User:Dcrjsr
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 High Sierra landscapes, or Sierra Nevada flowers.
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 the organizer, and 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[modifier]
Click here for the gallery of Dcrjsr/Protein Ribbon Drawings
- Dcrjsr/Protein Structure Detail images
CuZn SOD active site
Contacts between RNAse and U vanadate inhibitor
Selectivity region of K+ channel, from 1bl8
GCN4 Leu-zip hydrophobic core, with Asn (2zta)
Collagen Gly-Pro-hyPro triple helix (1cag)
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
Right-handed vs left-handed crossovers
- 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
- Crambin P41 hi-res map 3nir.tif
Ultra-high resolution electron density: crambin P41, 3nir
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
27 lysine rotamers
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
6 Ramachandran plots of wwPDB validation
- 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
TOP7 protein design, structure confirmed (1qys)
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 residueSuite diagram.jpg
RNA backbone - suite vs residue
RNA backbone - suite vs residue (tif format)
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
tRNA Phe, from PDB 1ehz
G-riboswitch binding site: map, contacts, conformers
G riboswitch RNA, 1u8d
Tetrahymena Group I self-splicing intron, 1grz
Twort groupI intron, stereo ribbon
5S ribosomal RNA, ribbons
E coli 70S ribosome structure, QuteMol
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
Dickerson DNA dodecamer, from 1bna
Holliday junction DNA, from the protein complex in 2crx
Nucleosome DNA & histone structure, round, 1aoi
Nucleosome DNA and histone structure, 1aoi
Nucleosome DNA/protein complex, ribbon schematic
CAP protein dimer on bent DNA, 1cgp
Coiled-coil transcription factor Max, on DNA
Zn-finger transcription factor Zif268, on DNA
BmrR/DNA/TPP complex, untwisting the DNA
Clamp-loader, open clamp, & DNA, 3u5z
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- Dcrjsr/NMR Structure images
2k49 NMR ensemble ribbons
2k5d NMR ensemble ribbons
144 NMR models for ubiquitin, from PDB 2nr2
NH RDC target curves on NMRmodels, D58 in 1d3z
- Dcrjsr/WikiProject Biophysics images
Original Richards box photo, 1968
Institute of BioPhysics, Beijing
IISc Tata Auditorium entrance, Bangalore
Tata Auditorium, Indian Inst Science, Bangalore
King-Way Yau 2008 ARVO
Jane S Richardson B&W 2002
Irwin Fridovich in Duke office, 1994
Heads & neck of kinesin motor, Goodsell MotM 64
Topoisomerase Type I on DNA, Goodsell MotM 73
Topoisomerase II composite, Goodsell MotM 73
Clathrin cage & triskelion, Goodsell MotM 88
Cu,Zn superoxide dismutase (SOD) dimer, Goodsell MotM 94
Human Cu,Zn superoxide dismutase, Goodsell MotM 94
Mn and Fe SOD dimers, Goodsell MotM 94
Ni SOD hexamer, Goodsell MotM 94
Kai A,B,C circadian clock, Goodsell MotM 97
70S bacterial ribosome, small subunit front, Goodsell MotM 121
70S initiation, with Shine-Delgarno mRNA, Goodsell MotM 121
3 stages of elongation in 70S: EF-Tu, peptide, EF-G, Goodsell MotM 121
RF-1release factor in ribosome, Goodsell MotM 121
Antibiotics bound to 70S bacterial ribosome, Goodsell MotM 121
Aquaporin water-channel tetramer, Goodsell MotM 173
Seven colors of GFP-like proteins, Goodsell MotM 174
Tetramer of GFP-like dsRed from coral, Goodsell MotM 174
Apoptosome subunit & complex, Goodsell MotM 177
Apoptosomes of 3 species, Goodsell MotM 177
Cross-section of Ebolavirus, with proteins, Goodsell MotM 178
three Ebolavirus matrix proteins, Goodsell MotM 178
TAL effector protein bound to DNA, Goodsell MotM 180
TALE/nuclease/DNA engineered complex, Goodsell MotM 180
Cascade complex of Type I CRISPR, Goodsell MotM 181
Cas1,2,3 proteins of CRISPR, Goodsell MotM 181
Cas9 Cascade complex of Type III CRISPR, Goodsell MotM 181
Glucagon hormone bound to its receptor, Goodsell MotM 184
ALAD enzyme in lead poisoning, Goodsell MotM 196
Zika virus capsid, Goodsell MoTM 197
Zika virus cross-section on cell, Goodsell MoTM 197
Section on Landscapes, Plants, etc[modifier]
Click here for the gallery of Dcrjsr/High Sierra landscape images, organized S to N by Wilderness area or Park
Click here for the gallery of Dcrjsr/Eastern Sierra images
Click here for the gallery of Dcrjsr/Sierra Nevada flower images, organized by genus & species
Click here for the gallery of Dcrjsr/Death_Valley_superbloom_2016 images
Click here for the gallery of Dcrjsr/Sierra Nevada shrub images, organized by genus & species
Click here for the gallery of Dcrjsr/Sierra Nevada tree images, organized by genus & species
Click here for the gallery of Dcrjsr/Duke Forest NC plant images
- Dcrjsr/Sedges, unidentified
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
Sedge (Carex sp) NW of Mono P (from BakerClaw)
Large sedge, seed head star, Oakland lawn
![Unknown sedge (Carex), Tantalus Road, Oahu.]]](https://upload.wikimedia.org/wikipedia/commons/thumb/d/d4/Sedge_TantalusRd_Oahu.JPG/120px-Sedge_TantalusRd_Oahu.JPG)
Unknown sedge (Carex), Tantalus Road, Oahu.]]
