diff --git a/test/3368/cutoff.txt b/test/3368/cutoff.txt new file mode 100644 index 0000000000000000000000000000000000000000..8b137891791fe96927ad78e64b0aad7bded08bdc --- /dev/null +++ b/test/3368/cutoff.txt @@ -0,0 +1 @@ + diff --git a/test/3368/emd_3368.map b/test/3368/emd_3368.map new file mode 100644 index 0000000000000000000000000000000000000000..2d5ee255b2dc5f5405640c2fd9934c83cabc1926 Binary files /dev/null and b/test/3368/emd_3368.map differ diff --git a/test/3368/header/emd-3368.xml b/test/3368/header/emd-3368.xml new file mode 100644 index 0000000000000000000000000000000000000000..1551bf66e32a75309cb6e8775fa56f232f722229 --- /dev/null +++ b/test/3368/header/emd-3368.xml @@ -0,0 +1,148 @@ +<?xml version="1.0" encoding="UTF-8"?> +<emdEntry accessCode="3368" version="1.9.6"> + <admin> + <lastUpdate>2016-07-13</lastUpdate> + </admin> + <deposition> + <status>REL</status> + <depositionDate>2016-03-08</depositionDate> + <depositionSite>PDBe</depositionSite> + <processingSite>PDBe</processingSite> + <headerReleaseDate>2016-04-13</headerReleaseDate> + <mapReleaseDate>2016-06-15</mapReleaseDate> + <title>Cryo-EM structure of yeast cytoplasmic exosome</title> + <authors>Liu JJ, Niu CY, Wu Y, Tan D, Wang Y, Ye MD, Liu Y, Zhao WW, Zhou K, Liu QS, Dai JB, Yang XR, Dong MQ, Huang N, Wang HW</authors> + <keywords/> + <primaryReference published="true"> + <journalArticle> + <authors>Liu JJ, Niu CY, Wu Y, Tan D, Wang Y, Ye MD, Liu Y, Zhao WW, Zhou K, Liu QS, Dai JB, Yang XR, Dong MQ, Huang N, Wang HW</authors> + <articleTitle>Cryo-EM structure of yeast cytoplasmic exosome</articleTitle> + <journal>cell research</journal> + <volume>26</volume> + <firstPage>822</firstPage> + <lastPage>837</lastPage> + <year>2016</year> + <externalReference type="pubmed">27174052</externalReference> + <externalReference type="doi">doi:10.1038/cr.2016.56</externalReference> + </journalArticle> + </primaryReference> + </deposition> + <map> + <file format="CCP4" sizeKb="2849" type="map">emd_3368.map.gz</file> + <dataType>Image stored as Reals</dataType> + <dimensions> + <numColumns>90</numColumns> + <numRows>90</numRows> + <numSections>90</numSections> + </dimensions> + <origin> + <originCol>0</originCol> + <originRow>0</originRow> + <originSec>0</originSec> + </origin> + <limit> + <limitCol>89</limitCol> + <limitRow>89</limitRow> + <limitSec>89</limitSec> + </limit> + <spacing> + <spacingCol>90</spacingCol> + <spacingRow>90</spacingRow> + <spacingSec>90</spacingSec> + </spacing> + <cell> + <cellA units="A">235.1772</cellA> + <cellB units="A">235.1772</cellB> + <cellC units="A">235.1772</cellC> + <cellAlpha units="degrees">90.0</cellAlpha> + <cellBeta units="degrees">90.0</cellBeta> + <cellGamma units="degrees">90.0</cellGamma> + </cell> + <axisOrder> + <axisOrderFast>X</axisOrderFast> + <axisOrderMedium>Y</axisOrderMedium> + <axisOrderSlow>Z</axisOrderSlow> + </axisOrder> + <statistics> + <minimum>-0.04306174</minimum> + <maximum>0.09575678</maximum> + <average>0.00022029</average> + <std>0.00855643</std> + </statistics> + <spaceGroupNumber>1</spaceGroupNumber> + <details>::::EMDATABANK.org::::EMD-3368::::</details> + <pixelSpacing> + <pixelX units="A">2.61308</pixelX> + <pixelY units="A">2.61308</pixelY> + <pixelZ units="A">2.61308</pixelZ> + </pixelSpacing> + <contourLevel