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boss jorgensen manualThey are freely available to academicThe BOSS programAlternatively, the energetics of the solutes can be represented with the QMExtensive capabilities are provided for easy setup ofEnergy minimizations canFree energy changes can be computed via FEPBy doing a few simple modifications it is possible to add PDDG support to. MOPAC while retaining backwards compatibility. Depression, ADHD, memory loss, agitation: These may seem like inevitable byproducts of modern lives spent multitasking, not getting enough sleep, and operating on digital overload. But while much of the brain’s work still remains a mystery, a growing body of scientific evidence suggests that the food you eat directly affects how well your brain functions. Brain health also pl.The guests range from super celebs (Jamie Foxx, Arnold Schwarzenegger, etc.) and athletes (icons of powerlifting, gymnastics, surfing, etc.) to legendary Special Operations commanders and black-market biochemists. For most of my guests, it’s the first time they. Molecular Modeling of Biological Molecules The first step is to download and read the users manual for BOSS from the Jorgensen Group website. The BOSS manual takes you through the parameter input file, defines the various parameters, goes through a sample zmatrix line-by-line, discusses various types of calculations, and defines variable definitions and portions of the output. We will also discuss the details in class. Under “pureliquid” are 3 directories: MCgasopt, MCgasruns, and MCliqruns which contain various files and scripts needed for the calculations. I would suggest copying over the contents of my pureliquid directory into a directory named “AMS536projects” in your home accounts on both the MATHLAB computers in the SINC site and also on the SEAWULF supercomputer. Note to copy files over to SEAWULF make a tar file (tar -cvf pureliquid.tar pureliquid )and then use the sftp protocol to copy the file “pureliquid.tar” the SEAWULF.https://www.acsmoz.com/fotos/boss-gt-6b-manual-pdf.xml

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Untar the file using: tar -xvf pureliquid.tar. Note that since you will be editing the various cmd scripts make sure your “vi” skills are up-to-date. FYI all the boss test jobs discussed in the manual are included in our boss distribution so feel free to explore. See (follow links to support and FAQ). Basically, for a “serial job” i.e. one processor you can just type as an example: qsub OPTcmdNodes without any jobs running show up in light blue. When in doubt consult the BOSS users manual. Look at the molecule visually and optimize a variety of molecules in the aazmat directory. Note that the optimized zmatrix from running OPTcmd is called “sum”. Open up sum with “vi” and look at it. The “plt” files are in PDB format and can visualized using a number of programs such as rasmol, vmd, or moe. Note that the “sum” file is a fully expanded zmatrix file which we will use for the other two BOSS calculations in directories MCgasruns and MCliqruns to compute pureliquid properties. Make any the necessary changes (i.e path names for where the files will be read and written) to the scripts MCgascmd and MCliqcmd and edit the parameter files so that the temperature is correct for the experimental data for which you want to compare. For example most jobs will be run either at 25 deg C or at the normal boiling point of the pure liquid. These jobs take some time so execute MCgascmd and MCliqcmd on Seawulf. Use Tables 9-10 from Jorgensen et al. J. Am. Chem. Soc. 1996, 118, 11225-11236 (Jorgensen002.pdf) to get the simulation temperature and the experimental density for which you will compare your computational results for your molecule(s) assigned in class.The purpose is not to just run the calculations but understand the process by which the calculations are actually setup so you can modify things in the future. Everyone please reply to these group questions so things don't get out of hand.http://cheumst.com/upload/fckeditor/boss-gt-6-user-manual-pdf.xml The set of methods that allow In essence, molecular simulations The Monte Carlo methodJorgensen at Yale ( ) The following tutorial Change into this subdirectory and verify that you have six files. The Z-matrix format BOSS z-matrices can be generated from otherThe first column defines the bonds and angles by Because BOSS is written in. Fortran, the position of fields in the parameter file should be kept as For the purpose The first part defines It also establishes connection between numerical atom types and For examples, both atom types 135 and 157 Torsional parameters are typically assigned based on atom classes. For CT-CT-OH-HO torsion because of connection between types and classes thatDuring the actual calculation of torsional A file suitable for the Monte Carlo. Notice that we are doing a simulation of ethanol in a box of 260 TIP4P. The meaning of entries