Re: [ccp4bb] SA-omit map
Would an omit map calculated after removing the ssDNA from the model and then
gently randomizing the remaining coodinates using the NOISE option in pdbset
(possibly not in the GUI version)
NOISE [maximum_shift] [subkeys]
Introduce random shifts into atom positions in orthogonal coordinates.
maximum_shift maximum shift (Angs)
defaults to 0.2 Angs, fails if greater than 0.5 Angs
be a possible alternative to a simulated annealing technique? Would it not be
similarly effective at removing any memory bias in the remaining coodinates,
and very easy to do?
Having said that, it is usually simplest to do what the referee requests, if at
all possible. And if your DNA isn't there in the omit map, then you have no
reason to suggest that it is there at all.
best wishes
Pete
On 4 Nov 2013, at 18:02, Mark Brooks mark.x.bro...@gmail.com wrote:
Maybe try CNS or SFCheck:
http://groups.yahoo.com/neo/groups/cnsbb/conversations/messages/1720
To improve Phenix maps, maybe try increasing the number of boxes (the
parameter IIRC n_box_target= )
http://www.phenix-online.org/documentation/autobuild.htm
In CNS, you can decrease the starting temperature in the annealing section,
to reduce the 'violence' of the simulated annealing:
http://cns-online.org/cgi-bin/cns_solve_1.2/cns_view.cgi?file=inputs/xtal_refine/composite_omit_map.inp
---8---Snip--8--
{* starting temperature *}
{===} temperature=500;
---8---Snip--8--
As said elsewhere, if your map is still poor, maybe it's trying to tell you
something...
Mark
On 4 November 2013 06:36, dengzq1987 dengzq1...@gmail.com wrote:
Dear all,
Recently, I received the comments from referees, they asked for the SA-omit
map of the ssDNA of our protein-DNA complex. They said that simulated
annealing omit map better than a biased 2Fo-Fc. The ssDNA consists of seven
thymidine nucleotide. Our data diffracted to 2.65A，but the data quality is
not good and twin. We tried to produce SA-omit map using phenix. The map is
really bad. Does anyone have suggestion to refine the map? Thank you!
Bests,
zq Deng
2013-11-04
dengzq1987
Prof Peter Artymiuk
Krebs Institute
Department of Molecular Biology Biotechnology
University of Sheffield
Sheffield
S10 2TN
ENGLAND
Re: [ccp4bb] SA-omit map
What does a straight difference map look like? i.e. omit one nucleotide at a time, do a few cycles of refinement and then inspect the weighted difference map - SA may be too violent for your structure. Eleanor On 4 Nov 2013, at 06:36, dengzq1987 wrote: Dear all, Recently, I received the comments from referees, they asked for the SA-omit map of the ssDNA of our protein-DNA complex. They said that simulated annealing omit map better than a biased 2Fo-Fc. The ssDNA consists of seven thymidine nucleotide. Our data diffracted to 2.65A，but the data quality is not good and twin. We tried to produce SA-omit map using phenix. The map is really bad. Does anyone have suggestion to refine the map? Thank you! Bests, zq Deng 2013-11-04 dengzq1987
Re: [ccp4bb] SA-omit map
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear zq Deng, you may actually have some anomalous signal from the P-atoms in your structure, even if you collected at short wavelength - if you have a data set collected at, say, 1.5A, it would be even stronger. In that case you could create an anomalous difference map (you need unmerged data). If that show peaks near the P-atoms, you have pretty model-bias confirmation for the position of your DNA. George Sheldrick's program anode is very convenient to use for such purpose, but you need unmerged Bijvoet-pairs in your data, of course. Best, Tim On 11/04/2013 07:36 AM, dengzq1987 wrote: Dear all, Recently, I received the comments from referees, they asked for the SA-omit map of the ssDNA of our protein-DNA complex. They said that simulated annealing omit map better than a biased 2Fo-Fc. The ssDNA consists of seven thymidine nucleotide. Our data diffracted to 2.65A?but the data quality is not good and twin. We tried to produce SA-omit map using phenix. The map is really bad. Does anyone have suggestion to refine the map? Thank you! Bests, zq Deng 2013-11-04 dengzq1987 - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.15 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFSd5pdUxlJ7aRr7hoRAvm8AKCMpTi6+U8pmcv9kTonB+7Rs9SQwQCff4Vg 0IedSwdjUXW6PIMwTMnURpY= =1RSo -END PGP SIGNATURE-
Re: [ccp4bb] SA-omit map
Hi Deng, Recently, I received the comments from referees, they asked for the SA-omit map of the ssDNA of our protein-DNA complex. They said that simulated annealing omit map better than a biased 2Fo-Fc. The ssDNA consists of seven thymidine nucleotide. Our data diffracted to 2.65A，but the data quality is not good and twin. We tried to produce SA-omit map using phenix. The map is really bad. Does anyone have suggestion to refine the map? it's not unexpected for an OMIT map to appear worse than the original map. Indeed, it would be naive to expect the map to improve by removing atoms from model. If you add SA on top of it, this may (or may not, given stochastic nature of SA) degrade the map further, as SA is good at correcting gross model errors but not good for well refined near to final models. The purpose of OMIT maps is not to make your map look nicer, but to prove or disprove something, like questionable density (whether it is real signal, model bias or noise) etc. It also depends what you call really bad. If you think the map looks worse beyond what one can expect from SA OMIT procedure, you may send us (Phenix) inputs necessary to reproduce the map you get and we will investigate. Pavel