source="author">0.02</contourLevel> + <annotationDetails>Reconstruction of Exosome-RNA18 complex</annotationDetails> + </map> + <supplement> + <maskSet/> + <sliceSet/> + <figureSet/> + <fscSet/> + </supplement> + <sample> + <numComponents>1</numComponents> + <name>Exosome complex</name> + <molWtTheo units="MDa">0.35</molWtTheo> + <molWtMethod>SDS-PAGE</molWtMethod> + <molWtExp units="MDa">0.35</molWtExp> + <sampleComponentList> + <sampleComponent componentID="1"> + <entry>protein</entry> + <sciName>Exosome complex</sciName> + <synName>PM/Scl complex</synName> + <molWtTheo units="MDa">0.35</molWtTheo> + <molWtExp units="MDa">0.35</molWtExp> + <protein> + <sciSpeciesName ncbiTaxId="4932">Saccharomyces cerevisiae</sciSpeciesName> + <recombinantExpFlag>false</recombinantExpFlag> + <synSpeciesName>Yeast</synSpeciesName> + <externalReferences/> + <natSource/> + <engSource/> + </protein> + </sampleComponent> + </sampleComponentList> + </sample> + <experiment> + <vitrification> + <cryogenName>ETHANE</cryogenName> + <humidity>100</humidity> + <instrument>FEI VITROBOT MARK IV</instrument> + </vitrification> + <imaging> + <electronSource>FIELD EMISSION GUN</electronSource> + <imagingMode>BRIGHT FIELD</imagingMode> + <illuminationMode>FLOOD BEAM</illuminationMode> + <detector>GATAN K2 SUMMIT (4k x 4k)</detector> + <microscope>FEI TITAN KRIOS</microscope> + <date>03-JAN-2015</date> + <specimenHolderModel>FEI TITAN KRIOS AUTOGRID HOLDER</specimenHolderModel> + <acceleratingVoltage units="kV">300</acceleratingVoltage> + </imaging> + <imageAcquisition/> + <fitting/> + <specimenPreparation> + <specimenState>particle</specimenState> + <specimenConc units="mg/ml">1.25</specimenConc> + </specimenPreparation> + </experiment> + <processing> + <method>singleParticle</method> + <reconstruction> + <software>EMAN2, IMAGIC, Relion-1.3</software> + <ctfCorrection>Ctffind3</ctfCorrection> + <resolutionByAuthor>13</resolutionByAuthor> + <resolutionMethod>FSC 0.143, gold-standard</resolutionMethod> + </reconstruction> + <singleParticle> + <appliedSymmetry>C1</appliedSymmetry> + <numProjections>55000</numProjections> + </singleParticle> + </processing> +</emdEntry> diff --git a/test/3368/header/map_analysis.txt b/test/3368/header/map_analysis.txt new file mode 100644 index 0000000000000000000000000000000000000000..4a3274a0ce7e39eae0e0d87fa606e035d95c492d --- /dev/null +++ b/test/3368/header/map_analysis.txt @@ -0,0 +1 @@ +)07[?1000h[?1002h[?1005l[?1015l[?1006h[1;1H[2J[1;1H[2J8 [?1000l [?1002l [?1006l \ No newline at end of file diff --git a/test/3368/images/EMD-3368.png b/test/3368/images/EMD-3368.png new file mode 100644 index 0000000000000000000000000000000000000000..215379b36b99a1085fbf8dfd35be0908b7e097d5 Binary files /dev/null and b/test/3368/images/EMD-3368.png differ diff --git a/test/3368/map/emd_3368.map.gz b/test/3368/map/emd_3368.map.gz new file mode 100644 index 0000000000000000000000000000000000000000..82e592e47950a59418eafc28e23aded3e8b9a68a Binary files /dev/null and b/test/3368/map/emd_3368.map.gz differ diff --git a/test/3368/resolution.txt b/test/3368/resolution.txt new file mode 100644 index 0000000000000000000000000000000000000000..b1bd38b62a0800a4f6a80c34e21c5acffae52c7e --- /dev/null +++ b/test/3368/resolution.txt @@ -0,0 +1 @@ +13