Remote Access to the PXRR Macromolecular ...

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Remote Access to the PXRR Macromolecular Crystallography Facilities at the NSLS a

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Alexei S. Soares , Dieter K. Schneider , John M. Skinner , Matt Cowan , Rick Buono a

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, Howard H. Robinson , Annie Héroux , Mary Carlucci-Dayton , Anand Saxena &

Robert M. Sweet

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Biology Department , Brookhaven National Laboratory , Upton, NY, USA Published online: 26 Sep 2008.

To cite this article: Alexei S. Soares , Dieter K. Schneider , John M. Skinner , Matt Cowan , Rick Buono , Howard H. Robinson , Annie Héroux , Mary Carlucci-Dayton , Anand Saxena & Robert M. Sweet (2008) Remote Access to the PXRR Macromolecular Crystallography Facilities at the NSLS, Synchrotron Radiation News, 21:5, 17-23, DOI: 10.1080/08940880802406067 To link to this article: http://dx.doi.org/10.1080/08940880802406067

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Remote Access to the PXRR Macromolecular Crystallography Facilities at the NSLS ALEXEI S. SOARES, DIETER K. SCHNEIDER, JOHN M. SKINNER, MATT COWAN, RICK BUONO, HOWARD H. ROBINSON, ANNIE HÉROUX, MARY CARLUCCI-DAYTON, ANAND SAXENA, AND ROBERT M. SWEET

Downloaded by [Brookhaven National Lab] at 06:38 24 August 2015

Biology Department, Brookhaven National Laboratory, Upton, NY, USA

The most recent surge of innovations that have simplified and streamlined the process of determining macromolecular structures by crystallography owes much to the efforts of the structural genomics community. However, this was only the last step in a long evolution that saw the metamorphosis of crystallography from an heroic effort that involved years of dedication and skill into a straightforward measurement that is occasionally almost trivial [1]. Many of the steps in this remarkable odyssey involved reducing the physical labor that is demanded of experimenters in the field. Other steps reduced the technical expertise required for conducting those experiments. Remote access to crystallography resources advances both of these objectives. By obviating the need for travel to a synchrotron, and by reducing the burden of safety and technical training needed after arriving at the facility, remote access significantly reduces the activation barrier to determination of novel structures. This draws new participants into the X-ray crystallography community. In addition, the technical advances that allow remote access improve the experience for those scientists who visit synchrotrons to take their own data. The ability to have scientists conduct their work while separated from the apparatus in space (remote) or while separated in time (asynchronous) is a tribute to the work of the pioneering developers who continue to improve crystallography today. Remote access would be impractical without the assistance of physical tools such as reliable cryogenic automounters [2], and computational tools such as push-button data analysis, data reduction, and structure solving [3]. Cryogenic automounters began arriving at synchrotrons around the turn of the century, first in the United States [4,5] and Europe [6,7], and soon in Japan [8]. These devices were inspired by a prototype developed at the Abbott pharmaceutical company [9] in response to the needs of the nascent structural genomics community for cost-effective tools to advance structure-based drug design. Academic users welcomed this resource for screening a large number of crystals for diffraction quality, particularly in the membrane crystallography community. However, even in cases where the number of specimens is small enough that the efficiency improvement is negligible, an automounter can still prove helpful. Scientists who are not busy with the mundane tasks of specimen mounting can instead focus on analyzing

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their data and characterizing their specimens. Also, in cases where the data collection needs for an experiment are better served at a different X-ray station, the specimens can be safely moved in order to obtain the best possible data. Without a database to facilitate the movement of information and ideas between machines, operators, and scientists, remote access would be of little value. Fortunately, many groups (including ours) implemented integrated experiment-tracking database systems in parallel with the introduction of cryogenic automounters [10]. The rationale is that automounters are most useful when one is handling a large number

Figure 1: Histogram of the growth of the productivity of the Mail-In Program according to two widely accepted criteria: structure depositions into the protein data bank (PDB) and peer-reviewed articles (2008 data for first six months).