in this file The command file that launches the. The command file tells Notice that the complete The short NVT The Boltzmann When the NVT equilibration has finished, you'll see a message 'Running NPT Equilibration'. At this time, open another UNIXPDB file in the program gOpenMol. You can inspect the First, hide everything by setting the Display state: Off and hitting Apply. Next, display the ethanol molecule by typing 1-9 into the Atom: field, setting the Display State: On and hitting Apply. You need to fill in Atom: fields with numbers corresponding to atom order in the PDB file. Inspection of the text in the PDB file reveals that the atom numbers that define the CC-OH dihedral are 4, 3, 1, 2. Close gOpenMol when you have finished the visual inspection of the structure. Inspection of the text Type xmgrace dihed1.xmgr Repeat the analysis for the Are these the expected results or do you spot Three most significant factors that affect the Perform the Monte Carlo simulation of Compare the observed probability You can easily obtain the gas phase energy of a conformation by using the xOPT script provided by BOSS.http://www.raumboerse-luzern.ch/mieten/bosch-maxx-wfl-2260-manualEstimate the percentage. Pyruvate and acetylacetone: a computational challenge. Giuliano Alagona, Caterina Ghio, Peter I. Nagy Chemistry, Medicine Physical chemistry chemical physics: PCCP 2010 References Publications referenced by this paper. BOSS is developed by Prof. William L. Jorgensen at Yale University, and distributed commercially by Cemcomco, LLC and Schrodinger, Inc.By using this site, you agree to the Terms of Use and Privacy Policy. If you need an account, please register here Barcelona 08028, Spain Darius Habibollahzadeh and Jiali Gao Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260 more. The results derived from these techniques are in reasonable agreement, which supports the reliability of the calculated polarization values. The polarization contribution to the free energy of hydration was partitioned into components to elucidate the nature of the polarization in the solvation process. Strategies to capture the polarization effects in force?field simulations are discussed. Chemistry, University of Toronto, Ontario, Canada. Version modified by R. Cammi, R. Bonaccorsi, and J. Tomasi, University of Pisa (1987). Google Scholar 27. D. A. Pearlman, D. A. Case, J. C. Caldwell, G. L. Seibel, U. C. Singh, P. Weiner, and P. Kollman, AMBER 4.0 Rev A, University of Californian, San Francisco (1991).Article views prior to December 2016 are not included. As founder Ikutaro Kakehashi approaches his 75th birthday, we begin a journey through the company's extraordinary history. The Judean Peoples' Front (or was it the Peoples' Front of Judea?) might well have replied as follows. But this is the story of a man as much as a company, so we'll start by turning our clock back to a time long before the birth of the hi-tech music. It's hardly surprising that the FR1 was successful.http://forgottenjustice.com/images/boss-jorgensen-manual.pdf Long before rhythm machines became commonplace, it offered 16 preset patterns that you could mix together simply by pressing two buttons simultaneously, so more than one hundred rhythm combinations were just a button press (or two) away. What's more, four additional buttons allowed you to defeat the cymbal, claves, cowbell and bass-drum sounds, thus allowing you to modify the sound still further. But perhaps most innovative of all were the FR1's sounds, now recognisable as archetypically 'Roland', and which were later destined to shape rock and pop music from the late '70s onwards. Indeed, the FR1 is the precursor of all Roland's great analogue rhythm machines. What's more, in an era of sometimes shoddy manufacturing and poor reliability, the FR1 was built like a tank, and also to last. Mine is approaching its 40th birthday, and its little heart beats as strongly today as it did back in the Summer of Love. He studied mechanical engineering and simultaneously worked as a schoolboy worker in the Hitachi shipyards where Japan's 'midget' suicide submarines were built. As a result, he witnessed a great deal of destruction in the last months of the war. This offered a far more rural existence and, to survive, he took a day job as a geographical survey assistant. But, at just 16 years old, he noticed that, with no watch or clock industry in post-war Japan, there was a thriving business to be had repairing existing timepieces. He was unaware of it at the time, but a chap named Torakusu Yamaha had also started out as a watch repairer, as had Matthias Hohner. Even the Hammond Organ Company started out as a sub-division of the Hammond Clock Company! This was a success, and he next decided to turn his enthusiasm for music into a business venture. It was no longer illegal to own a short-wave radio or to listen to foreign broadcasts and, scanning the airwaves for new music, Kakehashi learned the basics of