Dear Paul,
There seems to be a problem with the automatic asignment for F and SIGF when
using a file from phaser (processed by autoproc). The FCTR column seems to be
used instead of F but there is no reference what has been used in the logfile
(sample attached). Unfortunately the only
Hi!
Coot has to be told what columns to use for different programs. We've
coded fore refmac, phenix.refine and my density modification programs,
but not for phaser because no-one has asked.
Can you send me a dump of the mtz header with a list of the columns?
Which columns would you like used
Dear Alexander,
FCTR looks like it is coming from a BUSTER refinement:
http://www.globalphasing.com/buster/manual/buster/manual/chapter5.html#mlphas
This column is obviously only intended for looking at maps (however:
usually one looks at the 2FOFCWT/PH2FOFCWT and FOFCWT/PHFOFCWT maps).
So
Hi Kevin,
As Clemens pointed out it was not a phaser but a user problem. I accidently
used a buster mtz file for phaser. For autoproc - phaser everything works as
expected.
I have attached the mtzdump of a buster mtz-file. If you could support
auto-open for that it would be great.
Do you see a
Hi,
the automatic selection of structure factors for refinement happens in
Refmac and not in Coot. This is one for Garib. I dont know exactly how
Refmac chooses which structure factors to use, but it certainly should
write the selected ones in the log file (maybe newer versions of refmac
OK, so the map coefficients are:
1. FCTR PHICTR
2. 2FOFCWT PH2FOFCWT
3. FOFCWT PHFOFCWT
4. FOFRGSLV PHFOFRGSLV
5. FC PHIC
6. FOSC SIGFOSC
I think that auto-open (assuming you are using a 0.6pre from the last 6
months) should automatically pick up (2) and (3) for a normal and
difference map -
Bernhard is right, sorry. Ignore me!
Kevin
Bernhard Lohkamp wrote:
Hi,
the automatic selection of structure factors for refinement happens in
Refmac and not in Coot. This is one for Garib. I dont know exactly how
Refmac chooses which structure factors to use, but it certainly should
write
At the moment refmac does extremely simple selection. First structure
factor label and the first sigma that has similar name to the first
structure factor, if not then the first sigma.
It works for a class of cases but it cannot be universal. While we are
on this matter I think it would be
Alexander,
Do you see a way to include in the refmac-from-coot logfile which mtz columns were used?
No, since, as mentioned earlier, this is a refmac decision. However I
agree that the refmac log file should tell you which column was used
when automatically picking SF (maybe it does
Yes. It should and I will add it now. I do not think refmac writes
this info into the output file but it will do in one or two days time.
GArib
On 30 Nov 2009, at 11:32, Bernhard Lohkamp wrote:
Alexander,
Do you see a way to include in the refmac-from-coot logfile which
mtz columns were
Hi Kevin,
just for the record (even if the original question/thread was about
something slightly different):
On Mon, Nov 30, 2009 at 11:13:14AM +, Kevin Cowtan wrote:
OK, so the map coefficients are:
1. FCTR PHICTR
2. 2FOFCWT PH2FOFCWT
3. FOFCWT PHFOFCWT
4. FOFRGSLV PHFOFRGSLV
5. FC
Hi all
I am trying to find out if coot can export a map file that in text format.
I have created a difference map from two cns maps and want to export
it also in cns format (can be read in text eidtor). But till now, I
can only save it in xx.map format that in ASCII format.
How to do that?
pebbleped...@gmail.com wrote:
Hi all
I am trying to find out if coot can export a map file that in text format.
I have created a difference map from two cns maps and want to export
it also in cns format (can be read in text eidtor). But till now, I
can only save it in xx.map format that in
pebbleped...@gmail.com wrote:
Hi all
I am trying to find out if coot can export a map file that in text format.
I have created a difference map from two cns maps and want to export
it also in cns format (can be read in text eidtor). But till now, I
can only save it in xx.map format that in
pebbleped...@gmail.com wrote:
Hi all
I want to know possible method to get electron density map for ligand only.
The material are 2mFo-DFc map downloaded from EDS server and also
coordinates from PDB.
The electron density map contains protein, water and ligand. I want to
build a electron
Hi
There are some problems still existing.
The pdb file contain two domain A and B. As I do not know how to
select protein segid A and B and also waters at the same time, I do
mask as following:
First, I read .pdb file and then .ccp4 file. Then I use
ExtensionMapsMask map by atom
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