Hi Yogesh, in your first run the problem is exactly what the error
message says: the required columns are not present in the input MTZ
file for SIGMAA, i.e. the file
'/tmp/yogeshgupta/nme_phasecombination_11_1.tmp' contains only column
labels 'H K L FP SIGFP FC PHIC' as shown in the file header listing in
the SIGMAA output. I guess what you wanted to do was copy over all
the columns from your original input MTZ file, not just 'H K L FP
SIGFP'. According to the documentation for SFALL: "If you want to
copy everything over, use ALLIN on the LABOUT line." - there's also an
option in the CCP4I interface for SFALL to do this.
Personally, I wouldn't use SFALL anyway for this, I would use REFMAC
with refinement mode 'unrestrained' and 'NCYC 0'. You also need to be
sure to use the Fcalc columns with the solvent contribution included:
FC_ALL & PHIC_ALL. The reason is that SFALL doesn't use a solvent
model which is likely to cause big problems with the low resolution
shells in SIGMAA (of course you could always cut them out, but that's
hardly an ideal solution). Also SFALL can't handle TLS or ADP models.
I also tried your second run - I had to make a couple of changes in
your script to make it work - the LABIN line should be:
LABIN FP=FP SIGFP=SIGFP PHIBP=PHIB WP=FOM -
HLA=HLA HLB=HLB HLC=HLC HLD=HLD -
FC=FCalc PHIC=PHICalc
(HLA, HLB, HLC & HLD labels were wrong). Also I deleted the LABOUT
line - the label 'PHWT' should be 'PHFWT' (see sigmaa.doc - yes I know
that's very confusing!). But if you want to keep the default output
column labels, you don't need LABOUT anyway.
With these changes it ran without error (see attached log file). I'm
very puzzled how you got the error you did since given your input data
it's physically impossible for the program to access that line number
in the source code! i.e.
At line 771 of file
/sw64/src/fink.build/ccp4-6.1.13-1/ccp4-6.1.13/src/sigmaa.f (unit = 5,
file = 'stdin')
I note you are using a Mac, and can only conclude that this is the
result of some kind of bug in the OSX Fortran compiler. I can't help
you there, as I use PC/Linux & no-one else here uses a Mac. I'm
reposting this on the BB in the hope that any Mac users out there will
recognise the problem.
Cheers
-- Ian
On Thu, May 19, 2011 at 9:51 PM, Yogesh Gupta <[log in to unmask]> wrote:
> Hi Ian,
> Thanks for your prompt reply. First, i tried using SIGMAA through CCP4 GUI
> and defined the correct labels. It gave the errors that i mentioned in my
> previous email. I tried both options, first, calculaed phases from the model
> and merge them with experimental phases using CAD and use this CAD output in
> SIGMAA or used this option 'generate structure factors using SFALL' and
> supplied the partial model. Got the same error (see below).
> Below is the log of the run:
> #CCP4I VERSION CCP4Interface 2.0.6
> #CCP4I SCRIPT LOG sigmaa
> #CCP4I DATE 16 May 2011 18:23:35
> #CCP4I USER yogeshgupta
> #CCP4I PROJECT nme_phasecombination
> #CCP4I JOB_ID 11
> #CCP4I SCRATCH /tmp/yogeshgupta
> #CCP4I HOSTNAME horatio.1425mad.mssm.edu
> #CCP4I PID 28212
>
> ###############################################################
> ###############################################################
> ###############################################################
> ### CCP4 6.1: SFALL version 6.1 : 01/07/09##
> ###############################################################
> User: yogeshgupta Run date: 16/ 5/2011 Run time: 18:23:35
>
> 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.
