The Facility's equipment presently consists of one Enraf-Nonius CAD4 diffractometer, one 486DX2-66/VLB (hostname: lonsdale.chem.ncsu.edu) for diffractometer control, one P5-60/PCI (hostname: laue.chem.ncsu.edu) for crystallographic computing and other Facility duties and an HP LaserJet 4M+ for it's printing needs. The Facility also has a stereomicroscope for manipulating and mounting samples. The Facility posseses 2 metal and 1 plastic goniometer heads which are suitable for mounting samples on the CAD4 diffractometer.
With this equipment the vision for the Facility which I presented last Fall has been largely realized. On the whole the equipment is working well with the exception of generator problems which are probably related to the cooling system of the diffractometer as outlined below. In order to make more regular and rigorous back-ups, I will need to upgrade laue. This will be discussed in the hardware upgrade section of the report.
Synopsis of Generator failures.
14 May - generator down; restart ok
22 May - generator down; restart ok
5 Jun - generator down; restart ok
12 Jun - generator down; restart ok
23 Jul - generator down; needed to pull tube and clean screen,
filter changed, re-align instrument
7 Aug - generator down; restart ok
8 Aug - generator down; restart ok
10 Aug - generator down; restart ok
11 Aug - generator down; restart ok
21 Aug - generator down; restart ok
22 Aug - generator down; restart ok
23 Aug - generator down; restart ok
24 Aug - generator down; restart ok
25 Aug - generator down; needed a couple of tries restarted ok
27 Aug - generator down; restart ok
29 Aug - Nonius service person changes the amplifier in generator
30 Aug - generator kicked out when turning down mA, restart ok
18 Sep - generator down; needed to pull tube and clean screen,
filter changed, re-align instrument
27 Sep - generator down; needed to pull tube and clean screen,
filter changed, re-align instrument
28 Sep - generator down; needed to pull tube and clean screen,
re-align instrument
I think the problem with the generator failing comes from the fact that we are using tap water to cool the X-ray tube. This is contrary to the recommedation of the vendor. It is likely that we will continue to have problems of this nature until a chiller is installed for the generators. It will be interesting to see if the second diffractometer will have these problems also.
Statistics of Samples Submitted and Structures Solved
There have been approximately 42 - 45 samples submitted since I started working at NCSU. This number is approximate because when I first began I went to UNC-CH several times to run samples there. Some of these resulted in structures and some did not. For the first couple initial samples, I did not keep track of those which did not yield structure determinations. The following statistics are for the samples which are documented and/or billed by the Facility.
Notes
Samples submitted 42
Complete structure determinations 14
Unit cell determinations only 6 (a)
Data Collection only 3 (b)
Partial structures pending 2
Samples in queue at present 1
Unsuitable samples (no diffraction, multiple xtals, etc.) 16
(a) Some of these were submitted as structure determinations, but were
then aborted either because the cell matched a known compound, or the
crystal did not diffract out to high enough angle to make structure
solution a likely event had the analysis continued.
(b) - this is includes dataset for sample x95008. This was a partial
structure determination. A complete structure determination of this
compound was completed based data collected on a different crystal
(sample x95026). No charge for x95008, full charge for x95026.
Financial Status of Facility
Here is the current rate schedule for the Facility:
Current Rates for X-ray Structure Determination Single Crystal Structure Determination $350. Data Collection Only $250. Cell Determination Only $ 30. Liquid N2 costs (1/2 tank increments) at cost Single Crystal Structure Determination (external) $700.Here is a summary of the Facility finances:
(A) Expenditures for fiscal year 1995: $ 10,384.43 (B) "Facility Contribution" to buy used CAD4: $ 7,311.22 (C) "Actual" Facility Expenses for FY 1995: C = A - B $ 3,073.21According to Ken Hanck, the Facility operating costs for FY95 have been absorbed by the department. The only charges to be levied against the user charges (see below) are those incurred from 1 July 1995 onwards.
