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[ccp4bb]: Refmac5 libraries
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I have had a struggle helping a student with refmac5 libraries and am
still not totally able to do what we want. The structure is of a
peptide containing ALPHA-AMINOISOBUTYRIC ACID in the chain. A minimal
file exists for this as AIB but this is for an isolated amino acid not
as an L-peptide. Anyway by changing the residue name to AIC in the PDB,
we managed eventually to get a cif file that worked. The programme at
this stage wanted to define the C-N distance between residues to 3.5.
With a bit more playing we got the programme to write out links to a cif
file of 1.330 A C-N and I guess this would do. However for a council of
perfection I wanted to use the full TRANS peptide bond parameters so we
added explicit links to the PDB file
eg
LINK C GLY B 3 1.330 N AIC B 4
TRANS
This worked (once, eventually)as we had hoped, however when we made some
further hand modifications to the cif file (see diff below) this fails
and links called TRANS1 TRANS2 etc are written to an output cif file.
Can anyone explain this?
I presume L-polymer entries should resmble those in mon_lib_prot.cif.
The file I think works is more or less a manual hack of the ALA entry.
Whenever we used Sketcher it seemed to add inapporiate extra hydrogens
(eg making the C atom into an aldehyde)?
What is the role of .CCP4/monomers ? Is this read after the $CLIB and
before the ccp4i specified libfile ?
diff aic.cif tric-trans-aic2.cif
18c18
< AIC AIC 'ALPHA-AMINOISOBUTYRIC ACID '
L-peptide 13 6 .
---
> AIC AIC 'AMINO WHATSIT ' L-peptide 13 6 .
40,52c40,52
< AIC N N NH1 0.204
< AIC H H HNH1 -0.204
< AIC CA C CT 0.104
< AIC CB1 C CH3 -0.120
< AIC HB11 H HCH3 0.040
< AIC HB12 H HCH3 0.040
< AIC HB13 H HCH3 0.040
< AIC CB2 C CH3 -0.120
< AIC HB21 H HCH3 0.040
< AIC HB22 H HCH3 0.040
< AIC HB23 H HCH3 0.040
< AIC C C C 0.318
< AIC O O O -0.422
---
> AIC N N NH1 0.000
> AIC H H HNH1 0.000
> AIC CA C CT 0.000
> AIC CB1 C CH3 0.000
> AIC HB11 H HCH3 0.000
> AIC HB12 H HCH3 0.000
> AIC HB13 H HCH3 0.000
> AIC CB2 C CH3 0.000
> AIC HB21 H HCH3 0.000
> AIC HB22 H HCH3 0.000
> AIC HB23 H HCH3 0.000
> AIC C C C 0.000
> AIC O O O 0.000
79,83c79,83
< AIC H N single 0.860 0.020
< AIC CA N single 1.458 0.020
< AIC C CA single 1.525 0.020
< AIC CB1 CA single 1.521 0.020
< AIC CB2 CA single 1.521 0.020
---
> AIC H N single 1.010 0.020
> AIC CA N single 1.450 0.020
> AIC C CA single 1.507 0.020
> AIC CB1 CA single 1.524 0.020
> AIC CB2 CA single 1.524 0.020
85,90c85,90
< AIC HB11 CB1 single 0.960 0.020
< AIC HB12 CB1 single 0.960 0.020
< AIC HB13 CB1 single 0.960 0.020
< AIC HB21 CB2 single 0.960 0.020
< AIC HB22 CB2 single 0.960 0.020
< AIC HB23 CB2 single 0.960 0.020
---
> AIC HB11 CB1 single 1.059 0.020
> AIC HB12 CB1 single 1.059 0.020
> AIC HB13 CB1 single 1.059 0.020
> AIC HB21 CB2 single 1.059 0.020
> AIC HB22 CB2 single 1.059 0.020
> AIC HB23 CB2 single 1.059 0.020
98,104c98,104
< AIC H N CA 114.000 3.000
< AIC N CA CB1 110.400 3.000
< AIC N CA CB2 110.400 3.000
< AIC N CA C 111.200 3.000
< AIC CB1 CA CB2 123.000 3.000
< AIC CB1 CA C 110.200 3.000
< AIC CB2 CA C 110.200 3.000
---
> AIC H N CA 118.500 3.000
> AIC N CA CB1 110.000 3.000
> AIC N CA CB2 110.000 3.000
> AIC N CA C 111.600 3.000
> AIC CB1 CA CB2 111.000 3.000
> AIC CB1 CA C 109.470 3.000
> AIC CB2 CA C 109.470 3.000
117c117
< AIC CA C O 120.800 3.000
---
> AIC CA C O 120.500 3.000
--
Dr Nicholas H. Keep
Department of Crystallography,
Birkbeck College,
University of London,
Malet Street,
LONDON
WC1E 7HX
email n.keep@mail.cryst.bbk.ac.uk
Telephone 0171-631-6852 (Room 122, Office)
0171-631-6868 (Laboratory)
0171-631-6800 (Department Office)
Fax 0171-631-6803