>
> FORMATTED OLD file opened on unit 45
> Logical name: ATOMSF, Filename:
> /sw64/share/xtal/ccp4-6.1.13/lib/data/atomsf.lib
> Data line--- title combine experimental phases with model phases
> Data line--- LABIN FP=FP SIGFP=SIGFP
> Data line--- labout FC=FC PHIC=PHIC
> Data line--- MODE SFCALC XYZIN HKLIN
> Data line--- symmetry 'P 62'
> Spacegroup information obtained from library file:
> Logical Name: SYMINFO Filename:
> /sw64/share/xtal/ccp4-6.1.13/lib/data/syminfo.lib
> Reciprocal space symmetry:
> Space group: "P 62" Point group: "PG6" Laue group: "6/m"
> Reference asymmetric unit: "l>=0 and ((h>=0 and k>0) or (h=0 and k=0))"
> (change of basis may be applied)
> Spacegroup 171 "P 62"
> Original indices for reflection hkl with symmetry number ISYM
> Bijvoet positive
> ISYM ISYM ISYM ISYM
>
> ISYM 1 +h,+k,+l 3 -k,+h+k,+l 5 -h-k,+h,+l 7 -h,-k,+l
>
> ISYM 9 +k,-h-k,+l 11 +h+k,-h,+l
> Bijvoet negative
> ISYM ISYM ISYM ISYM
>
> ISYM 2 -h,-k,-l 4 +k,-h-k,-l 6 +h+k,-h,-l 8 +h,+k,-l
>
> ISYM 10 -k,+h+k,-l 12 -h-k,+h,-l
> Data line--- end
> OPENED INPUT MTZ FILE
> Logical Name: HKLIN Filename:
> /Users/yogeshgupta/scott_mme/nme/Nme_from_Rapidata/YGBuild/phase_combination/eden.mtz
> * Title:
>
> * Base dataset:
> 0 HKL_base
> HKL_base
> HKL_base
> * Number of Datasets = 0
> * Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
>
> * Number of Columns = 37
> * Number of Reflections = 19584
> * Missing value set to NaN in input mtz file
> * Column Labels :
> H K L NUMORB FB PHIB FOM HX HY FH PHIH FP SIGFP HLA HLB HLC HLD HL0 Fcent
> PHIcent FOMcent Fmap PHImap FHref PHIHref Fav SIGFav Ap Bp Ap2 ApBp Bp2 Aph
> Bph Aph2 AphBph Bph2
> * Column Types :
> H H H I F P W R R F P F Q A A A A R F P W F P F P F Q R R R R R R R R R R
> * Associated datasets :
> 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 0 0 0 0 0 0 0
> * Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
> 177.9730 177.9730 66.0660 90.0000 90.0000 120.0000
> * Resolution Range :
> 0.00004 0.09621 ( 154.129 - 3.224 A )
> * Sort Order :
> 0 0 0 0 0
> * Space group = 'P 62' (number 171)
> <html> <!-- CCP4 HTML LOGFILE -->
> <hr>
> <pre>
> Memory allocation (logical name, type, elements):
> MEMSIZE R 5000000
> MEMSIZE I 5000000
>
> $TEXT:Warning: $$ comment $$
> WARNING: Reflections not sorted as H slow, K medium, L fast
> $$
> Reciprocal space symmetry:
> Space group: "P 62" Point group: "PG6" Laue group: "6/m"
> Reference asymmetric unit: "l>=0 and ((h>=0 and k>0) or (h=0 and k=0))"
> (change of basis may be applied)
> Spacegroup 171 "P 62"
> Original indices for reflection hkl with symmetry number ISYM
> Bijvoet positive
> ISYM ISYM ISYM ISYM
>
> ISYM 1 +h,+k,+l 3 -k,+h+k,+l 5 -h-k,+h,+l 7 -h,-k,+l
>
> ISYM 9 +k,-h-k,+l 11 +h+k,-h,+l
> Bijvoet negative
> ISYM ISYM ISYM ISYM
>
> ISYM 2 -h,-k,-l 4 +k,-h-k,-l 6 +h+k,-h,-l 8 +h,+k,-l
>
> ISYM 10 -k,+h+k,-l 12 -h-k,+h,-l
> Logical name: XYZIN File name:
> /Users/yogeshgupta/scott_mme/nme/Nme_from_Rapidata/YGBuild/phase_combination/nmemodel-PolyAla.pdb
> PDB file is being opened on unit 1 for INPUT.
