Hi Todd Thanks for the pointer to mama2ccp4 . I just successfully used it to convert a mama mask to ccp4 format and could successfully use this in dmmulti.
I thought that lx_mapman did indeed convert the mama mask to ccp4 format since I could display and check the lx_mapman converted mask correctly in COOT. I didnt realize that the CCP4 format "map" from mapman as seen by dmmulti is different from from the CCP4 format mask as generated by mama2ccp4 and ncsmask. So lesson learnt : to convert mama masks to ccp4 format use mama2ccp4 . Thanks a tonne Hari On Mon, Jul 13, 2009 at 2:50 PM, Green, Todd <[email protected]> wrote: > Hello Hari- > > I'm not following exactly what you have done because i can't see the > commands that you have used. However to the best of my knowledge mapman will > not convert to ccp4 mask format. if you have a mask from MAMA, then you can > use mama2ccp4 to convert to ccp4 mask format, ie from the commandline: > > mama2ccp4 maskin input.mask maskout output.mask > > probably you are reading in a mask and writing out a ccp4 map but as i said > before I don't know because you haven't provided the commands that you have > used. see if the above command works, if not, give us a little more info on > what you have done and it should be an easy fix. > > cheers- > todd > > -----Original Message----- > From: CCP4 bulletin board on behalf of hari jayaram > Sent: Mon 7/13/2009 11:11 AM > To: [email protected] > Subject: [ccp4bb] mama/mapman converted CCP4 format in dmmulti gives > logical*1 error > > Hi everyone > Dmmulti seems to not like masks converted in mapman to the CCP4 format. > I get the following error > > dmmulti: domnin - Mask file is not logical*1 > > > I know the masks are fine because I can display them fine in coot which > reads CCP4 masks .I can also get ncsmask to read them fine. > Now in ncsmask run if I ask ncsmask to do operations which I have already > done in mama and write out the mask . Now dmmulti does not give me the > logical*1 error. > > I am attaching the mapman statistics for the mask which does not work ( > mama to ccp4 in mapman) and the working mask ( mama-to-ccp4-then-ncsmask) > here. > They seem very similar so I am wondering why I have to have ncsmask touch > my > CCP4 mask file before dmmulti is happy with it. > > Thanks for your help > Hari > > > ############## > Not working mask > ############## > > File name for input map file on unit 1 : nottedmask.msk > file size = 261328 ; logical name > nottedmask.msk > > > Number of columns, rows, sections ............... 51 29 44 > Map mode ........................................ 2 > Start and stop points on columns, rows, sections 21 71 > -6 22 -227 -184 > Grid sampling on x, y, z ........................ 80 103 154 > Cell dimensions ................................. 79.81400 > 102.63900 153.62700 82.46000 75.53000 73.45000 > Fast, medium, slow axes ......................... Y X Z > Minimum density ................................. 0.00000 > Maximum density ................................. 1.00000 > Mean density .................................... 0.19175 > Rms deviation from mean density ................. 0.39367 > Space-group ..................................... 1 > Number of titles ................................ 2 > > Titles : > > > Created by MAPMAN V. 080625/7.8.5 at Mon Jul 13 11:27:06 2009 for > hari > > > Parameters as read from the map file > Origin ...................... -6 21 -227 > Extent ...................... 29 51 44 > Grid ........................ 80 103 154 > Cell axes ................... 79.81 102.64 153.63 > Cell angles ................. 82.46 75.53 73.45 > UVW (fast, medium, slow) .... Y X Z > > Header done > Not in core > Reading levels ... > Level number : ( 10) > Level number : ( 20) > Level number : ( 30) > Level number : ( 40) > Closing BINARY CCP4 map on unit : ( 1) > Map read into memory - calculating statistics > Sum of density in map : ( 1.248E+04) > Requested dynamic range : 0.0000E+00 1.0000E+00 > Value of Prod and Plus : 2.5500E+02 0 > Actual dynamic range : 0.0000E+00 1.0000E+00 > > ############## > Working mask: > ############## > > Logical Name: nottedmask_mod1.msk Filename: nottedmask_mod1.msk > <!--SUMMARY_END--></FONT></B> > > > File name for input map file on unit 1 : nottedmask_mod1.msk > file size = 66180 ; logical name > nottedmask_mod1.msk > > > Number of columns, rows, sections ............... 44 29 51 > Map mode ........................................ 0 > Start and stop points on columns, rows, sections -227 -184 > -6 22 21 71 > Grid sampling on x, y, z ........................ 80 103 154 > Cell dimensions ................................. 79.81400 > 102.63900 153.62700 82.46000 75.53000 73.45000 > Fast, medium, slow axes ......................... Z X Y > Space-group ..................................... 1 > Number of titles ................................ 1 > > Titles : > > > > > Parameters as read from the map file > Origin ...................... -6 21 -227 > Extent ...................... 29 51 44 > Grid ........................ 80 103 154 > Cell axes ................... 79.81 102.64 153.63 > Cell angles ................. 82.46 75.53 73.45 > UVW (fast, medium, slow) .... Z X Y > > Header done > Closing BINARY CCP4 map on unit : ( 1) > Map read into memory - calculating statistics > Sum of density in map : ( 1.248E+04) > Requested dynamic range : 0.0000E+00 1.0000E+00 > Value of Prod and Plus : 2.5500E+02 0 > Actual dynamic range : 0.0000E+00 1.0000E+00 > > > This email was scanned with Mcafee's Anti-Virus appliance, but this > is no guarantee that no virus exists. You are asked to make sure you > have virus protection and that it is up to date. > >
