Dear All,
A quick question about Refmac on ccp4i. When refining an RNA oligonucleotide
structure using the findwaters option, the pdb output labels all the atoms as
HETATM (inluding the original RNA atoms which were not so labelled in the input
pdb). It is of course trivial to correct this, but
the CCP4 gui does just that - provides map coeffs by default..
You can seek out the full REFMAC output if needed but it is not there by
default.
Eleanor
On 3 August 2017 at 02:04, Pavel Afonine wrote:
> Hi Ed,
>
> your suggestion makes perfect sense to me, and it's trivial to add an
> option to
Hi Ed,
your suggestion makes perfect sense to me, and it's trivial to add an
option to do what you want. This will be available in next Phenix nightly
build (clearly not tomorrow given today's power outage).
Command line: use "write_map_coefficients_only=True" (by default is is
False).
Refinemen
On Wednesday, 02 August, 2017 16:12:30 Edwin Pozharski wrote:
> Just to clarify, how do you use the extra columns in this scenario? My
> suggestion was to have the output file that includes only the map
> coefficient columns, so you still can look at the map. IIRC, FP/SIGFP
> columns from refmac
Just to clarify, how do you use the extra columns in this scenario? My
suggestion was to have the output file that includes only the map
coefficient columns, so you still can look at the map. IIRC, FP/SIGFP
columns from refmac output are actually modified from the input (scaled
with Boverall), so
Yes, I agree! This (“Please look at my structure, and here are my files from
the last cycle of refinement") happens to me almost every week. :)
Diana
**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
University of Texas Sout
As someone who uses those "superfluous" columns all the time, I would
like to chime in in favor of keeping the default output columns of
refmac. If only I had a nickle for every time someone asked me to "look
at" a structure and only gave me the output files of refinement. Kind
of ties your h
>
> I know space is cheap these days, but is there a reason for Refmac to
> generate all those extra columns in the output mtz file? Refmac (as well
> as phenix.refine and buster-tnt) output mtz file is almost always used for
> only one purpose - look at the map in coot. You only need 4 columns f
Perhaps a good opportunity for getting rid of (scaled) F and SIGF too?
Certain pipelines need Refmac's phase estimates (Buccaneer and Crank2 off
the top of my head), but I can't see how activating an 'expert mode' or
'developer mode' in order to get them would be a problem for their authors.
Chee
I know space is cheap these days, but is there a reason for Refmac to
generate all those extra columns in the output mtz file? Refmac (as well
as phenix.refine and buster-tnt) output mtz file is almost always used for
only one purpose - look at the map in coot. You only need 4 columns for
that, n
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