> MATRICES DERIVED FROM CRYST1 CARD IN COORDINATE FILE
>
> RF RO
> 0.006 0.003 -0.000 -0.000 177.973 -88.986 0.000 -0.000
> -0.000 0.006 -0.000 0.000 0.000 154.129 0.000 0.000
> 0.000 -0.000 0.015 0.000 0.000 0.000 66.066 -0.000
> -0.000 0.000 -0.000 1.000 -0.000 0.000 -0.000 1.000
>
> WRITTEN OUTPUT MTZ FILE
> Logical Name: FFTHKLSCR Filename: /tmp/yogeshgupta/sfall_IO4.28214
>
> OPENED INPUT MTZ FILE
> Logical Name: FFTHKLSCR Filename: /tmp/yogeshgupta/sfall_IO4.28214
>
> WRITTEN OUTPUT MTZ FILE
> Logical Name: HKLOUT Filename:
> /tmp/yogeshgupta/nme_phasecombination_11_1.tmp
> * Title:
>
> * Base dataset:
> 0 HKL_base
> HKL_base
> HKL_base
> * Number of Datasets = 0
> * Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
>
> * Number of Columns = 7
> * Number of Reflections = 19584
> * Missing value set to NaN in input mtz file
> * Column Labels :
> H K L FP SIGFP FC PHIC
> * Column Types :
> H H H F Q F P
> * Associated datasets :
> 0 0 0 0 0 0 0
> * Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
> 177.9730 177.9730 66.0660 90.0000 90.0000 120.0000
> * Resolution Range :
> 0.00004 0.09621 ( 154.129 - 3.224 A )
> * Sort Order :
> 0 0 0 0 0
> * Space group = 'P 62' (number 171)
> SFALL may fail or give unreliable output later on.
> *** Calculation symmetry using space-group CalcSpaceGroup 145 ***
>
>
> Form factors used are
> AtomName - formfac number - (AI BI),I=1,NGauss - sum(AI)
> Default value is 5 term gaussian
> H 1 0.49300 10.51090 0.32291 26.12570
> 0.14019 3.14236 0.04081 57.79970 0.00304
> 0.00000 0.99995
> C 2 2.31000 20.84390 1.02000 10.20750
> 1.58860 0.56870 0.86500 51.65120 0.21560
> 0.00000 5.99920
> N 3 12.21260 0.00570 3.13220 9.89330
> 2.01250 28.99750 1.16630 0.58260 -11.52900
> 0.00000 6.99460
> O 4 3.04850 13.27710 2.28680 5.70110
> 1.54630 0.32390 0.86700 32.90890 0.25080
> 0.00000 7.99940
> S 5 6.90530 1.46790 5.20340 22.21510
> 1.43790 0.25360 1.58630 56.17200 0.86690
> 0.00000 15.99980
> Title: combine experimental phases with model phases
> Structure Factor Calculation
> Structure Factor Calculation to match existing FOBS file
> - Atom file Read ***
>
> Chain Names - First Residue - Last Residue - serial Kcount
> INPUT X USED AS X
> INPUT Y USED AS Y
> INPUT Z USED AS Z
> Title
> combine experimental phases with model phases
> Unit CELL Parameters are = 177.9730 177.9730 66.0660 90.0000
> 90.0000 120.0000
> Space Group Number = 145
>
>
> Hmin, Kmin, Lmin, Hmax, Kmax, Lmax are 0 0 -20 55 55 20
>
> Sampling Intervals NX,NY,NZ are 396 396 144
>
> Map dimensions are X = 0 to 395 Y = 0 to 395 Z = 0 to
> 47
>
> Minimum,Maximum 4(SNTH/L)**2 are 0.0000 and 0.0962
> intervals of s for rfactor analysis are 1./ 20
>
> ie Resolution Limits 154.1 to 3.2 Angstroms
>
> BADD = 0.00
>
> Initial Value of Atom radius in "fc" MAP 2.50
> This is modified by a factor Sqrt(B+25)/2PI to "spread" the density for
> atoms with high B factors
> Weight Omit 0.00 1000.00
>
> Scale BfactOverall 1.00 0.00
> FCALC is scaled by SCALE*exp(-BfactOverall*S/4)
>
> DSmin DSmax 3.22 4.47
> in refinement overall Scale and B are refined using