(D) Expenditures to date for fiscal year 1996 $ 171.94
(includes both FA109 and CS109 accounts)
(E) Invoices for X-ray Facility $ 4,880.00
(F) Invoices processed by accounting $ 1,900.00
(G) Pending G = E - F $ 2,980.00
(H) Total Net Debt or Credit H = E - D $ +4,708.06
I will bring copies of the report I received from Ken Hanck to the meeting
of anyone would like to have a more detailed look at the statements. The
invoices are for all the work I have done since last Winter, however, the
X-ray Trust fund was not set up until 1 July 95 and the billing was not
performed until FY96.
In the past year we did not have the usage which would enable the the Facility to be financially self-sufficent. According to the budget submitted as part of the NSF proposal, the Facilty needs to be completing about 60 structure determinations per year to be financially self-sufficent. I would appreciate some discussion during the meeting as to how this goal could be met.
Facility Renonvation
I spoke with Ken Hanck about the Facility renovation on 19 Oct; the following is a summary of what he said. The revised plans are back from the designers. Copies of these plans are being sent to the department and to University construction. Contractors could be walking through 737 with plans in hand as early as the end of next week (27 Oct). Bids should be received by the end of the first full week of November (Nov 10). Demolition and construction work should begin shortly after that. Ken stated that the Facility renovation should be done by 15 Jan. 96. According to an agreement with Enraf-Nonius the CAD4-MACH is to be delivered by 31 Dec 95. Given these time frames, it is likely that the CAD4-MACH will sit in Central Stores for a couple of weeks. After the renovation actually begins it should be possible to work out installation plans in greater detail. I would like for the old CAD4 to be moved and re-installed by Nonius personnel at the same time that the CAD4-MACH is being installed. Logistically, I think it will be easier to do this than to have to schedule two appointments for Nonius service people to come here.
Hardware/Software Upgrades
Hardware
Workstation
The largest hardware upgrade planned for the Facility is to use equipment grant money to purchase a RISC based workstation. At this point, I am considering either a Silicon Graphics (SGI) R4x00 based system or a Digital Equipment Corporation (DEC) Alpha system. Several of you have expressed interest in using the Facility computers for molecular modelling calculations. If any of you are still interested in this, I would appreciate it if you could bring the name of the software package and information about the vendor to the meeting. There are a number of technical and financial issues I am considering for this purchase and I am willing to bring non-crystallographic, but related software needs into the equation.
laue.chem.ncsu.edu
I am planning on upgrading laue's hardware to increase the disk space and add a CD-ROM and a tape back-up. The list of items would be a PCI based SCSI card, 4xCD-ROM (SCSI), 2 GB drive (SCSI) and tape back-up (SCSI). I was originally planning to implement a back up scheme using the university AFS realm, however, getting the 40 or 50 MB of hard drive space doesn't appear practical at this point. In lieu of this, I would like to institute a local back-up scheme using additional disk space and a tape drive. Cost estimate: $ 2000.
lonsdale.chem.ncsu.edu
The monitor originally supplied with the computer is not of high enough quality to display an X-windows graphical enivironment. I am planning to upgrade to a monitor which has proper specifications for this task. A ViewSonic 15 (15" monitor) should be sufficent to accomplish this. Cost estimate: $ 400.
Other Hardware
There are several other pieces of equipment which need to purchased or replaced. The first of which is the purchase of polarizing microscope. This piece of equipment was itemized in the NSF grant. I am working with a Nikon sales person in putting a system together for the Facility. The Facility needs also a new stereo-microscope as the one we have now is old and tends to defocus due to slippage in the focusing gears. The Facility should also have a refridgerator for temperature sensitive materials. The Facility should also have 3 or 4 more goniometer heads. When working with several crystals of the same compound it is desirable to have a number of goniometer heads available. If a crystal is removed from a goniometer head after it's orientation matrix has been determined, the martix is lost. Having to redetermine the orientation matrix for a crystal after taking it off and putting it back on is very inefficent. This problem will just get worse after the second diffractometer arrives. Cost estimate for stereo-microscope, refridgerator and 4 goniometer heads: $ 3000
Software
I have recently purchased the update to the Cambridge Database. It should be arriving shortly. At present we are using the VAX/VMS version on one of M. Whangbo's computers. After the upgrading the Facility's hardware, I will be moving the Database into the Facility and changing over to the UNIX version of the database. The US representatives of CSD have agreed to send the UNIX version for free when that time comes.
