u can get Phaser to only take
account of the top peak by setting the minimum peak height.
If you post or email the list of peaks, I might be able to give some specific
advice (although I'll be on my way to the Cold Spring Harbor school most of the
day).
Best wishes,
Randy Read
----
Ran
I suspect the problem is that sftools hasn't been modernised to alter all the
cell dimension records used in current MTZ files. I can't remember right now
but maybe the DCELL command in cad might fix it.
Randy Read
----
Randy J. Read
> On 2 Oct 2013, at 17:13, wtempel wrote:
&g
wever if you get a
large TFZ with the latest version of Phaser then this means something, because
it's already accounting for the modulation.
Best wishes,
Randy Read
----
Randy J. Read
On 16 Mar 2012, at 18:33, xiaoyazi2008 wrote:
> Thanks all!
>
> In addition to the pseudo
I'm worried when you say that you use the initial job's output MTZ. Refmac
replaces F with a detwinned F in the output file so you wouldn't be refining
against your measured data in the subsequent round.
Best wishes
Randy Read
----
Randy J. Read
On 2 Mar 2012, at 02:00,
tes that it found.
Best wishes,
Randy Read
On Nov 26 2011, Yuri Pompeu wrote:
Hi Boaz, Yes indeed, the phosphate group of the molecule looks quite
beautiful at 1.17A and it has a really big peak 18sigma! Is there a
utility for calculating anomalous maps, or is it simply an option in the
refinemen
I thought it would be good to follow up with the solution to this problem,
in case someone else has been suffering with it in silence.
It turns out that, at some point, the Windows version of CCP4 release
6.1.13 included a newer version of Phaser (2.2.1), but the ccp4i interface
for that relea
Dear Ylva,
If you're running from the ccp4i interface, it looks like a mismatch
between Phaser version and ccp4i version. Some of the syntax changed
between the version of Phaser released with CCP4 6.1 and the version that
will be coming out with the imminent 6.2 release. So, for instance, you
In this case, I'm more on ZO's side. Let's say that the refinement program
can't get an atom to the right position (for instance, to pick a reasonably
realistic example, because you've put a leucine side chain in backwards).
In that case, the B-factor for the atom nearest to where there should b
Sorry for the late reply -- I've been travelling.
You're correct, the current version of Phaser produces figures of merit
(and HL coefficients) based entirely on the initial guess about the quality
of model. The version currently in Phenix (and coming soon to the upcoming
CCP4 release) can ref
I think that message should mean that there's more than one symmetry
equivalent of at least one reflection. From memory (sitting in a workshop
at the moment), you could try reading the data into sftools and typing
"checkhkl" then looking at what it says.
Regards,
Randy Read
On Jun 15 2010, J
There's OpenMP parallelization of some of the most CPU-intensive parts of
molecular replacement in Phaser, in the versions released recently in
Phenix and hopefully in the next CCP4 release. However, OpenMP is not
turned on by default in the compilation of the binaries released with
Phenix, so
Hi,
If you search with a dimer, then the version of Phaser in CCP4 doesn't know
that there is internal symmetry in your model, and it will find two
solutions that are equivalent by the internal symmetry, but would not be
equivalent if the model were not symmetric. The latest version of Phaser
For the first part of your question, I usually use sftools from the command
line to combine things from different MTZ files, so you could give that a
try if cad is giving you trouble.
For the second part of the question, if you're staying within CCP4, then
cphasematch is probably the program y
Hi,
If you were desperate for BRUTE, I could probably dig out the source code.
My somewhat newer program BEAST also does a brute-force search, and you
could get that by downloading an older version of CCP4 or, again, directly
from me.
Our new program Phaser also has brute-force rotation and
Hi,
I've just double-checked this on my installation (6.0.99e still, but
shouldn't make a difference), and this command works.
I think that you've ended up with an older version of Phaser coming first
in your path. The syntax of the PACK command has changed (to allow it to
behave in a way th
We are looking to expand the team developing our program Phaser, for use
within both the CCP4 and Phenix packages. Our goals include expanding the
functionality to new phasing experiments (in addition to the options for
molecular replacement and SAD that exist in the current version), and
enhanci
This turns out to be a failure in the (rarely exercised) code to read in
the substructure with a .ha file. We almost always use PDB files from Hyss
or SHELXD to enter the initial substructure, then Phaser .sol files if
there's a reason to carry on refinement.