> reflections with DSMN < = D < = DSmax
>
>
>
> Reflections for which FOBS < -1.0 SIGMA Omitted
>
> Breset is -1.00
> Limits for atoms: AXIS MIN MAX
> 1 0.00000 1.00000
> 2 0.00000 1.00000
> 3 -0.03784 0.37116
>
>
> Upper limits are: AXIS MIN MAX
> 1 0.01405 0.98595
> 2 0.01405 0.98595
> 3 0.03784 0.29548
>
>
>
> First 10 atoms of atsort - orthog coordinates
> 1N ALA 361 66.3240 53.2960 30.4270 1.00 0.00 3
> fractional coordinates 0.54556 0.34579 0.46055
> 2CA ALA 361 67.4260 54.0090 31.0550 1.00 0.00 2
> fractional coordinates 0.55406 0.35041 0.47006
> 3C ALA 361 67.0020 55.4240 31.4240 1.00 0.00 2
> fractional coordinates 0.55627 0.35959 0.47565
> 4O ALA 361 66.0410 55.9520 30.8750 1.00 0.00 4
> fractional coordinates 0.55258 0.36302 0.46734
> 5CB ALA 361 68.6120 54.0650 30.1010 1.00 0.00 2
> fractional coordinates 0.56091 0.35078 0.45562
> 6N ALA 362 67.7080 56.0560 32.3750 1.00 0.00 3
> fractional coordinates 0.56229 0.36369 0.49004
> First 10 atoms of sorted file in asym unit -
> 30.64922 0.21013 0.12229 502.00 1.00 2 361CB ALA
> 60.35078 10.78987 0.12229 502.00 1.00 2 361CB ALA
> 30.65421 0.19977 0.12722 102.00 1.00 3 361N ALA
> 60.34579 10.80023 0.12722 102.00 1.00 3 361N ALA
> 60.36302 10.81044 0.13400 402.00 1.00 4 361O ALA
> 30.63698 0.18956 0.13400 402.00 1.00 4 361O ALA
> 60.35041 10.79635 0.13673 202.00 1.00 2 361CA ALA
> 30.64959 0.20365 0.13673 202.00 1.00 2 361CA ALA
> 60.35960 10.80332 0.14231 302.00 1.00 2 361C ALA
> 30.64041 0.19668 0.14231 302.00 1.00 2 361C ALA
> First atom of sorted file in atsort
> 50.75483 20.41129 -0.03750 120102.00 51.00 10CB ALA
> Number of atoms input = 2794
> Number of atoms in sort = 6816
> Number in density generation = 6816
> Number completely within fft box = 0
> Minimum B = 2.00
> Maximum B = 79.26
> Average B = 25.79
> Number of Bs < BfactReset = 1641
> Number of Bs > 99.99 = 0
>
> Number of reflections used = 19436
> Number of reflns. on file = 19584
> Old value of SCALE is = 1.000
> New value of SCALE is = 0.670
>
>
> to match FOBS , FC = Scale*Exp(-BfactOverall*SSQ/LL)*FCALC.
> Old values of SCALE and B overall are 0.6696E+00 0.0000E+00
>
> New values of SCALE and BfactOverall 0.278E+01 0.772E+02 Based on
> 12062 reflections with s**2 between 0.050 and 0.096
>
> Used values of SCALE and B overall are
> SCALE 0.2776E+01 B Value 0.7717E+02
> NB: Number of "possible" reflections is an underestimation - Centrics
> Kcounted at reduced multiplicity
> $TABLE: Rfactor analysis v resln :
> $GRAPHS:<Rfactor> v. resln combine experimental phases with model p:N:1,6:
> :<Nrefs> and <Nposs> v. resln combine experimental phases with model
> p:N:1,2,3:
> :<Fobs> and <Fc> v. resln combine experimental phases with model p:N:1,4,5:
> $$
> 1/resol^2 NO_OF_REF N_POSS <Fobs> <Fc> Rfactor
> Wdelta**2(Fobs_Scale) $$
> $$
> 0.025 7374 14146 280.18 559.58 1.22 74.33
> 0.075 12062 25865 116.07 121.37 0.58 22.70
> $$
> Total no. of reflections used 19436
> Overall Reliability index is 0.9600
> SIGMA W DELTA SQUARED (PII) ABSOLUTE SCALE 0.2773E+10
> SFALL: Normal Termination of structure factor calc.
