[COOT] Novel maps...
Dear cootbb, When building into density I use a map generated from the FWT amplitudes column and PHWT phases columns which I think is my 2Fo-Fc, and a second map generated from DELFWT and PHDELWT which I think is my Fo-Fc. This keeps me happy and in known territory. However today someone in the lab asked what it means to generate a map using FWT and PHDELWT. Does anyone know what type of map this would be in the Fo Fc terminology? Thanks, Simon
Re: [COOT] Novel maps...
Simon Kolstoe wrote: Dear cootbb, When building into density I use a map generated from the FWT amplitudes column and PHWT phases columns which I think is my 2Fo-Fc, and a second map generated from DELFWT and PHDELWT which I think is my Fo-Fc. Me too (more or less). This keeps me happy and in known territory. However today someone in the lab asked what it means to generate a map using FWT and PHDELWT. Not much. Does anyone know what type of map this would be in the Fo Fc terminology? "A mistake". Actually, the PHWT and PHDELWT are related. AFAIU, somewhere in Refmac there is something like this: if DELFWT < 0: DELFWT = - DELFWT PHDELWT = 180 + PHWT else: PHDELWT = PHWT
[COOT] Symops: coot vs ccp4
Hi, any particularly cogent reason why the order of symops is different in coot and ccp4? (E.g. below: P6522.) It's fantastically annoying, e.g. when trying to reconstruct symmetry mates via ccp4, if the symop number is not what is shown in the coot status bar. Or e.g. when trying to sort out inter-unit cell disulphides. Etc. phx. . CCP4 (SYMOP.LIB) X,Y,Z -Y,X-Y,2/3+Z Y-X,-X,1/3+Z -X,-Y,1/2+Z Y,Y-X,1/6+Z X-Y,X,5/6+Z Y,X,2/3-Z X-Y,-Y,-Z -X,Y-X,1/3-Z -Y,-X,1/6-Z Y-X,Y,1/2-Z X,X-Y,5/6-Z COOT (syminfo.lib) symop x,y,z symop x-y,x,z+5/6 symop -y,x-y,z+2/3 symop -x,-y,z+1/2 symop -x+y,-x,z+1/3 symop y,-x+y,z+1/6 symop -y,-x,-z+1/6 symop x-y,-y,-z symop x,x-y,-z+5/6 symop y,x,-z+2/3 symop -x+y,y,-z+1/2 symop -x,-x+y,-z+1/3
Re: [COOT] Symops: coot vs ccp4
On Wednesday 17 June 2009 15:10:52 Frank von Delft wrote: > Hi, any particularly cogent reason why the order of symops is different > in coot and ccp4? (E.g. below: P6522.) Hmm. I thought that the symops were taken from the *.mtz file in preference to any external source. Over on the ccp4bb list we're just thrashing a related set of problems that seems to arise from _not_ using the info in the *.mtz file, and I think the consensus seems to be that any remaining programs/libraries that look them up all over again will be changed so that they don't. I may have that wrong about the proposed change, but in any event the topic is under consideration. Ethan > It's fantastically annoying, e.g. when trying to reconstruct symmetry > mates via ccp4, if the symop number is not what is shown in the coot > status bar. Or e.g. when trying to sort out inter-unit cell > disulphides. Etc. > > phx. > > > . > CCP4 (SYMOP.LIB) > X,Y,Z > -Y,X-Y,2/3+Z > Y-X,-X,1/3+Z > -X,-Y,1/2+Z > Y,Y-X,1/6+Z > X-Y,X,5/6+Z > Y,X,2/3-Z > X-Y,-Y,-Z > -X,Y-X,1/3-Z > -Y,-X,1/6-Z > Y-X,Y,1/2-Z > X,X-Y,5/6-Z > > COOT (syminfo.lib) > symop x,y,z > symop x-y,x,z+5/6 > symop -y,x-y,z+2/3 > symop -x,-y,z+1/2 > symop -x+y,-x,z+1/3 > symop y,-x+y,z+1/6 > symop -y,-x,-z+1/6 > symop x-y,-y,-z > symop x,x-y,-z+5/6 > symop y,x,-z+2/3 > symop -x+y,y,-z+1/2 > symop -x,-x+y,-z+1/3 > -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742
Re: [COOT] Symops: coot vs ccp4
Frank von Delft wrote: Hi, any particularly cogent reason why the order of symops is different in coot and ccp4? (E.g. below: P6522.) It's fantastically annoying, e.g. when trying to reconstruct symmetry mates via ccp4, if the symop number is not what is shown in the coot status bar. Or e.g. when trying to sort out inter-unit cell disulphides. Etc. I thought that syminfo.lib was standard ccp4 - and that symop.lib was only hanging around for historical reasons. Perhaps the symmetry order problem would be somewhat ameliorated if you used expanded labels? Draw -> Cell & Symmetry -> Expanded Symmetry Atom Labels -> [Tick] Perhaps [Tick] should be the default. Paul.
Re: [COOT] Symops: coot vs ccp4
Indeed Paul is right - symop.lib is historical, syminfo.lib is the up-to-date version Phil > Frank von Delft wrote: >> Hi, any particularly cogent reason why the order of symops is >> different in coot and ccp4? (E.g. below: P6522.) >> >> It's fantastically annoying, e.g. when trying to reconstruct symmetry >> mates via ccp4, if the symop number is not what is shown in the coot >> status bar. Or e.g. when trying to sort out inter-unit cell >> disulphides. Etc. >> > > I thought that syminfo.lib was standard ccp4 - and that symop.lib was > only hanging around for historical reasons. > > Perhaps the symmetry order problem would be somewhat ameliorated if you > used expanded labels? > Draw -> Cell & Symmetry -> Expanded Symmetry Atom Labels -> [Tick] > > Perhaps [Tick] should be the default. > > Paul. >
