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 <[email protected]>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 <[email protected]> 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 <[email protected]>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> >>> >>> >--------------------------------------------------------------------------------------------------------------------------------------------------------- >>> > >>> >>> ======================================================== >>> >>> >>> >>> >>> >> >
