[ccp4bb] alt conformations and solvent structure
Hi folks: Is there a simple way to attach partially occupied solvent sites with a specific conformer when dealing with multiple conformations of side chains or nucleotides, for purposes of PDB deposition? (In this case the resolution is quite high.) Thanks. Bill William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
Re: [ccp4bb] Conflicting Qt on OS X 10.6
It looks like it should be doing the right thing, i.e., zsh-% otool -L qtrview qtrview: @executable_path/../Frameworks/QtWebKit.framework/Versions/4/QtWebKit (compatibility version 4.9.0, current version 4.9.3) @executable_path/../Frameworks/QtXmlPatterns.framework/Versions/4/QtXmlPatterns (compatibility version 4.8.0, current version 4.8.4) @executable_path/../Frameworks/QtGui.framework/Versions/4/QtGui (compatibility version 4.8.0, current version 4.8.4) @executable_path/../Frameworks/QtXml.framework/Versions/4/QtXml (compatibility version 4.8.0, current version 4.8.4) @executable_path/../Frameworks/QtNetwork.framework/Versions/4/QtNetwork (compatibility version 4.8.0, current version 4.8.4) @executable_path/../Frameworks/QtCore.framework/Versions/4/QtCore (compatibility version 4.8.0, current version 4.8.4) If you have $DYLID_LIBRARY_PATH set, try unsetting it. On Oct 28, 2013, at 9:00 AM, Dmitry Rodionov d.rodio...@gmail.com wrote: Good day! I'm having problems with qtrview (on OS X 10.6): it crashes or hangs after spitting out a screenful of messages like objc[2975]: Class QCocoaMenu is implemented in both /Applications/ccp4-6.4.0/bin/../Frameworks/QtGui.framework/Versions/4/QtGui and /Library/Frameworks/QtGui.framework/Versions/4/QtGui. One of the two will be used. Which one is undefined. Just like the message says, I have Qt 4 installed in the standard location. It seems like the global Qt it is being used instead of the one supplied with CCP4 6.4 since moving /Library/Frameworks/Qt* elsewhere fixes the problem. Oddly enough, qtrview of CCP4 6.3 worked fine under the same conditions. Is there a way to make qtrview use CCP4's Qt and ignore other versions? Thanks! Best regards, Dmitry
Re: [ccp4bb] OT: Has anyone experienced problems with Apple laptop battery expansion?
Presumably then it was running Linux? On Nov 20, 2012, at 7:39 AM, George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: I have never understood why Macs are so popular, although in this part of the world they are appreciably more expensive. My vintage 2005 Dell laptop does not have the sex appeal of a MacBook, but it has survived a fire (not its fault) as well as being under water (to put out the fire) and then bounced down a stone staircase (my wife fortunately caught it on the way down). Despite all my efforts to destroy it, it never needed servicing or replacement parts and still works perfectly! George (PS I should add that I have no connection with or shares in Dell) On 11/20/2012 10:25 AM, Charles Ballard wrote: To add to the general list (and future class action). I have just had the battery expansion on one for the second time. Added to the number of them I have bricked by letting the charge run down to low by unplugging them. Interestingly apple agreed to replace the bricked batteries free of charge, for their US customers. But, us foreigners had to pay for the pleasure... Charles On 18 Nov 2012, at 17:30, Bosch, Juergen wrote: Bill I think that's crap. I had issues on a 2005 MacBook Pro with inflating battery and it was replaced (after about 6 months). There were troubles with those batteries and impurities but mine still had apple care at that time and the batteries were exchangeable. I have not heard of the build in batteries to have problems but yours sure did. Send Tim Cook an email with the picture. This should not have happened and also keeping the power cord on leading to this problem should not have happened. For what did they introduce the trickling charging ? If you can't leave the coord plugged in how many nice wooden US households gave caught fire due to Apple products ? Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://lupo.jhsph.edu On Nov 17, 2012, at 16:28, William G. Scott wgsc...@ucsc.edu wrote: Hi folks: I'm trying to get a sense for how frequently this sort of thing occurs: CIMG4451.jpeg That was a macbook air that served me well for four years, but then self-destructed. (I took it to the Apple store. They generously offered to repair it for $800 or to sell me a new one, and suggested this was normal if you leave the power cord attached after the battery charges, even while giving a lecture or seminar.) It strikes me as a bit dangerous. --Bill Scott William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582
Re: [ccp4bb] Linux vs MacOS for crystallographic software
opinion on the virtues of different OS environments for two days It might be of interest to look back on the original poster's question, because all she asked were a few questions about a specific computer (HP Z210 8 GB with a low end Quadro Nvidia 400 512 MB) running any Linux, and a specific computer (IMAC 4 GB 2.5 GHz with AMD Radeon HD 6750M 512 MB) running OS X 10.7. Although she asked if the latter was platform advisable for crystallographic software for the coming years, there wasn't any question about the merits of various operating systems. Presumably, she can determine that as well as anyone else, assuming accurate answers to her questions. No one ever suggested operating system monogamy was a virtue. Besides, both are simply unix variants, and are far more alike than evangelists for either Linux or OS X seem to want to admit. If you like or dislike the iCandy apps, then there might be a compelling reason for/against OS X vs. Linux. Likewise, if you refuse to use closed-source, proprietary operating systems and software on principle, as advocated by Richard Stallmann, there is a compelling reason to use strict GNU/Linux (albeit without the NVidia proprietary driver). But then, you probably wouldn't be using much apart from COOT and other GPL software. OS X users, in that respect, are kind of like vegetarians who eat fish. --Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA
Re: [ccp4bb] Rigaku high voltage tank