The bug has now been fixed for the
On Apr 4 2008, hari jayaram wrote:
Hi everyone, I have a phaser molecular replacement solution for my
membrane protein which crystallized in spacegroup P3. The diffraction
data is good to about 3.3 A. The model I used had 39% homology to the
given protein. A solvent content analysis suggests t
As suggested earlier, you can use the TOPFILES command to get Phaser to
produce the files for more solutions. However, instead of rerunning the
whole job, you can produce the PDB files alone by feeding the .sol file
into a packing (MR_PAK) job, or both PDB and MTZ files by feeding the .sol
file
The procedure of cutting out electron density, putting it into a large unit
cell, and backtransforming to get structure factors can be tricky (as
you've discovered), so we put some instructions on our webpage:
http://www-structmed.cimr.cam.ac.uk/phaser/density_as_model.html
The last time I tri
On Nov 3 2007, Randy J. Read wrote:
Depends on the purpose. From the LLG, I want to see that it is positive
(negative means that I'm being too optimistic about the quality of the
model, i.e. the RMS error is higher or the completeness lower than
assumed), and I would like to see it inc
If you take a PDB file from the solution for the hexagonal form as your
input model for a translation search in P1, then the cross-rotation peaks
that rotate the hexagonal data onto the P1 data should be the correct
orientations. (Phaser uses the same definition for Euler angles as ALMN.)
I'd g
On Nov 2 2007, Bryan W. Lepore wrote:
neglecting e-density, packing, etc. - what matters most to people when
running phaser - LLG or Z-score? in what function (RF, TF)?
Depends on the purpose. From the LLG, I want to see that it is positive
(negative means that I'm being too optimistic about
On Sep 18 2007, Bryan W. Lepore wrote:
i wrote
"(ensemble) / (sequence)" to get a percent composition
i forgot to emphasize that i do not mean the Vm or the "Z" composition,
but the composition as one would enter e.g.
COMPosition ENSEmble mol1 FRACtional 0.22
or
COMPosition SCAttering
-b
On Aug 31 2007, Bryan W. Lepore wrote:
if it doesn't now, will phaser be able to run a phased translation
function in the future?
-bryan
Yes, that's on our long to-do list!
Randy Read
On Aug 16 2007, Eleanor Dodson wrote:
The weighting in REFMAC is a function of SigmA ( plotted in log file).
For this example it will be nearly 1 for all resolutions ranges so the
weights are pretty constant. There is also a contribution from the
"experimental" sigma, which in this case seems
Yes, this is an inconsistency between the version of the Phaser executable
and the version of ccp4i. To get around the problem that filenames,
particularly in Windows, can have spaces in them, the ccp4i GUI now wraps
filenames with quotation marks. But this required a corresponding change in
th
On Mar 15 2007, Yi Xue wrote:
So far, the native crystals diffracted best to 2.4A. The MAD data
diffracted to 2.6~2.7A. We attempted to use phenix.hyss to identify copper
atoms, and the program had hard time to identify the sites.
The protein: Cu ratio is around 1:1, which is decided by ICP-A
On Mar 12 2007, Andy Purkiss wrote:
Quoting Andrew Wong <[EMAIL PROTECTED]>:
I was using Phaser for some MR with a data set in P1 (may not actually
be P1, but..), and in every run I always got a list of "solutions" that
all have TFZ=100.0, with a very small LLG (around 0 or even in the
negat
I would agree mostly with what Dale said, and point out that it applies as
well to the SigmaA estimation that is a necessary part of ML refinement.
When we were developing the ML targets that went into CNS, we did a number
of tests to see how many cross-validation reflections were needed. The
f
On Jan 22 2007, Eaton Lattman wrote:
Will someone knowledgeable tell me what the present state of full 6
dimensional searches in molecular replacement?
Presumably you're referring to systematic 6D searches, not stochastic ones
like in EPMR or QoS. Do you mean "can it be done on current hardw
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