how radios worked.http://www.maoles.com/wp-content/plugins/formcraft/file-upload/server/content/files/1626f0fabd8369---bosch-security-programming-manual.pdf He was soon cannibalising broken sets to create working ones, and his repair shop started handling broken radios in addition to watches and clocks. Nonetheless, he still supplemented his income with agricultural work. Still just 20, he returned but was struck down by tuberculosis in both lungs, the treatment for which quickly consumed all the money he had earmarked for his education. So, as the months in Sengokuso hospital turned into years, Kakehashi supported himself by repairing watches and radios for the staff and other patients. He borrowed enough money to purchase a cathode-ray tube and, still confined to hospital, assembled his own receiver. Amazing though this was, it is almost incredible when you understand that Kakehashi had by this time spent three years in hospital. Indeed, his condition was gradually becoming terminal when he was selected as a guinea-pig for the newly developed drug, Streptomycin. Kakehashi's improvement was immediate; within a year he had left hospital. In retrospect, he was extremely lucky.This loophole, caused by a need for prior Japanese publication of a given idea, was a severe impediment to the fledgling Japanese manufacturers of the time. So Kakehashi and 16 colleagues (including Tsutomu Katoh, President of the Keio Organ Company, later to become Korg) collated all the information they could, and in January 1966 published two books: Everything About Electric Instruments and Everything About Electronic Instruments. This stopped foreign manufacturers from patenting anything except genuinely new ideas and techniques, thus allowing Japanese companies to design and build products using technology in the public domain, and thereafter to improve upon it. The two books became the first Japanese reference books for electric and electronic musical instrument design. He changed the name to the Ace Electrical Company, and was soon employing around 20 staff.www.drpaullampl.com/userfiles/files/comptia-security2B-2B-manual.pdf But as early as 1955, he had decided to branch out, combining his electrical skills and his interest in music to develop products for the music market. Like Bob Moog in the USA, his aim was to produce an electronic instrument capable of producing simple monophonic melodies, so he started by building a Theremin. However, he was disappointed to find how difficult this was to master. Later, exposure to an Ondes Martenot convinced him that a keyboard-based instrument was more likely to be successful, so he built a four-octave organ using parts from a reed organ, bits of telephones, and simple transistor oscillators. Kakehashi admits that Prototype No. 1 sounded rather different from how he had hoped, so it never entered production. Sure, his contact with Matsushita (who owned the Technics brand name) came courtesy of a friend of a friend, and it was unlikely that Ace could have raised the capital to manufacture and distribute the instrument, so Kakehashi must have leapt at the chance. Nonetheless, the birth of the SX601 was no small achievement, and Ace Electronic were up and running as a manufacturer of musical equipment. Three years later, in 1963, the company added guitar amplifiers to its product range, but Kakehashi's ambitions lay elsewhere. Ace Electronics' first commercial product, the unsuccessful R1 Rhythm Ace. So, in 1964, he developed the Ace Electronics R1 Rhythm Ace, and took it — along with the Canary, a simple monophonic instrument heavily influenced by the Clavioline — to the NAMM show in Chicago. The Rhythm Ace was possibly the world's first fully transistorised rhythm machine but, despite interest and sample orders from American manufacturers, Kakehashi did not seal any manufacturing or distribution deals. The technological problems of producing repeating rhythms were themselves non-trivial, but Kakehashi and his colleagues overcame them by inventing a 'diode matrix' that determined the position of each instrument in a pattern.http://slowjamsundays.com/wp-content/plugins/formcraft/file-upload/server/content/files/1626f0fc57811e---bosch-service-manuals-dishwasher.pdf Having done so, they were able to release the FR1 Rhythm Ace, which appeared in 1967 (see the above box). The positive response was immediate, and the FR1 was adopted by the Hammond Organ Company for incorporation within its latest line of organs. Ace Electronic were on their way. The following year (1968) the companies formed a joint venture called Hammond International Japan, and in 1969 Kakehashi raised the capital to take over a derelict piano and organ manufacturer, Zenon Gakki Seizou, in Hamamatsu. This factory was soon to become a major source of Hammond organs and, of course, the sole source of Ace Tone organs. These included the TOP3 (1965), the TOP1 (1969), TOP5, TOP6, TOP7, TOP8, and TOP9, plus the more