i should rtfm but don't you just need a mask per domain?
On 16 May 2012 22:54, Yu Feng <yufengc...@gmail.com> wrote: > Hi Eleanor, > > If you have a large protein and want to apply different ncs operations to > different domains, then you might need to give multiple masks and matrices. > > Yu > > > On Wed, May 16, 2012 at 8:26 AM, Eleanor Dodson <eleanor.dod...@york.ac.uk > > wrote: > >> It is a long time since I did this, but don't you need just one master >> mask - then that is converted using your rotation matrix to mask the >> related part of the structure ? >> >> Eleanor Dodson >> >> >> On 15 May 2012 15:56, Yu Feng <yufengc...@gmail.com> wrote: >> >>> Dear De-Feng Li, >>> >>> Thank you for your reply. Actually, I already used the script. The >>> script and the log file are at the bottom of the email. >>> >>> Best wishes, >>> Yu >>> >>> >>> On Tue, May 15, 2012 at 3:18 AM, lidefeng <lidef...@moon.ibp.ac.cn>wrote: >>> >>>> Dear Yu Feng, >>>> >>>> You could try it in script, but not in the CCP4i. The >>>> same problem could be found in DMMulti. >>>> >>>> Your sincerely >>>> De-Feng Li >>>> 2012-05-15 >>>> >>>> De-Feng Li, Ph.D, >>>> National Laboratory of Biomacromolecules >>>> Institute of Biophysics, Chinese Academy of Sciences >>>> 15 Datun Road, Chaoyang District >>>> Beijing 100101, PR China >>>> >>>> >>>> ======= 2012-05-15 18:44:48 You writed in your letter:======= >>>> >>>> >>>> >Dear CCP4ers, >>>> > >>>> >I have a problem when I use DM to do NCS averaging. If I input 9 NCS >>>> >averaging masks, DM works OK. However, if I input 10 NCS averaging >>>> masks, >>>> >DM can not open input map file. The masks should be OK because they are >>>> >generated by the same method. Do you have any idea how to solve the >>>> problem? >>>> > >>>> >Thank you in advance! >>>> >Yu >>>> > >>>> > >>>> >DM script is as below: >>>> >>>> >-------------------------------------------------------------------------------------------------------------------------------------------------------------------- >>>> >/usr/share/CCP4-6.0.2/ccp4-6.2.0/bin/dm \ >>>> >hklin >>>> >>>> >/home/crystal/Documents/Ecoli/datasets/F111062011/130_10/reprocess/DM/xxxxx_refine33_phase.mtz >>>> >\ >>>> >ncsin1 E.msk \ >>>> >ncsin2 F1.msk \ >>>> >ncsin3 F2.msk \ >>>> >ncsin4 D4.msk \ >>>> >ncsin5 D5.msk \ >>>> >ncsin6 D3.msk \ >>>> >ncsin7 D2.msk \ >>>> >ncsin8 D1.msk \ >>>> >ncsin9 C5.msk \ >>>> >ncsin10 C6.msk \ >>>> >hklout xxxxx_dm.mtz <<EOF-dm >>>> >SOLC 0.62 >>>> >#RESOL 50 4.0 >>>> >#NCSMASK SIZE 100000000 >>>> >#NCSMASK UPDATE 3 >>>> >#GRID 144 144 144 >>>> >MODE SOLV hist AVER MULTI >>>> >combine weight 0.15 >>>> >combine pert >>>> >scheme res from 4.5 >>>> >NCYCLE 10 >>>> >ncsmask overlap >>>> >AVER DOMAIN 1 REFINE >>>> >ROTATE EULER 0.000 0.000 0.000 >>>> >TRANSLATION 0.000 0.000 0.000 >>>> > >>>> >AVER DOMAIN 1 REFINE >>>> >ROTA MATRIX -0.26665 0.52763 0.80654 0.60893 -0.55642 0.56533 0.74706 >>>> >0.64187 -0.17293 >>>> >TRAN -31.41600 172.23766 -96.59856 >>>> > >>>> >AVER DOMAIN 1 REFINE >>>> >ROTA MATRIX 0.82271 0.34200 -0.45406 -0.55866 0.63407 -0.53465 0.10506 >>>> >0.69353 0.71272 >>>> >TRAN -141.48692 39.40455 -17.81890 >>>> > >>>> >AVER DOMAIN 1 REFINE >>>> >ROTA MATRIX -0.35001 0.06658 0.93438 0.03939 -0.99554 0.08569 0.93592 >>>> >0.06679 0.34582 >>>> >TRAN -75.12174 220.50938 35.16329 >>>> > >>>> >AVER DOMAIN 2 REFIN >>>> >ROTATE EULER 0.000 0.000 0.000 >>>> >TRANSLATION 0.000 0.000 0.000 >>>> > >>>> >AVER DOMAIN 2 REFINE >>>> >ROTA MATRIX -0.42731 0.24363 0.87066 0.39149 -0.81818 0.42109 0.81494 >>>> >0.52080 0.25424 >>>> >TRAN -7.42336 185.84557 -68.83428 >>>> > >>>> >AVER DOMAIN 2 REFINE >>>> >ROTA MATRIX -0.42918 0.04126 0.90228 0.01801 -0.99837 0.05422 0.90304 >>>> >0.03952 0.42774 >>>> >TRAN -74.51554 219.69878 39.63858 >>>> > >>>> >AVER DOMAIN 2 REFINE >>>> >ROTA MATRIX 0.94716 0.32039 -0.01558 -0.30765 0.89358 -0.32691 -0.09082 >>>> >0.31442 0.94493 >>>> >TRAN -121.99072 28.41423 20.60830 >>>> > >>>> >AVER DOMAIN 3 REFINE >>>> >ROTATE EULER 0.000 0.000 0.000 >>>> >TRANSLATION 0.000 0.000 0.000 >>>> > >>>> >AVER DOMAIN 3 REFINE >>>> >ROTA MATRIX -0.42590 0.08845 0.90044 -0.00887 -0.99557 0.09361 0.90473 >>>> >0.03188 0.42480 >>>> >TRAN -77.38764 220.87816 40.52480 >>>> > >>>> >AVER DOMAIN 4 REFINE >>>> >ROTATE EULER 0.000 0.000 0.000 >>>> >TRANSLATION 0.000 0.000 0.000 >>>> > >>>> >AVER DOMAIN 4 REFINE >>>> >ROTA MATRIX -0.34404 0.07038 0.93631 -0.03070 -0.99750 0.06370 0.93845 >>>> >-0.00683 0.34534 >>>> >TRAN -79.74300 222.43433 43.52758 >>>> > >>>> >AVER DOMAIN 5 REFINE >>>> >ROTATE EULER 0.000 0.000 0.000 >>>> >TRANSLATION 0.000 0.000 0.000 >>>> > >>>> >AVER DOMAIN 5 REFINE >>>> >ROTA MATRIX -0.35957 -0.00781 0.93309 -0.00716 -0.99991 -0.01113 >>>> 0.93309 >>>> >-0.01068 0.35948 >>>> >TRAN -70.14525 224.81303 43.77335 >>>> > >>>> >AVER DOMAIN 6 REFINE >>>> >ROTATE EULER 0.000 0.000 0.000 >>>> >TRANSLATION 0.000 0.000 0.000 >>>> > >>>> >AVER DOMAIN 6 REFINE >>>> >ROTA MATRIX -0.35957 -0.00781 0.93309 -0.00716 -0.99991 -0.01113 >>>> 0.93309 >>>> >-0.01068 0.35948 >>>> >TRAN -70.14525 224.81303 43.77335 >>>> > >>>> >AVER DOMAIN 7 REFINE >>>> >ROTATE EULER 0.000 0.000 0.000 >>>> >TRANSLATION 0.000 0.000 0.000 >>>> > >>>> >AVER DOMAIN 7 REFINE >>>> >ROTA MATRIX -0.35957 -0.00781 0.93309 -0.00716 -0.99991 -0.01113 >>>> 0.93309 >>>> >-0.01068 0.35948 >>>> >TRAN -70.14525 224.81303 43.77335 >>>> > >>>> >AVER DOMAIN 8 REFINE >>>> >ROTATE EULER 0.000 0.000 0.000 >>>> >TRANSLATION 0.000 0.000 0.000 >>>> > >>>> >AVER DOMAIN 8 REFINE >>>> >ROTA MATRIX -0.35957 -0.00781 0.93309 -0.00716 -0.99991 -0.01113 >>>> 0.93309 >>>> >-0.01068 0.35948 >>>> >TRAN -70.14525 224.81303 43.77335 >>>> > >>>> >AVER DOMAIN 9 REFINE >>>> >ROTATE EULER 0.000 0.000 0.000 >>>> >TRANSLATION 0.000 0.000 0.000 >>>> > >>>> >AVER DOMAIN 9 REFINE >>>> >ROTA MATRIX -0.35957 -0.00781 0.93309 -0.00716 -0.99991 -0.01113 >>>> 0.93309 >>>> >-0.01068 0.35948 >>>> >TRAN -70.14525 224.81303 43.77335 >>>> > >>>> >AVER DOMAIN 10 REFINE >>>> >ROTATE EULER 0.000 0.000 0.000 >>>> >TRANSLATION 0.000 0.000 0.000 >>>> > >>>> >AVER DOMAIN 10 REFINE >>>> >ROTA MATRIX -0.35957 -0.00781 0.93309 -0.00716 -0.99991 -0.01113 >>>> 0.93309 >>>> >-0.01068 0.35948 >>>> >TRAN -70.14525 224.81303 43.77335 >>>> > >>>> >LABIN FP=FOBS SIGFP=SIGFOBS PHIO=PHIFMODEL FOMO=FOM >>>> >LABOUT PHIDM=PHIDM FOMDM=FOMDM >>>> >EOF-dm >>>> >>>> >------------------------------------------------------------------------------------------------------------------------------------------------------ >>>> > >>>> > >>>> > >>>> > >>>> >Part of the log file is as below: >>>> >>>> >------------------------------------------------------------------------------------------------------------------------------------------------------ >>>> > Grid dimensions 96 108 162 must contain the following prime >>>> > factors for agreement with symmetry restrictions- 2 2 2 >>>> > >>>> >>>>>>> CCP4 library signal library_file:Cannot open file (Error) >>>> > raised in ccp4_file_open2 <<<<<< >>>> >>>>>>> CCP4 library signal ccp4_map:Cannot open file (Error) >>>> > raised in ccp4_cmap_open <<<<<< >>>> >>>>>>> CCP4 library signal ccp4_map:Cannot open file (Error) >>>> > raised in MRDHDS <<<<<< >>>> > dm: Error in opening input map file. >>>> >Times: User: 0.1s System: 0.0s Elapsed: 0:00 >>>> ></pre> >>>> ></html> >>>> ><!--SUMMARY_END--></FONT></B> >>>> >>>> >--------------------------------------------------------------------------------------------------------------------------------------------------------- >>>> > >>>> >>>> ======================================================== >>>> >>>> >>>> >>>> >>>> >>> >> >
