[phenixbb] omit map for protein-DNA complex

Mon Jul 8 16:24:03 PDT 2013

Sorry about this - I guess the BREAK record is a non-standard
extension used by CNS and a few other programs (including Phenix,
obviously).  We'll see if we can get rid of it in our output files.

On Sat, Jul 6, 2013 at 6:57 PM, Wei Shi <wei.shi118 at gmail.com> wrote:
> 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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