Xmipp

Frequently Asked Questions

Below, we have listed the most frequently asqued questions about Xmipp package as we receive them from users. If you did not find any answer to your doubt in the Documentation section and it is not solved here, then let us know.

About XMIPP

What is XMIPP?

Xmipp is a specialized suite of image processing programs, primarily aimed at obtaining the 3D reconstruction of biological specimens from large sets of projection images acquired by transmission electron microscopy... (Continues in history section).

Is XMIPP for free?

This package is open source and is published under the GNU General Public License version 2 (or later). You can find the code in our repository at sourceforge.net.

My favorite flavor of Linux isn't on the list of supported distributions. Will you support it?

We have tested the installation of XMIPP in many distributions, but you can compile it from the source code in any other distribution by following the installation steps. Just be sure you solve all the required external dependencies. Please send us some report about your installation, so we can include it in our list.

Can I run XMIPP in a virtual machine?

Yes, actually we have a virtual machine available with XMIPP already installed for developing purposes.

Technical questions

I have developed some algorithms that could be useful, may I collaborate developing for XMIPP?

If you have some interest in your algorithms to be included in XMIPP or want to collaborate developing XMIPP, just contact us.

I just found a bug, how do I report it?

You can use the bugs report application at sourceforge, or simply by mailing it to us (More info at Report section).

I also use other microscope images reconstruction packages and I think Euler angles are a mess, Which is the XMIPP angles convention?

Yes, we understand you, and you can find the information about how XMIPP manages angles in conventions section.

Where is the center of an image?

In the conventions section there is an explanation about which pixel has (0,0) coordinates, depending whether the image size is even or odd.

Is there an easy way to convert .box-Files from EMAN's boxer (i.e. a list of x/y coordinates + box_xdim + box_ydim) to a .pos-File?

Yes, from the Xmipp Particle Picker GUI you can import .box files from EMAN and other formats. You can import a .box file for a single micrograph or just several files inside the same folder. For the latter to work it is needed that each .box file have the same name (without extension) than the micrograph name. You can find the import dialog from File -> Import coordinates. In this dialog you can play with some parameters such us scale (when you are picking in a binned micrographs) or invert x or y axis.

May I change Xmipp protocols fonts?

Sure, Xmipp protocols use the font/size defined by the variables XMIPP_FONT_NAME and XMIPP_FONT_SIZE. If you want to chage the fonts for all users edit the file $XMIPP_HOME/.xmipp.bash and modify lines

# To change the font used in protocols
export XMIPP_FONT_NAME=Verdana
export XMIPP_FONT_SIZE=12   

If you have .xmipp.cfg in the user home folder you may set fonts for individual users.