Re: [ccp4bb] How to obtain an oca file?
We miss the MSD target service a lot. Is there a real reason why it's gone? Jan Dohnalek Eleanor Dodson wrote: Thwe MSD target service has gone, and that was the way I created oca files comparing sequences? Is there another web site which will give back the same format? Eleanor -- == Mr. Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Laboratory of Structural Analysis of Molecules Heyrovskeho nam. 2 16206 Prague 6 Tel: +420 296809205 Fax: +420 296809410 ==
[ccp4bb] Announcement... New CCP4 documentation wiki
We've set up a new way of documenting the CCP4 software, which the aim of being more accessible to GUI and novice users. The new documentation is in the form of a wiki, which you can visit here: http://ccp4wiki.org/ Unlike Kay Deidrich's community wiki, the aim of this site is not to be editable by most users (the wiki engine is just used for convenience), but rather to be an easier-to-maintain and update way of documenting the software. The focus will be on how to user the software through the user interface. As a result, the contributors will mainly by program authors, and a few expert users. It's not complete, but based on feedback at a recent course, it is already good enough to be useful. The site is divided into two main areas: 1. How to use the software. This has been organised to mirror the steps you might take in solving your structure, and the modules of the user interface. 2. Knowledge base. This contains a fairly extensive glossary of terms used in the software documentation, along with some other information. There is also a collection of lectures from recent workshops. Please have a look and see if it useful to you. Feedback is very welcome. If you like the format but think specific articles need work (or indeed are missing), please tell me and I'll pass on the requests. Kevin
[ccp4bb] Negative density around C of COO-
Dear all: I am noticing that in some of my structures, at 1.5 A resolution, 1) there is some negative density around the C of the carboxyl groups. 2) I also notice the negative density around S in a disulfide region. It is as though the disulfide is broken. Could some body enlighten me on this feature?
Re: [ccp4bb] Negative density around C of COO-
I would suspect radiation damage for the S density . I have not seen radiation damage of only COO carbons, but then again, I do not routinely get such good diffraction. Kevin P Madauss V-161a US Structural Biology GlaxoSmithKline Office: 919.483.3759 5 Moore Drive Cell: 919.924.6436 RTP, NC 27709
Re: [ccp4bb] Negative density around C of COO-
Narayanan Ramasubbu wrote: Dear all: I am noticing that in some of my structures, at 1.5 A resolution, 1) there is some negative density around the C of the carboxyl groups. 2) I also notice the negative density around S in a disulfide region. It is as though the disulfide is broken. Could some body enlighten me on this feature? Synchrotron radiation can cause free radical mediated damage to proteins. The most frequently observed consequences are decarboxlation of Asp and Glu, and the breakage of disulfide bonds. See, for example, Wiek et al. (2000) PNAS 97, 623-628, and Leiros et al. (2001) Acta Cryst. D 57, 488-497. Cheers, -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [EMAIL PROTECTED]
[ccp4bb] Summary: Negative density around COOH
Thanks for the quick reply and pointing out t bunch of references. Radiation damage has been pointed out as a cause for such feature. The following references were pointed out. Ravelli, R.B.G. McSweeney, S.M. (2000). The 'fingerprint' that X-rays can leave on structures. Structure 8:315-328. Wiek et al. (2000) PNAS 97, 623-628, and Leiros et al. (2001) Acta Cryst. D 57, 488-497. Subbu
[ccp4bb] question on how crystals form
Dear colleagues, I have a structure with two identical dimers per asymmetric unit. If the dimers are identical in different crystalline environments and in different crystal forms they should be particularly stable. How does such a stable dimer crystallize? Is it necessay to pre-exist in the specific conformation in solution (even to a lesser extent than a major monomeric form) or a very stable dimer can assemble from the very beginning durnig crystallization? And can the same dimer form during crystallization in different crystalline environments without it being present in solution to any (even infinitesimal) extent? I would appreciate all responses. Thanks. Mike Colaneri