On Sep 28, 2011, at 7:15 AM, Artem Evdokimov wrote: Are you indeed referring to the oil-filled high voltage transformer core in the older model generators? Yes. (Newer ones tend to use solid state voltage multipliers). That sounds much more sane. I recall that there were issues with those things that were eventually traced to elevated humidity. Now, that was humidity around 80% which should not be the case for most systems these days since most of us seem to prefer humidity controlled environments (for the sake of the cryostreams) but it might be worth checking some local leaks etc. Well, I'm at DIY-U, so this very likely is a potential source of the problem. We have to supply our own hamsters for the electrical generators, too. One more reason that the tank transformer might go bad would be inadequate matching between power input and drain, especially high-drain situation caused by an undetected high current (like a parasite current too weak to cause arcing, but strong enough to damage transformer over time). Did your/Rigaku's engineer check the voltages and currents in the tube tower? Do you have the option to record currents while no one is attending the instrument (in the even that the problem is intermittent)? I don't think anything like that was ever done, but I am not sure. We shipped it back to them, and they need more money to continue diagnosis, so we are probably just going to cut our losses on this decade-long nightmare. Artem On Tue, Sep 27, 2011 at 8:51 AM, Patrick Loll pat.l...@drexel.edu wrote: Bill, What do you mean by high voltage tank? When I hear this term, I think of the oil- (and PCB-) filled tank housing the transformer on an old generator; but there's nothing like that on the R-Axis. Do you mean the blue box housing the detector controller? If so, then I can tell you that we've had ours plugged into a 1000 VA UPS (APC Back UPS Pro) for 10 years, with never a glitch (and I'm told that Philly power is not pretty). If instead you're referring to the high voltage tank on the generator, then I have no idea of what to do (although replacing the power cable doesn't sound like a bad idea)...you'd probably need to steal an entire 7-11 to pay for a UPS large enough to condition power for that. Pat On 26 Sep 2011, at 10:15 PM, William G. Scott wrote: Hi Citizens: We seem to run through high voltage tanks on our Raxis IV like guano goes through a goose. Has anyone else had this problem, and, more importantly, what is the best way to protect them. I am assuming it might have something to do with our electrical supply, which is a bit unreliable. Also, does anyone have an extra used functional one they want to get rid of? We've run out of 7-11s to rob to pay for this, and our friendly and helpful radiation safety staff think the best way to deal with this problem is to hack apart the power cable, so it is a current (so to speak) source of frustration. Thanks in advance. Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
Re: [ccp4bb] Mac OSX 10.7 Lion
Hi Phil: I've found few, if any advantages. I fear for the future. I've had problems getting coot to run stereo due to the X11 implementation in 10.7. Apart from that, no major problems with crystallographic software. Lion greedily uses memory, and any computer I have with less than 4 gig of memory has become extremely sluggish as a consequence of the upgrade. Ideally, you need 8 gig. Even with that, on my 2010 mini that I use for music playback, I regressed to 10.6.8, because of the audio interface. (It seems less robust, more prone to dropouts and now lacks integer mode output). Sara has been screaming at me for the last two weeks (nothing us usual in of itself) because Apple decided to get rid of Save As. Xcode and the compiler set is free again on 10.7. I've put some suggestions here for how to get rid of the most annoying new features: http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Lion_upgrade_notes All the best, Bill On Sep 9, 2011, at 1:28 AM, Phil Evans wrote: Is there any opinion or experience about whether Lion is ready for crystallographic use? Should I upgrade? Phil William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
Re: [ccp4bb] Mac OSX 10.7 Lion
On Sep 9, 2011, at 11:09 AM, William Scott wrote: (nothing us usual in of itself) I forgot to mention how delightful the spelling auto-correction feature can be. (It should have read nothing unusual in and of itself). That, at least, can be turned off.
Re: [ccp4bb] BLT wish
Yeah, it was a totally delightful interaction. So much for the Ubuntu spread
the love of humanity theme.
They have successfully migrated from figure 3 to figure 2:
http://bandcamp.tv/linux-demotivators/
As for BLT, my sense (being the unfortunate maintainer for it on fink) is that
it is dead in the water, and if CCP4 could free itself of this dependency,
those who insist upon using the GUI instead of the infinitely simpler and more
elegant command-line interface could use the OS X native port of tcl/tk.
--Bill
On Aug 17, 2011, at 6:34 AM, Edward A. Berry wrote:
Seems to me the CCP4 change is exactly in line with the developers'
response to wgscott's bug report at:
https://bugs.launchpad.net/ubuntu/+source/blt/+bug/19148
You have to have the BLT package, whether you shell bltwish or wish.
Modern BLT package doesn't contain bltwish, because
not a bug. It doesn't make sense to provide a separate shell for each Tcl
Extension. . . .
just use wish for your scripts:
#!/usr/bin/wish
package require BLT
[...]
Phil Evans wrote:
In previous CCP4 releases CCP4/ccp4i/bin/loggraph used bltwish
exec $CCP4I_TCLTK/bltwish $0 -- ${1+$@}
In 6.2.0 this has mutated to
exec $CCP4I_TCLTK/wish $0 -- ${1+$@}
which doesn't work on our systems, see error below
I've fixed it by changing back to the previous exec bltwish, but does this
new version work for other people? Should it work for me, and with what
version of TCL?
(I look forward to replacing loggraph!)
Phil
Error in startup script: can't find package BLT
while executing
package require BLT
(file /public/xtal/CCP4/ccp4-64/ccp4-6.2.0-c5/ccp4i/bin/loggraph.tcl
line 47)
invoked from within
source [file join $env(CCP4I_TOP) bin loggraph.tcl]
(file /public/xtal/CCP4/ccp4-64/ccp4-6.2.0-c5/ccp4i/bin/loggraph line 5)
William G. Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott/
Re: [ccp4bb] BLT wish
On Aug 17, 2011, at 3:25 PM, Harry wrote: Hi Bill I don't think this includes BLT, does it? No. That was what I was trying to say (apparently not very well, sorry!): On 17 Aug 2011, at 22:33, William Scott wrote: if CCP4 could free itself of this dependency... …then it could make use of the no-BLT version of tcl/tk provided with OS X 10.6 and 10.7.
Re: [ccp4bb] off-topic: Synchrotron look alike
Yeah, I know what you mean. That Zalman 3D LCD monitor put me back almost $300, and the mac mini I hooked it to, nearly another $600. My SGIs only cost $12K each in 1998. On Jun 9, 2011, at 9:43 AM, Mayer, Mark (NIH/NICHD) [E] wrote: The sad thing is, although Macs are great crystallography platforms, stereo is hard at best, ridiculously expensive compared to Linux systems, and still requires the use of CRTs which have not been manufactured for years ...
