User:Dcrjsr

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Dcrjsr is a user created by Jane Shelby Richardson at Duke University. This user page is mainly intended as a way to help organize the uploaded images.

Small galleries are on this page, while larger ones are linked - such as those for Protein ribbon drawings or for High Sierra landscapes.

One section pertains to structural bioinfomatics: ribbon drawings of 3D protein and RNA structures, illustrations of aspects of crystallographic or NMR models and methodology, and examples of structural motifs. More background information can be found at our lab web site. I am a participant in WikiProject Biophysics

The second section includes images of landscapes, flowers, and animals - mostly photographed in the Sierra Nevada mountains of California and mostly with geolocations. Note that I keep my camera set on Eastern US time zone, so the metadata does not show local time if taken elsewhere.


  • Dcrjsr/POTD, featured, quality, & valued images

  • TIM ribbon pastel - featured image on Commons

  • 1GWE antiparallel beta sheet - valued image on Commons

  • Ranger's buttons - quality image on Commons

  • Sierra arctic gentians (Gentiana newberryi var. tiogana) - valued image

  • Banner Peak & 1000-Island Lake - valued image on Commons


Section on Protein and Nucleic Acid Structures [edit]

Click here for the gallery of Dcrjsr/Protein Ribbon Drawings

Example protein ribbon drawing: CuZn SOD











  • Dcrjsr/Protein Structure Detail images

  • CuZn SOD active site

  • Contacts between RNAse and U vanadate inhibitor

  • Phi-Psi-Omega backbone dihedral angles

  • PhiPsi diagram with plane and labels

  • Alpha vs 310 helix end views

  • Helical wheel diagram of alpha helix

  • Wenxiang diagram of alpha helix

  • Antiparallel beta sheet from 1GWE, face & edge views

  • Classic beta-bulge schematic


  • Dcrjsr/Protein Crystallography images

  • Asymmetric Staph nuclease crystals

  • CuZn SOD precession photo

  • Staph nuclease brass model to UV worm

  • Staph nuclease Arg-Phe on glass map stack

  • Helix in high-resolution electron density

  • Hydrogens in protein electron density

  • 4fc1 Arg17 neutron H vs D in map

  • Modeling alternate conformers in KiNG


  • Dcrjsr/Structure Validation images

  • Structure validation concept

  • Incredulase: the model is not the molecule

  • Good all-atom contacts, 1gci Ala methyls

  • Low vs hi resolution hemoglobin detail

  • MolProbity Logo

  • Validation outlier legend, MolProbity

  • MolProbity clashscore vs year thru 2011

  • MolProbity validation outliers in 3D, on-line

  • Ramachandran plot, original 1963 outlines

  • 1acx PCNA ProCheck Rama plot

  • Ramachandran plot for general amino acids

  • Ramachandran plot for Glycine

  • Ramachandran plot for Proline

  • Top8000 general-case Ramachandran plot

  • Glycine Ramachandran plot, Top8000

  • Top8000 trans Pro Ramachandran plot

  • Ramachandran redux, Gly, 3600x3600px color-coded


  • Dcrjsr/Protein Design images & audios

  • Betabellin model, early de novo design

  • Betabellin sequence incantation

  • Felix model, early 4-helix bundle de novo design

  • Felix sequence incantation

  • PheA redesign template, gramicidin synthase


  • Dcrjsr/3D Structure Prediction images

  • Target structure, with 354 predicted models (CASP8)

  • Cumulative plot of Calpha accuracy, CASP8 T0398


  • Dcrjsr/RNA Structure images

  • RNA backbone - suite vs residue

  • All-atom contacts for two GC base pairs of RNA

  • GNRA tetraloop motifs, 3 superimposed & annotated

  • S-motif in RNA, with backbone conformer labels

  • Kissing Loop motif (1zci), from GJKapral

  • Kissing Loop motif, blinking (1zci), from GJKapral

  • G-riboswitch binding site: map, contacts, conformers

  • G riboswitch RNA, 1u8d

  • Twort groupI intron, stereo ribbon

  • 5S ribosomal RNA, ribbons

  • Ecoli 70S ribosome pair w/ tRNA, mRNA

  • Ecoli 70S ribosome pair vs gentamicin drug

  • 70S E coli ribosome outline

  • 50S subunit archaeal ribosome, outline

  • RNA backbone rebuild 3cc2 5S 77


  • Dcrjsr/DNA Structure images

  • Nucleosome DNA/protein complex, ribbon schematic

  • Coiled-coil transcription factor Max, on DNA

  • Zn-finger transcription factor Zif268, on DNA

  • BmrR/DNA/TPP complex, untwisting the DNA


  • Dcrjsr/NMR Structure images

  • 2k49 NMR ensemble ribbons

  • 2k5d NMR ensemble ribbons

  • NH RDC target curves on NMRmodels, D58 in 1d3z


  • Dcrjsr/WikiProject Biophysics images

  • Original Richards box photo, 1968

  • King-Way Yau 2008 ARVO


Section on Landscapes, Plants, etc [edit]

Click here for the gallery of Dcrjsr/High Sierra landscape images, organized S to N by Wilderness area or Park

Example high Sierra image









Click here for the gallery of Dcrjsr/Eastern Sierra images

Example Eastern Sierra image










Click here for the gallery of Dcrjsr/Sierra Nevada flower images, organized by botanical family

Example flower image










Click here for the gallery of Dcrjsr/Sierra Nevada shrub images, organized by genus & species

Example shrub image










Click here for the gallery of Dcrjsr/Sierra Nevada tree images, organized by genus & species