complex, dual-manual GT7. Of these, the GT7 is the most interesting, because it appears to be the direct precursor of the Hammond X5. Furthermore, it was perhaps the only Japanese organ to use sine waves as the building blocks of its sounds rather than the brighter sawtooth and pulse waves favoured by the likes of Lowrey, Baldwin, Wurlitzer, Vox, and, indeed, all previous Ace instruments. The project was later unveiled at the NAMM show in Miami, and the Piper Organ — the world's first single-manual organ to incorporate a rhythm accompaniment unit — became one of the most successful products ever produced by Hammond. This had not been a problem when the major investor was a company named Sakata Shokaim, because Kakehashi and Kazuo Sakata shared an interest in organs, and enjoyed a good professional relationship. Unfortunately, an industrial company, Sumitomo Chemical, accidentally acquired Ace when it purchased Sakata Shokai. Sumitomo's staff had no understanding of or sympathy for the music industry, and Kakehashi found the situation intolerable so, despite 18 years of hard work and commitment, he decided to resign and walk away. It was time for something new. AS1 sustain pedal. RHYTHM PRODUCTS TR33. TR55. TR77.https://cffcommunications.nl/wp-content/plugins/formcraft/file-upload/server/content/files/1/1626f0fd583172---bosch-service-manual-washing-machine.pdf However, he did not choose the name because of the French romantic poem, Chanson de Roland. This is an oft-repeated story repeated in dozens of places on the Internet. In fact, Kakehashi chose the name for phonetic reasons: he wanted two syllables with soft consonants, and Roland satisfied his criteria nicely. However, he had no wish to be the junior partner in his own company for a second time, so he decided to forge ahead on his own. Using his considerable reputation as collateral, Kakehashi managed to persuade parts suppliers to offer 90-day payment terms, and then aimed for the unbelievable target of designing, manufacturing, and exporting a rhythm unit before the bills fell due. The decision to export was not as strange as it may seem. The dominance of Yamaha and Kawai in Japan's music markets made it impossible for Roland to compete if the new company launched an established type of product, and it was unlikely that an innovative product could make an impact in time for Roland to earn enough cash to survive. Therefore, foreign markets offered more hope, provided that Kakehashi could find distributors capable of delivering Roland products across the key markets of the USA and Europe. Next, he visited the Multivox Corporation in New York, the US importer for Ace products (and the company which, somewhat later, would be linked to the somewhat cloudy Multivox copies of Roland instruments). In Europe, he contacted Brodr Jorgensen, a Danish company that had subsidiaries in the UK, Switzerland and Germany, and which distributed Ace across the continent. In each case, he obtained orders for a number of units, sufficient for him to start purchasing components and undertake assembly. Consequently, he rented a small factory there, and production of Roland products started in both locations.www.dqnjl.com/userfiles/files/comptia-network2B-lab-manual.pdf Roland were later to move in their entirety to Hamamatsu, establishing a number of factories in the area, but for the first few years, Kakehashi would commute overnight by train between the two. The first Roland product, the TR77 rhythm box. This is not surprising; Kakehashi had extensive experience in designing such products, the development cycle was short, and the costs were low. The organ-industry heritage of these products was obvious, and the TR33 had the cut-out body shape that showed that it was intended for mounting underneath a piano or organ keyboard. The TR55 was more of a tabletop design, but the long, flat TR77 (which was, if truth be told, little more than an updated version of the Ace Tone FR7L) was the pick of the bunch. When Hammond rebadged the TR77 as the Hammond Rhythm Unit, it was clear that Kakehashi had made the best use of his contacts, and that Roland were on their way. The most polite one can be is to say that it wasn't worth ?250. Roland's first synthesizer was Japan's first synthesizer, predating the Korg 700 by a handful of weeks. It was a strange instrument, offering 10 preset tones to which you could add vibrato, growl and portamento. At the time, the fat, punchy patches of Moogs and ARPs were the preferred sounds of a generation, so the little Roland was considered weak and uninspiring. What's more, it lacked any redeeming qualities such as pressure sensitivity, performance controls, duophony, a spring reverb, or interconnectivity with other synths, all of which had appeared on other manufacturers' instruments over the previous three years. Nonetheless, two things made the SH1000 special. Kakehashi understood that electronic music products needed to be affordable and