Re: [ccp4bb] CCP4 for iphones
Until tcl/tk gets ported, this might tide you over: http://www.readpixel.com/remotetap/index.html It is a VNC display optimized for iPod/iPhone/iPad use. -- Bill - On Feb 25, 2011, at 11:54 AM, Jacob Keller wrote: Hello All, is there a ccp4 app for iphones yet? Has any structure been solved on an iphone? I know BR uses an iphone to drive his robots, but what about structures? (A question for Friday afternoon...) JPK *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu *** William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
Re: [ccp4bb] Could someone can help me to explain why EDTA-2Na can formate salt crystals
What other cations are present? Any divalent cations like Mg++ or Ca++? The Ksp of magnesium phosphate is about 10^-24, so even if you have a very small amount present, say as a contaminant with citrate or EDTA, it will crystallize. On Feb 21, 2011, at 1:22 PM, Yibin Lin wrote: Dear all, I got a lot of salt crystals in reservior solution (well solution), which contains 0.1 M phosphate/citrate ph 4.2, PEG200 47%, EDTA-2Na 0-22mM. Reservior solution appears crystals from 12mM EDTA. Could someone help me to explain why? Thank you very much! Yibin William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
Re: [ccp4bb] Problem installing CCP4 on MacOSX behind firewall?
Two ideas: 1. Create a file in your home directory called ~/.curlrc and in it put the following line: -P - ftp 2. Use wget first, install wget with fink Then put the line DownloadMethod: wget into the file /sw/etc/fink.conf (or /sw64/etc/fink.conf ). I use wget. It seems to be more robust somehow. On Oct 14, 2010, at 2:20 AM, Mads Gabrielsen wrote: I have a problem installing CCP4 on a MacOSX 10.6.4. When I follow the procedure on Bill Scott's web-pages to install the precompiled version, I get an error message saying Err http://sage.ucsc.edu stable/main Packages 403 Forbidden When trying to install it via the normal Fink way, I get curl (56) FTP response reading failed ###execution of curl failed, exit code 56 Downloading the file ccp4-6.1.13-core-src.tar.gz failed. I think there is an issue with our firewall, but apart from setting the http_proxy to what has been suggested by our IT services I don't really know how to proceed. Does anyone have any suggestions? I know I can download the disk images from the ccp4 pages, but I would like to understand what is going wrong. Cheers, Mads
[ccp4bb] embarrassingly simple MAD phasing question
Hi Citizens: Try not to laugh. I have an embarrassingly simple MAD phasing question: Why is it that F in this picture isn't required to be vertical (purely imaginary)? http://www.doe-mbi.ucla.edu/~sawaya/tutorials/Phasing/phase.gif (Similarly in the Harker diagram of the intersection of phase circles, one sees this.) I had a student ask me and I realized that there is this fundamental gap in my understanding. Many thanks in advance. -- Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA phone: +1-831-459-5367 (office) +1-831-459-5292 (lab) fax:+1-831-4593139 (fax)
[ccp4bb] Summary : [ccp4bb] embarrassingly simple MAD phasing question
Thanks for the overwhelming response. I think I probably didn't phrase the question quite right, but I pieced together an answer to the question I wanted to ask, which hopefully is right. On Oct 13, 2010, at 1:14 PM, SHEPARD William wrote: It is very simple, the structure factor for the anomalous scatterer is FA = FN + F'A + iFA (vector addition) The vector FA is by definition always +i (90 degrees anti-clockwise) with respect to the vector FN (normal scattering), and it represents the phase lag in the scattered wave. So I guess I should have started by saying I knew f'' was imaginary, the absorption term, and always needs to be 90 degrees in phase ahead of the f' (dispersive component). So here is what I think the answer to my question is, if I understood everyone correctly: Starting with what everyone I guess thought I was asking, FA = FN + F'A + iFA (vector addition) for an absorbing atom at the origin, FN (the standard atomic scattering factor component) is purely real, and the f' dispersive term is purely real, and the f absorption term is purely imaginary (and 90 degrees ahead). Displacement from the origin rotates the resultant vector FA in the complex plane. That implies each component in the vector summation is rotated by that same phase angle, since their magnitudes aren't changed from displacement from the origin, and F must still be perpendicular to F'. Hence the absorption term F is no longer pointed in the imaginary axis direction. Put slightly differently, the fundamental requirement is that the positive 90 degree angle between f' and f must always be maintained, but their absolute orientations are only enforced for atoms at the origin. Please correct me if this is wrong. Also, since F then has a projection upon the real axis, it now has a real component (and I guess this is also an explanation for why you don't get this with centrosymmetric structures). Thanks again for everyone's help. -- Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA phone: +1-831-459-5367 (office) +1-831-459-5292 (lab) fax:+1-831-4593139 (fax)
Re: [ccp4bb] Zalman
Hi Allen: I have a smaller Zalman monitor, but I defined buttons to set the screen size (and toggle stereo) like this: coot_toolbar_button(FullScreen, set_graphics_window_size(1680,999), gtk-network) Making the vertical dimension an odd number seems to be required to ensure that stereo is the right way around. Even if a saved state changes the dimensions, this will change it back, and therefore presumably reset the stereo the correct way. (It might need to be an even number for different setups, but once you find what you need, it should be reproducible). HTH, Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA phone: +1-831-459-5367 (office) +1-831-459-5292 (lab) fax:+1-831-4593139 (fax) On Oct 1, 2010, at 8:57 AM, Sickmier, Allen wrote: I recently got the 24 inch Zalman and when the coot window is maximized the 3D is reversed. I know I can minimize it slightly and move it up and down a pixel to fix it. Has anyone found a trick to leave it maximized and correct the 3D. I have tried adjusting screen position but have not found a good way to do it yet. I am using linux WS4 with nivida video card. Allen Sickmier Amgen MS 14-2A, Drop Zone: B14 DZ 2C 1 Amgen Center Dr. Thousand Oaks, CA 91320-1789
[ccp4bb] Assistant Professor faculty position: Santa Cruz, CA
Dear Colleagues: If you know of anyone who might be interested in an assistant professor position, would you please be kind enough to bring the following advertisement to their attention? http://www.nature.com/naturejobs/science/jobs/154054-Assistant-Professor Many thanks. Bill Scott
Re: [ccp4bb] how to improve Rfree?