[ccp4bb] HKL2000 and gcc4
Basically, the newest version of HKL2000 won't run on Linux machines that do not have the libg2c.so.0 library (part of gcc3) in /usr/lib/ . This is a problem for us, as every new computer we acquire uses a version of Linux (that is no longer terribly new) that uses gcc4 (which does not have the libg2c.so.0 library) and not gcc3. We've tried pointing our LD_LIBRARY_PATH to a directory that has this old library in it, but HKL2000 won't recognize it. I have tried an experiment of putting the library into the /usr/lib/ folder, and HKl2000 runs, but our sys-admin refuses to let it stay there. Has anyone made this work (i.e. Am I missing something that is probably quite simple)? Thanks, Chris -- Dr. Christopher A. Waddling, Ph.D. University of California at San Francisco MC 2140 S126C 600 16th St., San Francisco, CA 94158-2517 (415) 476-8288 (office) (415) 502-7779 (lab) (415) 514-4142 (fax) (415) 810-7556 (cell) [EMAIL PROTECTED] AIM duckie2k1 Skype chriswaddling
Re: [ccp4bb] HKL2000 and gcc4
Get a new sys-admin. He is getting in the way of your research. There is no good reason to be paranoid about this particular shared library sitting in /usr/lib. James On May 5, 2008, at 1:32 PM, Chris Waddling wrote: I have tried an experiment of putting the library into the /usr/lib/ folder, and HKl2000 runs, but our sys-admin refuses to let it stay there. -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com
Re: [ccp4bb] question on how crystals form
Hi Mike, how does your protein look on a sizing column ? Perhaps a dimer ? That would then explain the tendency to form dimers in different crystal forms, as it is a biological relevant dimer. for the eventuality that you have no clue how the sizing looks like, run one and find out. Juergen Michael Colaneri wrote: Dear colleagues, I have a structure with two identical dimers per asymmetric unit. If the dimers are identical in different crystalline environments and in different crystal forms they should be particularly stable. How does such a stable dimer crystallize? Is it necessay to pre-exist in the specific conformation in solution (even to a lesser extent than a major monomeric form) or a very stable dimer can assemble from the very beginning durnig crystallization? And can the same dimer form during crystallization in different crystalline environments without it being present in solution to any (even infinitesimal) extent? I would appreciate all responses. Thanks. Mike Colaneri -- Jürgen Bosch University of Washington Dept. of Biochemistry, K-426 1705 NE Pacific Street Seattle, WA 98195 Box 357742 Phone: +1-206-616-4510 FAX: +1-206-685-7002 Web: http://faculty.washington.edu/jbosch
Re: [ccp4bb] Negative density around C of COO-
I don't mean to single anyone out, but the assignment of free radicals as the species mediating radiation damage at cryo temperatures is a pet peeve of mine. Free radicals have been shown to mediate damage at room temperature (and there is a VERY large body of literature on this), but there are a great many good reasons to think that free radicals do NOT play a role in radiation damage under cryo. This assignment of free radicals to damage is often made (flippantly) in the literature, but I feel a strong need to point out that there is NO EVIDENCE of a free radical diffusion mechanism for radiation damage below ~130K. To the contrary there is a great deal of evidence that water, buffers and protein crystals below ~130 K are in a state of matter known as a solid, and molecules (such as free radicals) do not diffuse through solids (except on geological timescales). If you are worried that the x-ray beam is heating your crystal to 130 K, then have a look at Snell et. al. JSR 14 109-15 (2007). They showed quite convincingly that this just can't happen for anything but the most exotic situations. There is evidence, however, of energy transfer taking place between different regions of the crystal, but energy transfer does not require molecular diffusion or any other kind of mass transport. In fact, solid-state chemistry is generally mediated by cascading neighbor-to-neighbor