reliable as well as creative. So he designed his synthesizer to use fewer op-amps than other synths, and this enabled him to reduce the cost considerably. Secondly, the SH1000 was well built, and it exuded reliability. At the time of writing, mine is almost 30 years old, but looks as good as it did the day it was built, and still performs faultlessly. All of the knobs and slider heads are present and correct, without a single crackly pot to indicate the instrument's age. It has never needed tuning or servicing either. If anything justifies Roland's ensuing success, it is this. SH3 monosynth. Establishing domestic and export markets is hard enough without your former employer trying to block your efforts to create a distribution channel, but this is what Ace did, threatening to disenfranchise any dealership that carried Roland products. Fortunately, most refused to be bullied, and Kakehashi was able to continue marketing and selling his products in Japan, North America and Europe. Least amongst these were the AW10 wah pedal, the more advanced AD50 Double Beat (which, by virtue of combining wah, fuzz and a simple phaser, was possibly the ancestor of all today's multi-effects pedals), and the AG5 'Funny Cat' auto-wah. Then there were the EP10 and EP20, Japan's first fully electronic pianos. These proved to be sturdy and reliable, but in common with other electronic pianos of the 1970s, they sounded truly horrid. They were no competition for the Fender Rhodes and Wurlitzer pianos that dominated the era so, despite their places in history, they are probably best forgotten. However, you wouldn't want to forget the other four products launched in 1973. His announcement machine was quickly modified, and the RE100 and RE200 tape-echo units became the precursors of the landmark 'Space Echo' products that were soon to appear. The Roland SH3. Any resemblance to the Ace Tone SH3 is purely coincidental. or is it? An instrument of the 'synth-in-its-own-flightcase' school of design, the SH3 shared the SH1000's ability to mix waveforms, offering sawtooth, pulse and square waves, freely mixable in any proportions at each of the 32', 16', 8' 4' and 2' footages. The SH3 sported two conventional LFOs (the PWM had its own, dedicated rate control) with a neat routing system for pitch modulation, filter modulation, and tremolo. What's more, there was a sample-and-hold section, portamento, a self-oscillating filter, a full ADSR contour generator, and two preset envelope shapes — one brassy, one percussive — for the VCF and VCA. But this is not quite the impressive accolade that it might seem. After all, the SH3 was only the third synth manufactured in Japan, the Roland SH1000 and Korg 700 being the others! Distortion, wah-wah and phasing existed, but chorus and ensemble effects were still in the future, as were the complex delay, modulation and spectral effects that we now take for granted. The heart of an echo — an RE201 seen from above with the cover removed, revealing the tape and associated control circuitry. OK, the RE201 was not the first Space Echo, having been preceded by the RE100 and RE200, but both of these seem to have disappeared without trace. It was also launched alongside the RE101, but this lacked six of the modes, the EQ and the all-important reverb, so it was the RE201 that became the Space Echo. That it looked superb, and was as rugged as a Chieftain tank were added bonuses that ensured that the RE201 became de rigueur on the road as well as in the studio. Later Space Echoes offered extra controllability and a modified range of effects. The RE301 added chorus and a sound-on-sound head, while the RE501 and the rackmount SRE555 added chorus, sound-on-sound, a fourth echo head and a balanced (XLR) input. There was even a cut-down model, the RE150, but this stepped all the way back to the RE101 specification (ie.But it was the RE201 that embodied the perfect combination of price, facilities, and performance. It was a classic and, amazingly, it remained a current product until 1990. A digital version, the RE3, was launched in 1988, and, although it was a good unit in its own right, it was not a great success. But when, and where, does the Ace Tone EC1 fit into this story. In many ways, it's a dead ringer for the RE101, with the same three-channel input configuration and prominent VU meter. Sure, the Ace's controls are different, with buttons rather than the rotary knobs of the Space Echoes, but the family resemblance is unmistakable. EFFECTS AP5 Phase 5. RE101 Space Echo. RE201 Space Echo. PIANOS EP30 touch-sensitive electronic piano. SH3A monosynth. So a new version appeared in 1974. Externally, the SH3A was almost identical to the SH3, but it sported a new VCF and VCA, and it was this model that Vangelis and a handful of other famous keyboard players adopted in the mid-1970s. This offered a number of facilities that made it more flexible than other single-oscillator synths of the era. For example, the