> Times: User: 1.4s System: 0.1s Elapsed: 0:02
> </pre>
> </html>
>
> ###############################################################
> ###############################################################
> ###############################################################
> ### CCP4 6.1: SIGMAA version 6.1 : 02/06/09##
> ###############################################################
> User: yogeshgupta Run date: 16/ 5/2011 Run time: 18:23:37
>
> 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.
> Data line--- title combine experimental phases with model phases
> Data line--- labin FP=FP SIGFP=SIGFP PHIBP=PHIB WP=FOM HLA=HLA HLB=HLB
> HLC=HLC HLD=HLD FC2=FB
> Data line--- labout DELFWT=DELFWT PHDELFWT=PHDELFWT FWT=FWT PHFWT=PHFWT
> WCMB=WCMB PHCMB=PHCMB
> Data line--- ranges 20 1000
> Data line--- error
> Data line--- symmetry 'P 62'
> Spacegroup information obtained from library file:
> Logical Name: SYMINFO Filename:
> /sw64/share/xtal/ccp4-6.1.13/lib/data/syminfo.lib
> Data line--- combine part 1 damp 1.0 1.0
> Data line--- end
> OPENED INPUT MTZ FILE
> Logical Name: HKLIN Filename:
> /tmp/yogeshgupta/nme_phasecombination_11_1.tmp
> * Title:
>
> * Base dataset:
> 0 HKL_base
> HKL_base
> HKL_base
> * Number of Datasets = 0
> * Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
>
> * Number of Columns = 7
> * Number of Reflections = 19584
> * Missing value set to NaN in input mtz file
> * HISTORY for current MTZ file :
>
> * Column Labels :
> H K L FP SIGFP FC PHIC
> * Column Types :
> H H H F Q F P
> * Associated datasets :
> 0 0 0 0 0 0 0
> * Cell Dimensions : (obsolete - refer to dataset cell dimensions above)
> 177.9730 177.9730 66.0660 90.0000 90.0000 120.0000
> * Resolution Range :
> 0.00004 0.09621 ( 154.129 - 3.224 A )
> * Sort Order :
> 0 0 0 0 0
> * Space group = 'P 62' (number 171)
> Error in LABIN: label PHIB not found in file!
> Error in LABIN: label FOM not found in file!
> Error in LABIN: label HLA not found in file!
> Error in LABIN: label HLB not found in file!
> Error in LABIN: label HLC not found in file!
> Error in LABIN: label HLD not found in file!
> Error in LABIN: label FB not found in file!