Two very low-brow suggestions that might help: 1. Do a round of idealization in Refmac, to tighten up the geometry as much as possible. Then return to your current approach. 2. Try using phenix.refine (with the same mtz, test reflections, latest PDB, etc). The difference can sometimes be rather dramatic, especially after simulated annealing. Best of luck. Bill On Mon, October 19, 2009 5:49 am, Sylvia Fanucchi wrote: Dear all I have been refining my structure using refmac5 restrained refinement and the model currently has an R-factor of 0.19. What is concerning me is that there is quite a big discrepancy between the Rfree and the R-factor, with the Rfree being around 0.27. Furthermore, after about 10 rounds of refinement, the R-free actually starts to increase slightly although the R-factor continues to decrease. Does this mean that there is significant bias in my model? Does anybody know how I could go about addressing this problem? Thanks for any help :-) Sylvia Fanucchi Ph.D Protein Structure-Function Research Unit East Campus, Gate House Room 416 School of Molecular and Cell Biology University of the Witwatersrand Johannesburg 2050 South Africa Tel: +27 (11) 717-6348 Fax: +27 (11) 717-6351 E-mail: sylvia.fanuc...@wits.ac.za mailto:sylvia.fanuc...@wits.ac.za htmlpfont face = verdana size = 0.8 color = navyThis communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorized signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary./font/p/html William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
Re: [ccp4bb] Jobs
I always Look on the Bright Side of Life, so I take a certain solace in the fact that while this may be true, most postdoc positions pay about as well as my job, if not better. On Wed, September 30, 2009 5:52 pm, Artem Evdokimov wrote: I personally am not peeved at all, but I am getting concerned that most of the jobs advertised are postdocs. Mighty and mysterious market forces have cut very deep into the heart of structural science and this is not good. Artem
Re: [ccp4bb] Jobs
No, just California Dollars, which I think are on a par with those printed in Zimbabwe prior to April 12th. On Wed, September 30, 2009 8:27 pm, aaleshin wrote: Are the salaries compared in orders of magnitude? Or you mean other pays? On Sep 30, 2009, at 8:30 PM, William Scott wrote: I always Look on the Bright Side of Life, so I take a certain solace in the fact that while this may be true, most postdoc positions pay about as well as my job, if not better. On Wed, September 30, 2009 5:52 pm, Artem Evdokimov wrote: I personally am not peeved at all, but I am getting concerned that most of the jobs advertised are postdocs. Mighty and mysterious market forces have cut very deep into the heart of structural science and this is not good. Artem William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
Re: [ccp4bb] mosflm and hkl2000
Is it the gui or mosflm itself that crashes? The new gui is dependent upon a number of external dependencies, so you are at the mercy of the stability of those. The old gui still works fine, at least last time I checked. On Thu, July 30, 2009 4:40 pm, Marius Schmidt wrote: We have a little internal project where we want to compare the quality of data reduced with HKL2000 and IMOSFLM (mosflm) to 1.3 A. Unfortunately, imosflm with its standard settings crashes always even at lower resolution whereas HKL2000 is rock stable. Why is that so? Any experience with that? Data collected at a synchrotron, axis set to reversephi in imosflm (newest release). Suse Linux, Swap space 2 GB. Anyway, even if (i)mosflm looses orientation, it should complain and not crash. Thanks, Marius Dr.habil. Marius Schmidt Asst. Professor University of Wisconsin-Milwaukee Department of Physics Room 454 1900 E. Kenwood Blvd. Milwaukee, WI 53211 phone: +1-414-229-4338 email: m-schm...@uwm.edu http://users.physik.tu-muenchen.de/marius/ William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
Re: [ccp4bb] ccp4i, OS X 10.5.7, security enforcement
When I do this with /bin/zsh, it does the right thing. The source command
in the bltwish shell gives me ccp4i.
When I run the commands interactively in bash or sh (which is bash on os
x), the command
exec ${CCP4I_TCLTK}/bltwish $0 -- ${1+$@}
terminates the shell session instead of turning it into a bltwish shell.
So I think your process is getting killed before you look at the cat in
the box. If it is a question of ${CCP4I_TCLTK} not getting assigned, the
error you should see looks like this:
bash: /bltwish: No such file or directory
bash: exec: /bltwish: cannot execute: No such file or directory
or
sh: /bltwish: No such file or directory
sh: exec: /bltwish: cannot execute: No such file or directory
Likewise, with quantum mechanics, the mysteries disappear if you allow
that the probability function is an objective statement about where a
particle might be located, rather than a subjective statement about our a
priori knowledge of the particle's location (i.e., you reject
wave-particle duality in favor of a particle interpretation).
On Sun, July 26, 2009 2:34 pm, James Stroud wrote:
Hello All,
It seems that sh has a variable that exists and doesn't exist at the
same time (see my shell session below). Isn't such transition between
existence and non-existence reserved for quantum mechanics and eastern
philosophy? My guess is that sh has become more vigilant about
security and the exec statement. Can anyone venture a better guess as
to how the output below might happen? What's the best way around
this? But the real question is: Can the people at ccp4 look at this
and make changes to the code base before these kinds of security
features become more commonplace (for the good reason to prevent
injection attacks)?
For example:
http://www.theregister.co.uk/2009/07/21/critical_ddwrt_router_vuln/
Here is my shell session:
chernev 10% cat `which ccp4i`
#!/bin/sh
# Start ccp4i interface
# \
echo CCP4I_TCLTK is $CCP4I_TCLTK
exec ${CCP4I_TCLTK}/bltwish $0 -- ${1+$@}
source [file join $env(CCP4I_TOP) bin ccp4i.tcl]
chernev 11%
chernev 12% ccp4i
CCP4I_TCLTK is /usr/local/X11/bin
Error in startup script: can't read CCP4I_TCLTK: no such variable
while executing
exec ${CCP4I_TCLTK}/bltwish $0 -- ${1+$@}
(file /usr/local/ccp4-6.1.1/bin/ccp4i line 5)
William G. Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott/
Re: [ccp4bb] ccp4i, OS X 10.5.7, security enforcement
On Sun, July 26, 2009 5:38 pm, Edward A. Berry wrote:
William Scott wrote:
..
