IVE Problems and Limitations

The known problems have been categorized by application; those which apply to many applications can be found in the general category. This document covers IVE 3.3. For IVE 4, consult http://msg.ucsf.edu/IVE/IVE4_HTML/Limitations.html

General Problems

Priism does not clean up properly if you log out or the X server dies while Priism is running. Use of ivekill (see the answer to question 7 in the IVE 3.3 FAQ) can complete the cleanup job.
A Priism session that did not terminate cleanly can prevent image windows from working when Priism is restarted. A workaround is to exit Priism, run ivekill (see the references for the problem above), and restart.
The HTML-based help system assumes that Netscape is installed and can be run from the command line with a -remote option. If this is not the case, you can use the old-style help viewer (this can be set from the Help menu on the Priism menu bar) so that help buttons in applications will work. The documentation in the HTML directory of the Priism distribution can, of course, be viewed on its own in an HTML browser of your choice. Also, the HTML-based help response is slow.
Copy Region and other applications based on the same platform have the option when writing to append their output to an existing file as additional wavelengths. If the existing file has an extended header, it is not modified; this may confuse applications which process the results.
Applications which have the option of writing to a scratch window can crash with the following sequence of operations: write to the scratch window, close the scratch window from the window's menu, and have the application write to it again.
The layout of directories and files in the Priism distribution is not compatible with those for an application in /opt according to the Filesystem Hierarchy Standard.
Some documentation, not directly related to deconvolution, references the deconvolution documentation which is not included with the publicly distributed version.
(IRIX only) When a value is entered into a field and the next action is to click on an adjacent menu, if the new entry causes an error dialog to be displayed, the system becomes unresponsive to most keyboard input or the mouse buttons (the mouse pointer will still move). Pressing the escape key or the enter key on the numeric keypad usually works to make the system responsive. Logging in remotely and killing the offending application also works. It is reported that the system will become responsive without intervention after a long delay (tens of minutes); if that is too long, pressing the ctrl-shift-f12-numeric key pad / keys simultaneously will force the X server to restart (the side effect of this is that all the X applications attached to that server will exit).

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Image Windows

The effect of different offsets for different waves (i.e. as set with the Align program) is not taken into account when drawing graphics on top of the images (except for object library graphics which are used by Clouds).
The section number display in the lower left of the image is not properly cleared if it is longer or taller than the image itself.
When a scratch window is not full, it is possible to step past the end of the sections that have been used so far.
If an application is interested in mouse events from an image window and the mouse pointer is in the image window when the application starts, the application may not notice changes due to the mouse until the pointer leaves and reenters the image window.
Applications are not notified when the monitor window changes size. So if they have graphics which are drawn in window coordinates (rather than the coordinates for the image data), they will be not be able to update their graphics are not able to update their graphics appropriately (this affects picking regions in EMRECON).
(IRIX only) When Priism is used simultaneously with an application that uses a 12-bit color-indexed visual, colormap flashing occurs. Examples of such applications include showcase, snapshot, and jot from SGI and Chimera from UCSF's Computer Graphics Laboratory. If may be possible to avoid the colormap flashing if the other application's uses colors from the first 1000 entries in the 12-bit color table. If this is the case (as it is with showcase, snapshot and jot), then setting the environment variable, IVE_FAST_GREYSCALE, to no before Priism is started will help (at the expense of drawing speed for greyscale images). If the other application uses the full 12-bit color table (this is true for Chimera), then colormap flashing is unavoidable with IVE 3.3.
(IRIX only) Copying an image from an image window into showcase with the image gizmo frequently just grabs a black image or an image of a different section (the Priism window is double-buffered and showcase may be reading from the wrong buffer). Forcing a redraw of the image window, which is possible by selecting the Redraw option in the image window's Image menu, can cause Showcase to grab the correct image. For an alternative to the image gizmo, SGI's mediarecorder is recommended; it reliably captures images from image windows.

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Processing Applications

The convolution, Filter 2D, and Filter 3D applications do not work with complex data.
CCDCor and Convolution are missing documentation in the old-style format.
CCDCor assumes a maximum image size of 1024 x 1024.
CTFPlot is missing documentation.
The bead alignment and EMRECON user interfaces occasionally die because of X window errors when parameter subdialogs are displayed or hidden.
In EMRECON, if Massnorm's IprmFile is not set then can not find a parameter file for X/Y region selection.
EMRECON's Massnorm user interface has a new option to turn on and off the identification of jumps in the background intensity. That option has not been implemented yet in the backend which always tries to identify and fit jumps.
The documentation for EMRECON's Massnorm does not describe the sigma parameter.
The local contrast enhancement application will crash if the z field is modified and no input file has been specified.
The elliptically-weighted backprojection in EMRECON only handles tilt series with widths up to 16384.
For simplex, the extended header on the output is likely not correct if the input wavelengths are drawn from multiple files or if there is one input file and the wavelengths are reordered.

