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Re: [ccp4bb]: PDB2CIF (summary)
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The CIF file has a lot of information that you don't wan't.
Why the dickens would you need scattering factors to write a
PDB file?
You probably only want a list of atoms with coordinates, in PDB format.
Even occupancy and B-factor could be set throughout to 1.0 and 20.
You can edit out the coordinates entries and awk them into pdb format.
Unfortunately due to the free format of CIF, you have to edit the
awk command for each new file you convert. Heres what worked for
Deisenhofer's antimycin coordinates:
Here's what worked for me:
awk '$7~/Uani|Uiso/' antimycin.cif \
|sed -e 's/(..)//g' |sed -e 's/(.)//g' \
| awk '{printf("%5d%10.5f%10.5f%10.5f%10.5f%5.2f%5d%14s%5s\n",
1,$3,$4,$5,0.00,$8,1,0,$1,"ANT") }' \
>! ant.frc
coordconv XYZIN ant.frc \
XYZOUT antimycinh.pdb <<EOF-coordconv
INPUT FRAC
OUTPUT PDB ORTH 1
CELL 15.385 8.027 12.471 90.00 96.34 90.00
END
EOF-coordconv
this was for a cif file that has atom records like:
O1 O -0.9870(5) -0.6339(10) -0.0623(8) 0.100(3) Uani 1 d . .
O2 O -0.8438(4) -0.0991(8) -0.0864(5) 0.059(2) Uani 1 d . .
H1 H -0.8106(4) -0.0181(8) -0.0947(5) 0.071 Uiso 1 calc R .
O3 O -0.7115(4) 0.0493(8) -0.1450(5) 0.060(2) Uani 1 d . .
O4 O -0.4292(4) 0.2193(8) -0.1652(5) 0.048(2) Uani 1 d . .
O5 O -0.4937(4) 0.4549(8) -0.2355(5) 0.051(2) Uani 1 d . .
O6 O -0.4745(3) 0.1501(8) -0.3709(4) 0.046(2) Uani 1 d . .
O7 O -0.4626(4) -0.1185(9) -0.3174(6) 0.064(2) Uani 1 d . .
O8 O -0.2716(4) 0.3356(9) -0.4259(5) 0.056(2) Uani 1 d . .
O9 O -0.3152(5) 0.4986(13) -0.5639(6) 0.085(3) Uani 1 d . .
N1 N -0.9373(5) -0.3670(11) -0.0674(7) 0.068(2) Uani 1 d . .
H1A H -0.9523(5) -0.2648(11) -0.0518(7) 0.081 Uiso 1 calc R .
N2 N -0.6027(4) -0.0870(10) -0.2097(6) 0.052(2) Uani 1 d . .
H2A H -0.5774(4) -0.1833(10) -0.2196(6) 0.062 Uiso 1 calc R .
C1 C -0.9932(7) -0.4892(16) -0.0457(9) 0.071(3) Uani 1 d . .
Pete wrote:
>
> *** For details on how to be removed from this list visit the ***
> *** CCP4 home page http://www.ccp4.ac.uk ***
>
> Here is my "success-story" on the conversion of CIF-files to PDB files.
> According to your suggestions I tried the following:
>
> I downloaded PLATON
> - conversion of the first CIF-file caused the program to crash
> - conversion of the second CIF-file produced a useful PDB file!!
> => success rate 50%
>
> I tried to use "libcheck"
> - there is a typo in the manual _FILE_OUT and _FILE_O are mixed up
> - the warning message was:
> WARNING : residue: C00 1 chain:AA - not found in the library
> WARNING: can't find atomic scatt.factors for :
> default symbol is "N "
> - no PDB file was produced
> => success rate 0%
>
> Pete Duntan suggested "Rasmol will read the small molecule cif file and
> output a pdb file."
> - Rasmol was able to read one of my three CIF-files
> - It did output a PDB-file but the coordinates were completely screwed up
> => success rate ~10%
>
> BABEL cannot read CIF-format (at least not the version we have installed)
>
> As I reported before:
> - CIFTr (from http://pdb.rutgers.edu/mmcif/). Gives a run time error.
> - CIF2PDB (from http://www.bernstein-plus-sons.com/software/cif2pdb/DISCUSS.cif2pdb.html)
> doesn't compile properly - at least in my hands.
>
> I hardly can believe. Is CIF-format even worse than any language
> produced in Babel
> that noone can understand. Any hints and suggestions are still appreciated!
>
> Pete
>
> ________________________________________________________________________
>
> PD Dr. Peter Burkhard
> M.E. Müller Institut (MSB)
> Klingelbergstr. 70
> CH-4056 BASEL, Switzerland
>
> Phone: ++41 61 267 20 91
> Fax: ++41 61 267 21 09
> E-mail: Peter.Burkhard@unibas.ch
> Web: http://www.biozentrum.unibas.ch/burkhard