Input data description ====================== Map --- | Modeling means atomic interpretation of a map. This map can be the result of our own reconstruction process or can be obtained from a database. In this tutorial we use the haemoglobin map *EMD-3488*, that can be downloaded from `PDBe `_ (:numref:`model_building_PDBE`). | ``WARNING`` In case you use your own map obtained from cryo-EM images: Take into account that cryo-EM 3D maps benefit significantly of an “optimizing” step, normally referred to as “sharpening” or “density improvement“, that tends to increase signal at medium/high resolution. Therefore, we recommend to sharp the map before tracing the atomic model. Either two *Scipion* protocols consecutively applied, **xmipp3-local MonoRes** :cite:p:`vilas2018` and **xmipp3-localdeblur sharpening** :cite:p:`ramirez2018`, or the protocol **xmipp3-deepEMhancer** :cite:p:`Sanchez-Garcia2020.06.12.148296`, allow map sharpening. Details about the parameters of these protocols are shown in Appendices :ref:`Local MonoRes `, :ref:`Local Deblur Sharpening ` and :ref:`DeepEMhancer Sharpening `, respectively. .. figure:: Images/Fig3.svg :alt: Downloading the volume from *PDBe*. :name: model_building_PDBE :align: center :width: 95.0% Downloading the volume from *PDBe*. Once downloaded the volume, unpack it (command line: ``gunzip emd-3488.map.gz``) and save it in your tutorial folder. .. _`section_input_seq`: Sequences --------- The sequences of *Hgb* :math:`\alpha` and :math:`\beta` subunits are included in *UniProtKB*. Accession numbers are `P69905 `_ and `P68871 `_, respectively. Next, we show both sequences in fasta format: :: >sp|P69905|HBA_HUMAN Haemoglobin subunit alpha MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG KKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTP AVHASLDKFLASVSTVLTSKYR >sp|P68871|HBB_HUMAN Haemoglobin subunit beta MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPK VKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFG KEFTPPVQAAYQKVVAGVANALAHKYH These protein sequences were determined by direct translation from the experimental sequence obtained from complementary *DNA (cDNA)*, i.e., *DNA* synthesized or retro-transcribed from messenger *RNA (mRNA)*. In this way, it is quite unlikely that these sequences include post-translational modifications. Although methionine is added with the translation *Met-tRNA* initiation factor, the removal of methionine aminoacid from the N-terminus of a polypeptide is a common post-translational modification. Since *Met* appears at the N-terminal end of both proteins, we can predict that these are not the polypeptide mature forms and *Met* will be removed in the mature ones that are present in the atomic structures. Those two sequences can be retrieved from *UniProtKB* using *Scipion* **import sequence**  protocol, which allows direct downloading from the database.