3/9/2023 0 Comments Color residues jmol![]() Once open, go to the command line in PyMOL and enter ‘run colour.py’ (or subbing in whatever you’ve called your file). Then, from the same directory as this new file, open PyMOL with any suitable structure. You can call it whatever you like, as long as it has ‘.py’ at the end. You can see in the script that every residue has its own unique colour, with names as imaginative as ‘deepsalmon’, ‘smudge’ and ‘wheat’ (whether or not Theresa May keeps a high tyrosine diet is beyond the scope of this blog post).Ĭopy the text and paste into a new file called – for example – ‘colour.py’. # COLOUR BY RESIDUE - PATRICK BRENNAN, UNIVERSITY OF OXFORD - AUGUST 2020Ĭmd.select ('backbone_carbons','name C+CA')Ĭmd.select ('ALA','name CB and resn ALA')Ĭmd.select ('ARG','name CB+CG+CD+CZ and resn ARG')Ĭmd.select ('ASN','name CB+CG and resn ASN')Ĭmd.select ('ASP','name CB+CG and resn ASP')Ĭmd.select ('CYS','name CB and resn CYS')Ĭmd.select ('GLN','name CB+CG+CD and resn GLN')Ĭmd.select ('GLU','name CB+CG+CD and resn GLU')Ĭmd.select ('HIS','name CB+CG+CD2+CE1 and resn HIS')Ĭmd.select ('ILE','name CB+CG1+CG2+CD1 and resn ILE')Ĭmd.select ('LEU','name CB+CG+CD1+CD2 and resn LEU')Ĭmd.select ('LYS','name CB+CG+CD+CE and resn LYS')Ĭmd.select ('MET','name CB+CG+CE and resn MET')Ĭmd.select ('PHE','name CB+CG+CD1+CD2+CE1+CE2+CZ and resn PHE')Ĭmd.select ('PRO','name CB+CG+CD and resn PRO')Ĭmd.select ('SER','name CB and resn SER')Ĭmd.select ('THR','name CB+CG2 and resn THR')Ĭmd.select ('TRP','name CB+CG+CD1+CD2+CE2+CE3+CZ2+CZ3+CH2 and resn TRP')Ĭmd.select ('TYR','name CB+CG+CD1+CD2+CE1+CE2+CZ and resn TYR')Ĭmd.select ('VAL','name CB+CG1+CG2 and resn VAL')Ĭode = This, I felt, had two advantages: firstly, it allows the viewer to easily pick out the trajectory of the backbone when the side chains are all visible and secondly it highlights glycine’s role as a ‘blank’ amino acid that has no side chain to speak of, as it blends into the overall backbone. Secondly, whilst the NGL Viewer option colours the backbone portion of every residue the same as the side chain, and colours glycine (which is just the backbone) as white, I decided to colour the backbone region of every residue as white. Firstly, whereas in the NGL Viewer option every atom in the residue was coloured the same, I decided to keep the heteroatoms (oxygen, nitrogen and cysteine) as their standard colours (red, blue and yellow respectively). With this in mind I decided to write a script to colour residues in PyMOL according to a similar colour scheme – with two important differences. leucine and isoleucine are slightly different shades of green), allowing for both easy identification of residue type and easy inspection of the overall geography of a protein structure: for instance, similarly blue-coloured lysines and arginines are often seen on the outskirts of the protein, whilst the core is often a mix of greens (leucine and isoleucine) and grey (phenylalanine). This setting assigns a unique colour to every residue such that similar amino acids have similar but distinguishable hues (e.g. one colour for hydrophobic, one for hydrophilic, one for positively charged, one for negatively charged), but the best I had encountered so far was the ‘colour by residue’ option in NGL Viewer – previously the default viewer option on the RCSB Protein Data Bank’s website. Looking online I found a few scripts which loosely coloured residues according to properties (e.g. Whist you can easily differentiate atom types based on colour in the colour menu, and even choose which colour you wish carbons to show up as whilst keeping heteroatoms different colours, this assigned carbon colour would be constant throughout the entire protein. However one thing I felt that PyMOL lacked was an easy way to visually distinguish residues based on type. – which all have their own pros and cons. It allows you to toggle between different representations of the protein – such as cartoon, surface, sticks, etc. PyMOL is a handy free way of viewing three dimensional protein structures.
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Take your kitchen to the next level with a LG smart refrigerator that lets you control key features from your smartphone via the LG ThinQ app. ![]() *Purchase an LG Refrigerator or Laundry product and receive Free Installation and Haul-Away. ![]() Magnification of second McMinnville UFO photograph.Īnother well-documented specific comparison of the objects to saucers was the Kenneth Arnold sighting on June 24, 1947, while Arnold was flying near Mount Rainier. Other designs have followed, such as the American Vought V-173 / XF5U " Flying Flapjack", the British GFS Projects flying saucer, or the British "S.A.U.C.E.R." ("Saucer Aircraft Utilising Coanda Effect Reactions") flying saucer, by inventor Alf Beharie. The first flying disc craft was called the Discopter and was patented by Alexander Weygers in 1944. īeyond the common usage of the phrase, there have also been human-made saucer-like craft. ![]() The flying saucer is now considered largely an icon of the 1950s and of B movies in particular, and is a popular subject in comic science fiction. ![]() Many of the alleged flying saucer photographs of the era are now believed to be hoaxes. However, unknown saucer-like objects are still reported, such as in the widely publicized 2006 sighting over Chicago-O'Hare airport. In fact, the term UFO was invented in 1952, to try to reflect the wider diversity of shapes being seen. More recently, the flying saucer has been largely supplanted by other alleged UFO-related vehicles, such as the black triangle. Many sightings of cigar or dirigible-shaped UFOs were reported following it. Such sightings were once very common, to such an extent that "flying saucer" was a synonym for UFO through the 1960s before it began to fall out of favor. Although Arnold never specifically used the term "flying saucer", he was quoted at the time saying the shape of the objects he saw was like a "saucer", "disc", or "pie-plate", and several years later added he had also said "the objects moved like saucers skipping across the water." Both the terms flying saucer and flying disc were used commonly and interchangeably in the media until the early 1950s.