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 <[log in to unmask]> wrote:
i should rtfm  but don't you just need a mask per domain?


On 16 May 2012 22:54, Yu Feng <[log in to unmask]> 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 <[log in to unmask]> 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 <[log in to unmask]> 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 <[log in to unmask]> 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>
>---------------------------------------------------------------------------------------------------------------------------------------------------------
>

========================================================