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Modeling Applications

In 3D Model, connecting a branch point in one object to a branch point in another causes parts of the objects to be lost.
In 3D Model, an attempt to connect an object to itself causes an infinite loop.
In 3D Model, deleting an object or point list does not update the graphics shown in image windows.
In 3D Model, dots added with the "just dots" option are not visible unless lighting is on and the background is not black.
If EditPolygon is instructed to load a file that is not in the standard polygon format (for instance, an image file) then it complains about the file having the incorrect format but dies anyways.
Closing FindPoints via the window manager controls does not cause the graphics generated by FindPoints to be removed from image windows.
Pick Points watches for presses of the tab key in the image window to change the current picking mode, but Motif uses the tab key to transfer focus from one dialog control to another.
In Region Growing or Find Points, if region growing results for the mask or masked input are only generated for a subset of the input z, time, or wavelength values, then the extended header of the generated data is not appropriately shuffled.
Using the Region Growing application on a subset of the input data has a number of problems (processing the full data set is ok): the masked input data that is generated is incorrect, a mask that is written will have the same size as the input data, the z and time step values are present in the interface but are not used, and the origin and time start values in the header of the output are not updated appropriately.
Tracer only works with image windows.
With a synthetic test case (an image with two greylevels), Tracer and 3D Model's automodel did not perform because an early termination condition in the search is sensitive to round-off error.

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Other Applications

View File and Volume Viewer are missing documentation in the old-style format.
EMACT occasionally hangs (typically because eminfo, the application responsible for maintaining the EMACT Information window, crashes); the apparent cause is a race condition but its source has not been The problem occurs much more frequently on machines with less RAM memory (it commonly occurs when the machine has 64 MB or less).
Flip may thrash badly if the input is an image window and even more so if the output is another image window.
Line Profile's x, y, or diagonal profiles are not handled correctly when the source image window displays multiple sections and the step direction is not z.
Line Profile's graphics in the image windows are aligned to the left or bottom edge of a pixel rather than the center.
The rendering of graphics drawn on images is different in MonToPS than it is in the image window: graphics in window coordinates are not clipped at the window edges; the scale bar label is not shown if it appears in the image window; graphics from 3D Model are not shown.
The Priism menu bar does not need resize handles.
The Priism .hlp file is out of date.
Projection algorithm in Rotfast breaks down as the tilt approaches +90 or -90 degrees (for instance get completely black image at +90).
With tiffmovie on an O2, images in the movie may have rows or columns along the edge whose image values are those of a previous section. The output appears to be ok if the zoom on the image window is one.

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IM Library

The mechanism for detecting when byte-swapping is necessary limits the x or y dimensions of a data set to be less then 65536. The library can not detect if byte-swapping is necessary if the x and y dimensions of a data set are both zero.
When an application uses IM calls without any calls to IWAlScl or IWAlSecScl and writes a result to an image window, the results often do not appear "right" because each section is scaled separately. The default scaling done in this case should be drawn the minimum and maximum values from the header.
The result of writing to an image window or to a file with the same data can be different because the automatic conversion of floating-point values to integers handles rounding and extreme values (those beyond the limits of the destination integer type) differently for image windows and files.
If IMRdHdr needs to swap bytes in the header and an extended header is present with a symmetry group number of 0, IMRdHdr can corrupt the heap if the number of bytes in the extended header is less than the number of sections times the size needed to store the integer and floating-point extended header values for each section.
Passing a nonpositive stream number to IMOpen is not rejected though its behavior is undefined.
IMPutHdr does not adjust the internally allocated extended header space if the new header values changed the size of the extended header.
Writing partial sections to resolutions other than the highest resolution gives different results depending on whether the destination is an image window or file.
IMFixExHdr does not properly change the extended header if wavelengths are rearranged (it does correctly handle the case where some waves are omitted).

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IW Library

Many functions have no documentation or very rudimentary documentation. IWAlCursor is one.
The Fortran versions of the functions assume that the Fortran compiler mangles names by converting to lowercase and appending one underscore. Any logical arguments are assumed to be false if, when treated as an integer, the argument is zero and true otherwise; this is not compatible with some Fortran compilers.
IWCopyPartialData and IWTransformPartialDataType do not work with data in the IW_COMPLEX_SHORT format.

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WM Library

The Fortran function interface has not been documented.
The Fortran versions of the functions assume that the Fortran compiler mangles names by converting to lowercase and appending one underscore. Any logical arguments are assumed to be false if, when treated as an integer, the argument is zero and true otherwise; this is not compatible with some Fortran compilers.

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IP Library

Assumes at least one input file and only allows one output file that is under the management of the framework.
The required and window only parameters to IPAddInput are not honored.
IPSetDisChgHandler assumes that the file's IM stream is one.
A CLEAN_UP_PROC function registered with IPSetCustRoutine is not invoked when the application is closed via the window manager controls.
A UN_REG_DIS_CHG function registered with IPSetCustRoutine is always passed one as the argument.
For the FOUR_D and FOUR_D_WAVE options, the framework does not allocate sufficient space for the input and output arrays.
With the FOUR_D_WAVE option, the scaling is only set for the first output wavelength and not any of the others.
LoadFile in the EXAMPLE directory does not compile.
The automatic allocation of input and output buffers could be smarter; it always allocates space as if the application were processing complex data.
The argument passed along with the callback function to IPSetCustRoutine is not used as expected for the CLEAN_UP_PROC, AFTER_DO_IT, and NEW_XYAREA functions. Instead, the function registered with CLEAN_UP_PROC is not passed anything, the function registered with AFTER_DO_IT is passed the argument registered for CLEAN_UP_PROC, and the function registered with NEW_XYAREA is passed the argument registered for NEW_REGION.

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modified November 15, 2003

IVE Development Team (ive-web@msg.ucsf.edu)
Macromolecular Structure Group, UCSF (http://msg.ucsf.edu)