Īrnold's sighting was followed by thousands of similar sightings across the world. The highly publicized sighting by Kenneth Arnold on June 24, 1947, resulted in the popularization of the term "flying saucer" by U.S. "Some who saw the weird light described it as a huge comet, a flaming flying saucer, a great red glow, a ball of fire." The term "flying saucer" had been in use since 1890 to describe a clay pigeon shooting target, which resembles a classic UFO shape. Īnother early recorded use of the term "flying saucer" for an unidentified flying object was to describe a probable meteor that fell over Texas and Oklahoma on June 17, 1930. Martin, according to the newspaper account, said it appeared to be about the size of a saucer from his perspective, one of the first uses of the word "saucer" in association with a UFO. On January 25, 1878, the Denison Daily News printed an article in which John Martin, a local farmer, had reported seeing a large, dark, circular object resembling a balloon flying "at wonderful speed". Early reported sightings of unknown "flying saucers" usually described them as silver or metallic, sometimes reported as covered with navigation lights or surrounded with a glowing light, hovering or moving rapidly, either alone or in tight formations with other similar craft, and exhibiting high maneuverability.ĭisc-shaped flying objects have been interpreted as being sporadically recorded since the Middle Ages. The term was coined in 1947 but has generally been supplanted since 1952 by the United States Air Force term unidentified flying objects (or UFOs for short). ![]() Ī flying saucer (also referred to as "a flying disc") is a descriptive term for a type of flying craft having a disc or saucer-shaped body, commonly used generically to refer to an anomalous flying object. Nearly a year before the Flying Disc wave of 1947, pulp magazine Amazing Stories featured disc-shaped spacecraft. 3/8/2023 0 Comments Macos server hostingOn both the employee’s desktop Mac Computer and laptop Mac Computer, or multiple students For example, a single employee may use the Apple Software One (1) copy of the Apple Software for use either: (a) by a single individual on each of the MacĬomputer(s) that you own or control, or (b) by multiple individuals on a single shared MacĬomputer that you own or control. (ii) If you are a commercial enterprise or educational institution, to download, install, use and run Mountain Lion or OS X Lion (“Mac Computer”) that you own or control MacOS High Sierra, macOS Sierra, OS X El Capitan, OS X Yosemite, OS X Mavericks, OS X Software directly on each Apple-branded computer running macOS Catalina, macOS Mojave, (i) to download, install, use and run for personal, non-commercial use, one (1) copy of the Apple Limited, non-transferable, non-exclusive license: ![]() Permitted by the Services and Content Usage Rules set forth in the Apple Media Services Terms andĬonditions () (“Usage Rules”), you are granted a Through an automatic download, then subject to the terms and conditions of this License and as If you obtained a license for the Apple Software from the Mac App Store or ![]() Here is the EULA the quote below is from. ![]() Most hosted solutions are just leased devices which Apple formally allowed with Big Sur for 1:1 usage. I recommend looking in to something like Mac Stadium, or Amazon's hosted Mac Solutions. Apple typcially does not enforce this vary much, but good luck getting your employer to agree to the risk. Unfortunately macOS's EULA generally kills this. 3/8/2023 0 Comments Navicat premium 11.2.17![]() Whether you're also pinning a rectangular indication or something not square at all, Full Pin Tracker has you protected. Consider your chroma entering results even more by making use of Primatte in mixture with Supercomp's i9000 post-keying tools.Monitoring CleanupVFX Collection functions lighting-fast, precise planar tracking, correct inside of After Results - no need to action out of AE for great corner-pin tracking results any more. Primatte's cleanup equipment help change even the nearly all difficult pictures into strong and expert composites. Whether you are making use of a natural display or azure display screen, Primatte Keyer can regularly draw a perfect key with a one click. 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An empty result, where there should be a result, is however many times the symptom of an unhandled exception or timeout. One thing contradicting this theory however is, that you use RaiseError => 1, and as such you should get an exception when you fail to acquire the lock. Googling i stumbled across which mentions locking in combination with sqlite_busy_timeout. the file is locked through another process, and your call times out, while trying to acquire a lock. "Perl takes several seconds may return no rows, even where there are matching candidates."