Dear all,
Sorry for a non-ccp4
question. I am trying to refine a structure of protein-RNA complex. The RNA
have two 5-iodo-U in one chain. I used the following patch in
generate.inp so that an I5 atom is added to the C5 atom of the
Uracil.
I add patch statement at the bottem
of generate.inp
{* any special nucleic acid patches can be applied here
*}
{===>}
patch
U5I
reference=nil=((residue
3 or residue 12 ) and segid B )
end
{<===}
However when I run generate.inp, the result is like
this:
CNSsolve> {* any special nucleic acid patches can be
applied here *}
CNSsolve>
{===>}
CNSsolve> patch
U5I
PATCH> reference=1=((residue
3 or residue 12) and segid B)
SELRPN: 0
atoms have been selected out of
1941
PATCH> end
%PATCH-ERR: to be
modified atom C5 not found in molecular
structure.
%PATCH-ERR: no set found for atom to be
added
%PATCH-ERR: to be deleted bond C5
I5 not found in molecular structure.
%PATCH-ERR: to
be deleted angle I5 C5 C4
not found in molecular structure.
%PATCH-ERR: to be deleted angle
I5 C5 C6 not found in
molecular structure.
%PATCH-ERR: to be deleted improper
I5 O4 C6
C5 not found in molecular structure.
SCRATC-warning:
STORe selections erased.
The coordinate 5-iodo-U is like this :
ATOM 1025 P URI
B 3 -18.359 16.541
7.430 1.00
65.41
P
ATOM 1026 C5' URI B 3
-16.935 17.944 5.725 1.00
69.03 C
ATOM 1027 O5' URI B 3
-17.951 17.909 6.722 1.00
66.63
O
ATOM 1028 C4' URI B 3
-16.596 19.372 5.379 1.00
70.65 C
ATOM 1029 O4' URI B 3
-17.740 20.001 4.747 1.00
70.93
O
ATOM 1030 C3' URI B 3
-16.296 20.265 6.571 1.00
71.94 C
ATOM 1031 O3' URI B 3
-14.944 20.125 6.990 1.00
73.84
O
ATOM 1032 C2' URI B 3
-16.593 21.652 6.017 1.00
71.82 C
ATOM 1033 O2' URI B 3
-15.535 22.175 5.239 1.00
71.73
O
ATOM 1034 C1' URI B 3
-17.805 21.366 5.127 1.00
71.42 C
ATOM 1035 O1P URI B 3
-17.114 15.829 7.818 1.00
65.41 O
ATOM 1036 O2P URI B 3
-19.387 16.843 8.460 1.00
64.75 O
ATOM 1037 N1 URI B
3 -19.094 21.594 5.810 1.00
20.00 N
ATOM 1038 C2 URI B
3 -19.526 22.901 5.911 1.00
20.00 C
ATOM 1039 N3 URI B
3 -20.737 23.073 6.553 1.00
20.00 N
ATOM 1040 C4 URI B
3 -21.528 22.084 7.090 1.00
20.00 C
ATOM 1041 C5 URI B
3 -20.995 20.751 6.941 1.00
20.00 C
ATOM 1042 C6 URI B
3 -19.820 20.544 6.314 1.00
20.00 C
ATOM 1043 I5 URI B
3 -21.972 19.056 7.556 1.00
50.00 I
ATOM 1044 O2 URI B
3 -18.892 23.841 5.468 1.00
20.00
O
ATOM 1045 O4 URI B
3 -22.599 22.360 7.646 1.00
20.00
O
I used 1.1 version, it seems that all the porgram in my
linux machine is OK.
It seems that the patch which I add didn't work and 0
atoms have been selected out of 1941 atoms.
Could anybody know
how to add patch statement correctly in generate.inp?
Another question is how to precess phosphate group in 5'
in the RNA? It seems patch also needed to be state in generate.inp.
Thanks very much in advance!
Hai-Feng Hou
Biological macromolecule group
Beijing Synchrotron
Radiation Facility
Institute of High Energy Physics
Chinese Academy of
Sciences
Beijing, China
Tel: +86-10-88234208
E-mail: [log in to unmask]
2008-02-29