So I think your process is getting killed before you look at the cat in
the box. If it is a question of ${CCP4I_TCLTK} not getting assigned,
the
error you should see looks like this:
bash: /bltwish: No such file or directory
bash: exec: /bltwish: cannot execute: No such file or directory
It seems bash treats undefined variables as the null string:
bash-3.2$ echo ${wxyz}/abc
/abc
while csh prints an error message, but not like the OP's:
oswego 185% echo ${wxyz}/abc
wxyz: Undefined variable.
apparently tcl gives the error message reported:
oswego 187% tclsh
% printf ${wxyz}/abc
can't read wxyz: no such variable
So I think the exec is successful but some ensuing tcl script is
not inheriting the environment.
The exec is working both with bash/sh and zsh examples, but the string
source [file join $env(CCP4I_TOP) bin ccp4i.tcl] isn't getting passed
into the wish shell in any of these. The script as written doesn't work.
Maybe you need a here string. If you run the bash/sh example without the
$0 -- ${1+$@} stuff, and then paste in the source string manually
after the prompt, it does what he wants (i.e., works).
Re: [ccp4bb] ccp4i, OS X 10.5.7, security enforcement
On Sun, July 26, 2009 6:07 pm, William Scott wrote:
On Sun, July 26, 2009 5:38 pm, Edward A. Berry wrote:
William Scott wrote:
..
So I think your process is getting killed before you look at the cat in
the box. If it is a question of ${CCP4I_TCLTK} not getting assigned,
the
error you should see looks like this:
bash: /bltwish: No such file or directory
bash: exec: /bltwish: cannot execute: No such file or directory
It seems bash treats undefined variables as the null string:
bash-3.2$ echo ${wxyz}/abc
/abc
while csh prints an error message, but not like the OP's:
oswego 185% echo ${wxyz}/abc
wxyz: Undefined variable.
apparently tcl gives the error message reported:
oswego 187% tclsh
% printf ${wxyz}/abc
can't read wxyz: no such variable
So I think the exec is successful but some ensuing tcl script is
not inheriting the environment.
The exec is working both with bash/sh and zsh examples, but the string
source [file join $env(CCP4I_TOP) bin ccp4i.tcl] isn't getting passed
into the wish shell in any of these. The script as written doesn't work.
Maybe you need a here string. If you run the bash/sh example without the
$0 -- ${1+$@} stuff, and then paste in the source string manually
after the prompt, it does what he wants (i.e., works).
I think the trick is to put single quotes around the here string, eg, in
zsh, this will work:
exec ${CCP4I_TCLTK}/bltwish 'source [file join $env(CCP4I_TOP) bin
ccp4i.tcl]'
By the way, why do all this instead of just issuing the command ccp4i ?
Re: [ccp4bb] Ligand PDB
Dear protein.chemist: Try elbow.builder or phenix.elbow or whatever it is currently called. It will optimize the geometry. Good.luck Bill.Scott On Tue, July 21, 2009 1:23 pm, protein.chemist protein.chemist wrote: Dear All, What is the best way to find the coordinates of a ligand. I do not find teh ligand in Pdb.org. I am trying to draw it in prodrug but the server is showing error. Also if I draw it how do I make sure that the geometry is correct. Thanks, Mariah -- Mariah Jones Department of Biochemistry University of Florida William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
Re: [ccp4bb] ccp4i permission problem
% fink describe ccp4 Information about 9170 packages read in 3 seconds. snip Invoke optional ccp4i gui for the first run using sudo ccp4i on 10.4, or sudo /bin/zsh followed by source /sw/bin/init.sh ;ccp4i on 10.5 to permit global configuration. Thereafter, you can invoke ccp4i without sudo. /snip On Thu, July 9, 2009 1:25 pm, Raja Dey wrote: Hi, I just finished installation of ccp4 current version in a new macbook pro using fink. When I typed ccp4i in a console and press enter I got the following message: You are the first person to run this version of CCP4i and it is trying to automatically configure and save information to the file: /sw/share/xtal/ccp4-6.1.1/ccp4i/etc/UNIX/configure.def but you do not have write permission for this directory. Please get the permission who installed CCP4i to run it and do the configure. It is OK to continue running CCP4i. Every time the same message is coming at the beginning. Could you please tell me what I should do at this point. Thanks... Raja See the Web#39;s breaking stories, chosen by people like you. Check out Yahoo! Buzz. http://in.buzz.yahoo.com/ William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
[ccp4bb] small-angle scattering and radiation damage control
Hi folks: A colleague of mine here is doing small angle X-ray scattering at SSRL and finding his samples are suffering significant radiation damage. He asked me for advice as to what potential radical scavengers might be useful. I told him to take 10 mg of ascorbic acid and to call me in the morning. Anyone have a better suggestion that I might be able to pass along to him? Many thanks in advance. Bill William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ LinkedIn: http://www.linkedin.com/in/wgscott
Re: [ccp4bb] error in ccp4i
The answer to this was to ensure that the file /etc/hosts is present and contains the line 127.0.0.1 localhost William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ On May 16, 2009, at 6:38 AM, Sebastiano Pasqualato wrote: hi there, I'm using ccp4 installed via fink on my macbook pro, and suddenly the program complains that it cannot connect to the database server and won't let me run a combat job with the following error: Using CCP4 programs from /sw/share/xtal/ccp4-6.1.1/bin CCP4i failed to connect to database server after 1 attempt(s) Accessing the project database directly for this session ERROR opening socket connection in NotifyDatabase: Arguments: 159 hect UpdateStatus RUNNING -pid 916 SERVER_HOST: localhost SERVER_PORT: 4441 Error : couldn't open socket: host is unreachable ERROR opening socket connection in NotifyDatabase: Arguments: 159 hect UpdateStatus FINISHED SERVER_HOST: localhost SERVER_PORT: 4441 Error : couldn't open socket: host is unreachable Any clue? thanks a lot, ciao s
Re: [ccp4bb] CCP4 updates and the problem pages
I just did the same today. Those that are missing from the 4-03 patch (at least the src version) included: scala.f version.fh refmac5.tcl scalepack2mtz.com dtrek2mtz.com pname2.com import_scaled.script also there was a tcl++ fix William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ On May 11, 2009, at 3:35 PM, Ben Eisenbraun wrote: If I download and apply a patch; e.g.: ftp://ftp.ccp4.ac.uk/ccp4/6.1.1/updates/ccp4-6.1.1-linux-i386-patch-04_03_09.tar.gz Can I assume that all the problems listed on the problem pages prior to April 3, 2009 will be in that patch? Or do I still need to go through the problem pages and update things by hand? Thanks. -ben -- | Ben Eisenbraun | Software Maintainer| | Structural Biology Grid | http:// sbgrid.org | | Harvard Medical School | http:// hms.harvard.edu |
Re: [ccp4bb] imosflm in ccp4 6.1.0 in linux problems
Hi Paula:
Here is more info:
http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/CCP4-6.1.0_on_Ubuntu_Ibex
(There is no reason why you would have to do step 1.)
