News and Bugs

News

SPIDER for Irix

We are discontinuing support for SPIDER and Web on SGI Irix in 2008. RIP.

"Free" License

SPIDER source code is now 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 Windows 2000 and Windows XP

We have discontinued support for SPIDER and Web for Windows 2000. We may still provide an untested executable for SPIDER and will provide a Makefile which might be usefull to compile SPIDER on your own system.

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.

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Recent Bugs

CP TO CCP4

CL CLA

? --> Dec. 2007 (Fixed in: version 15.13) Gave incorrect class assignments when certain numbers of factors requested. Also always used first factors even when factor list was specified.

12/20/07 AL

? --> 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

? --> Feb. 2006 (Fixed in: version 14.11) 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

CE VAR

--> Oct. 2002 (version 8.05) Did not calculate "variance".

10/7/02 AL

PW

On some 64 bit SGI machines with 7.3.13m FORTRAN, SPIDER encounters a bad memory leak.

Install SGI patch 4511 (7.3 FORTRAN runtime #3 for IRIX 6.5) to fix this. (We have introduced a "work-around" which avoids most of the leak.)

8/14/02 AL

CA S

June 2001 --> Feb. 2002 (version 8.02). With small problems the Coran option used the wrong formulation and never finished processing.

8/14/02 AL

RF & RF 3

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

10/10/01 AL

Integers larger than 99999 are incorrect when placed in doc files.

?--> Aug. 2000 (version 6.34). Numbers in document files were stored with G12.5 Fortran format so that integers greater than 99999 lack precision. As of version 6.35 integers > 999999 show the same "error" but integers < 999999 can be used OK. Keeping precise integers > 999999 in a document file will require major changes in SPIDER document files. This will be done in a subsequent release.

8/22/00 AL

Inline Stack File Memory Leak

?-->present. SPIDER has a memory leak on SGI Irix 6.5 which sometimes occurs when one alternately creates and deletes an inline stack file. We have introduced a workaround which will lessen the occurance.

10/10/99 AL

FT, AC, and CC

--> present. SGI's version of "libblas" routines have a slow memory leak in routines necessary for Fourier transforms. When performing these operations millions of times in a single run you may exhaust system memory and SPIDER may crash. SGI acknowledges a problem, and suggests that users switch to the "CRAY Subroutine Library" which is not included with the Irix OS, which we are reluctant to use.
We have introduced a work-around that minimizes the effect of this bug under most circumstances. Details.

3/20/99 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 previous releases of SPIDER.