Re: [PyMOL] about Display CCP4 Maps

[Joel T. <joe...@ot...>]

Hi Lina,

Could you be more specific about what you are trying to do. E.g." I have a structure from the pdb and I would like to display the density."

If it is this option then you can automatically generate ccp4 type maps from http://eds.bmc.uu.se/eds/ assuming the structure factors have been deposited. You can them load these into pymol (file.ccp4)

"Or I am determining the structure of a protein ligand complex and I wish to calculate the electron density map ."

If this is the case I would suggest some further reading of the ccp4 tutorials. These come with ccp4i

Hope this helps

Joel

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Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
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-----Original Message-----
From: lina [mailto:lin...@gm...] 
Sent: Wednesday, 26 October 2011 1:27 a.m.
To: Thomas Holder
Cc: pym...@li...
Subject: Re: [PyMOL] about Display CCP4 Maps

On Tue, Oct 25, 2011 at 7:56 PM, Thomas Holder <sp...@us...> wrote:
> Hi Lina,
>
> do you already have any electron density or reflection file (*.map, 
> *.mtz,
> ...) or do you want to create a "fake" density from your structure? 
> It's not


I don't have the reference electron density file.

mainly wish to calculate a density map based on the structure?

> clear from your question.
>
> Cheers,
Thanks for asking.

>  Thomas
>
> On 10/25/2011 10:28 AM, lina wrote:
>>
>> Hi,
>>
>> I went through the pymolwiki and cross this page:
>>
>> http://www.pymolwiki.org/index.php/Display_CCP4_Maps
>>
>> I have some questions:
>>
>> 1] do I need generate the map from ccp4
>>
>>  (I have already installed the ccp4i, but seems not easy to know how 
>> to get the map)
>>
>> 2] For small molecular (ligand), the ccp4 is the best way to obtain 
>> its  electron density map?
>>
>> Seems those questions are not so-pymol-related, but I wish if someone 
>> are familiar with this, can give me some advice??
>>
>> Those questions might be easy, but to me at present it seems very 
>> confusing.
>>
>> Thanks with best regards,
>
> --
> Thomas Holder
> MPI for Developmental Biology
>

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