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 Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
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From: lina [mailto:lina.lastname@...]
Sent: Wednesday, 26 October 2011 1:27 a.m.
To: Thomas Holder
Subject: Re: [PyMOL] about Display CCP4 Maps
On Tue, Oct 25, 2011 at 7:56 PM, Thomas Holder <speleo3@...> wrote:
> Hi Lina,
> do you already have any electron density or reflection file (*.map,
> ...) 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.
Thanks for asking.
> On 10/25/2011 10:28 AM, lina wrote:
>> I went through the pymolwiki and cross this page:
>> 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
>> Thanks with best regards,
> Thomas Holder
> MPI for Developmental Biology
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