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of specimens, and the resulting super-abundance of data is best handled by a database. The protein crystallography database (PXDB) allows users and staff to access and manage organized information regarding their specimens, experiments and projects. The PXDB also serves as an access portal into PXRR capabilities such as beam-time requests, robot operations, and remote access. Remote and asynchronous participation are now maturing fields. The initial “vertical” push into new territory was accomplished early in this decade by multiple groups [11]. Recent developments are largely “horizontal.” Staff at synchrotron facilities around the world continue to work to reach more users, and in more ways, than ever before [12,13]. Successful programs developed at one institution are replicated elsewhere. From the user’s point of view, this means that an ever-increasing number of options are available to use X-ray resources. Mail-in crystallography The first remote participation option that was embraced by users of the protein crystallography research resource (PXRR) beamlines at the

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National Synchrotron Light Source (NSLS) was the Mail-In Program [14]. The appeal of this popular program is its flexibility. Some participating users are looking for a no-frills data collection service where they retain detailed control of the experiment. Other users defer control of experimental details to the expertise of the mail-in scientist. Still others invite the mail-in scientist to contribute beyond the structure determination, and deep into interpretation and evaluation efforts. In this way, mail-in constitutes a continuous soft boundary between conventional synchrotron visits and the ultimate expression of remote access where physical, technical, and even scientific tasks are outsourced to the data collection facility. The inherent flexibility with which each mail-in collaboration is tailored to the needs of the user is partly responsible for the popularity of the program. However, we have found that the fast turnaround and the low activation barrier to data collection motivates a paradigm shift that our clients find equally valuable. Users of the program begin to view the synchrotron facility as an extension of their own lab. Reducing the penalty for “failure” is one more step in the gradual transformation of the synchrotron visit from the hierarchical summit of a substantial

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effort (in which failure is a catastrophe) into a simple measurement with an overhead that is small enough that it can generate value even in highrisk, low-reward scenarios such as screening, space group determination, and initial characterization. The Mail-In Program also transformed our whole operation. Immediate benefits of the program to the PXRR include an increased flexibility of scheduling, the ability to use unexpected machine availability on short notice, a decreased need for training, and an inherent increase in safety. In the longer term, our group has found that mail-in provides the ideal platform upon which to test new initiatives and apply quality assurance. Each technology is road-tested by the mail-in scientists before handing the keys to the general user base. By continuously using our own facilities, we ensure that they are kept in optimum condition, and we quickly uncover problems before they become serious. The utility of the Mail-In Program is reflected in its popularity and productivity (Figure 1). We continue to be surprised by the resilience of the geometric growth phase of mail-in, as our forecasts of an eventual plateau fail to materialize. Similar programs continue to germinate and

grow around the world, and these also frequently report unanticipated large demand [15,16]. Given the user-defined flexibility of these mailin programs, this across-the-board popularity suggests that there exists a deep untapped well of demand for other forms of remote access. Conventional remote access The program offered by the PXRR for conventional remote access to its facilities at the NSLS is built upon the NX remote desktop. When a user requests remote access, he or she is walked through two prerequisite steps: (i) obtain a CRYPTOCard™ for authentication; and (ii) install and configure the NX client. Use of a CRYPTOCard™ virtually guarantees positive authentication, which is a requirement for remote access to Brookhaven National Laboratory (BNL). The installation and configuration of the NX client is done by a web-based utility. In most cases, the push-button installation should conclude normally with no need for additional support from our staff. However, in case of an anomaly, the user will be contacted by a member of our computer support group.

Figure 2: Push-button access to the NX desktop environment is a key feature of our conventional remote program. Once the desktop is active, all tools normally available onsite can be used.

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Once the NX client is operating properly, the remote user can log into our data-collection computer. Doing so invokes a virtual desktop that exactly mirrors the familiar version that the user may have experienced during a previous onsite visit. All of the capabilities that are normally available onsite can be run via the virtual desktop (Figure 2). If the user is disconnected for some reason, re-establishing the connection restores the original desktop, which will accurately reflect the up-todate status of data collection, or whatever other actions might have been in progress. A typical remote access experiment proceeds as follows: 1. The user requests beam time for remote access using the PXDB. 2. If this is the first remote visit, the user obtains a CRYPTOCard™ by mail, and uses our browser-based utility to install and configure the NX client. 3. The user may request to borrow robot tools and equipment for the proposed experiments. Instructions for robot-compatible specimen preparation are also available on the web as a streaming video. 4. The remote user receives a beam time assignment according to his or her needs, enters identification of the specimens into our online database, and forwards the sample dewar to the NSLS. 5. Our staff notifies the remote user when the specimens are loaded and the automounter is ready to go. The user is also given instructions for paging PXRR staff should the need arise.

Figure 3: The Q project combines existing productivity tools for screening and automatic crystal centering with a novel off-line feature to define the exposure point on the crystal and to queue one or more data collection plans. Participants use the simplified interface to review the results from automated screening, select an exposure point on their specimen, and choose a suitable data collection strategy. The actual experiment then proceeds automatically at a later time.


