Hi Pavel, Can I please cast my vote for option 2 ("add this option to PHENIX"). This is something I find myself wanting to do fairly often (it accelerates the disappointment of finding out your active site is empty *again* : ) Cheers, Stephen 2009/4/28 Pavel Afonine :

Hi Charlie,

there is no specific tool in PHENIX to do so. However, I remember I wrote such script using PHENIX components for someone a while ago...

Here are the options:

- I can just sent you that script, where you will have to put in your file names, Fobs labels, etc, and run it as: phenix.python script.py

- I can add this option to PHENIX, so it will be something like: "phenix.fo_minus_fo_map". In this case it will take a day or two before it appears in a nightly build and you can download the updated version of PHENIX where it will be available.

- You can send me the data and I compute this map for you. I think I will add this option to PHENIX anyway.

Once it's available, it would be helpful if you me some feedback, like tell if it works as expected, etc.

Pavel.

On 4/27/09 6:15 PM, chandra bose wrote:

Hi,

I was wondering how to make fobs-fobs difference electron density maps with phenix using data sets from two crystals. I know cns has a script for this...

thanks Charlie

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-- Dr Stephen Graham Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549

HI Pavel, I was wondering if you could add something to the fobs-fobs and create a special output script. If you look at the cns output script you will find that there is some columns/Table that indicates how similar the structure factors between the two data sets are. I believe that you can use this to judge whether the two data sets can really be compared to each other. thanks Raj

Hi Charlie,

there is no specific tool in PHENIX to do so. However, I remember I wrote such script using PHENIX components for someone a while ago...

Here are the options:

- I can just sent you that script, where you will have to put in your file names, Fobs labels, etc, and run it as: phenix.python script.py

- I can add this option to PHENIX, so it will be something like: "phenix.fo_minus_fo_map". In this case it will take a day or two before it appears in a nightly build and you can download the updated version of PHENIX where it will be available.

- You can send me the data and I compute this map for you. I think I will add this option to PHENIX anyway.

Once it's available, it would be helpful if you me some feedback, like tell if it works as expected, etc.

Pavel.

On 4/27/09 6:15 PM, chandra bose wrote:

...

Hi,

I was wondering how to make fobs-fobs difference electron density maps with phenix using data sets from two crystals. I know cns has a script for this...

thanks Charlie ------------------------------------------------------------------------

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_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb