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

7 Jul 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  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:
...
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:
...
Okay, this makes sense.  Wei, are you trying to model methylated DNA,
or are those C7 atoms there by accident?
-Nat
...
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
...
-Tom T
On Jul 2, 2013, at 1:07 PM, Nathaniel Echols wrote:
...
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
On Tue, Jul 2, 2013 at 12:11 PM, Terwilliger, Thomas C
 wrote:
part of a DA nucleotide.
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