reactions that do not involve diffusion in the traditional sense. Electricity is an example of this kind of chemistry, and these reactions are a LOT faster than diffusion. The closest analogy to diffusion is that the propagating reaction can be seen as a species of sorts that is moving around inside the sample. Entities like this are formally called quasiparticles. Some quasiparticles are charged, but others are not. If you don't know what a quasiparticle is, you can look them up in wikipedia. Some have tried to rescue the free radical statements about radiation damage by claiming that individual electrons are radicals. I guess this must come from the pressure of such a large body of free-radical literature at room temperature. However, IMHO this is about as useful as declaring that every chemical reaction is a free radical reaction (since they involve the movement of electrons). I think it best that we try to call the chemistry what it is and try to stamp out rumors that mechanisms are known when in reality they are not. Just my little rant. -James Holton MAD Scientist
Re: [ccp4bb] HKL2000 and gcc4
Chris Waddling wrote: Basically, the newest version of HKL2000 won't run on Linux machines that do not have the libg2c.so.0 library (part of gcc3) in /usr/lib/ . This is a problem for us, as every new computer we acquire uses a version of Linux (that is no longer terribly new) that uses gcc4 (which does not have the libg2c.so.0 library) and not gcc3. We've tried pointing our LD_LIBRARY_PATH to a directory that has this old library in it, but HKL2000 won't recognize it. I have tried an experiment of putting the library into the /usr/lib/ folder, and HKl2000 runs, but our sys-admin refuses to let it stay there. Has anyone made this work (i.e. Am I missing something that is probably quite simple)? Thanks, Chris -- Dr. Christopher A. Waddling, Ph.D. University of California at San Francisco MC 2140 S126C 600 16th St., San Francisco, CA 94158-2517 (415) 476-8288 (office) (415) 502-7779 (lab) (415) 514-4142 (fax) (415) 810-7556 (cell) [EMAIL PROTECTED] AIM duckie2k1 Skype chriswaddling Have you installed the compatibility libraries compat-libstdc++-33 and libstdc++296? This is easily accomplished using yum if it is installed, e.g., $ yum -y install compat-libstdc++-33 compat-libstdc++-296 These libraries are required for programs compiled using GCC 3.x Cheers, -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [EMAIL PROTECTED]
Re: [ccp4bb] HKL2000 and gcc4
On Mon, 05 May 2008 13:48:00 -0600, James Stroud [EMAIL PROTECTED] wrote: Get a new sys-admin. He is getting in the way of your research. There is no good reason to be paranoid about this particular shared library sitting in /usr/lib. James On May 5, 2008, at 1:32 PM, Chris Waddling wrote: I have tried an experiment of putting the library into the /usr/lib/ folder, and HKl2000 runs, but our sys-admin refuses to let it stay there. I'd echo James, but to say that there is no reason that you cannot have both gcc3 and gcc4 installed. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 [EMAIL PROTECTED]http://pldserver1.biochem.queensu.ca/~rlc
Re: [ccp4bb] HKL2000 and gcc4
Hi Chris, On Mon, 05 May 2008 12:57:17 -0700, Chris Waddling [EMAIL PROTECTED] wrote: Robert, that's exactly what I keep asking him to do maybe I should take James Stroud's advice... Yes, maybe you should, if you cannot convince him of the error of his ways. :) BTW, nice to hear from my M.Sc. alma mater... I worked in Donal Macarntney's Chemistry lab from '91-93. I haven't crossed paths with Donal, just with a couple of others like Victor Snieckus and David Zechel in the Chemistry department here. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 [EMAIL PROTECTED]http://pldserver1.biochem.queensu.ca/~rlc
[ccp4bb] negative LLG in Phaser run
Phaser experts, When running Phaser I see LL gain becoming negative closer to the end. What would that mean? Resolution ~3.0 A, s.g. I222, 2 complexes per a.u. Here is the line from log file: ANNOTATION: RFZ=7.6 TFZ=8.9 PAK=0 LLG=142 RFZ=6.6 TFZ=18.0 PAK=0 LLG=150 RFZ=4.6 TFZ=12.8 PAK=0 LLG=-44 RFZ=3.8 TFZ=5.8 PAK=19 LLG=-908 Thank you in advance. __ Oganesyan Vaheh, Ph.D Antibody Discovery MedImmune, Inc. To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.
