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Hello Christoph--
>
> I have 2 cis-prolines (as judged from chemical shifts and NOE connectivities)
> in my structure.
>
> I included a cipp-patch (for implementing cis-settings) in the
> generate_seq.inp, but despite of this the mtf-file that was generated is
> identical (apart from the file names) with the mtf-file which was generated
> without the cipp-patch. >> although the cipp-patch was used (but didn't
> actually effect any change of the mtf-file) the subsequently generated
> pdb-file and the calculated ensemble obviously came out trans.
>
mtf files are called psf files in Xplor-NIH. Are you using CNS?
In Xplor-NIH, you can generate your files using the script:
simWorld.setRandomSeed(3421) #set random seed
import protocol
from psfGen import seqToPSF, cisPeptide
seqToPSF('prot.seq') #prot.seq contains the sequence in 3-char codes
cisPeptide(42) #change 42 and 43 to the proper resids.
cisPeptide(43)
# the following two lines will write out
# psf and pdb files
xplor.command("write psf output=file.psf end")
protocol.genExtendedStructure("file.pdb",verbose=1)
If you have some issue(s) with the above, please contact us.
best regards--
Charles
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