Hell Sir,
I am using this input script to run the mlphare
#!/bin/sh
set -e
# bug # 3192 - run-all examples produce harvest files - well to counteract
# this here set HARVESTHOME to somewhere in $CCP4_SCR
HARVESTHOME=$CCP4_SCR
export HARVESTHOME
mlphare hklin /home/skumaran/Desktop/testmad/commandMAD.mtz \
hklout /home/skumaran/Desktop/testmad/mlphr.mtz << eof
TITLE 9 refining cycles + 1 phasing cycle
RESO 15.0 3.45
SCALE SIGFP 1.0
CYCLE 30
THRES 2.5 0.5
ANGLE 10
PRINT AVE AVF
LABIN FP=F SIGFP=SIGF DPH1=DANO SIGDPH1=SIGDANO
LABOUT PHIB=PHIB FOM=FOM HLA=HLA HLB=HLB HLC=HLC HLD=HLD
DERIV AU20
DCYCLE PHASE ALL REFCYC ALL KBOV ALL
RESO 10.0 3.45
ISOE
ANOE
ATOM Se1 0.552 0.732 0.91 0.918 BFAC 25.000
ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL
ATOM Se2 0.611 0.448 0.769 4.877 0.901 BFAC 25.000
ATREF X ALL Y ALL Z ALL OCC ALL AOCC ALL
DERIV MM11
DCYCLE PHASE ALL REFCYC ALL KBOV ALL
RESO 15.0 3.45
ISOE
ATOM Se 0.651 0.532 0.292 BFAC 0.812 25.000
ATREF X ALL Y ALL Z ALL OCC ALL
DERIV I100
DCYCLE PHASE ALL REFCYC ALL KBOV ALL
RESO 15.0 3.45
ISOE
ATOM Se 0.183 0.979 0.855 0.718 BFAC 25.000
ATREF X ALL Y ALL Z ALL OCC ALL
END
eof
and out of this script is as follow
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<html> <!-- CCP4 HTML LOGFILE -->
<hr>
<!--SUMMARY_END--></FONT></B>
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<pre>
###############################################################
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### CCP4 6.2: MLPHARE version 6.2 : 28/04/08##
###############################################################
User: unknown Run date: 20/ 6/2012 Run time: 22:38:38
Please reference: Collaborative Computational Project, Number 4. 1994.
"The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50,
760-763.
as well as any specific reference in the program write-up.
<!--SUMMARY_END--></FONT></B>
Data line--- TITLE 9 refining cycles + 1 phasing cycle
Data line--- RESO 15.0 3.45
Data line--- SCALE SIGFP 1.0
Data line--- CYCLE 30
Data line--- THRES 2.5 0.5
Data line--- ANGLE 10
Data line--- PRINT AVE AVF
Data line--- LABIN FP=F SIGFP=SIGF DPH1=DANO SIGDPH1=SIGDANO
Data line--- LABOUT PHIB=PHIB FOM=FOM HLA=HLA HLB=HLB HLC=HLC HLD=HLD
Data line--- DERIV AU20
** MLPHARE **
** Heavy Atom Phasing and Refinement Program **
** **
Title for this run: "9 refining cycles + 1 phasing cycle"
OPENED INPUT MTZ FILE
Logical Name: HKLIN Filename:
/home/skumaran/Desktop/testmad/commandMAD.mtz
* Title:
Generate F+/- columns for derivative data
* Base dataset:
0 HKL_base
HKL_base
HKL_base
* Number of Datasets = 1
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
1 unknown
unknown
unknown190612:22:03:40
76.8390 83.2080 95.3160 90.0000 90.0000 90.0000
0.97100
* Number of Columns = 11
* Number of Reflections = 8541
* Missing value set to NaN in input mtz file
* Column Labels :
H K L F SIGF DANO SIGDANO F_se+r SIGF_se+r F_se-r SIGF_se-r
* Column Types :
H H H F Q D Q G L G L
* Associated datasets :
0 0 0 1 1 1 1 1 1 1 1
* Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
76.8390 83.2080 95.3160 90.0000 90.0000 90.0000
* Resolution Range :
0.00025 0.08451 ( 62.683 - 3.440 A )
* Sort Order :
0 0 0 0 0
* Space group = 'P 21 21 21' (number 19)
(spacegroup is known)
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename:
/home/programs/ccp4/ccp4-6.2.0/lib/data/syminfo.lib
Number of alternate origins for spacegroup: P 21 21 21 is: 8
Norigin Ox Oy Oz
1 0.0000 0.0000 0.0000
2 0.0000 0.0000 0.5000
3 0.0000 0.5000 0.0000
4 0.0000 0.5000 0.5000
5 0.5000 0.0000 0.0000
6 0.5000 0.0000 0.5000
7 0.5000 0.5000 0.0000
8 0.5000 0.5000 0.5000
****** CENTRIC ZONES ******
CENTRIC Zone 1
Reflections of type 0kl
CENTRIC Zone 2
Reflections of type h0l
CENTRIC Zone 3
Reflections of type hk0
****** EPSILON ZONES - Reflection Classes and their multiplicity
******
EPSILON Zone 1
Reflections of type h00
Multiplicity 2
EPSILON Zone 2
Reflections of type 0k0
Multiplicity 2
EPSILON Zone 3
Reflections of type 00l
Multiplicity 2
EPSILON Zone 4
Reflections of type hkl
Multiplicity 1
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
SUMMARY INFORMATION FOR INPUT PARAMETERS:
=========================================
Protein Resolution Limits are from 15.00 to 3.45 Angstroms
Native Sigmaas will be scaled by 1.000
Parameter Shifts greater than 2.500
Sigma will be scaled by 0.500
Number of Phasing and Refinement Cycles = 30
Input Phasing Flags for each Cycle are
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
If phasing flag NE 0 - input phases will be combined with calculated
phases.
