[phenixbb] Will phenix.refine read CNS *.cv files?

[Scott Classen]

Hi Nick,

I think I tried that at some point, but the problem lies in the IOBS.
Some are regular float fortran format:

INDE     3    0    0 FOBS=   100.142 SIGMA=     1.478 IOBS= 10028.400
                    SIGI=   293.800 TEST=         0

while other IOBS are large and for some reason CNS decided to put them  
in scientific notation such as

INDE     5    0    0 FOBS=   492.449 SIGMA=    17.677 IOBS=     
0.242506E+06
                    SIGI= 17098.000 TEST=         0

As far as I can tell this requires two sets of fortran format  
statements for f2mtz to work properly.

format '(6X,3F5.0,6X,F10.3,7X,F10.3,6X,E15.3,/,24X,F10.3,6X,F10.0)'
or
format '(6X,3F5.0,6X,F10.3,7X,F10.3,6X,F10.3,/,24X,F10.3,6X,F10.0)'

I'm playing around with with grep to separate the original cv file  
into reflections with IOBS in F10.3 format and those with IOBS in  
E15.3 format, convert with f2mtz, then CAD them together, but this is  
bloody cumbersome. I was hoping phenix.refine would just automagically  
figure it all out.

Scott


On Jan 14, 2009, at 5:35 PM, Noinaj, Nicholas (NIH/NIDDK) [F] wrote:

> Scott,
>
> <not sure if anyone has remedied your problem yet>
>
> I don't know if you can read cns file directly into phenix.refine.   
> but
> here is another option....convert the cns file to *.mtz using CCP4.   
> If
> you use the CCP4i GUI --> Reflection Data utilities --> Convert
> to/modify/extend MTZ.  You can also retain the original flagged
> reflections here also.  You can then use the *.mtz file in
> phenix.refine.
>
> If you need further help, just drop me a quick email.  I can also  
> try it
> here if you supply me with the data file, but this may be too 'top
> secret' (lol).  Best of Luck!
>
>
>
>
>
> Cheers,
> Nick
>
>
>
> -----Original Message-----
> From: Scott Classen [mailto:sclassen at lbl.gov]
> Sent: Wednesday, January 14, 2009 8:06 PM
> To: PHENIX user mailing list
> Subject: [phenixbb] Will phenix.refine read CNS *.cv files?
>
> Hi all,
> I'm embarking on a collaboration with someone who is providing me with
> CNS cross validated data files. They look something like this.
>
>
>  NREFlection=     92086
>  ANOMalous=FALSe { equiv. to HERMitian=TRUE}
>  DECLare NAME=FOBS                   DOMAin=RECIprocal   TYPE=REAL END
>  DECLare NAME=SIGMA                  DOMAin=RECIprocal   TYPE=REAL END
>  DECLare NAME=IOBS                   DOMAin=RECIprocal   TYPE=REAL END
>  DECLare NAME=SIGI                   DOMAin=RECIprocal   TYPE=REAL END
>  DECLare NAME=TEST                   DOMAin=RECIprocal   TYPE=INTE END
>  INDE     3    0    0 FOBS=   100.142 SIGMA=     1.478 IOBS= 10028.400
>                    SIGI=   293.800 TEST=         0
>  INDE     4    0    0 FOBS=   158.996 SIGMA=     2.329 IOBS= 25279.600
>                    SIGI=   735.200 TEST=         0
>  INDE     5    0    0 FOBS=   492.449 SIGMA=    17.677 IOBS=
> 0.242506E+06
>                    SIGI= 17098.000 TEST=         0
>  INDE     7    0    0 FOBS=   246.492 SIGMA=     3.127 IOBS= 60758.400
>                    SIGI=  1531.800 TEST=         0
>  INDE     8    0    0 FOBS=    32.790 SIGMA=     0.549 IOBS=  1075.200
>                    SIGI=    35.700 TEST=         1
>  INDE     9    0    0 FOBS=   426.866 SIGMA=     8.886 IOBS=
> 0.182215E+06
>                    SIGI=  7507.000 TEST=         0
>  INDE    10    0    0 FOBS=   411.347 SIGMA=     8.597 IOBS=
> 0.169206E+06
>                    SIGI=  6999.000 TEST=         0
>  INDE    11    0    0 FOBS=    87.275 SIGMA=     1.346 IOBS=  7617.000
>                    SIGI=   233.200 TEST=         0
>
> When I try to run phenix.refine --dry_run my_model.pdb  
> my_CNS_cv_file.cv
>
> I get the following error:
>
> Processing inputs. This may take a minute or two.
> Sorry: Unknown file format: my_CNS_cv_file.cv
>
>
> Any ideas?
>
> Thanks,
> Scott
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Scott Classen, Ph.D.
> SIBYLS Beamline 12.3.1
> http://bl1231.als.lbl.gov
> Advanced Light Source
> Lawrence Berkeley National Laboratory
> 1 Cyclotron Rd
> MS6R2100
> Berkeley, CA 94720
> C) 510.206.4418
> O) 510.495.2697
> Beamline) 510.495.2134
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
>
>
>
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Scott Classen, Ph.D.
SIBYLS Beamline 12.3.1
http://bl1231.als.lbl.gov
Advanced Light Source
Lawrence Berkeley National Laboratory
1 Cyclotron Rd
MS6R2100
Berkeley, CA 94720
C) 510.206.4418
O) 510.495.2697
Beamline) 510.495.2134
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~