> SIGMAA: Error in label assignments in LABIN
> Times: User: 0.0s System: 0.0s Elapsed: 0:00
> </pre>
> </html>
> <html> <!-- CCP4 HTML LOGFILE -->
> <hr>
> <a name="sigmaasigmaa"><h1>SIGMAA</h1></a>
> <pre>
> <pre>
> Program prints lots of information about every nmon th reflection - nmon
> = 1000
>
> Partial weights will be multiplied by 1.000
> Phase combination and Fourier coefficients
> Option COMBINE with partial structure--
> Phase combination of several sets of information:
> Combined map coefficients
> (a) Fourier map: 2mFo-DFc PH2mFo-DFc
> (b) Difference map: 2(mFo-DFc) PHFo-DFc
> HKLOUT contains columns H K L ... FWT DELFWT DFC WCMB
> SigmaA determination for 1 partial structure(s)
> ***************************************************************************
> * Information from CCP4Interface script
> ***************************************************************************
> The program run with command: /sw64/share/xtal/ccp4-6.1.13/bin/sigmaa HKLIN
> "/tmp/yogeshgupta/nme_phasecombination_11_1.tmp" HKLOUT
> "/Users/yogeshgupta/mylocation/eden_sigmaa1.mtz"
> has failed with error message
> SIGMAA: Error in label assignments in LABIN
> ***************************************************************************
>
> #CCP4I TERMINATION STATUS 0 " SIGMAA: Error in label assignments in LABIN"
> #CCP4I TERMINATION TIME 16 May 2011 18:23:37
> #CCP4I MESSAGE Task failed
>
> Then i tried to run it through command line using following script:
> sigmaa HKLIN merged-exp-model.mtz
> HKLOUT merge-exp-model-sigmaa.mtz
> << END-sigmaa
> TITLE Combine model phases with experimental phases
> RANGES 10 1000 ! Number of analysis bins, monitor interval
> RESOLUTION 50 3.2 ! Resolution limits in 4(sintheta/lambda)**2
> ERROR ! Use sigmaA v resolution for coordinate error
> COMBINE PART 1 ! Combine isomorphous + 1 partial model
> LABOUT PHCMB=PHCMB WCMB=WCMB FWT=FWT PHWT=PHWT
> LABIN FP=FP SIGFP=SIGFP PHIBP=PHIB WP=FOM -
> HLA=A HLB=B HLC=C HLD=D -
> FC=FCalc PHIC=PHICalc
> END
> END-sigmaa
> This gave the error:
> At line 771 of file
> /sw64/src/fink.build/ccp4-6.1.13-1/ccp4-6.1.13/src/sigmaa.f (unit = 5, file
> = 'stdin')
> Fortran runtime error: Bad real number in item 1 of list input
> I am attaching the original experimental phases that came from SHARP
> (eden.mtz) and second file where i merged the calculated phases from the
> model (merged----.mtz).
> Your help will be much appreciated.
> Thanks,
> Yogesh
>
> On Thu, May 19, 2011 at 5:12 AM, Ian Tickle <[log in to unmask]> wrote:
>>
>> Hi Yogesh
>>
>> I was probably the last person to update the SIGMAA source code, but I
>> have been using it without any problems. Could you post more info,
>> specifically the shell script you are using and an mtzdump listing of
>> the MTZ file header. If the problem can't be resolved from that info
>> I may need to ask you for the MTZ file itself, if that's possible.
>>
>> Cheers
>>
>> -- Ian
>>
>> On Wed, May 18, 2011 at 10:45 PM, Yogesh Gupta <[log in to unmask]>
>> wrote:
>> > My goal is to combine experimental phases to calculated phases from
>> > partial
>> > model. I am using SIGMAA in CCP4, which gave the following error, all
>> > labels
>> > that program can not find are present in the input file though.
>> >
>> > Error in LABIN: label PHIB not found in file!
>> > Error in LABIN: label FOM not found in file!
>> > Error in LABIN: label HLA not found in file!
>> > Error in LABIN: label HLB not found in file!
>> > Error in LABIN: label HLC not found in file!
>> > Error in LABIN: label HLD not found in file!
>> > Error in LABIN: label FB not found in file!
>> > SIGMAA: Error in label assignments in LABIN
>> >
>> > Could someone help me fix this or point me to other program that could
>> > do
>> > the phase combination similar to SIGMAA?
>> >
>> > Thanks for your time.
>> >
>> > -Yogesh
>> >
>> > --
>> > --------------------------------------------------
>> > Yogesh K. Gupta, Ph.D.
>> > Dept of Structural & Chemical Biology
>> > Mount Sinai School of Medicine
>> > Icahn Medical Institute
>> > 1 Gustave L. Levy Place, Box 1677
>> > New York, NY, USA 10029
>> >
>> > Tel:+1 212-659-8639
>> > --------------------------------------------------
>> >
>
>
>
>
|
