Re: [scipion-users] Map is not visible in COOT

[Dmitry S. <Sem...@gm...>]

Dear Marta,

Thank you for your answer.

The issue is that the post processed map is not visible by external COOT.
So the map you can open without errors but you see nothing – we tried to center it and to magnify/demagnify – nothing.

The only hint that you get is the very wide map histogram in COOT comparable to the other maps (as in my previous email).


 

I would like to open it inside SCIPION. But currently, I got an error message when I want to do the ccp4 - coot refinement that the ccp4 is not installed (although I did it via SCIPION plugins): Binary file does not exits. Please install CCP4 software suit.

Do you know if I need to install CCP4 separately? Out of SCIPION?

Thank you

Sincerely,
Dmitry

> On 12. Feb 2020, at 19:48, Marta Martinez <mm...@cn...> wrote:
> 
> Hi Dmitry,
> I suppose that you are performing a modeling work inside Scipion. The reality is that we have never started the modeling process without importing the map (we haven't modified the output of the rest of the protocols to use directly the map generated yet). Even if you have generated the map in Scipion, import it to stablish the appropriate format and the origin of coordinates in the map header (you can choose in the protocol import volumes the origin, maybe yoy want to maintain the already existing origin or maybe you would like to have another one; by default we place maps centered at the origin of coordinates and you can check it in Chimera by pressing Analyze Results). If the map is properly located you have to be sure that the atomic model fits in the map to open Coot in Scipion and load map and model. By default Coot (in Scipion) requires a model to be launched, because we use Coot to visualize atomic structures or to perform the refinement of structures according to the map.
> 
> Try to import the map and tell me if you still have problems to open the map in Coot. Is the name of the map in
> the tap "Display Manager" in Coot?, Can you read the name of the map but you don't see anything? Does the model fit in the map?
> I hope this help, otherwise clarify a little bit what you're doing, and if you're in or outside Scipion.
> 
> Cheers,
> MARTA
> 
> 
> Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> escribió:
> 
>> Dear colleagues,
>> 
>> I have cryo-em map obtained with relion in SCIPION.
>> 
>> But when we want to open it in with COOT the map is not visible. (Chimera can read it)
>> 
>> Could you please give me any suggestions?
>> 
>> Please see the image in the attachment the histogram differences — on the left is readable file (made with relion itself) and from the right is unreadable one (made by relion in SCIPION).
>> 
>> 
>> Thank you
>> 
>> Sincerely,
>> Dmitry
> 
> 
> -- 
> Marta Martinez Gonzalez
> 
> Biocomputing Unit (Lab B13)
> National Center for Biotechnology-CSIC
> Darwin, 3. Campus de la Universidad Autonoma de Madrid
> 28049 Madrid. Spain
> Tel:+34 915854510 Fax:+34 913720112
> E-mail: mm...@cn... <mailto:mm...@cn...>
> 
> 
> 
> _______________________________________________
> scipion-users mailing list
> sci...@li... <mailto:sci...@li...>
> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users>