Re: [scipion-users] using MonoRes from command line

[JOSE L. V. P. <jl...@cn...>]

Dear Gabriella,

Thank you for your interest in MonoRes.

Most of algorithm that are integrated in Scipion can run with a  
command line, in particular MonoRes.

To run MonoRes, first you need Xmipp installed in your  
computer/machine (probably it is already installed if you use Scipion,  
if not...

Here you can fin the instructions: https://github.com/I2PC/xmipp

Once you hace installed Xmipp its time to run MonoRes. To do that  
first Xmipp enviroment need to be loaded

1. Load Xmipp enviroment, executing next command (you have to  
substitute the path)

source /folderWhereXmippIsInstalled/build/xmipp.bashrc

2. Run MonoRes comand with your data, for example (Detailed  
instructions will be given below)

xmipp_resolution_monogenic_signal  --vol betaGal.mrc:mrc --mask  
binarized_mask.mrc --sampling_rate 3.540000 --minRes 1.000000 --maxRes  
25.000000 --step 0.250000 --mask_out  
Runs/000214_XmippProtMonoRes/extra/output_Mask.mrc -o mgresolution.mrc  
--volumeRadius 50.000000 --exact --chimera_volume  
MG_Chimera_resolution.mrc --sym c1 --significance 0.950000  
--md_outputdata mask_data.xmd

-----------------------------------------------------
%% Specific information about MonoRes
IMPORTANT: MonoRes requires that your maps present noise otherwise it  
is not able to compute the local resolution of the map. The  
alternative is the map is nosie free, is the use of two half maps.

MonoRes requires next fields to run (for a single map):

xmipp_resolution_monogenic_signal

--vol            File name of the map to estimate its resolution
--mask           File name of a binary mask that define where the  
protein is. Outside the mask there is only noise. It defines the  
boundary between noise and protein.
--sampling_rate  Pixel size of your protein
--minRes         The highest resolution (you can set to 0.5A)
--maxRes         The lowest resolution. probably you will work at high  
resolution, so you can set it to 8A
--step           [By default 0.25A] Local resolution will be analyzed  
in steps of the given number, for instance
--mask_out       This is not important for you. The provided mask is  
refined by MonoRes. It is an output of MonoRes. Just right a file name  
like outputmask.mrc
-o
--volumeRadius   This is important, many maps present areas free of  
noise (usually they are out of a sphere), this radiues tells MonoRes  
the radius of that sphere. If the map is not masked with an sphere,  
then this volume radius is the half of the boxsize.
--exact          It is a flag about the algorithm just write it
--chimera_volume MonoRes produces a map for the visualization in  
chimera. So provide the file name for that, for instance  
chimeraResolution.mrc.
--sym            In the first verion of MonoRes symmetry was required,  
now you can set it as c1
--significance   The significance for statistical calculus, set it to 0.95
--md_outputdata  This is a metadata created for scipion nor relevant  
for you. Just write a file name metadata.xmd
ammaple:
xmipp_resolution_monogenic_signal  --vol betaGal.mrc:mrc --mask  
binarized_mask.mrc --sampling_rate 3.540000 --minRes 1.000000 --maxRes  
25.000000 --step 0.250000 --mask_out  
Runs/000214_XmippProtMonoRes/extra/output_Mask.mrc -o mgresolution.mrc  
--volumeRadius 50.000000 --exact --chimera_volume  
MG_Chimera_resolution.mrc --sym c1 --significance 0.950000  
--md_outputdata mask_data.xmd

More considerations:

As you can see, MonoRes requires a binary mask for running. The  
creation of such mask must be carried out before running MonoRes as it  
follows

First, known the boxsize of the map, the map is filtered with a  
gaussian kernel

setSize = 0.02*boxsize

xmipp_transform_filter -i volumeFileName --fourier real_gaussian  
setSize -o gaussianMapFileName

Then, the filtered map is thresholded to obtain a binary mask. It  
requires to determine the maximum intensity of the map

max_val = 0.05*max(gaussianMapFileName)

xmipp_transform_threshold -i gaussianMapFileName --select below  
max_val --substitute binarize -o binaryMaskFileName

Please feel you free and do not hesitate of asking anything you want.  
I know that in a first approach it can seem complex, but it is not,  
trust me.

Kind regards

Jose Luis Vilas



Quoting Pablo Conesa <pc...@cn...>:

> Sorry Gabriella for the late reply....your email was stuck in the admin site.
>
> Scipion is written in python and you can almost do anything from a  
> python script. Let me know if you'd like to try this idea.
>
> Now, monores is part of xmipp and there is a program (binary behind)  
> but not sure if calling it from a terminal will render what you get.
>
> Best person to answer is Jose Luis, I think he is reading this list.  
> He might be able to help you.
>
> On 28/8/19 19:41, Gabriella Reggiano wrote:
>> Hi all,
>>
>> I have been looking for alternatives to ResMap because I need to  
>> calculate resolution estimates for a large number of maps, and I  
>> wanted something that required very little user input (ideally,  
>> without masks). MonoRes is the closest to what I need. Do you have  
>> any advice for getting MonoRes/Scipion to run through the command  
>> line, rather than the GUI?
>>
>> Thank you,
>> Gabriella Reggiano
>> --
>> Ph.D. Student
>> DiMaio Lab
>> Department of Biochemistry
>> University of Washington
>>
>>
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
> -- 
> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*