technically different from the traditional
>> isomorphous difference map where the SF amplitudes of the two data sets are
>> subtracted prior to the map calculation.
>>
>> Philip
>>
>
> Should be the same, due to linear property of the Fourier transform,
> EXCEPT for possible scaling differences and treatment of missing data.
> This latter could be significant, since presumably the traditional methods
> omits reflections unless present in both datasets, whereas in Tim's method
> each map will be made with all data available in that dataset. As a result,
> the largest coefficients in Tim's difference map might be the reflections
> which are absent in one map and present in the other.  But if both have
> good completeness, it  may not matter.
>
> eab
>
>
>
>> On Tue, May 12, 2015 at 9:24 AM, Tim Gruene <tg at shelx.uni-ac.gwdg.de
>> <mailto:tg at shelx.uni-ac.gwdg.de>> wrote:
>>
>>     Dear crystallogrphy,
>>
>>     you can open the PDB file with Coot, then use File -> Open MTZ to
>> read one
>>     mtz-file after the other into Coot. Coot will offer to generate the
>> map
>>     coefficients from the previously loaded PDB file.
>>
>>     Once you have both maps, you can go to Extensions -> Maps -> Make a
>> Difference
>>     Map to create the difference map.
>>
>>     In order to see both positive and negative density, you choose
>> Extensions ->
>>     Maps -> Set Map is a Difference Map.
>>
>>     Regards,
>>     Tim
>>
>>     On Tue, May 12, 2015 at 08:43:45PM +0800, crystallogrphy wrote:
>>      > Hi,
>>      >
>>      > I am trying to generate an isomorphous difference map with phenix
>> GUI. I
>>      > input reflection 1 and 2 with mtz format and a PDB model, I got an
>> MTZ
>>      > format map file. Because I want to load it to coot or pymol with
>> negative
>>      > and positive density, I need to transform this mtz map to ccp4 map.
>>      > However, FFT map cannot work.
>>      > Does any know how can I get a ccp4 format maps with positive or
>> negative
>>      > density?
>>      >
>>      > Thanks!
>>
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>>
>>     --
>>     --
>>     Dr Tim Gruene
>>     Institut fuer anorganische Chemie
>>     Tammannstr. 4
>>     D-37077 Goettingen
>>     phone: +49 (0)551 39 22149 <tel:%2B49%20%280%29551%2039%2022149>
>>
>>     GPG Key ID = A46BEE1A
>>
>>
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