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6. The remote user establishes a connection to our data collection computer using NX. Once the NX desktop is active, the user can use all software on our local computers. This includes the Crystallography at Brookhaven Acquisition Software System (CBASS), crystal centering, adxv frame display, database experiment tracking, and data-reduction software. 7. When the remote user concludes the experiment, he/she can copy the data onto DVDs using our DVD-burning robots. The data are returned to the user along with the specimen dewar. If immediate access to the data is needed, reduced data can be downloaded by FTP. The technical and scientific staff of the PXRR must closely coordinate the support of the remote user. Our group first introduced the “PX operator” staff position as a way to provide near continuous support for the troubleshooting of common problems and for handling of typical offhour requests. The position has since evolved, and our expert operators now coordinate complex mechanical and administrative reconfigurations as needed to deal with emergencies or to take advantage of opportunities for improved science. This type of expertise and self-assurance is also critical to help bridge any confidence gap that may occur when novice users first access our facilities remotely. The remote-access program is fully commissioned and has been tested by our mail-in scientists conducting experiments from home. The program is new and consequently it has accommodated few general users. We have seen substantial interest in conventional remote services from some of our mail-in clients. This user group is accustomed to almost immediate results, which necessarily implies access to the kind of unscheduled beam time that has been so popular in the Mail-In Program. Since conventional remote access operates on a scheduled basis, we developed an asynchronous remote program in parallel to the conventional program. Asynchronous remote access and the “Q” project The minimal necessary set of instructions needed for automated collection of a data set is: (i) the coordinates used for specimen centering; (ii) the minimum crystal quality to merit data collection; and (iii) a plan for executing that data collection. The tools to perform steps (ii) and (iii) asynchronously were already in place at the PXRR when the “Q” project was conceived. The Q project introduces off-line crystal centering capability, and simplifies the overall process of asynchronous data collection by providing a single platform for users to submit seamlessly all information needed for their experiment to be carried out (Figure 3). The system relies on the C3D automated crystal centering software [17] that our group has adopted to identify the face-on (i.e. “flattest”) view of the crystal and to find a reproducible reference point in that view. This reference point is used to identify the coordinates of the user’s desired exposure point. Since the majority of Q projects will likely involve robotic crystal handling, a typical data collection visit partly mirrors the previously

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discussed sequence of events (steps 1, 3 and 7 would be similar). Notably, there is no need for authentication or installation of new software since the Q project interface is entirely web-browser based (although the NX desktop still delivers an increase in utility for tasks such as data reduction and backup). When the user’s specimens arrive, they are automatically cycled through the facility for preliminary screening. During this cycling, the face-on view of each user specimen is identified, a photo of each crystal is saved to our database, and diffraction data adequate for specimen characterization is presented. The user is notified by e-mail when screening and pictures of his crystals are available for inspection. For each picture, the user selects an exposure point and enters a data-collection strategy. The next available slot of uptime is then used to perform the user’s desired experiment automatically. The big picture The intent of the suite of PXRR remote-access programs is to provide our users with an assembly of productivity tools that are as diverse as possible in terms of their capabilities, while being as similar as possible in terms of the interface and mechanics used to access them. Each of our programs can alternately serve as a favorite warhorse that experienced crystallographers use to optimize productivity, or as an occasional shortcut used by multi-project groups with diverse needs. However, our group’s most sublime mission is fulfilled when our programs serve as a “low activation barrier” enticement to attract an entirely new member into the X-ray crystallography community. In all cases, our staff is happy to don whatever hat best serves the requirements of each unique project. Our experience with mail-in has taught us that our users much prefer to customize our programs to fit their needs, rather than having to package their experiments to conform to our expectations. Using an NX remote desktop, users will seamlessly transition between mail-in, conventional remote, and asynchronous remote. In all of our programs, we continue to strive for unity of form while maximizing diversity of function. Acknowledgments Financial support for this work, performed within Brookhaven National Laboratory’s Biology Department and the NSLS, comes principally from the Offices of Biological and Environmental Research and of Basic Energy Sciences within the U.S. Department of Energy, and from the National Center for Research Resources of the National Institutes of Health. Use of the NSLS is supported by the U.S. Department of Energy’s Office of Basic Energy Sciences under contract number DE-AC02-98CH10886. References 1. Z. Dauter, Current state and prospects of macromolecular crystallography, Acta Cryst. D62, 1–11 (2006). 2. E. Abola, P. Kuhn, T. Earnest, and R.C. Stevens, Automation of X-ray crystallography, Nature Struc. Biol., structural genomics supplement, 973–977 (2000). 3. V.S. Lamzin and A. Perrakis, Current state of automated crystallographic data analysis, Nature Struc. Biol., structural genomics supplement, 978–981 (2000).



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