Hi Eleanor, You are right, I just need a mask per domain. In my case, the protein has more than 10 domains, and I want to input their masks at the same time. It seems that I have to re-compile DM to run large proteins.
Yu On Thu, May 17, 2012 at 4:38 AM, Eleanor Dodson <[email protected]>wrote: > i should rtfm but don't you just need a mask per domain? > > > On 16 May 2012 22:54, Yu Feng <[email protected]> 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 < >> [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> >>>>> >>>>> >--------------------------------------------------------------------------------------------------------------------------------------------------------- >>>>> > >>>>> >>>>> ======================================================== >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>> >> >