Within the next month I am planning to do a major upgrade of the operating systems for laue and lonsdale. There are several reasons for this. First, there have been enough improvements in the networking code as well as other aspects of the operating system to make it worthwhile to do so. Second, according to Dr. Willis (Associate Provost for Academic Computing) there is now official university level support for the Linux operating system. It makes sense to for me to upgrade to the particular Linux distribution which NCSU is supporting. Third, a couple commercial implementations of OpenGL are now available for Linux. Putting this software on the Facilty's PC's will allow them to display advanced graphical output of applications running on the future Facility SGI or DEC Alpha.
Points for Discussion
The following several points are topics I would like the Committee to discuss and give feed back to me.
New Output Format
Several of you have asked about a different standard result format. At least one of you feels that the present format is contains too much information, while a couple of you do not like the accordian file folders used to organize the output. After thinking about this for a while, the idea I find most attractive is to present the result in a HyperText format (i.e. readable from a Web browser). The first point to make is that the results would be password protected. After clicking on the link you will be prompted for a passwd (which I will give you personally). After the passwd is successfully validated, there will be an index page which contains links to the following pages: Experimental page, Summary of Crystal Data, atomic coordinates, table of displacement parameters (thermal parameters), bond angles, torsion angles (if appicable), best plane calculations (if relevant) and a final Fobs / Fcalc table. The graphical output will be available in the form of both in line GIF files as well as PostScript files.
The most appealing aspect of this is that the crystallographic output can be cut and pasted directly from the HyperText form into a word processor document. Also, the researcher can also just select to print the Web page if a hardcopy is desired. Most errors in reporting crystallographic results are typographical in nature. This method would eliminate that source of error as well as eliminating the tedium of preparing tables of crystallographic results.
At present I have the software on hand which converts a variety of graphical format to one another. Using this, I have produced GIFs from PostScript files. The image quality is adequate for a Web page, but is inferior on printing. For this reason, I propose to distribute laser printed hardcopies of the PostScript files as well as softcopies of the the PostScript files.
I am currently working on a mock-up of what the results will look like in this format. It should be done by the middle of next week. I will inform you as to where to point your Web browsers to examine this new output format.
Statement of Policy for Facility
Over the past summer there was a discussion/disagreement bewteen Chuck and Jim and myself as to how samples should be prioritized in the queue. The subsequent up shot of this discussion was that I should put together a statement of policy for the X-ray Facility. I have hesitated doing this because after the discussion it seemed to me to be a better idea to either wait and see if the problem became recurrent issue or wait for the Committee to meet and discuss it. The central issue of last summer was does the Facility Director have the ability to commit to getting an outside sample done within a given time period when the queue doesn't have anyone else on it. This then opens up a more general discussion of what degree of flexibility should the X-ray queue have. At present, I do not see this as pressing issue because the diffractometer is running far below capacity. However, I would welcome comments of the Committee members. For food for thought, there are several policy statements from service crystallography facilities available from the Web. I urge the Committee members to take a look at the following hypertext documents to get a feel for what other facilities are doing: Indiana University Molecular Structure Center, Michigan State University and McMaster Unversity . I presented my own opinion on queue management at the Committee meeting last Fall. To reiterate briefly, the queue should be generally first come first serve with exceptions being made to accomodate special needs (e.g. chemical instability, someone needing a result for a poster in the very near future, etc.) Note that not all special needs are equal. Another consideration is to make the most efficent use of instrument time.
I don't to get into a position where several different, conflicting "precedences" are at work and I am have to follow some rote "formula" to resolve the conflict. I think the Director should have sufficent lattitude and flexibility to make queueing decisions which make the best use of instrument time, provide good service and accomodate special needs.
I would appreciate your comments on the issue of policy for the Facility as well as comments on other parts of this report.