Example tree image













Click here for the gallery of Dcrjsr/Duke Forest NC plant images

Example NC plant image











  • Dcrjsr/Sedges

  • Long sedge (Carex sp), edge of Hamilton Lake

  • Sedge (Carex sp) NW of Mono P (from BakerClaw)

  • Y-end sedge (Carex sp) close, Golden Lake

  • Y-end sedge (Carex sp) clump, Golden Lake

  • Round-end sedge close (Carex sp) Lake George

  • Round-end sedge (Carex sp) Lake George

  • Finger-end sedge close (Carex sp) Tioga

  • Finger-end sedge (Carex sp) by pond, Tioga

  • Large sedge (Carex sp) in edge of Lower Rock Creek

  • Large sedge close, Rock Creek Canyon

  • Large sedge (Carex sp) Rock Creek Canyon

  • Large sedge, seed head star, Oakland lawn


  • Dcrjsr/Gymnosperms

  • Green ephedra (Ephedra viridis) bush

  • Green ephedra (Ephedra viridis) close

  • Green ephedra, male cones & leaf scales


  • Dcrjsr/Animal images

  • Gray fox, cameo

  • Gray fox, full-face

  • Gray fox, back twirl

  • Gray fox, over shoulder

  • Gray fox, sniff

  • Yellow-bellied marmot, near Kaweah Gap

  • Beldings ground squirrels (Spermophilus beldingi)

  • Chipmunk stuffing cheeks with seeds

  • Pika in rocks, mouthful of dried grass

  • American pika (Ochotona princeps) camouflaged

  • Blacktail jackrabbit (Lepus californicus) Marin County

  • Pack llamas posing, meadow N of Purple Lake

  • Bison classic profile, Yellowstone

  • Two bison at riverbend, Yellowstone

  • Two baby mule deer, Oakland CA

  • Mule deer buck full-face, Swall Mdws

  • Mule deer doe backlit, Swall Mdws

  • Black-headed grosbeak, perched, front view

  • Stellers jay perched on antelope brush

  • Purple finch, on gravel, front view

  • California quail male, on antelope brush

  • California quail chicks hiding by path


  • Dcrjsr/Worldwide places images

  • Institute of BioPhysics, Beijing

  • Great Wall at Badaling, embrasure view

  • Great Wall at Badaling, view past tower

  • Gold lion in Forbidden City, Beijing

  • Hills in mist, Li River, China

  • "Big Temple" at Thanjavur, India

  • Temple elephant blessing, Thanjavur, India

  • Ramanujan museum, SASTRA, Kombakonam

  • Ramanujan statue, SASTRA, Kumbakonam

  • Tata Auditorium entrance, IISc, Bangalore, India

  • Tata Auditorium, Indian Inst Science, Bangalore

  • Guest House entrance, IISc, Bangalore

  • Trees with pepper vines, Coorg, India

  • Green peppercorns (Piper nigrum) Coorg, India

  • Coffee tree (Caffea arabica) with berries

  • Small boat on river, Coorg, India

  • Wash day at riverbank, Coorg, India

  • View of green hillside, from clifftop in Orvieto Italy

  • Monastery hillside from clifftop in Orvieto Italy

  • Small tower across rooftops, Orvieto Italy

  • Wisteria in cobblestone cul-de-sac, Orvieto Italy

  • Narrow cobblestone street, Orvieto Italy

  • Old ladies in sun under arbor, Ostia Antica, Italy

  • Closeup of Roman road stones, Ostia Antica, Italy

  • Ancient Roman ampitheater, Ostia Antica, Italy

  • Monte Cofano from Erice, Sicily

  • Acanthus mollis flower spikes, Erice, Sicily

  • Elymian stone theatre, Segesta, Sicily

  • Gaudi iron door, LaPedrera, Barcelona

  • Tarragona Spain: sea view from Balcon terrace

  • Fireworks from the Balcon terrace, Tarragona Spain

  • Kings College, Cambridge UK


  • Dcrjsr/US places images

  • Na Pali coast, Kauai - Hanakapi'ai Beach

  • Na Pali Coast profile, Kauai, from Kalalau Trail

  • Na Pali Coast, overlook of Kalalau Valley & cliffs

  • Marsh marigold bloom at edge of snowmelt WA

  • Marsh marigold (Caltha leptosepala)

  • Pacific Crest Trail in Washington woods

  • Observation tower, Wildflower Center TX

  • Bluebonnets by trail, Wildflower Center TX

  • Hedgehog cactus, Wildflower Center TX

  • Dragonfly sculpture, Wildflower Center TX

  • Piney Mtn Road, Duke Forest, Durham NC

  • Concrete Bridge Rd N, dogwood branch

  • Concrete Bridge Rd S, starting downhill

  • View down from end of Piney Mtn Rd

  • Concrete Bridge, late summer, Duke Forest

  • New Hope Creek with blooming fringetree

  • New Hope Creek, Duke Forest, Durham NC

  • Duke Forest, misty morning woods

  • Moon thru branch tips, Duke Forest, Durham NC

  • Duke Forest seed pines after timbering

  • Sunderland Bridge, from Sugarloaf Mtn, MA

  • Town center of Sunderland, Massachusetts

  • Boulder on granite-slab shoulder, Welsh Mtn NH

  • Stone breakwater S of Saco River, Maine

  • Saco River harbor, Biddeford Maine


en
This user is a native English speaker.
PH-2 This user is able to take good quality photographs.
BG-1 This user is able to contribute at a basic level to bitmap graphics.
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