VCO waveform passed through an octave-divider, enabling players to build complex voices using a mix of octave footages from 32' to 2'. Four families of waveform were available — sawtooth, five widths of pulse (including square), PWM, and noise — although only one could be used at a time. There were two LFOs (one with delay), three levels of filter tracking, a fixed filter that could be overdriven, a fully variable 12dB-per-octave resonant filter, and two independent envelope generators. While you could access all of these facilities more flexibly on the SH3A, the SH2000 was the more expressive, thanks to its five parameters of aftertouch sensitivity. A second revision (serial numbers 608900 onwards) featured an updated power supply. But whichever version was used, the SH2000 sounded good, and it eventually became widely used in mainstream rock and pop. That's not bad for something designed to sit on top of a domestic organ. Furthermore, like the SH1000 and SH3A, the SH2000 was still available in 1981, nearly a decade after its introduction. Clearly, Kakehashi had got things right first time. The famous RE201 Space Echo tape-based delay. A design classic that looks as good now as it did when first unveiled, the RE201 used a much longer tape loop than its predecessors or competitors, reducing wear on the tape, which in turn improved the sound quality and prolonged the useful life of the tape itself. The Space Echo was an instant hit, and remained in the Roland catalogue for the next 16 years. It was also the first Roland product to cross all the boundaries of popular music. A decade before the introduction of affordable digital multi-effects units, its combination of reverb, multi-tapped echo and EQ proved to be equally attractive to guitarists, vocalists and keyboard players, and it soon became impossible to avoid the ubiquitous box, whether on the road or in the studio. Nowadays, tapes for these are becoming harder to find, and owners are prone to forgetting that they need periodic servicing to maintain good performance, but you'll still find numerous RE201s in use. However, just before the product launch, somebody in Japan realised that Meg is a common girl's name in the west, so Kakehashi changed the brand name to something with 'leadership connotations'. I doubt that anybody reading this remembers the product in question, and it would now be of no interest but for one thing: Kakehashi's new brand name was Boss, and when the Boss B100 guitar preamp was released, another legend was born. By determining the amount of delay, the modulation rate and depth, and the relative phases between the three signal paths, Roland's designers could have selected between a wide range of delay, reverb, tremolo, vibrato, phasing and chorus effects, all of which can be generated by these chips. However, it seems that they got it just right. The sound of the Roland ensemble became a distinguishing feature of the company's synthesizers, and although the exact nature of the circuitry changed over the years, the sound remained consistently desirable, and continues to be so nearly three decades later. JC120 Jazz Chorus guitar amp. Revo 30 Leslie simulation system. Revo 120 Leslie simulation system. Revo 250 Leslie simulation system. AP2 Phase II. AP7 Jet Phaser. RHYTHM MACHINES TR66 Rhythm Arranger. SH5 monosynth. Many of the new products shown were destined to be significant, although it was not always obvious at the time. This was the first amp to include dual amplifiers and a chorus effect, but I doubt anybody realised in 1975 that this was to become one of the most popular amplifiers of all time. Yet a classic it quickly became, and spawned a dynasty of 'JC' amplifiers that are still in production today. The sadly under-appreciated RS101 ensemble keyboard. It might have been a leap forward for keyboard-based string sounds, but the mid-'70s synth-buying market didn't notice. This was a nice ensemble keyboard that failed to cause much of a ripple upon its release. It offered independent Strings I, Strings II, and Brass presets either side of a keyboard split. Each side of the split offered a Tone control, and independent Slow Attack, variable Sustain and Volume Soft options, thus allowing you to play bi-timbrally. There was also vibrato but, more importantly, the RS101 marked the first appearance of what was soon become to Roland's trademark: its Ensemble effect. Furthermore, the RS101 offered individual VCAs and envelopes for each note, so it could articulate sounds correctly. Physically, it was compact and sturdy, and much lighter than the Solina, so it was also the more convenient of the two. Yet it sank almost without trace. Nearly 30 years later, I still don't understand why this happened, and I suspect that its designers felt the same way. That it sold in moderate quantities has added to its collectability, and the fact that it is undoubtedly the prettiest of Roland's early synths only helps in this regard.