be JO Bi. wh 17 October 1987 Prof. Guiseppe Zaccai Institut Max Von Laue - Paul Langevin 156 X Centre de Tri 38042 Grenoble Cedex France Dear Joe, To help in interpreting the fourier maps, I have enclosed the following extracts from my research notebook: RAW DATA Each map indicates where the helix centers were taken for subsequent calculations. Notice that the origin is at the upper left hand corner, and that coordinates are measured in cm. The last page documents the conversion to Angstroms and summarizes the data. OVERALL RAW COORDINATES Summary of the raw data. X,Y AXIS PROJECTIONS I've included the x, and y projections of the computed helix centers for helices 2 and 3. The lines that are drawn between the points represent a least squares fit of all points. Doing this calculation with helix 2 results in a line that seems to fit well. For some reason, however, (despite the fact that the exact same computational procedure is followed), helix 3 doesn't fit as well by eye. The m (slope), r (correlation coefficient) and b (y-intercept) are given. 2-AKIS PROJECTIONS The projection of the helix axes is shown by arrows starting from inside the membrane to outside. Allhelices follow the expected tilts. Notice the slight tilts of the inner three helices, and their seemingly closely packed disposition: COORDINATE TRANSFORMATIONS Here I document the calculations that translate the Baldwin axes onto the helices that are described by the original HEPNN axes. In other words, I compute the overall center for both the Baldwin and HEPNN axes, and translate the overall Baldwin center to the overall HEPNN center. I then apply this translation to all other points in the Baldwin axes. 6. LEFT-HANDED COORDINATE SYSTEM Shows the final CTL file (HEPNN_10.CTL) and the relationships between the left-handed and right- handed coordinate systems. 7. SOME PROGRAMS For your convenience, I've included some of the programs that are used to compute structure factors (differences, scaling, phases, etc.) and the fourier maps. I hope this information is helpful. Once again, if there are any questions, please don't hesitate to give me a call at (212) 694-5620. Let me know of the latest status of the next BR experiments; when will we conduct them?, what are the caveats that the Approval Committee noted?, how can we resolve these?, etc. With reference to these, I'll check with some contacts here, as well as do some more detailed literature review. Best of luck at your analysis of the data using the fourier maps; I hope that the R-factor searches are going well. Sincerely, ogan Gurel Columbia University College of Physicians & Surgeons 630 West 168th Street Box 535 New York, NY 10032va To 2.wA 24 November 1987 Prof. Guiseppe Zaccai Institut Max Von Laue - Paul Langevin 156 X Centre de Tri 38042 Grenoble Cedex France Dear Joe, Thanks very much for your recent letter which clarified some of the conceptual and practical subtleties involved in even the most simple of statistical analyses. I will generate a new set of helix models using the revised data you have sent. Hopefully, I'll get a chance to do some of the model building during the Christmas recess; I'll be sure to keep you up-to-date on any interesting observations. With respect to the I of Tyr experiment, it is probably most practicable to do the biochemical preparations and characterizations in Grenoble. Firstly, continuous communication would be easier, and secondly it may be difficult to integrate into a lab here where experiments with BR are not ongoing. I would be glad to work on the samples in Grenoble. My schedule allows for a Spring vacation beginning on Saturday, 26 May 1988 thru Sunday, 3 April 1988. In addition, it should be possible to stay in Grenoble during the following week (up until the 10th of April) should that be necessary. As part of the advanced biochemistry seminar I am taking here, I am preparing a review paper on the structure of bacteriorhodopsin. I will send both you and Jean-Luc a copy sometime during the latter part of December. Thanks again for your letter. Looking forward to hearing from you regarding the model front. Sincerely, Ogan Gurel Columbia University College of Physicians & Surgeons 630 West 168th Street Box 535 New York, NY 10032