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 <ber...@upstate.edu> 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, herman.schreu...@sanofi.com 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:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von >> *Niu Tou >> *Gesendet:* Montag, 19. Mai 2014 23:25 >> *An:* CCP4BB@JISCMAIL.AC.UK >> *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: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