Re: [ccp4bb] HKL2000 and gcc4
Hi, Have you installed the compatibility libraries compat-libstdc++-33 and libstdc++296? This is easily accomplished using yum if it is installed, e.g., $ yum -y install compat-libstdc++-33 compat-libstdc++-296 These libraries are required for programs compiled using GCC 3.x Those packages don't provide libg2c but they are good to have. You need yum install compat-libf2c-34 for libg2c.so.0 assuming you're using RHEL5 or greater. In any case, we're using v0.98.698d and it doesn't seem to need libg2c: % ldd `which hkl2000` linux-gate.so.1 = (0x4000) libX11.so.6 = /usr/lib/libX11.so.6 (0x00ada000) libm.so.6 = /lib/libm.so.6 (0x00a7) libdl.so.2 = /lib/libdl.so.2 (0x00a99000) libc.so.6 = /lib/libc.so.6 (0x0092e000) libXau.so.6 = /usr/lib/libXau.so.6 (0x00acd000) libXdmcp.so.6 = /usr/lib/libXdmcp.so.6 (0x00ad2000) /lib/ld-linux.so.2 (0x0090d000) which version of HKL2000 are you using that requires libg2c?
Re: [ccp4bb] HKL2000 and gcc4
Basically, the newest version of HKL2000 won't run on Linux machines that do not have the libg2c.so.0 library (part of gcc3) in /usr/lib/ . This no doubt qualifies as an obvious question, but have you tried /usr/local/lib? That is often automatically searched for libraries on Linux systems, and is often used as a resting place for obsolete libraries for that reason. It's preferable, if they're available for your flavor of Linux, to use compatibility packages as Professor Rowlett mentions. You'll probably need compat-g77, or something similar, as libg2c is the old Fortran compatibility library for GCC. -- Michael Strickler, Ph.D. Research Specialist Center for Structural Biology Yale University 260 Whitney Ave, 355C JWG PO Box 208114 New Haven, CT 06520-8114
Re: [ccp4bb] HKL2000 and gcc4
On ubuntu, you can get this in the libg2c package. I agree with James Stroud. Fire the sysadmin and divvy the salary up amongst those who really need it. Time to raise the black flag and start slitting throats. On May 5, 2008, at 12:32 PM, Chris Waddling wrote: Basically, the newest version of HKL2000 won't run on Linux machines that do not have the libg2c.so.0 library (part of gcc3) in /usr/lib/ . This is a problem for us, as every new computer we acquire uses a version of Linux (that is no longer terribly new) that uses gcc4 (which does not have the libg2c.so.0 library) and not gcc3. We've tried pointing our LD_LIBRARY_PATH to a directory that has this old library in it, but HKL2000 won't recognize it. I have tried an experiment of putting the library into the /usr/lib/ folder, and HKl2000 runs, but our sys-admin refuses to let it stay there. Has anyone made this work (i.e. Am I missing something that is probably quite simple)? Thanks, Chris -- Dr. Christopher A. Waddling, Ph.D. University of California at San Francisco MC 2140 S126C 600 16th St., San Francisco, CA 94158-2517 (415) 476-8288 (office) (415) 502-7779 (lab) (415) 514-4142 (fax) (415) 810-7556 (cell) [EMAIL PROTECTED] AIM duckie2k1 Skype chriswaddling
Re: [ccp4bb] Negative density around C of COO-
I believe some, may not be all, negative density may be due to the choice of wavelength. C,O and N are not so sensitive to normally used wavelength (1-1.54A), but S does. This is more true when you have higher resolution and better quality data. You can estimate this by f'. By the way, although I am not a real supporter of radicals from damage, I believe that a photo-induced (here X-ray) chemical reaction is much different from a heat-induced one. Low temperature is not a problem. But this not for diffusion, as it is ~100% heat- related. Please point out if I am wrong. This assignment of free radicals to damage is often made (flippantly) in the literature, but I feel a strong need to point out that there is NO EVIDENCE of a free radical diffusion mechanism for radiation damage below ~130K. Lijun Liu, PhD Institute of Molecular Biology HHMI Department of Physics University of Oregon Eugene, OR 97403 541-346-4080
[ccp4bb] Refmac Error
