Version 3.8 (the version before 4.0) remains available.
The design error caused multiple problems. The initial display of uploaded ConSurf files was the asymmetric unit, but should have been biological unit 1. When biological unit 1 was smaller than the asymmetric unit, displaying biological unit 1 caused "solid" atoms to be too large, and erroneously reported that the model contained only alpha carbons. This error precluded use of the Vines/Sticks View, and most Tools.Examples:
|Biological Unit 1 of a clathrin cage (3iyv) constructed from the crystallographic asymmetric unit and simplified to every second alpha carbon by FirstGlance in JSmol. Colored by distance from center.|
Reovirus Core 1ej6.
300 chains: 60 duplicates of the 5 chains in the asymmetric unit.
Simplified to every 11th alpha carbon. Diameter ~725 Å.
|1. Five Duplicated Chains||2. Three Distinct Sequences||5. Color by Distance||6. Grayscale by Distance|
|Isolated: Chains sequence-identical with chain M in the asymmetric unit of 2GTL in its biological unit 1, colored by amino to carboxy rainbow.|
ConSurf PDB Files are Special Cases: Evolutionary conservation of amino acids in unpublished PDB files can be determined by uploading the PDB files to the ConSurf Server. ConSurf prepares a downloadable PDB file customized for FirstGlance, containing the conservation results. These ConSurf PDB files are handled by FirstGlance as special cases: the initial view will be Biological Unit 1 (instead of the asymmetric unit as is the case for other .pdb files), automatically simplified as needed. See examples, including important instructions for unpublished ConSurf PDB files.
|PDB Entry||Resolution, Å||Rfree||FirstGlance 3.8||FirstGlance 4.0|
|3a38||0.70||0.075||(no interpretation)||Better than average|
|1b13||1.5||0.191||Better than average||Average|
|1p5x||2.0||0.196||Much better than average||Better than average|
|2ic3||3.0||0.31||Worse than average||Unreliable|
|4yh7||4.4||0.325||(no interpretation)||Worse than average|
This requires FirstGlance version 3.8 or later, which may not yet be installed on the ConSurf Server. Therefore, at the ConSurf Server, you should download the PDB file for FirstGlance, and then upload it to the latest FirstGlance.Jmol.Org.
|ConSurf PDB File||Action||Seconds pre-optimization||Seconds post-optimization|
|1n73 12 K atoms†||Initial ConSurf View||8.3||6.3 (2 sec less)|
|''||Check chain F||2.3||0.3 (2 sec less)|
|''||Go to FirstGlance Control Panel||2.4||No change.|
|''||Check ConSurf Colors*||4.4||0.6 (4 sec less)|
|6cri 53 K atoms†||Initial ConSurf View||56||38 (18 sec less)|
|''||Check chain Q||21||1.3 (20 sec less)|
|''||Go to FirstGlance Control Panel||5.9||No change|
|''||Check ConSurf Colors*||44||10 (34 sec less)|
Protein Crosslinks of several types (beyond disulfide bonds)
are now detected and reported.
An alert for
Unusual Components or Features
reports these regardless of preference settings.
Counts of each type present are linked in the
Molecule Information Tab,
subject to a preference setting.
A new tool "Protein Crosslinks" the Tools tab is always available.
Clicking one of those links/tools
lists the individual bonds of that type. Clicking on an individual bond finds it (yellow
halos), zooms in, and labels it and its neighbors. Also in the Lower Left Panel
are listed a range of examples, and the
methods used to detect the crosslinks.
methods are also listed in the Notes.
Only models with resolution of 4.0 Å or better are evaluated for protein crosslinks. When alternate locations are present, only conformation 1 is evaluated. When there are multiple models, only model 1 is evaluated.
For most models, scanning for protein crosslinks adds no noticeable time to how long FirstGlance takes to stop being busy while initially characterizing the model. The median entry in the PDB has 3,600 non-hydrogen atoms. 90% of entries have < 13,000 non-hydrogen atoms. Comparing FirstGlance 3.0 vs. 3.5, ready time for 13,000 atoms (6RD5) is 9 sec for both. For 53,000 atoms (largest 1.5% of PDB, 6cri), ready times were 20 vs. 23 sec, respectively. For 99,600 atoms (largest 0.7% of PDB and maximum number of atoms compatible with the PDB format, 3J9Q), ready times were 34 and 37 sec, respectively. (PDB analysis: August, 2021. Timings: Chrome browser in Windows 10.)
A single example is given for each type of crosslink below. More examples are listed under each type of crosslink in FirstGlance: click Protein Crosslinks in the Tools tab.
Asymmetric Biological Code Method Unit? Units* •1d66: X-ray Diffraction Yes 0 •1hho: X-ray Diffraction Yes 1 •1b6b: X-ray Diffraction Yes 2 (monomers) •5cev: X-ray Diffraction Yes 2 (hexamers, neither = asymmetric unit) •1qrd: X-ray Diffraction Yes 2 (software determined more likely than author determined) •5mny: Neutron Diffraction Yes 0 •2yz4: Neutron Diffraction Yes 1 •6pkj: Electron Crystallography Yes 0 •6oiz: Electron Crystallography Yes 1 •2bbn: Solution NMR No 0† •5v7z: Solid State NMR ? 0 •2c0x: Solid State NMR ? 1 •6ef8: Electron Microscopy No 0 •6nef: Electron Microscopy Yes 1 *Not counting the asymmetric unit, which is sometimes designated as a biological unit. † A search of the PDB finds no solution NMR entries with biological unit assembly operations (Sept. 14, 2019).
New default "Shiny"|
now a preference option.
60K atoms3, 5
99.6K atoms3, 6
1. Min:sec between entering the PDB code and the final disappearance of "BUSY" after the tabs at
the top left had appeared.
Times measured after JSmol & FirstGlance were already in the browser cache (1d66 had previously been displayed in the same browser session).2. Edge and Internet Explorer operate JSmol unacceptably slowly. See browsers.
Italics: First load (times measured after the browser cache had been cleared).
Clocked on a mid-2014 MacBook Pro (Mojave, 2.2 GHz i7, 16 GB 1600 MHz DDR3).
Internet Explorer and Edge clocked in a Windows 10 virtual machine (VMWare, same hardware).
3. There are no hydrogen atoms in this model.
4. Atom count includes hydrogens. Non-hydrogen atom count for 7ahl=17K.
5. Mostly RNA: 36K atoms RNA, 24K atoms protein.
6. 99,999 atoms are the maximum possible in the PDB format. FirstGlance does not yet handle mmCIF.
Greater than 99% of entries in the PDB are available in the PDB format.7. Percentages of entries in the PDB determined January 23, 2019 by MW search,
when there were a total of 148K entries in the PDB.