Hi guys,

With the help of Tom and Nat, I fixed the errors in my pdb file and could generate the simulated annealing omit map for the protein-DNA complex structure!

But when I opened resolve_composite_map.mtz and *_ed.pdb in Coot, I could only see one monomer of the protein in Coot. It should be two dimers of the protein plus two pieces of DNA. And when I opened the *_ed.pdb in pymol, it showed the right thing: two dimers of the protein plus two pieces of DNA. It seems that something in� *_ed.pdb file is not recognized by Coot.� I don't know whether any of you had this before and would have any suggestions for me.
When I opened *_ed. pdb with text file and found out that the word "break" is used instead of "ter" between different chains, so I replaced all "break" with "ter", but this didn't help....

Thank you so much!

Best,
Wei

On Wed, Jul 3, 2013 at 10:36 AM, Wei Shi <wei.shi118@gmail.com> wrote:

Hi Nat and Tom,

Thank you so much for your help! I don't know why those C7 atoms are there.... I just added some nucleotides manually using coot to fit the density.� I am going to delete those C7 atoms in DA and see whether that would help. Thank you guys so much!

Best,
Wei

On Tue, Jul 2, 2013 at 5:22 PM, Nathaniel Echols <nechols@lbl.gov> wrote:

Okay, this makes sense. �Wei, are you trying to model methylated DNA,
or are those C7 atoms there by accident?

-Nat

On Tue, Jul 2, 2013 at 12:11 PM, Terwilliger, Thomas C
<terwilliger@lanl.gov> wrote:
> Hi Nat,
> I think it was the input file. Here is a little piece of it:
>
> ATOM � 3157 �P � DA �E � 8 � � -56.682 �44.723-118.292 �1.00 37.45 � � � � � P
> ATOM � 3158 �C5' DA �E � 8 � � -54.313 �44.743-117.204 �1.00 40.32 � � � � � C
> ATOM � 3159 �O5' DA �E � 8 � � -55.729 �44.807-117.015 �1.00 38.38 � � � � � O
> ATOM � 3160 �C4' DA �E � 8 � � -53.551 �44.795-115.886 �1.00 35.58 � � � � � C
> ATOM � 3161 �O4' DA �E � 8 � � -53.433 �46.172-115.429 �1.00 32.68 � � � � � O
> ATOM � 3162 �C3' DA �E � 8 � � -54.164 �44.027-114.709 �1.00 30.30 � � � � � C
> ATOM � 3163 �O3' DA �E � 8 � � -53.117 �43.597-113.848 �1.00 30.92 � � � � � O
> ATOM � 3164 �C2' DA �E � 8 � � -54.997 �45.106-114.029 �1.00 18.46 � � � � � C
> ATOM � 3165 �C1' DA �E � 8 � � -53.974 �46.233-114.120 �1.00 19.87 � � � � � C
> ATOM � 3166 �N1 �DA �E � 8 � � -52.933 �50.956-112.506 �1.00 �4.27 � � � � � N
> ATOM � 3167 �C2 �DA �E � 8 � � -52.179 �49.849-112.633 �1.00 �5.31 � � � � � C
> ATOM � 3168 �N3 �DA �E � 8 � � -52.515 �48.630-113.069 �1.00 �3.59 � � � � � N
> ATOM � 3169 �C4 �DA �E � 8 � � -53.816 �48.619-113.401 �1.00 �5.26 � � � � � C
> ATOM � 3170 �C5 �DA �E � 8 � � -54.722 �49.662-113.344 �1.00 �5.31 � � � � � C
> ATOM � 3171 �C6 �DA �E � 8 � � -54.237 �50.894-112.863 �1.00 �4.84 � � � � � C
> ATOM � 3172 �N6 �DA �E � 8 � � -55.010 �51.981-112.750 �1.00 �5.38 � � � � � N
> ATOM � 3173 �C7 �DA �E � 8 � � -56.909 �56.086-110.227 �1.00 �2.18 � � � � � C
> ATOM � 3174 �N7 �DA �E � 8 � � -55.973 �49.258-113.789 �1.00 �6.11 � � � � � N
> ATOM � 3175 �C8 �DA �E � 8 � � -55.803 �47.992-114.102 �1.00 �7.27 � � � � � C
> ATOM � 3176 �N9 �DA �E � 8 � � -54.525 �47.556-113.888 �1.00 �8.54 � � � � � N
> ATOM � 3177 �OP1 DA �E � 8 � � -56.215 �43.588-119.122 �1.00 44.46 � � � � � O
> ATOM � 3178 �OP2 DA �E � 8 � � -58.094 �44.785-117.853 �1.00 32.00 � � � � � O
>
> Notice the C7 that is not attached to anything and is not normally part of a DA nucleotide.
> -Tom T
>
> On Jul 2, 2013, at 1:07 PM, Nathaniel Echols wrote:
>
>> On Tue, Jul 2, 2013 at 9:03 AM, Wei Shi <wei.shi118@gmail.com> wrote:
>>> Below is the error message I got when I ran a plain refinement of the same
>>> PDB file and data file. I also ran phenix.ready-set of the PDB file using
>>> default setting (add hydrogen to model if absent, et al) and generate a
>>> updated PDB file and ran refine again, but still got the same error message
>>> as below:
>>
>> This sounds like a bug. �Could you please email us off-list with the
>> PDB file and any existing restraints? �(We can fake the data for
>> testing purposes.)
>>
>> -Nat
>