News and Bugs

News

SPIDER for Irix

We discontinued release of SPIDER/Web for SGI Irix in 2008. RIP.

"Free" License

SPIDER source code is licensed under GPL license. SPIDER documentation (manuals, tutorial, etc) is licensed under a Creative Commons Attribution 2.5 License.

New operations

New SPIDER operations or changes in usage of old operations.

Note that these changes may NOT be in the release of SPIDER that you have at your site now.

SPIDER for Linux Info

Slaton Lipscomb from the: Nogales Lab, UC Berkeley provides some tips on installing and using SPIDER

Older news

News on previous releases of SPIDER.

---

Recent Bugs

AP SR, CC, ..

? --> 17.11 Certain operations involving correlation e.g. 'AP SR' sometimes crash on OS X or when recompiled for Linux using Intel compiler.

AP REF

? --> 17.08 Register 10 ('Change in projection angle') of the alignment output file haa incorrect values when used with multiple images.

Nextresults

? --> 17.08 Nextresults script missing from distribution. Gave error message on starting SPIDER.

TF ED

? --> 17.07 Often crashed when compiled to run on Intel processors (OK on AMD).

AP SH

? --> 17.07 A "TRANSLATION SEARCH RANGE" that goes out of image reports an error message but fails to completely stop a parallel operation, leading to incorrect alignments.

CL CLA

? --> Dendrograms do not display image class assignments. It starts at class level. A design decision not a bug.

AP SR

16.** --> 17.01 Sometimes gave all all zero alignment angles.

BP CG

17.00 --> 17.01 Sometimes failed to find angles for projection. (Results were correct if it ran.)

CL CLA

? --> 15.12 Gave incorrect class assignments when certain numbers of factors requested. Also always used first factors even when factor list was specified.

? --> Mar. 2006, A BRIX volume converted from a SPIDER volume by using "CP TO BRIX" can be used to fit a PDB structure using "O" or Real Space Refinement (RSR). Usually, the coordinates of the PDB structure are changed to reflect its fitted position relative to the BRIX volume. The BRIX volume and the new PDB coordinates are in correct orientation and location with respect to each other. However, if the SPIDER volume used for fitting is now changed to a CCP4 volume by using SPIDER command "CP TO CCP4" then the resultant CCP4 volume will not be at correct location and orientation relative to the coordinates of the above fitted PDB structure. To put the CCP4 volume at the correct location and orientation with respect to the fitted PDB structure, one will have to use the SPIDER procedure "fit_ccp4_to_pdb.spi" (see CP TO CCP4). The inconsistency is due to different coordinate conventions used in SPIDER and "O".

Note :, Some of the earlier SPIDER volumes deposited at EMDB database by our group at Albany were converted to CCP format by directly using the SPIDER command "CP TO CCP4" (SPIDER procedure "fit_ccp4_to_pdb.spi" was not used). These volumes are not at the correct location and orientation with respect to the coordinates of the deposited fitted PDB structures. We have already resubmitted all these volumes with correct location and orientation which respect to the coordinates of the deposited fitted PDB structures. These volumes are now available under category "other" of the EMDB database download page.

03/9/06 BR

AP REF, CC & CC N

? --> 14.10 When running our precompiled executable: spider_linux_mpfftw_opt64 (only this executable), the output image (CC) or the translational shift (AP REF) may be WRONG. This was due to a complex arithmetic bug in the PGI compiler which we used. This problem has been fixed by rewriting the relevant code to avoid the use of COMPLEX variables.

02/14/06 BR and AL

RF & RF 3

--> Oct. 2005 (version 13.00) Gave low 3-sigma resolution

Number of voxels (fifth column in the output document file) too low by a factor of two and the 3-sigma criterion output (fourth column) was too HIGH by a factor of sqrt(2). This means that resolution is better than reported.

10/7/05 PP

RF & RF 3

--> present. NSAM must be equal to NROW for correct answers.

10/10/01 AL

RT 90

--> present. The "RT 90" operation reforms an image's columns and rows (or just rows for 180 degrees). The action of such an rotation is not the same as other "RT" rotations since the center of rotation differs. Thus "RT 90" is not interchangeable with other "RT" operations.

11/27/98 AL

Older bugs

Bugs in earlier releases of SPIDER.