įrom the behaviour this makes me think of a locking/timeout issue. Some random thought based on your description (might not apply): Seeing which line of code consumes most time, might help you in identifying the root cause, and as such fixing it. I do not have the answer for you, but if i had your problem, then i would try to identify the cause through benchmarking the code with Devel::NYTProf. Reinvent the wheel, then learn The Wheel may be one day you reinvent one of THE WHEELS. PPS have you checked for database and table fragmentation? To compact the db with VACUUM can help in such cases. PS then I suppose you need transactions and commit when you've done. ![]() Update 2: now ran it on windows 7 too and it was PDQ there as well. Update: Mea culpa: I botched the indexing (didn't commit.), and with the indexes fixed it worked all right: fast, and just as fast as postgres. (Sorry, I don't know the windows invocation.) Time sqlite3 ~/employee.db "select e.* from employees e, groups g where e.sam_account_name = g.sam_account_name and g.group_name = 'whatever' order by e.last_name, e.first_name" How fast is a SQLite commandline query? Maybe you can try something like: (Then again, I know next to nothing of SQLite it's always slow-ish in my hands so maybe I do something wrong.)įWIW, postgres runs this same query in less than a millisecond, with the same data.Ĭould sqllitestudio be caching the query, or the data? It seems likely sqllitestudio is just a wrapper, from what I read on its website. SQLite is not a particularly fast database. "select * from employees where sam_account_name = ''" takes 3 seconds. I tried to repeat this performance by making an SQLite database of those two tables + indexes, together 600 MB, employees with 18M rows, groups with just 3 rows. Re: DBD::Sqlite queries slow - and gives wrong results Also, that doesn't explain why the results are different between Perl and SQL Thanks, but I run exactly the same query against exactly the same database from SQLiteStudo, and the time goes from many seconds to milliseconds. Re^2: DBD::Sqlite queries slow - and gives wrong results ![]() All power corrupts, but we need electricity. 3/8/2023 0 Comments Renpy coding editra![]() This is what your game will look like at first when you launch it. The following screenshots are to show what each looks like as you open them. As you edit the coding of your game, I recommend launching your game often to check and make sure you don't have any errors pop up. ![]() Again, I recommend keeping your game folder open while you work for easy access to them. RPY files to your game depending on it's length, and just like with the directory, the files won't show up where the purple circle is. These are the files you'll be adding your coding to. The contents in the purple circle are your Ren'Py files. Any extra folders you add to your game won't show up on the Directory, so I recommend just keeping the original game folder open while you work, that way it's easy to access the other folders as well. Lines beginning with a single mark are commented-out code, and you may want to. In my next tutorial, I will be listing the default folders it has, as well as folders I personally add to it for the sake of organization. By clicking on the text in your directory list, it will open up folders where you can put your game's contents. The text inside the orange circle is your Directory. To work on it, all you have to do is click it once, and it will bring up the options on the right side of the screen. The red arrow is where your game will be listed. The Question is a short VN they added into the download, probably for an example of what a completed game may look like. The Tutorial game is a tutorial on how to use Ren'Py and what you can do with Ren'Py, however some people have complained that the way it's explained can be a bit confusing, especially for beginners that don't already have coding knowledge(Which is why I'm making these tutorials). Tutorial and The Question come with Ren'Py when you download it. You'll see that Ren'Py already has two games "Tutorial" and "The Question"(Ignore that my Ren'Py screen has more than that, the others listed on my screen are my own project). Open up Ren'Py and this screen should pop up. Whether you use Editra or a different program, you will have to select it so it knows which program to use to open up your script files later on. ***Since I have been working on my project for years, I can't remember when it will happen, but at some point Ren'Py will ask you which program you'll be using to code. The link to the Editra download can be found below. Please keep in mind that you'll have to do this on your computer, not your phone. You can find the download the latest version of Ren'Py in the following link. This first tutorial will probably seem obvious, but I figured I should still make this anyway, because I know how frustrating and confusing jumping into something new can be. Want to make a visual novel? Well, hopefully with these tutorials I can help you out! This is the first "official" tutorial for my Ren'Py Tutorial series. 