Dear All, I occasionally get the following error after running refmac: #CCP4I TERMINATION STATUS 0 Error from script /home/local/LINUX/ccp4-6.0.2/ccp4i/scripts/refmac5.script: error writing stdout: I/O error The above error is from the last lines of the log file. It seems that refinement runs fine (I see refinement cycle statistics etc.), however, no pdb or mtz file is written out. I use CCP4 version 6.0.2. Thanks for your suggestions, Kianoush * Kianoush Sadre-Bazzaz Graduate Student, Chris Hill Lab University of Utah Biochemistry Department 15 N Medical Drive East RM 4100 Salt Lake City UT 84112-5650 USA (801)585-7068 [EMAIL PROTECTED] - Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now.
Re: [ccp4bb] Refmac Error
Kianoush wrote: Dear All, I occasionally get the following error after running refmac: #CCP4I TERMINATION STATUS 0 Error from script /home/local/LINUX/ccp4-6.0.2/ccp4i/scripts/refmac5.script: error writing stdout: I/O error The above error is from the last lines of the log file. It seems that refinement runs fine (I see refinement cycle statistics etc.), however, no pdb or mtz file is written out. I use CCP4 version 6.0.2. Thanks for your suggestions, Kianoush * Kianoush Sadre-Bazzaz Graduate Student, Chris Hill Lab University of Utah Biochemistry Department 15 N Medical Drive East RM 4100 Salt Lake City UT 84112-5650 USA (801)585-7068 [EMAIL PROTECTED] Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://us.rd.yahoo.com/evt=51733/*http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ%20 The very first thing to check is whether or not you have permission to write in the directory where the PDB and MTZ files are to be written to. This might explain an intermittent error of the type you describe. Cheers, -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [EMAIL PROTECTED]
Re: [ccp4bb] HKL2000 and gcc4
I had similar problem with Mosflm due to odd combination of Suse and AMD-64. Copied those files from a different installation, everything runs just fine.. would agree with James.. lol.. On Mon, May 5, 2008 at 8:32 PM, Chris Waddling [EMAIL PROTECTED] wrote: Basically, the newest version of HKL2000 won't run on Linux machines that do not have the libg2c.so.0 library (part of gcc3) in /usr/lib/ . This is a problem for us, as every new computer we acquire uses a version of Linux (that is no longer terribly new) that uses gcc4 (which does not have the libg2c.so.0 library) and not gcc3. We've tried pointing our LD_LIBRARY_PATH to a directory that has this old library in it, but HKL2000 won't recognize it. I have tried an experiment of putting the library into the /usr/lib/ folder, and HKl2000 runs, but our sys-admin refuses to let it stay there. Has anyone made this work (i.e. Am I missing something that is probably quite simple)? Thanks, Chris -- Dr. Christopher A. Waddling, Ph.D. University of California at San Francisco MC 2140 S126C 600 16th St., San Francisco, CA 94158-2517 (415) 476-8288 (office) (415) 502-7779 (lab) (415) 514-4142 (fax) (415) 810-7556 (cell) [EMAIL PROTECTED] AIM duckie2k1 Skype chriswaddling -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: [EMAIL PROTECTED] Phone: + 44 208 816 2515
Re: [ccp4bb] Negative density around C of COO-
Hi James, We used to talk about primary and secondary radiation damage. The former operates at room temperature where free radicals were said to be formed in solution and diffuse around to damage proteins. Under cryoconditions this no longer happens, leading to greatly improved crystal life time, but we still have primary radiation damage, with the photons directly hitting the protein. It was my understanding that this was still considered to form a free radical at the affected atom without there being any diffusion involved. Sulfur atoms would be more sensitive as they have a larger X-ray cross-section or because they may act as free-radical sinks where free radicals generated nearby strip an electron from the sulfur, thereby satisfying their own electronic configuration and converting the sulfur into a radical