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 c
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 clear from your question.
Cheers,
Thomas
On 10/25/2011 10:28 AM, lina wrote:
> Hi,
>
> I went through the pymolwiki and cross this
On Tue, Oct 25, 2011 at 7:56 PM, Thomas Holder
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 calcula
Lina,
If you want to create an "omit" map for your ligand using CCP4i, you
can find instructions here for both Fo-Fc and 2Fo-Fc maps:
http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Model+Building+and+Validation#Creating_Omit_Maps_for_Ligands_using_Refmac
To display an omit map in Pym
On 10/25/2011 02:27 PM, lina wrote:
> On Tue, Oct 25, 2011 at 7:56 PM, Thomas Holder
> 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
> And read the help for the map_new command (there is no wiki page yet):
> PyMOL>help map_new
now the wiki page is there:
http://pymolwiki.org/index.php/Map_new
Cheers,
Thomas
--
Thomas Holder
MPI for Developmental Biology
Hi Lina,
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)
>
The CCP4 file is a map. Once the map is loaded into PyMOL you can choose how
you want to represent the data: isomesh, isosurface, slice, gradient, or the
n
On Wednesday 26,October,2011 12:55 AM, Jason Vertrees wrote:
Hi Lina,
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)
The CCP4 file is a map. Once the map is loaded into PyMOL you can
choose how you want
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 de