3/7/2023 0 Comments Hard drive idle timer![]() Device time is measured in power on hours, not physical time (as time with the disk powered off for extended periods of time does not count towards device wear). HDDs exhibit a bathtub curve for failures, with device failures increasing as time increases, rapidly accelerating after the 5 year warranty on most models. SMART is useful for finding predictive failures and removing a device before the data is lost, but this is tedious for novice users to understand (although I will show you how later). Hard drives have moving parts, and over time the motors, heads, and actuators fail. 16TB drives are 4x more space and power-efficient than 4TB drives (this is obvious, but is insanely important) Hard Drive Recommendationsįirst Choice: Ultrastar DC HC550 18 TB Hard Driveīack up plan: WD Elements 18TB Drives have an enterprise grade drive inside, which is an amazing deal but remember the warranty is void after you shuck the drive!! Internal drives with 5 year warranty will be less of a hassle, but generally, the same models can be found in high-capacity external HDDs if you are willing to “shuck” them and remove them from the enclosure. You will use 4-4.5x less space, have 4-16x fewer drive failures, and consume 4-4.5x less electricity (and power bill). TL:DR buy big drives, 16TB and 18TB are the sweet spots today. I have banished all the 4TB from my farm, and working on the 8TB next) Great right? There are two problems with this approach. 4TB and 8TB drives can be found for as little as $10/TB. It is tempting to buy old used hard drives that are very low cost. This helps us bring you quality content and keep this site running.” We only recommend products that we use ourselves and would never compromise the integrity of your build. “We have Amazon and CJ affiliate links in this article and we earn commission from qualifying purchases at no cost to you. 3/7/2023 0 Comments Babacad straight line![]() “I would disagree with you that we were lacking energy,” he said. Andonovski has generally not been the type to be critical of his players in public. Now, Andonovski didn’t agree when asked after the game if he thought the energy was lacking, and even if it was he’s not the type of coach who would say much about it. Maybe the locker room is missing too many of those wild-eyed players, like Kelley O’Hara and Julie Ertz, or even Lynn Williams, if you want to talk about pressing (and we do - see below). ![]() Perhaps that’s part of trying to transition this group and keeping that balance between veterans and new players. But it feels like there has been a distinct lack of just sheer, raw, brute determination. You can’t accuse these players of not wanting it enough - of course they want it. And it’s also a very nebulous thing to try to put your finger on for precisely that reason. Which is a tough thing to say about a bunch of athletes who still probably rank amongst the top 0.1 percent of overly competitive people on the planet. We’re not advocating for a flurry of borderline yellow card physicality, it just feels like the desire is lacking. They don’t go out there and bulldoze people to the ground with a wild look in their eyes. Looney Tunes goals aside, here are a few things that need improvement from the USWNT. Germany takes the 1-0 lead over the USWNT in Florida □□ /yzngnbTM5k Germany opened the scoring on a combination of a weird bounce, some quick countering, a possible blown offside call from the linesperson, and yet another extremely weird bounce that pinged the ball in from a rebound off the post that hit Casey Murphy in the back, like an old-timey cartoon where a character shoots an arrow off of a bunch of pots and pans and hits the bullseye. But against Germany, that 4-3-3 wasn’t getting totally exposed and was, in fact, generating quite a bit of good pressure on Germany for a solid hour or so. So what’s gone wrong in their 2-1 loss to England, 2-0 loss to Spain and now this against Germany? The team’s not necessarily a tactical disaster, although head coach Vlatko Andonovski’s rigid devotion to the 4-3-3 formation is concerning. goal, with Alex Morgan remaining grittily determined to stay on the ball and pick out Megan Rapinoe across the box. Indeed, that was the source of the night’s one U.S. In the past, that solution was often a straight-up dose of teeth-baring mental aggression, where the team would hustle their way to a goal. Flukes happen, though, and when the dice are coming up in statistically improbable ways, it’s on the team to find a solution. 3/7/2023 0 Comments Get plain text osx app![]() Option-Command-D: Show or hide the Dock.Shift-Command-U: Open the Utilities folder.Control-Shift-Command-T: Add selected Finder item to the Dock (OS X Mavericks or later).Shift-Command-T: Show or hide the tab bar in Finder windows.Shift-Command-R: Open the AirDrop window.Shift-Command-P: Show or hide the Preview pane in Finder windows.Shift-Command-O: Open the Documents folder.Option-Command-L: Open the Downloads folder.Shift-Command-K: Open the Network window.Shift-Command-H: Open the Home folder of the current macOS user account.Shift-Command-G: Open a Go to Folder window.Shift-Command-F: Open the Recents window, showing all of the files you viewed or changed recently.Shift-Command-D: Open the desktop folder.Shift-Command-C: Open the Computer window.(3) In Software Update, check for software updates again. ![]() (2) In some apps, such as Calendar or Safari, refresh or reload the page.
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