[phenixbb] hydrogen-bond restraints for Watson-Crick base pairs
Jeff Headd
jjheadd at lbl.gov
Tue Jun 22 15:41:32 PDT 2010
Hi Scott,
I'm not sure why that's not working, it looks to me to be formatted
correctly. Could you send me (directly to my email, not the board) a
larger section of DNA that should have WC base pairs? That will help
to trouble shoot what is going on.
Thanks,
Jeff
On Tue, Jun 22, 2010 at 3:17 PM, Scott Classen <sclassen at lbl.gov> wrote:
> Hi Nat,
>
> The Ad and * stuff comes from coot
>
> OK I renamed all my DNA residues and atom to the PDB version 3 "standard" Ad becomes DA and * becomes ' etc etc.
>
> HETATM 1 O5' DA D 1 -47.740 -49.121 -17.972 1.00 91.44 O
> ANISOU 1 O5' DA D 1 13002 6701 15042 3404 -258 -1747 O
> HETATM 2 C5' DA D 1 -47.012 -48.219 -17.145 1.00 89.95 C
> ANISOU 2 C5' DA D 1 12785 6488 14904 3328 -133 -1848 C
> HETATM 3 C4' DA D 1 -45.570 -48.166 -17.612 1.00 87.82 C
> ANISOU 3 C4' DA D 1 12704 6315 14346 3354 213 -1700 C
> HETATM 4 O4' DA D 1 -45.517 -47.624 -18.952 1.00 85.51 O
> ANISOU 4 O4' DA D 1 12694 6248 13549 3345 56 -1589 O
> HETATM 5 C3' DA D 1 -44.642 -47.267 -16.812 1.00 88.97 C
> ANISOU 5 C3' DA D 1 12860 6436 14508 3299 389 -1783 C
> HETATM 6 O3' DA D 1 -43.312 -47.719 -17.004 1.00 87.64 O
> ANISOU 6 O3' DA D 1 12793 6290 14216 3376 787 -1645 O
> HETATM 7 C2' DA D 1 -44.883 -45.902 -17.456 1.00 88.06 C
> ANISOU 7 C2' DA D 1 12951 6509 13998 3224 84 -1819 C
> HETATM 8 C1' DA D 1 -45.055 -46.290 -18.922 1.00 86.43 C
> ANISOU 8 C1' DA D 1 12944 6475 13420 3268 -4 -1650 C
> HETATM 9 N9 DA D 1 -46.030 -45.477 -19.640 1.00 88.99 N
> ANISOU 9 N9 DA D 1 13415 6923 13476 3202 -408 -1684 N
> HETATM 10 C8 DA D 1 -47.262 -45.061 -19.205 1.00 91.41 C
> ANISOU 10 C8 DA D 1 13632 7157 13943 3159 -766 -1828 C
> HETATM 11 N7 DA D 1 -47.919 -44.338 -20.086 1.00 91.51 N
> ANISOU 11 N7 DA D 1 13857 7306 13606 3115 -1076 -1814 N
> HETATM 12 C5 DA D 1 -47.057 -44.279 -21.180 1.00 89.60 C
> ANISOU 12 C5 DA D 1 13841 7242 12960 3112 -900 -1656 C
> HETATM 13 C4 DA D 1 -45.889 -44.979 -20.917 1.00 87.68 C
> ANISOU 13 C4 DA D 1 13517 6968 12828 3174 -500 -1580 C
> HETATM 14 N1 DA D 1 -46.108 -43.812 -23.301 1.00 83.38 N
> ANISOU 14 N1 DA D 1 13478 6809 11393 3063 -789 -1439 N
> HETATM 15 C2 DA D 1 -45.046 -44.522 -22.903 1.00 82.39 C
> ANISOU 15 C2 DA D 1 13235 6642 11427 3141 -430 -1387 C
> HETATM 16 N3 DA D 1 -44.840 -45.143 -21.741 1.00 83.98 N
> ANISOU 16 N3 DA D 1 13201 6650 12057 3203 -253 -1442 N
> HETATM 17 C6 DA D 1 -47.151 -43.666 -22.454 1.00 87.19 C
> ANISOU 17 C6 DA D 1 13821 7135 12171 3057 -1043 -1571 C
> HETATM 18 N6 DA D 1 -48.209 -42.954 -22.862 1.00 88.07 N
>
> Still no luck
>
>
>
> On Jun 22, 2010, at 3:03 PM, Nathaniel Echols wrote:
>
>> On Tue, Jun 22, 2010 at 2:56 PM, Scott Classen <sclassen at lbl.gov> wrote:
>> I set main.secondary_structure_restraints = True
>> and it appears that protein ss elements are found and added to the geo file, but watson crick pairs are not.
>>
>> My DNA looks like this:
>>
>> HETATM 1 O5* Ad D 1 -47.740 -49.121 -17.972 1.00 91.44 O
>> ANISOU 1 O5* Ad D 1 13002 6701 15042 3404 -258 -1747 O
>>
>> Is there any reason it wouldn't be recognized by PROBE?
>>
>> Jeff says that PROBE probably won't recognize "Ad" (it expects "dA" instead), and the default behavior probably requires O5', not O5*. The atom naming we can probably work around, the residue names are more difficult. What program generated these residues?
>>
>> If you can send us the model (or just enough of it to have base pairs, actually), we'll take a look.
>>
>> -Nat
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