[phenixbb] omit map for protein-DNA complex

[Wei Shi]

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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