Re: [phenixbb] omit map for protein-DNA complex

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 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 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 wrote:

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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 wrote:

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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 wrote:

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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:

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On Tue, Jul 2, 2013 at 9:03 AM, Wei Shi 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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