Re: [ccp4bb] cns .map in coot

[Paul Emsley]

On 14/12/10 20:01, Julian Nomme wrote:

I can easily convert my composite omit map from cns to ccp4 format and
open it into coot.


Very good, but no need to do that.


However, how can I make coot use this map to fit density to my structure ?
I can only use this map for visual support and for example, coot doesn't
assign any density on the bar graph generated by using the "Density fit
analysis" option to check the geometry.
Does anyone have any idea how to fix this problem?


It is not clear to me if the density is displayed in the wrong place 
(which might well be our problem) or that it's simply a matter of scale 
of the density fit graph begin wrong (which is your problem).


If the latter, use Extensions -> Refine -> Set Density Fit Graph Weight...

Paul

Re: [ccp4bb] cns .map in coot

[Ed Pozharski]

You should have also gotten the .coeff file - try converting it to mtz
and using with coot.

On Tue, 2010-12-14 at 14:01 -0600, Julian Nomme wrote:
> Hi all,
> 
> I can easily convert my composite omit map from cns to ccp4 format and 
> open it into coot.
> However, how can I make coot use this map to fit density to my structure ?
> I can only use this map for visual support and for example, coot doesn't 
> assign any density on the bar graph generated by using the "Density fit 
> analysis" option to check the geometry.
> Does anyone have any idea how to fix this problem?
> 
> Thanks,
> 
> Julian

-- 
"I'd jump in myself, if I weren't so good at whistling."
   Julian, King of Lemurs

[ccp4bb] cns .map in coot

[Julian Nomme]

Hi all,

I can easily convert my composite omit map from cns to ccp4 format and 
open it into coot.

However, how can I make coot use this map to fit density to my structure ?
I can only use this map for visual support and for example, coot doesn't 
assign any density on the bar graph generated by using the "Density fit 
analysis" option to check the geometry.

Does anyone have any idea how to fix this problem?

Thanks,

Julian

Re: [ccp4bb] cns map in coot

[Sabuj Pattanayek]

attempting to read CNS map: /Users/rajadey/yong/cns/coot/excl_comp.map
CNSMAPfile: can't get number of header lines
WARNING:: failed to read /Users/rajadey/yong/cns/coot/excl_comp.map
DEBUG:: Erasing the back molecule 1 which says that it has molecule number 1
Read map /Users/rajadey/yong/cns/coot/excl_comp.map failed


What does "head /Users/rajadey/yong/cns/coot/excl_comp.map" show? I just 
loaded 2fofc and fofc maps generated by cns 1.2 into coot 0.4.1


You should probably also post to the coot list specifically.

[ccp4bb] cns map in coot

[Raja Dey]

Hi,
I am using COOT 0.5-pre and getting the following error when opening a cns 
map. I can open that map in O. Of-course I can convert the cns map into ccp4 
format which is readable in coot. But, what's wrong with my coot that can not 
open cns map directly?

CCP4 map filename: /Users/rajadey/yong/cns/coot/excl_comp.map
INFO:: map file type was determined to be CNS type
allocating space in read_ccp4_map
attempting to read CNS map: /Users/rajadey/yong/cns/coot/excl_comp.map
CNSMAPfile: can't get number of header lines
WARNING:: failed to read /Users/rajadey/yong/cns/coot/excl_comp.map
DEBUG:: Erasing the back molecule 1 which says that it has molecule number 1
Read map /Users/rajadey/yong/cns/coot/excl_comp.map failed

 Thanks...Raja


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