Phase Probabilities will be calculated every 10 degrees
Flag for Calculation of Atomic form factors in electrons = 1
Flag for printing of Correlation Matrices = 0
Flag for printing of Statistics on the Derivative Scale = 1
<!--SUMMARY_END--></FONT></B>
Reciprocal matrix Real matrix
0.01301 0.00000 0.00000 76.84 0.00 0.00
0.00000 0.01202 0.00000 0.00 83.21 0.00
0.00000 0.00000 0.01049 0.00 0.00 95.32
The orthogonalisation code is:
B PARALLEL TO KO C* PARALLEL TO LO
B* PARALLEL TO YO C PARALLEL TO ZO
The real matrix pre-multiplies column vector {x y z} in
fractional coordinates to get orthogonal coordinates. The
reciprocal matrix is its inverse. This is not the same as
PDB standard NCODE 1. These matrices are used when
refining anisotropic temperature factors, although the
orthogonal axis definition is irrelevant.
Data line--- LABOUT PHIB=PHIB FOM=FOM HLA=HLA HLB=HLB HLC=HLC HLD=HLD
MtzParseLabin: neither label recognised: HLA HLA
MtzParseLabin: neither label recognised: HLB HLB
MtzParseLabin: neither label recognised: HLC HLC
MtzParseLabin: neither label recognised: HLD HLD
MLPHARE: Error in label assignments in LABOUT
MLPHARE: Error in label assignments in LABOUT
Times: User: 0.1s System: 0.0s Elapsed: 0:00
</pre>
</html>
<!--SUMMARY_END--></FONT></B>
it seems that it is having problem in label input
On 20 June 2012 16:16, Eleanor Dodson <[email protected]> wrote:
> You can View input command file, when working from the GUI.
> Could you cut and paste this into your message - obviously some inmportant
> parameter is not set, but I cant tell which without seeing that file.
>
> Eleanor
>
>
>
>
> On 20 June 2012 05:25, Appu kumar <[email protected]> wrote:
>
>> Thank you for your reply,
>> I am running Malphare through CCP4 GUI interface. I am giving mtz file
>> and Se.pdb file as input and running it. I do not know running Malphare
>> through script. Please help me with heavy atom refinement in Malphare.
>>
>> On 20 June 2012 03:49, Pete Meyer <[email protected]> wrote:
>>
>>> It's not clear without looking at your input script, but it appears that
>>> you've got a problem with either your LABIN, ATREF or ATOM lines. It might
>>> be helpful to check out some of the example scripts distributed with ccp4.
>>>
>>> Pete
>>>
>>>
>>> Appu kumar wrote:
>>>
>>>> Dear CCP4 user,
>>>> I am facing problem in running Mlphare
>>>> for HEAVY ATOM REFINEMENT and PHASE CALCULATO. It is running successfully
>>>> but in output log file i am not getting any FOM for acentric. Log file
>>>> output of one of the cycle is
>>>>
>>>> *** Finished refinement cycle 3
>>>> 0 reflections were rejected for refinement
>>>>
>>>> Figures of merit as functions of resolution shell
>>>> ------------------------------**-------------------
>>>> Resolution of each shell in angstroms:
>>>> 19.88 11.81 8.40 6.52 5.33 4.50 3.90 3.44
>>>>
>>>> Number of Measurements phased -ACENTRIC
>>>> TOTAL
>>>> 20 107 280 498 721 1092 1383 1342
>>>> 5443
>>>> Mean Figure of Merit
>>>> 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
>>>> 0.0000
>>>>
>>>> Number of Measurements phased -CENTRIC
>>>> TOTAL
>>>> 29 62 98 120 139 161 158 145
>>>> 912
>>>> Mean Figure of Merit
>>>> 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
>>>> 0.0000
>>>>
>>>> Number of Measurements phased -ALL
>>>> TOTAL
>>>> 49 169 378 618 860 1253 1541 1487
>>>> 6355
>>>> Mean Figure of Merit
>>>> 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
>>>> 0.0000
>>>>
>>>>
>>>> Compound 1 "Se"
>>>> -----------------------------
>>>> Scale Factor 1.0000 Shift 0.0000 S. D.
>>>> 0.0000
>>>> Overall B 0.0000 Shift 0.0000 S. D.
>>>> 0.000
>>>> ------------------------------**-----------------
>>>> Refinement Parameter = 0.000000
>>>> Anomalous Refinement Parameter = 0.000000
>>>> ------------------------------**-----------------
>>>>
>>>> ====== CYCLE 4 ==============================**
>>>> =============================
>>>>
>>>> One more thing Mlphare did not giving me anamolous shift for individual
>>>> Se site. Please guide me and suggest me your valuble ideas to overcome this
>>>> problem.
>>>>
>>>> Thank you
>>>> Appu
>>>>
>>>>
>>>
>>
>
