2,291 research outputs found
Hylemonella gracilis
No full textHylemonella gracilis. The rest of the files are in ~/Images/060816. This date's files are not good enough for motor averaging.<strong>Tilt Series Date:</strong> 2006-08-16</p>
<strong>Data Taken By:</strong> Gavin Murphy</p>
<strong>Species / Specimen:</strong> Hylemonella gracilis</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong> Single Axis, tilt range: (-60.0°, 60.0°), step: 1.1°, constant angular increment, dosage: 110.0 eV/Ų, defocus: -10.0 μm, magnification: 0x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod, bsoft</p>
<strong>Collaborators and Roles:</strong> Cells provided by Jared Leadbetter; Data collected and processed by Gavin Murphy</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grown in dilute media without salt. 0.5 g/L of Tryptone, 0.5 g/L YE. Cells grown for 2 days. OD never gets above 0.005. Centrifuged lightly, then concentrated 100x fold.</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity...</p>Files available via S3 at https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/gme2006-08-16-4</p>S10_S474G3_90e10d22k.mrc, Tilt Series (Pixel Size 0.98 nm), 931.3 MB
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Hylemonella gracilis
No full textHylemonella gracilis. The rest of the files are in ~/Images/060816. This date's files are not good enough for motor averaging.<strong>Tilt Series Date:</strong> 2006-08-16</p>
<strong>Data Taken By:</strong> Gavin Murphy</p>
<strong>Species / Specimen:</strong> Hylemonella gracilis</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong> Single Axis, tilt range: (-60.0°, 60.0°), step: 1.1°, constant angular increment, dosage: 110.0 eV/Ų, defocus: -10.0 μm, magnification: 0x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod, bsoft</p>
<strong>Collaborators and Roles:</strong> Cells provided by Jared Leadbetter; Data collected and processed by Gavin Murphy</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grown in dilute media without salt. 0.5 g/L of Tryptone, 0.5 g/L YE. Cells grown for 2 days. OD never gets above 0.005. Centrifuged lightly, then concentrated 100x fold.</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity...</p>Files available via S3 at https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/gme2006-08-16-5</p>S11_S474G3_90e10d22k.mrc, Tilt Series (Pixel Size 0.98 nm), 981.6 MB
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Hylemonella gracilis
No full textHylemonella gracilis. The rest of the files are in ~/Images/060913. The analysis consists of motor picking. Some ctf correction.<strong>Tilt Series Date:</strong> 2006-09-13</p>
<strong>Data Taken By:</strong> Gavin Murphy</p>
<strong>Species / Specimen:</strong> Hylemonella gracilis</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong> Single Axis, tilt range: (-63.0°, 60.0°), step: 0.9°, constant angular increment, dosage: 75.0 eV/Ų, defocus: -12.0 μm, magnification: 0x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod, bsoft</p>
<strong>Collaborators and Roles:</strong> Cells provided by Jared Leadbetter; Data collected and processed by Gavin Murphy</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grown in dilute media without salt. 0.5 g/L of Tryptone, 0.5 g/L YE. Cells grown for 2 days. OD never gets above 0.005. Centrifuged lightly e.g. 3500x g, then concentrated 50-100x fold.</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity...</p>
H14_060913_tilt.jpg: * associated to rawdata H14_060913_rec.jpg: file associated to 3D Image #79Files available via S3 at https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/gme2006-09-13-1</p>A14_S474G3_34kx12d90eC.mrc, Tilt Series (Pixel Size 0.67 nm), 973.2 MB
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A14NoCTFrec0.27.mrc, Reconstruction (Pixel Size 0.0 nm), 313.6 MB
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A14NoCTFhigh_44_part.pif, Reconstruction (Pixel Size 0.0 nm), 9.5 MB
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Pyruvate dehydrogenase
No full textE. coli's pyruvate dehydrogenase. The rest of the files are in ~/Images/040824.<strong>Tilt Series Date:</strong> 2004-08-24</p>
<strong>Data Taken By:</strong> Gavin Murphy</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> purified pyruvate dehydrogenase</p>
<strong>Tilt Series Settings:</strong> Dual Axis, tilt range: (-63.0°, 63.0°), step: 3°, constant angular increment, dosage: 120.0 eV/Ų, defocus: -8.0 μm, magnification: 0x. </p>
<strong>Acquisition Software:</strong> UCSF Tomo</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod, bsoft</p>
<strong>Collaborators and Roles:</strong> Protein provided by Terrence Wagenknecht, Wadsworth, Albany, NY; Data collected and processed by Gavin Murphy</p>
<strong>Purification / Growth Conditions / Treatment:</strong> E. coli. Pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase obtained from Terrence Wagenknecht at Wadsworth, Albany, NY. Fortunately, I didn't have to purify anything. Protein was diluted to I think 8 mg/ml and applied to grids.</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity...</p>