Sorry, but I couldn't figure out how to append the link using my iPod
while undergoing mind-numbing boredom in an interminable faculty
meeting.
As for the MOSDIR, I found this alias helpful:
alias imosflm='MOSDIR=${PWD} imosflm'
The single quotes are crucial. This makes whatever directory from
whence you issue the command the $MOSDIR.
HTH,
Bill
On Jan 6, 2009, at 3:18 PM, William G. Scott wrote:
The ActiveTcl distribution can be installed anywhere, eg /opt
Then point imosflm to the wish binary in that.
William G. Scott
(via iPod and gmail -- forgive the typos and brevity)
Please reply to wgsc...@chemistry.ucsc.edu
On Jan 6, 2009, at 3:03 PM, Salgado, Paula
p.salg...@imperial.ac.uk wrote:
Hi everyone
I've been trying to run the new imosflm version from ccp4i 6.1.0
gui on ubuntu 8.0.4, but keep having problems. After struggling
with it to search for the correct MOSDIR directory path, it then
complained it was missing several packages from wish8.4. I did
manage to find some of them, but after searching the web I still
can't find:
treectrl 2.1
img::png 1.3
img::gif 1.3
img::jpeg 1.3
can anyone tell me where I can download them or what other
solutions to get imosflm to run properly?
Thanks a lot
Paula
Re: [ccp4bb] imosflm in ccp4 6.1.0 in linux problems
On Jan 6, 2009, at 7:10 PM, William Scott wrote: (There is no reason why you would have to do step 1.) Sorry, that should have been no reason ... to do step THREE.
[ccp4bb] OS X 10.4.11 and mmdb in ccp4-6.1.0 libtool: internal link edit command failed
Hi Citizens: When compiling ccp4 on OS X v. 10.4.11, I get the following failure for libmmmdb.dylib: It works fine on 10.5.5, and mmdb v. 1.19 itself (used for coot) compiles fine under the same conditions. gcc -dynamiclib -flat_namespace -undefined suppress -fPIC -fno-common - install_name /sw/lib/ccp4-6.1.0/libmmdb.dylib -all_load libmmdb.a -o libmmdb.dylib -lstdc++; gcc -dynamiclib -flat_namespace -undefined suppress -fPIC -fno-common -install_name /sw/lib/ccp4-6.1.0/ libccp4c.dylib -all_load libccp4c.a -o libccp4c.dylib ld: multiple definitions of symbol ___floatdisf /usr/lib/gcc/i686-apple-darwin8/4.0.1/libgcc.a(_floatdisf.o) private external definition of ___floatdisf in section (__TEXT,__text) /usr/lib/gcc/i686-apple-darwin8/4.0.1/../../../libgcc_s. 10.4.dylib(_floatdisf_s.o) definition of ___floatdisf ld: multiple definitions of symbol ___floatdidf /usr/lib/gcc/i686-apple-darwin8/4.0.1/libgcc.a(_floatdidf.o) private external definition of ___floatdidf in section (__TEXT,__text) /usr/lib/gcc/i686-apple-darwin8/4.0.1/../../../libgcc_s. 10.4.dylib(_floatdidf_s.o) definition of ___floatdidf ld: multiple definitions of symbol ___divdi3 /usr/lib/gcc/i686-apple-darwin8/4.0.1/libgcc.a(_divdi3.o) private external definition of ___divdi3 in section (__TEXT,__text) /usr/lib/gcc/i686-apple-darwin8/4.0.1/../../../libgcc_s. 10.4.dylib(_divdi3_s.o) definition of ___divdi3 ld: multiple definitions of symbol ___udivdi3 /usr/lib/gcc/i686-apple-darwin8/4.0.1/libgcc.a(_udivdi3.o) private external definition of ___udivdi3 in section (__TEXT,__text) /usr/lib/gcc/i686-apple-darwin8/4.0.1/../../../libgcc_s. 10.4.dylib(_udivdi3_s.o) definition of ___udivdi3 ld: multiple definitions of symbol ___umoddi3 /usr/lib/gcc/i686-apple-darwin8/4.0.1/libgcc.a(_umoddi3.o) private external definition of ___umoddi3 in section (__TEXT,__text) /usr/lib/gcc/i686-apple-darwin8/4.0.1/../../../libgcc_s. 10.4.dylib(_umoddi3_s.o) definition of ___umoddi3 /usr/libexec/gcc/i686-apple-darwin8/4.0.1/libtool: internal link edit command failed William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
Re: [ccp4bb] COOT Problem
Does ccp4i work? On Thu, December 11, 2008 8:06 pm, Jayashankar wrote: since its a same coot problem, i have one more, i am using mac 10.5 leopord osx the thing is, i dont get any pop upped table even after i do a translate and do a real space refinement . is it a bug or is it a problem in setups of other supportive libraries S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany. On Fri, Dec 12, 2008 at 2:22 AM, Ethan Lai tf...@imcb.a-star.edu.sg wrote: Dear all, I have recently installed Coot version 0.5 on Fedora 9. However, when I tried to open a mtz file, the following error occurs. CCP4 library signal library_file:Bad mode (Error) raised in ccp4_file_readchar Any advices? Thanks! William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
Re: [ccp4bb] O/T: can a protein which dimerizes in solution crystallize as a monomer?
