Does
unset normalize_ccp4_maps
in pymol (http://www.pymolwiki.org/index.php/Normalize_ccp4_maps)
overcome your problem?On Wed, Jul 21, 2010 at 11:01:20AM -0400, Andy Torelli wrote: > I just realized it's the "mapmask" program. Documentation at: > www.ccp4.ac.uk/dist/html/mapmask.html > > The SCALE [SIGMA [c1 [c2]]] seems to be promising. I'll give that a > try. > > Thanks, > -Andy > > On 7/21/2010 10:34 AM, Andy Torelli wrote: >> Kevin, >> >> Thank you for the reply. Your suggestion works well. >> >> As a follow-up question, I noticed that extending the map has changed >> the sigma level that must be chosen in PyMOL in order to match the view >> in COOT. Is this because the sigma level is defined based on the >> distribution of electron density and by changing the extent of the map I >> have changed the distribution of electron density peaks? >> >> If so, I'd like to normalize the new map to the original map in order >> to get the sigma contouring to match. I expect the program >> documentation may help with this. Do you know which program is used for >> the "Extend a map/mask file" function you mentioned? >> >> Thank you very much for your time, >> -Andy >> >> On 7/21/2010 10:02 AM, Kevin Cowtan wrote: >>> The ccp4 program mapmask does what you want. From ccp4i, select: >>> Map and Mask Utilities/Edit-Rotate Map& Mask/Extend a map-mask file >>> >>> Andy Torelli wrote: >>>> Hi everyone, >>>> >>>> I produced an NCS-averaged map in COOT that I would like to output >>>> and load into PyMOL to make a figure. The map loads successfully into >>>> PyMOL, but of course the density only covers a portion of my molecule >>>> that is fully covered when viewed in COOT. I know/believe this is >>>> because COOT generates maps with electron density that is only defined >>>> explicitly for certain regions of the unit cell and dynamically displays >>>> electron density (based on symmetry) for the regions that are not defined. >>>> >>>> I e-mailed the PyMOLbb regarding this issue some time ago and >>>> learned that symmetry-expansion was in the works, but it doesn't seem to >>>> be working in version 1.2r3pre. I was wondering if there is any way to >>>> tell COOT to output a map with electron density values explicitly >>>> defined for a given region (e.g. a protein chain, defined region of >>>> space or a ligand/ion). >>>> >>>> Things I've tried: >>>> - making a mask (Extensions->Maps->Mask Map by Atom Selection) and >>>> loading that map into PyMOL based on a previous post suggestion, but the >>>> (lack of) coverage was the same. >>>> - loading the map into MAPMAN and converting to a different file >>>> format. The map was too big to be loaded and I'm not sure if I can >>>> re-define the area for which electron density will be defined. >>>> >>>> Thanks for your help and suggestions, >>>> -Andy Torelli >>> >>> >> -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
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