• RSS
  • Facebook
  • Twitter
  • Linkedin
Home > Error In > Error In Detector Gain Mosflm

Error In Detector Gain Mosflm


If integration proceeds smoothly but postchk does not, try using dps_refine or mosflm refinement, or skip refinement entirely. Transfer them to the "Beam X" and "Beam Y" fields in the "Processing params" area of the mosflm display, and also to the "X Beam" and "Y Beam" fields in the Crystallization and data collectionCrystals of insulin, lysozyme and thaumatin were grown and cryoprotected as summarized in Table 1 ▶ and described pre­viously (Nanao et al., 2005 ▶). Set the starting and ending image numbers to include 10-20 frames.

At finer rotation angles, when more images contribute to spot intensities and the spot is better sampled along ϕ, spot centroids can be determined more accurately (Kabsch, 2010a ▶). If "Done." does not appear, something went wrong. Other general parameters are shown, and can be changed, in the windows which you can pop up using the buttons at the top right (5). If this doesn't work it is probably best to screen your crystals carefully and next time collect data on a crystal that isn't twinned.

Mosflm Download

The "Refine cell" procedure allows you do define a separate orientation matrix for each segment of images. SDfac accounts for noise proportional to the square root of intensity, and only shot noise (like photon counting) behaves like that. It may also be necessary to keep the cell fixed if only a small range of spindle angle is covered by the frames, particularly if symmetry is low.

Rossmann & E. Data acquired using CCD detectors are affected by both detector noise and potential shutter jitter, which restricts the applicability of fine-slicing (Pflugrath, 1999 ▶). A peak intensity P is composed of the reflection intensity I and its background B. Mosflm Indexing To do this click on "Read image" and then type 90.

The blank, grey image displayed for the first image when a New Session is started has been fixed. Mosflm Tutorial The system returned: (22) Invalid argument The remote host or network may be down. For more detailed information, examine the log file, by scrolling back in the window or using an editor or xloggraph. Thus if, for example, the program has generated reflections from phi=10 to phi=100 then it not possible to try: START 0 END 30 GO or ROTATE 100 at the STRATEGY prompt

This must be consistent with the phi values used during indexing! Mosflm Reference corrections have already been done; assumes 16-bit unsigned integer pixel values on a linear scale) Clicking "Show Detector Parameters" posts a window containing information about the current detector: number of pixels e.g. The state of this checkbutton (and that for 'Automatically index after spot finding') are saved to the user's profile between runs.

Mosflm Tutorial

Other data-collection parameters such as flux and exposure time, which can be optimized to take detector characteristics such as count-rate limitation or read­out time into account, are the subject of separate Adjust if necessary in the parameter list on the left side of the window and try "Autoindex" again. Mosflm Download Postrefinement for fine-phi slicing (POSTREF MULTI) has been improved and is now the default. Mosflm Show Resolution Rings A possible explanation for this observation is that summing the finest-sliced images results in poorer diffraction data, but the reflection intensities can be estimated more accurately by the integration software from

You also need to set your own highest resolution with the RESOLUTION command, and set your images and phi angle (ANGLE) on the PROCESS line. If one number is given, the starting phi is calculated from the image number, assuming that all images have the same delta phi, there are no discontinuities in the sequence of Click on "Scaling:DPS" to bring up the "Scaling Parameters" window. If this is a good image and the program is using the correct distance, wavelength, and direct beam position, a good solution can generally be obtained. Mosflm Citation

  1. To save them to a new parameter file, enter a new name in "Parameter File" and click "SAVE".
  2. Strategy Run the strategy option.
  3. If you know the unit cell very well and it differs slightly from the one determined by indexing, you can force a change by entering the desired cell in the "Cell
  4. or RAXIS (for RAXIS II) or DIP2000 etc If not processing Mar Research, ADSC, R-axis or Mac Science images: => WAVE 0.91 !
  5. The 'View' menu has been renamed 'Settings' in the main iMosflm interface window.
  6. This file can be input to xloggraph for graphical representation.(Ascii) 4) When running interactively, all output written to the terminal window is also written to the file "mosflm.lp". (Ascii) Temporary Files
  7. D62, 867–876. [PubMed]Dauter, Z. (2010).
  8. Therefore, the different results obtained with two sets of parameters cannot be attributed to a single parameter but originate from a combination of several parameters.
  9. Other per-image-based errors may arise from the crystal goniometer and the X-ray shutter.

Obviously, fine-slicing reduces the problem of overlapping reflections from intersecting lunes. the difference between the widest-sliced data set and the best fine-sliced data set of a series can be in the range 20–80%. Differences are all relative to one lattice, which will display a split angle as "-". As long as the "Peaks" toggle button is on, new peaks will be automatically calculated whenever a new frame is loaded.

Details for the three refinement options are given below. Ccp4i Single or multiple frames may be used. Cryst. 30, 1036-1040) or Wolfgang Kabsch's REFIX program (Kabsch, 1988, 1993) both of which have been incorporated into the MOSFLM program.

improved command line autoindexing (AUTOINDEX DPS) and mosaicity estimation (MOSAIC ESTIMATE).

If box location is correct, answer "y" to the question. I/σ(I) and R ...Three-dimensional reflection profiles are represented in XDS on a grid in a coordinate system specific for each reflection. For indexing, and initial refinement, you will probably use only a subset of the complete set of frames (as specified in the indexing and refinement windows); "sequence" gives the range that Pdb Maximum length of command line increased to 400 characters.

Accuracy of intensity estimatesThe aim of a diffraction experiment is to accurately determine the intensities of Bragg reflections. The output directory can now be specified so that it does not have to be in the same directory as that in which Mosflm is started. Additionally, the negative sign is no longer lost when editing a negative missetting angle value by clicking a highlighted line in the Images browser. The wide rotation range leads to a smaller number of images for a complete data set that need to be read out from the detector, stored and processed.

Integration proceeds in exactly the same way as when integrating a single lattice, except that for overlapping reflections (from different lattices) the total intensity of all the reflections is measured. M. & Ravelli, R. Bad spots identified during processing and whose numbers are plotted during integration can now be displayed in the Image display window. Current values are displayed in the "Machine Parameters" window.

For Mar Research, ADSC, R-AxisIV and Mac Science detectors the wavelength and distance will automatically be taken from the header records in the image file, for other types of image the See the help library (Subsection Novel detectors of DETECTOR) for details on how to do this. Position and size of beam stop shadow, specified in "Machine Parameters".