Yo Thierry: The periplasmic domain of the aspartate receptor, in the absence of ligand, 1lih, is a dimer, but crystallizes as a monomer in the sense that there is one monomer per asymmetric unit. There is a disulphide bond between two Cys36 that maintains it as a dimer (and indeed reduction of this bond inhibits crystallization). Each of two ligand binding sites spans both monomers. So based on that, the biologically relevant form is definitely a dimer, so you can't conclude otherwise based on the fact that it crystallizes as one monomer per asymmetric unit. Now if it were to crystallize in a space group lacking a crystallographic 2-fold coincident with the natural dimer axis, that might be a different story. When you add aspartate, it crystallizes as a dimer with only one of two potential binding sites occupied by the ligand. Bill William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ On Dec 1, 2008, at 2:47 PM, Fischmann, Thierry wrote: Dear fellow crystallographers, This is a question which is not CCP4-related. Is anybody aware of a protein which is known to be a dimer in solution (say by SEC), and yet crystallizes as a monomer? Wouldn't the high concentration in the crystallization drop further favor dimerization? In other words, if a protein crystallizes as a monomer, can I conclude that it does not form biologically relevant dimers in solution? Thank you in advance for your replies. Thierry * This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited -- Please immediately and permanently delete.
Re: [ccp4bb] Crystallographic computing platform recommendations?
Hi Anna: I think the main thing to emphasize in summary is that any of the options various people have suggested would be far more than adequate to do refinement or model building with coot. In my limited personal experience, unless you have something as big as the ribosome, you won't be forced to resort to 64-bit OS. I have the slowest first- generation iMac at home, and that is more than adequate for anything we have done. Computers simply aren't rate-limiting anymore, so finding an operating system and hardware that you are comfortable with should probably be your main priority. Bill William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ On Nov 18, 2008, at 10:41 AM, Anna S Gardberg wrote: Dear list, Thank you all for the helpful and thoughtful advice about crystallographic computing systems. Before I get into the (first day's) summary, I have a followup question: Has anyone worked with refinement or coot rebuilding of 1.0 Ang. structures on an iMac? If so, what was your experience of it? Here is a summary of the advice so far: OPERATING SYSTEM 1. There was nearly unanimous agreement that Windows isn't really an option. Since I feel antipathy for Vista anyway, that part of the decision will be easy! 2. While many replies suggested 64-bit operating systems, especially if RAM exceeds 4 GB, many also warned of problems I might face compiling coot and CCP4 under a 64-bit OS, and their solutions seem to require more Linux-fu than I currently possess. However, it seems that compiling programs as 32 bit will work fine under a 64-bit OS, and can be recompiled as 64- bit (with lots of cursing and asking for advice, presumably) when an application demands it. 3. For ease of maintenance, Ubuntu Linux was generally recommended over others, but there were several Red Hat/Fedora proponents, as well as support for other Linux systems (Linuces?). 4. Many recommended MacOSX for least-hassle use by a non-guru. I must say, this sounds blissful, for I have lost many days of my life to the hassles of stressful software installation. HARDWARE 1. Many of the suggestions involved constructing systems from components, a feat beyond my current skill and inclination. Thus, I will purchase a pre-built system. 2. If going with OSX, there was disagreement about the necessity for a Mac Pro; some responders thought a high-end iMac would be fine. Has anyone worked with 1.0 A structures on an iMac? 3. Eddie Snell made the point that most crystallographic software cannot take advantage of multiple processors yet. Still, as some people pointed, it is often convenient to try several refinement options at the same time, so there would be greater convenience with more processors. GRAPHICS/ DISPLAY 1. NVidia graphics cards were recommended over ATI. There was concern that Linux drivers would not be available for the very newest ones. 2. Some recommended dual-monitors, to give you a place to put all of your open windows.
Re: [ccp4bb] Crystallographic computing platform recommendations?
The main differences aren't cosmetic, but rather free accessibility of updates and distributions, as well as attitude aka philosophy. Advantages of Ubuntu include frequent OS updates, debian-based package management system (which admittedly is a matter of taste, but it is one of the original package management systems), an active user-based support community, extremely good internationalization support, and a major financial commitment to keeping everything free and open: http://www.ubuntu.com/community/ubuntustory/foundation from the Canonical corporation, headed by Mark Shuttleworth, a South African anti-racist entrepreneur who manages to defy the cynics: http://rixstep.com/2/1/20060712,00.shtml Any software that runs on RH/Fedora will run on Ubuntu and vice versa, so that should not be an issue. I'm running Xubuntu by the way (xfce4), but I also have the options of logging into KDE or gnome (Kubuntu and vanila Ubuntu) as well as other window managers. For me, installing vanilla ubuntu first and then xfce4 worked fine. I made the transition by installing on a new partition (new disk) and booting into it, back when Breezy was introduced. I never looked back. I've put some more propaganda here: http://sage.ucsc.edu/xtal/wiki/index.php/Scientific_Computing_on_Ubuntu Bill On Nov 18, 2008, at 9:23 AM, Andreas Förster wrote: Re: Switching from Fedora to Ubuntu. Don't. Stick with Fedora if it works for you. If you're tempted by Ubuntu because of the coolness, the bling, the color, the limited customizability or the lack of root, a Mac will get you all of this much more abundantly. If you're used to Redhat/Fedora, stick with it. Everything crystallography related works on it. I tried to set an ancient Vaio up with xUbuntu and went back to Redhat 9 after too much frustration. Things are not where they're supposed to be and don't work as they should. This is from a Redhat perspective, obviously, which I've been using since 5.2. Andreas Edward Snell wrote: That would have saved me a lot of time and frustration! Now if only I can remember this for the next time JI have a 64bit Fedora 9 system running on an Lenovo Thinkstation D10 – you can buy this without the operating system. I used the 64bit option as I’m processing very high resolution X-ray data and needed to use more memory. I was able to get a 16 GB system for a reasonable cost. If you are a tinkerer and want a few days of ‘fun’ this is a way to go. If not, commercially available Linux systems are available but I found few with a large memory capacity. Coot and CCP4 were a pain to compile in 64 bit