state. For instance, in ribonucleotide reductase a tyrosine free radical is formed spontaneously (using oxygen and an dinuclear iron site) and jumps over 20 Angstrom from one subunit to another to form a thiyl free radical in the active site. It then jumps back to the tyrosine upon completion of the catalytic cycle. Although we don't know how it jumps, certainly not by diffusion, there is general agreement that it does happen. People have also observed broken disulfides in cryocrystal structures with the sulfurs at a distance that is too long for a disulfide but too short for a normal non-bonded sulfur-sulfur interaction. I seem to remember that this distance was suggested to indicate the presence of a thiyl free radical. I'm no chemist of physicist so can't evaluate if that claim is reasonable but if it is then that would be direct evidence to support the involvement of a free radical state in radiation damage. So I guess my questions/comments are - what are the great many good reasons to think that free radicals do NOT play a role in radiation damage under cryo. - although diffusion does not happen below 130K, radicals do appear to teleport, at least over short distances. Bart James Holton wrote: I don't mean to single anyone out, but the assignment of free radicals as the species mediating radiation damage at cryo temperatures is a pet peeve of mine. Free radicals have been shown to mediate damage at room temperature (and there is a VERY large body of literature on this), but there are a great many good reasons to think that free radicals do NOT play a role in radiation damage under cryo. This assignment of free radicals to damage is often made (flippantly) in the literature, but I feel a strong need to point out that there is NO EVIDENCE of a free radical diffusion mechanism for radiation damage below ~130K. To the contrary there is a great deal of evidence that water, buffers and protein crystals below ~130 K are in a state of matter known as a solid, and molecules (such as free radicals) do not diffuse through solids (except on geological timescales). If you are worried that the x-ray beam is heating your crystal to 130 K, then have a look at Snell et. al. JSR 14 109-15 (2007). They showed quite convincingly that this just can't happen for anything but the most exotic situations. There is evidence, however, of energy transfer taking place between different regions of the crystal, but energy transfer does not require molecular diffusion or any other kind of mass transport. In fact, solid-state chemistry is generally mediated by cascading neighbor-to-neighbor reactions that do not involve diffusion in the traditional sense. Electricity is an example of this kind of chemistry, and these reactions are a LOT faster than diffusion. The closest analogy to diffusion is that the propagating reaction can be seen as a species of sorts that is moving around inside the sample. Entities like this are formally called quasiparticles. Some quasiparticles are charged, but others are not. If you don't know what a quasiparticle is, you can look them up in wikipedia. Some have tried to rescue the free radical statements about radiation damage by claiming that individual electrons are radicals. I guess this must come from the pressure of such a large body of free-radical literature at room temperature. However, IMHO this is about as useful as declaring that every chemical reaction is a free radical reaction (since they involve the movement of electrons). I think it best that we try to call the chemistry what it is and try to stamp out rumors that mechanisms are known when in reality they are not. Just my little rant. -James Holton MAD Scientist -- == Bart Hazes (Assistant Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax:1-780-492-7521 ==
Re: [ccp4bb] HKL2000 and gcc4
Thanks all for your suggestions. It turns out that I was mis-defining the LD_LIBRARY_PATH (using 'set' instead of 'setenv'). Dumb mistake, but thanks to our sysadmin pointing this out, all's good. Chris