![Unknown sedge (Carex), Tantalus Road, Oahu.]]](/wiki/File:Sedge_TantalusRd_Oahu.JPG)
- Dcrjsr/Ferns & lower Gymnosperms
Equisetum arvense lining streambank, Aspendell
Equisetum arvense, sterile stem close
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
Desert cottontail (Silvilagus audubonii) under sage bush
Desert cottontail (Silvilagus audubonii) back view
Desert cottontail (Silvilagus audubonii) front view
Desert cottontail (Silvilagus audubonii) side view
Blacktailed jackrabbit (Lepus californicus) Marin County
Pika in rocks, mouthful of dried grass
American pika (Ochotona princeps) camouflaged
Yellow-bellied marmot, near Kaweah Gap
Marmota flaviventris, on rock in meadow, 20-Lakes Basin
Marmota flaviventris standing, S of Donahue
Beldings ground squirrels (Spermophilus beldingi)
Chipmunk stuffing cheeks with seeds
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
Striped skunk (Mephitis mephitis) Las Trampas
Black-headed grosbeak male, perched front
Black-headed grosbeak female, perched
Rufous hummingbird female, perched, front
Stellers jay perched on antelope brush
Purple finch, on gravel, front view
California quail male, on ceanothus bush
California quail chicks hiding by path
Great horned owl, closeup of mother and nestling
Green sea turtle (Chelonia mydas) onTurtle Beach Oahu
Green sea turtle (Chelonia mydas) looking around
Green sea turtle turning to leave the beach, Oahu
Green sea turtle heading back toward the sea, Turtle Beach
Green sea turtle partly wet by wave, heading seaward
Green sea turtle back in the water again, Turtle Beach
Orthoceras fossil cluster, black marine nautiloids
_front_view.jpg)
- 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
Ramanujan museum, SASTRA, Kombakonam
Ramanujan statue, SASTRA, Kumbakonam
IISc Tata Auditorium entrance, Bangalore
Guest House entrance, IISc, Bangalore
Trees with pepper vines, Coorg, India
Green peppercorns (Piper nigrum) Coorg
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
Large hole through island off La'ie Point, Oahu
View south from La'ie Point to Ka'a'awa, Oahu
Chinaman's Hat Island, off Ka'a'awa peninsula, Oahu
Diamond Head & Waikiki, from Tantalus Rd, Oahu
Marsh marigold bloom at edge of snowmelt WA
Marsh marigold (Caltha leptosepala)
Pacific Crest Trail in Washington woods
View SE from paved trail, Las Trampas
N along Rocky Ridge top, Las Trampas
California bay tree (U. californica) Las Trampas
View W into EBMUD watershed. Las Trampas
compressed-fossil rock, Las Trampas
Striped skunk (Mephitis mephitis) Las Trampas
Observation tower, Wildflower Center TX
Cafe & tower, Wildflower Center TX
Texas bluebonnet field (Lupinus texensis), with oaks
Path by bluebonnets, Wildflower Center TX
Bluebonnets by trail, Wildflower Center TX
Hedgehog cactus, Wildflower Center TX
Dragonfly sculpture, Wildflower Center TX
Great horned owl (Bubo virginianus) mother and nestling
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
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