[phenixbb] omit map for protein-DNA complex
Wei Shi
wei.shi118 at gmail.com
Sat Jul 6 18:57:57 PDT 2013
Hi guys,
I got the suggestions from Paul Emsley and after deleting all the "BREAK"
in the PDB file, I could view the whole molecule in coot!
Best,
Wei
On Wed, Jul 3, 2013 at 9:36 PM, Wei Shi <wei.shi118 at gmail.com> wrote:
> 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 at 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 at 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 at 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 at 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
>>> >
>>>
>>
>>
>
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