Oh no, I’ve been meaning to update that page for a while! It’s much easier to cut out density now than it was when I wrote that. In CCP4, Kevin Cowtan has the program cmapcut, and in Phenix Tom Terwilliger has the program phenix.cut_out_density. For most purposes, I think you’ll find those programs easier to use.
Best wishes,
Randy Read
On 20 May 2014, at 14:52, Edward A. Berry <[log in to unmask]> wrote:
> But, if you convert to structure factors and recalculate the map in a different cell,
> the features will be "stretched" to fill the cell, which I take it is the original problem.
>
> I found Kleywegt's RAVE package very convenient for doing this,
> but i believe the functionality is now available in
> ccp4 mapmask and maprot programs.
>
> The Phaser Wiki has a page with instructions
> for cutting out electron density within a mask,
> and putting it in a large P1 cell for use as a molecular
> replacement model. Perhaps you could modify that to achieve
> your aims.
>
> http://www.phaser.cimr.cam.ac.uk/index.php/Using_Electron_Density_as_a_Model
> eab
>
> On 05/20/2014 03:07 AM, [log in to unmask] wrote:
>> Dear Niu,
>>
>> Provided you have a complete asymmetric unit (unit cell in P1), you could also convert this map to
>> structure factors and manipulate those, e.g. with sftools. To calculate structure factors you could use
>> sfall and also clipper has utilities to convert a map to structure factors.
>>
>> Best,
>>
>> Herman
>>
>> *Von:*CCP4 bulletin board [mailto:[log in to unmask]] *Im Auftrag von *Niu Tou
>> *Gesendet:* Montag, 19. Mai 2014 23:25
>> *An:* [log in to unmask]
>> *Betreff:* [ccp4bb] map manipulation questions
>>
>> Dear All,
>>
>> I have a ccp4 format map file in P1 spacegroup, I would like to manipulate it in several ways:
>>
>> 1. enlarge the cell dimension . When I tried "CELL" keyword in MAPMAN, the density scaled up together
>> with the cell dimension. Does anybody know how to do it without changing the density?
>>
>> 2. Change the space group to P2.
>>
>> 3. Move the density away from its original place, i.e. apply a translocation vector to it.
>>
>> Does anybody know the answers? Thanks in advance!
>>
>> Regards,
>>
>> Niu
>>
------
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: + 44 1223 336500
Wellcome Trust/MRC Building Fax: + 44 1223 336827
Hills Road E-mail: [log in to unmask]
Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
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