ParticlePick.jpg: file associated to 3D Image #125Files available via S3 at https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/gme2004-08-24-1</p>P4b_S46G3_60e10d27kx.mrc, Tilt Series (Pixel Size 0.82 nm), 377.6 MB
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P4a_S46G3_60e10d27kx.mrc, Tilt Series (Pixel Size 0.82 nm), 369.2 MB
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P4.mrc, Reconstruction (Pixel Size 0.0 nm), 838.9 MB
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P4_40_part.pif, Reconstruction (Pixel Size 0.0 nm), 42.5 MB
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Hylemonella gracilis
No full textHylemonella gracilis. The rest of the files are in ~/Images/070507. The analysis consists of motor picking. Some ctf correction. Ctf correction never helped.<strong>Tilt Series Date:</strong> 2007-05-07</p>
<strong>Data Taken By:</strong> Gavin Murphy</p>
<strong>Species / Specimen:</strong> Hylemonella gracilis</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong> Single Axis, tilt range: (-63.0°, 60.0°), step: 1.1°, constant angular increment, dosage: 80.0 eV/Ų, defocus: -8.0 μm, magnification: 0x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod, bsoft</p>
<strong>Collaborators and Roles:</strong> Cells provided by Jared Leadbetter; Data collected and processed by Gavin Murphy</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grown in dilute media without salt. 0.5 g/L of Tryptone, 0.5 g/L YE. Cells grown for 2 days. OD never gets above 0.005. Centrifuged lightly e.g. 3500x g, then concentrated 50-100x fold.</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity...</p>
H01_070507_tilt.jpg: * associated to rawdata H01_070507_rec.jpg: file associated to 3D Image #121Files available via S3 at https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/gme2007-05-07-1</p>H1_S672G1_34k80e8d.mrc.gz, Tilt Series (Pixel Size 0.64 nm), 614.1 MB
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H1b2_0.32.mrc, Reconstruction (Pixel Size 0.0 nm), 170.4 MB
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H1b2_0.46_44_part.pif, Reconstruction (Pixel Size 0.0 nm), 4.1 MB
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Hylemonella gracilis
No full textHylemonella gracilis. The rest of the files are in ~/Images/061020. The analysis consists of motor picking. Some ctf correction. Ctf correction never helped.<strong>Tilt Series Date:</strong> 2006-10-20</p>
<strong>Data Taken By:</strong> Gavin Murphy</p>
<strong>Species / Specimen:</strong> Hylemonella gracilis</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong> Single Axis, tilt range: (-63.0°, 60.0°), step: 0.9°, constant angular increment, dosage: 75.0 eV/Ų, defocus: -12.0 μm, magnification: 0x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod, bsoft</p>
<strong>Collaborators and Roles:</strong> Cells provided by Jared Leadbetter; Data collected and processed by Gavin Murphy</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grown in dilute media without salt. 0.5 g/L of Tryptone, 0.5 g/L YE. Cells grown for 2 days. OD never gets above 0.005. Centrifuged lightly e.g. 3500x g, then concentrated 50-100x fold.</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity...</p>
A06_061020_tilt.jpg: * associated to rawdata A06.jpg: * associated to rawdata H06_061020_rec.jpg: file associated to 3D Image #91Files available via S3 at https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/gme2006-10-20-2</p>A6_S443G2_34k12d75e4nm.mrc, Tilt Series (Pixel Size 0.67 nm), 1.2 GB
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A06NoCTFrec0.29.mrc, Reconstruction (Pixel Size 0.0 nm), 229.5 MB
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A06NoCTFhigh_44_part.pif, Reconstruction (Pixel Size 0.0 nm), 6.8 MB
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A06.tif, * associated to rawdata, 8.4 MB
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Hylemonella gracilis
No full textHylemonella gracilis. The rest of the files are in ~/Images/060816. This date's files are not good enough for motor averaging.<strong>Tilt Series Date:</strong> 2006-08-16</p>
<strong>Data Taken By:</strong> Gavin Murphy</p>
<strong>Species / Specimen:</strong> Hylemonella gracilis</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong> Single Axis, tilt range: (-60.0°, 60.0°), step: 1.1°, constant angular increment, dosage: 110.0 eV/Ų, defocus: -10.0 μm, magnification: 0x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod, bsoft</p>
<strong>Collaborators and Roles:</strong> Cells provided by Jared Leadbetter; Data collected and processed by Gavin Murphy</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grown in dilute media without salt. 0.5 g/L of Tryptone, 0.5 g/L YE. Cells grown for 2 days. OD never gets above 0.005. Centrifuged lightly, then concentrated 100x fold.</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity...</p>Files available via S3 at https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/gme2006-08-16-14</p>S15_S474G3_90e10d22k.mrc, Tilt Series (Pixel Size 0.98 nm), 956.4 MB
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S15s.mrc, Reconstruction (Pixel Size 0.0 nm), 175.3 MB
