Computational Needs and Resources in Crystallography Proceedings of a Symposium, Albuquerque, New Mexico, April 8, 1972. (1973) / Chapter Skim
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What are the Needs of Crystallographers?
What are the Needs of Crystallographers?
Pages 17-46
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From page 17... ...
Session I What Are the Needs of Crystallographers? Session Chairman: Philip Coppens 17
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In outlining computational needs, I will comment also on the operation of the Vogelback Computing Center at Northwestern University. In my position as Chairman of the University Computing Committee over the past four or so years, I have gained some insight into the support problems of a large computer in a private educational institution and I hope information on this subject will be of interest to others.
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Those familiar with our work know that without triphenylphosphine as a ligand to stabilize a transition metal in a low-valence state, we would feel very lost indeed. In this respect our computational needs may not be typical of structural chemists; even with the theoretical dodges we use, such as treating the phenyl rings as rigid groups, our problems tend to be large by ordinary standards.
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Over the years we, at Northwestern University, have devised various schemes for the distribution of soft money, one in particular is this: If Professor X brings in large amounts of hard money, he is rewarded with similar amounts of soft money, and the reward is on a graduated scale. This procedure has worked very well.
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I return to this point later. Hard money: $15 000 Soft money: $30 000 Loss to university computing center if CDC 7600 is used off campus: $10 000 Figure 4 Payment for Crystallographic Computations Figure 5 presents a rough breakdown of the sources of support for our computing center.
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Administrative processing should remain separate 3. Additions to hardware are necessary to handle many of the tasks (expanded core storage, expanded discs, additional printer and plotter, at a total cost of about $500 000)
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We have recently been performing remote calculations on the CDC 7600 at Lawrence Berkeley Laboratory. Transmission to and from the 7600 is done over telephone lines through the 200 User's Terminal at our Computer Center.
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Difficulty of tape and disk storage 5. Government bureaucracy Figure 9 Problems in Remote Computation On the basis of this limited test I am pleased with the results and am optimistic that remote computing on problems too large or too expensive to handle locally will become commonplace among crystallographers.
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But should we get heavily involved in computer-aided instruction, then money will not be spent at the computer center but will possibly buy renote terminals for a tie-in with the Plato system at Illinois. In any event, I too have been around the computer game for many years, and know your worries when you imply that estimates on computer usage always fall short.
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From page 26... ...
Sayre: You have indicated that crystallographers may often want to turn to special off-campus machines for their large number-crunching computations. You have pointed out two associated problems, that of data transmission and that of administrative complexity.
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considers only operating costs in arriving at an hourly charge. They do not consider amortization or the initial expense of buying the machine.
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We have a Bell Telephone Data Set which modulates and demodulates digital data to go over the analog common carrier. It operates over a public dial-switched network and allows a maximum transmission rate of 2000 bits per second.
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Buffer Storage: 256-Character capacity - Two 128-character core memory buffers Translation Capabilities: Card Code/Transmission Code, Hollerith/ ASC-II, Hollerith/XS-3 (DLT compatible) Special Features - Error detection and retransmission, telephone alert, select character capability, short block capability, peripheral Input/Output channel, unattended operation 29
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One company gave us a private line to encourage us to dedicate all our computing to them. Our intensity data are collected on magnetic tape and sent via mail or messenger service to the computer center.
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The unreliability of the telephone lines causes us to be disconnected about twice in an eight hour period. Appraisal of Remote Terminals In general we are satisfied with our computing system, with some reservations which I shall outline.
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The public telephone lines are not reliable and as a result the transmission rates are slowed. The telephone rates are high for long distance calls.
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We do overnight computing but it really doesn't save us much. Dewar: In my experience these terrible troubles about telephone lines are confined to the east coast in general, or non-Bell Telephone areas.
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We had a lot of trouble with telephone lines there too, and this was card input-output. It was very difficult, and this indicates something about distance transmission.
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Suddath: Our 370 is tied with Harvard by microwave and my understanding is that it's working out quite well, very high transmission rates. Berman: Just using the leased telephone line makes all the difference in the world.
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Berman: If we had done that, it would have dedicated us to one computer center, and we haven't yet found the computer center we are willing to make that dedication to. Meyer: There are several commercial firms that plan within the next few years to blanket the country with data transmission networks.
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calculated using these phases and fitted by some model giving approximate atomic positions usually is the final step in the structure determination. This is so for a number of reasons, including the difficulty of obtaining good higher-resolution data and the limitations of present-day computers.
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However, the most demanding use of computers in the near future is going to be in the refinement of protein structures to produce much more accurate models. Since the phased data in even a "high resolution" protein structure do not approach the precision required to resolve individual atomic positions, the current protein models are poor by regular crystallographic standards.
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From page 39... ...
However, it must be noted that refinement of a model by electron-density maps has several disadvantages when errors exist in the data or when atoms are not resolved. Computer requirements for this type of refinement are not particularly large, but the model produced would be considered only a reasonable starting model for refinement according to regular crystallographic standards.
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From page 40... ...
Also, it is a good structure on which to test protein refinement because of its relatively small sizg and because significantly observable data exist to a resolution of 1.5 A (approximately atomic resolution)
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Therefore the matrix was partitioned into blocks of about 240 parameters associated with neighboring atoms and requiring 10 passes through the computer to complete one full cycle of refinement. One cycle of refinement requires approximately 17 hours of central processor time and costs about $5400 to $6000 as compared with about $600 and a week of hard work for AF refinement.
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From page 42... ...
New methods of least-squares refinement are required that take into account the overlap of electron densities of neighboring atoms and allow more nearly diagonalized matrices, so as to increase speed and efficiency of refinement. However, in final analysis, the dynamic growth of protein crystallography is dependent on the increasing availability of larger and higher-speed computers.
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1972. A rapid data acquisition system for protein crystallography.
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From page 44... ...
Watenpaugh: In starting out, for example, we've used the X-ray system designed for people who are solving lots of different structures and lots of different space groups, but when we come to protein structures we're going to spend a significant amount of time on refinement so that it will be very important that we optimize the system for a particular space group and a particular protein. Stewart: People tend to refer to this X-ray system as being mine.
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The amount required for the solution of protein structures has been small, and this is about where protein people have stopped. However, as more proteins are going to be refined, you're going to see an astronomical increase in the amount of computing time on the part of protein crystallographers.
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From page 46... ...
Being members of the University of California, perhaps we might have a better chance. Jeffrey: I seem to remember a paper where someone related differential synthesis to a diagonal matrix refinement.
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