Re: [ccp4bb] SA-omit map
Hi Deng - Can you tell why the reviewer was asking for the SA-omit map? Is there some doubt about the conformation of your ssDNA, or even whether it is present in the first place? Is there a question about the sequence, or the sequence register (which nucleotides go in which positions)? Even a poor-quality map should let you locate the phosphate backbone of the DNA. This should convince most reviewers that the DNA is present and in the general position you have modeled. You can't resolve concerns about nucleotide base position or conformation without a better quality map. I imagine that you built the protein model first during your structure determination, and only added the ssDNA later in the refinement. If this is correct, you could present the maps from the last refinement cycle before you added the DNA. This is even less model biased than what the reviewer wants. Hope that helps, Matt On 11/4/13 1:36 AM, dengzq1987 wrote: Dear all, Recently, I received the comments from referees, they asked for the SA-omit map of the ssDNA of our protein-DNA complex. They said that simulated annealing omit map better than a biased 2Fo-Fc. The ssDNA consists of seven thymidine nucleotide. Our data diffracted to 2.65A,but the data quality is not good and twin. We tried to produce SA-omit map using phenix. The map is really bad. Does anyone have suggestion to refine the map? Thank you! Bests, zq Deng 2013-11-04 dengzq1987 -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374
Re: [ccp4bb] SA-omit map
I have two bits of advice. 1. If the SA omit map for the ssDNA is really bad, perhaps you should reconsider whether your model is a faithful representation of the experimental data. 2. You could use anomalous difference Fourier analysis to locate the P atoms of the DNA backbone. We did this for ssDNA bound to a Fab using a data set collected at wavelength=1.74 A. See Figure 3 of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2516951/ John J. Tanner Professor of Biochemistry and Chemistry University of Missouri-Columbia 125 Chemistry Building Columbia, MO 65211 Phone: 573-884-1280 Fax: 573-882-2754 Email: tanne...@missouri.edumailto:tanne...@missouri.edu http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html On Nov 4, 2013, at 10:42 AM, Matthew Franklin mfrank...@nysbc.orgmailto:mfrank...@nysbc.org wrote: Hi Deng - Can you tell why the reviewer was asking for the SA-omit map? Is there some doubt about the conformation of your ssDNA, or even whether it is present in the first place? Is there a question about the sequence, or the sequence register (which nucleotides go in which positions)? Even a poor-quality map should let you locate the phosphate backbone of the DNA. This should convince most reviewers that the DNA is present and in the general position you have modeled. You can't resolve concerns about nucleotide base position or conformation without a better quality map. I imagine that you built the protein model first during your structure determination, and only added the ssDNA later in the refinement. If this is correct, you could present the maps from the last refinement cycle before you added the DNA. This is even less model biased than what the reviewer wants. Hope that helps, Matt On 11/4/13 1:36 AM, dengzq1987 wrote: Dear all, Recently, I received the comments from referees, they asked for the SA-omit map of the ssDNA of our protein-DNA complex. They said that simulated annealing omit map better than a biased 2Fo-Fc. The ssDNA consists of seven thymidine nucleotide. Our data diffracted to 2.65A，but the data quality is not good and twin. We tried to produce SA-omit map using phenix. The map is really bad. Does anyone have suggestion to refine the map? Thank you! Bests, zq Deng 2013-11-04 dengzq1987 -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374
Re: [ccp4bb] SA-omit map
Maybe try CNS or SFCheck:
http://groups.yahoo.com/neo/groups/cnsbb/conversations/messages/1720
To improve Phenix maps, maybe try increasing the number of boxes (the
parameter IIRC n_box_target= )
http://www.phenix-online.org/documentation/autobuild.htm
In CNS, you can decrease the starting temperature in the annealing section,
to reduce the 'violence' of the simulated annealing:
http://cns-online.org/cgi-bin/cns_solve_1.2/cns_view.cgi?file=inputs/xtal_refine/composite_omit_map.inp
---8---Snip--8--
{* starting temperature *}
{===} temperature=500;
---8---Snip--8--
As said elsewhere, if your map is still poor, maybe it's trying to tell you
something...
Mark
On 4 November 2013 06:36, dengzq1987 dengzq1...@gmail.com wrote:
Dear all,
Recently, I received the comments from referees, they asked for the
SA-omit map of the ssDNA of our protein-DNA complex. They said that simulated
annealing omit map better than a biased 2Fo-Fc. The ssDNA consists of seven
thymidine nucleotide. Our data diffracted to 2.65A，but the data quality
is not good and twin. We tried to produce SA-omit map using phenix. The map
is really bad. Does anyone have suggestion to refine the map? Thank you!
Bests,
zq Deng
2013-11-04
--
dengzq1987
[ccp4bb] SA-omit map
Dear all, Recently, I received the comments from referees, they asked for the SA-omit map of the ssDNA of our protein-DNA complex. They said that simulated annealing omit map better than a biased 2Fo-Fc. The ssDNA consists of seven thymidine nucleotide. Our data diffracted to 2.65A,but the data quality is not good and twin. We tried to produce SA-omit map using phenix. The map is really bad. Does anyone have suggestion to refine the map? Thank you! Bests, zq Deng 2013-11-04 dengzq1987