<a role="button" class="ui compact mini button" href="https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/gme2006-08-16-14/3dimage_77/S15s.mrc"
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Hylemonella gracilis
No full textHylemonella gracilis. The rest of the files are in ~/Images/060816. This date's files are not good enough for motor averaging.<strong>Tilt Series Date:</strong> 2006-08-16</p>
<strong>Data Taken By:</strong> Gavin Murphy</p>
<strong>Species / Specimen:</strong> Hylemonella gracilis</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong> Single Axis, tilt range: (-60.0°, 60.0°), step: 1.1°, constant angular increment, dosage: 110.0 eV/Ų, defocus: -10.0 μm, magnification: 0x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod, bsoft</p>
<strong>Collaborators and Roles:</strong> Cells provided by Jared Leadbetter; Data collected and processed by Gavin Murphy</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grown in dilute media without salt. 0.5 g/L of Tryptone, 0.5 g/L YE. Cells grown for 2 days. OD never gets above 0.005. Centrifuged lightly, then concentrated 100x fold.</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity...</p>Files available via S3 at https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/gme2006-08-16-6</p>S3_S474G3_110e10d22k.mrc, Tilt Series (Pixel Size 0.98 nm), 939.7 MB
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S3s.mrc, Reconstruction (Pixel Size 0.0 nm), 174.4 MB
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gm2006-08-16-6ribosegnew.am, Ribosome segmentation.am file created from post-processed Molmatch data.Created by David J. Rosenman., 1.8 MB
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Hylemonella gracilis
No full textHylemonella gracilis. The rest of the files are in ~/Images/061020. The analysis consists of motor picking. Some ctf correction. Ctf correction never helped.<strong>Tilt Series Date:</strong> 2006-10-20</p>
<strong>Data Taken By:</strong> Gavin Murphy</p>
<strong>Species / Specimen:</strong> Hylemonella gracilis</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong> Single Axis, tilt range: (-63.0°, 60.0°), step: 0.9°, constant angular increment, dosage: 75.0 eV/Ų, defocus: -12.0 μm, magnification: 0x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod, bsoft</p>
<strong>Collaborators and Roles:</strong> Cells provided by Jared Leadbetter; Data collected and processed by Gavin Murphy</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grown in dilute media without salt. 0.5 g/L of Tryptone, 0.5 g/L YE. Cells grown for 2 days. OD never gets above 0.005. Centrifuged lightly e.g. 3500x g, then concentrated 50-100x fold.</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity...</p>
H18_061020_tilt.jpg: * associated to rawdata H18_061020_rec.jpg: file associated to 3D Image #109 gme2006-10-20-8_slicer5148.jpg: Chemoreceptors gme2006-10-20-8_slicer5157.jpg: unknownFiles available via S3 at https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/gme2006-10-20-8</p>A18a_S474G4_34k12d75e4nm.mrc, Tilt Series (Pixel Size 0.67 nm), 1.2 GB
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A18NoCTFrec0.30.mrc, Reconstruction (Pixel Size 0.0 nm), 368.2 MB
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A18NoCTFhigh_44_part.pif, Reconstruction (Pixel Size 0.0 nm), 9.5 MB
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Hylemonella gracilis
No full textHylemonella gracilis. The rest of the files are in ~/Images/061020. The analysis consists of motor picking. Some ctf correction. Ctf correction never helped.<strong>Tilt Series Date:</strong> 2006-10-20</p>
<strong>Data Taken By:</strong> Gavin Murphy</p>
<strong>Species / Specimen:</strong> Hylemonella gracilis</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong> Single Axis, tilt range: (-63.0°, 60.0°), step: 0.9°, constant angular increment, dosage: 75.0 eV/Ų, defocus: -12.0 μm, magnification: 0x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod, bsoft</p>
<strong>Collaborators and Roles:</strong> Cells provided by Jared Leadbetter; Data collected and processed by Gavin Murphy</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grown in dilute media without salt. 0.5 g/L of Tryptone, 0.5 g/L YE. Cells grown for 2 days. OD never gets above 0.005. Centrifuged lightly e.g. 3500x g, then concentrated 50-100x fold.</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity...</p>
H05_061020_tilt.jpg: * associated to rawdata A05.jpg: * associated to rawdata H05_061020_rec.jpg: file associated to 3D Image #88Files available via S3 at https://renc.osn.xsede.org/ini210004tommorrell/tomography_archive/gme2006-10-20-1</p>A5_S443G2_34k12d85e4nm.mrc, Tilt Series (Pixel Size 0.67 nm), 1.2 GB
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A05NoCTFrec0.3.mrc, Reconstruction (Pixel Size 0.0 nm), 197.7 MB
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A05NoCTFhigh_44_part.pif, Reconstruction (Pixel Size 0.0 nm), 4.1 MB
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A05.tif, * associated to rawdata, 8.4 MB
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