card 7 in v9.07 and v9.08

Submitted by donghua on Thu, 2014-05-08 15:49

Forums

Frealign

Dear Niko,

I have one question about card 7. In my log file attached at the end, there is one line:
RESOLUTION RECONST., REFINE LOW/HIGH, CLASSIFY, DFSTD, RBFACT ?
And the input was shown as
3.0 200.0 3.4 3.4 100.0 150.0

Does this mean RBFACT=150.0? or RBFACT not shown in the log file?
Is DFSTD ( DFSIG ? ) defaulted to be 100.0?
In fact RBFACT was set to zero and DFSIG was 150.0 in my mparameters file.

Thanks!
Donghua

------------
FREALIGN - Fourier REconstruction and ALIGNment
V9.08 - 05.05.14
Copyright 2013 Howard Hughes Medical Institute.
All rights reserved.
Use is subject to Janelia Farm Research Campus Software Copyright 1.1
license terms ( http://license.janelia.org/license/jfrc_copyright_1_1.html )

CFORM,IFLAG,FMAG,FDEF,FASTIG,FPART,IEWALD,
FBEAUT,FFILT,FBFACT,FMATCH,IFSC,FDUMP,IMEM,INTERP?
M 1 F F F F 0 F F F F 0 F 0 0
RO,RI,PSIZE,MW,WGH,XSTD,PBC,BOFF,DANG,ITMAX,IPMAX?
CARD 2: Error. Trying old CARD 2 input...
360.0 265.0 1.07 0.000 0.070 0.000 5.0 75.0 1.0 10 10
PMASK for parameter refinement (e.g. 1,1,1,1,1)
1 1 1 1 1
FIRST, LAST PARTICLES ?
101 110
SYMMETRY CARD ?
I2
Entering GETSYMMAT with ASYM,NASYM I 2
Symmetry point group I2 redundancy 60
MAGNIFICATION, STEPSIZE, TARGET & THRESH SCORE LIMIT, CS, KV, BEAM TILT X,Y ?
1.0 6.4 0.9 0.9 4.1 300.0 0.0 0.0
NSET= 1, RELMAG= 1.000, DSTEP= 6.40
RESOLUTION RECONST., REFINE LOW/HIGH, CLASSIFY, DFSTD, RBFACT ?

CARD 7: Error. Trying old CARD 7 input...

3.0 200.0 3.4 3.4 100.0 150.0
PARTICLE IMAGE STACK ?

Axel Thu, 2014-05-08 15:57

Hi Donghua,

Does this mean RBFACT=150.0? Yes

I suspect there is a mistake in your script somewhere, with some value missing, which caused Frealign to assume you were using an older frealign card 7 format, where the individual values are not what you intend them to be.

This is reflected in the line:
CARD 7: Error. Trying old CARD 7 input...

You should double-check your scripts, and hopefully this error will go away once you determine its source.

Best,

Axel

niko Thu, 2014-05-08 15:58

It looks like you did not enter all the information on Card 7 that should be entered. You should provide 6 reals, for example

3.0,200.0,3.4,8.0,100.0,0.0

donghua Thu, 2014-05-08 16:53

Thanks Axel and Niko.
Originally I thought the new version could be compatible with older script.