mode (not the developers problem, just mine for trying to get them to work in 64 bit). I had to play with some header definitions, lop h’s off etc, add using namespace std and, install a lot of libraries but they now work well. Coot reads all the svg files and displays all the pretty icons. I like the PC Linux route mainly because the hardware is less expensive and easier to swap out components. I am used to Fedora and manage my own system so for the moment I plan to stick with that but it sounds like Ubuntu looks like an interesting way to go. Has anyone had any experiences in transitioning from Fedora to Ubuntu? Is it something to think about, a Thanksgiving project mainly? Cheers, Eddie Edward Snell Ph.D. Assistant Prof. Department of Structural Biology, SUNY Buffalo, Hauptman-Woodward Medical Research Institute 700 Ellicott Street, Buffalo, NY 14203-1102 Phone: (716) 898 8631 Fax: (716) 898 8660 Email: [EMAIL PROTECTED] Telepathy: 42.2 GHz Heisenberg was probably here! *From:* CCP4 bulletin board [mailto:[EMAIL PROTECTED] *On Behalf Of *Michel Fodje *Sent:* Tuesday, November 18, 2008 10:28 AM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] Crystallographic computing platform recommendations? On Tue, 2008-11-18 at 09:40 -0500, James M. Vergis wrote: 2) Graphics Cards: I like the Nvidia cards since they provide linux drivers. ATI also does now. I would say the only thing I don't like about them is when you do a kernel update you have to remake the driver. I would just add that for those using Fedora, you can avoid having to remake the driver by using the RPMFusion repositories to install the Nvidia drivers. This way updating the kernel automatically installs the corresponding Nvidia kernel module. The same applies to AMD/ATI drivers. -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London
Re: [ccp4bb] terminal window
If you installed fink, in a startup file you need to issue source /sw/bin/init.sh or source /sw/bin/init.csh depending on whether you are using bash/zsh or tcsh. This will set up the ccp4 environment for you automatically. If you installed ccp4 in some other way (eg /usr/local), then you have to source the appropriate environment file in $CCP4/include This will define $CBIN for you, and then the arp/warp environment definitions should then work. Bill William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ On Oct 20, 2008, at 12:22 PM, Jayashankar wrote: Dear Friends, I recently followed William Scott page and followed his advice to install fink and crystallographic softwares... But out of my curiosity i once tried to install arpwarp as per the instructions and it was done successfully, no problem, but whenever i open a new terminal window,i see the following lines Cannot setup ARP/wARP Variable $CBIN is not defined Please install CCP4 first i dont know how to get rid of them, or do they mean something. (Mac OS X 10.5) thank you S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany.
[ccp4bb] off-topic: Enzymology textbook recommendations?
Hi Folks: I just found out that in a couple of weeks I am going to be teaching a graduate student-level enzymology course. Can anyone recommend a good text, and possibly good websites authored by people who are predisposed to consider plagiarism the highest form of complement? Many thanks in advance. Panically-stricken yours, Bill Scott William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
Re: [ccp4bb] CCP4i on MacPro under Leopard
Glad it worked. I should have written sudo /bin/bash or sudo /bin/zsh or sudo /bin/tcsh followed by sourcing the appropriate startup script. However, if I run the tcsh command, I get this error: limit: stacksize: Can't remove limit (Invalid argument) oddly, this does not happen with a non-root version of tcsh. It is easier I think just to use /bin/bash or /bin/zsh in this case. On Aug 25, 2008, at 9:09 AM, Anita Bentley wrote: Thanks a lot for this hint: it works! Including REFMAC, which ran to completion and used Arp/Warp to add waters successfully. Anita Le 25 août 08 à 16:04, William G. Scott a écrit : Under 10.5.X, sudo doesn't inherit the environment. So the best thing to do is start a root process like this: /bin/bash (or /bin/zsh or /bin/tcsh ) source /usr/local/ccp4-6.0.2/include/ccp4.setup-bash (or whatever it is for your shell) Then issue ccp4i William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ On Aug 25, 2008, at 6:05 AM, Anita Bentley wrote: My faithful old Mac G5 siezed up and I have to use a brand new MacBook Pro from now on. It's an Intel machine with Leopard. I managed to install CCP4 together with TLK/BLK programmes. After a long while searching for bltwish routines I discovered that they are automatically installed in /usr/local/bin and not in /sw/bin as suggested in the ccp4 setup files (!). With this problem sorted out, I was able to start ccp4i GUI fine. I get the message that I am the first person to run this version ... and should get the right person to configure the interface However, when I try to run ccp4i with sudo in order to have the priviledges to configure it, I am unable to run it: macbookpro-bentley 7% sudo ccp4i /usr/local/ccp4-6.0.2/bin/ccp4i: line 4: /bltwish: No such file or directory /usr/local/ccp4-6.0.2/bin/ccp4i: line 4: exec: /bltwish: cannot execute: No such file or directory I've modified the -sh and -csh files (I have a one-line login.com to get me under csh as user) to no avail. What do I have to do to be able to configure the interface??? The underlying problem is that I cannot run REFMAC in the present state of things, I get the following error: Error from script /usr/local/ccp4-6.0.2/share/ccp4i/scripts/refmac5.script: can't read cell: no such variable which makes me think the configuration of the interface is not quite right. Any help is greatly appreciated! Anita Anita Lewit-Bentley LBPA Ecole Normale Supérieure de Cachan 61, avenue du Président Wilson 94235 Cachan cedex FRANCE tel: 33-(0)1-47 40 76 65 fax: 33-(0)1 47 40 76 71 e-mail: [EMAIL PROTECTED]
Re: [ccp4bb] DNA building program
coot On Aug 12, 2008, at 3:35 PM, Raja Dey wrote: Dear Friends, Does anyone can refer a reliable program for building 3D model of a double stranded straight DNA from sequence? Thanking you in advance... Raja
Re: [ccp4bb] Ammonium citrate tribasic buffer
Wikipedia claims Hasselbach is a misspelling: http://en.wikipedia.org/wiki/Henderson-Hasselbalch_equation Since Wikipedia has now replaced the social consensus as the final arbiter of truth ... On Aug 7, 2008, at 3:22 PM, Juergen Bosch wrote: Just on a side note, can someone clarify why Hasselbach is not Hasselbalch or vice versa ? Or is that the same guy just somewhere sometime misspelled and for ever in the records ? See here: http://www.britannica.com/EBchecked/topic/261188/Henderson-Hasselbach-equation Jürgen On 7 Aug 2008, at 15:12, [EMAIL PROTECTED] wrote: Good points! Not only citrate is inappropriate for buffers in the pH 6.5-7.5 range, but also (as pointed out by your colleagues at UCSC, but probabbly elsewhere, polyprotic acids are hard to handle, as their pKa change in a significant fashion depending on their concentration. In this case, the Henderson-Hasselbalch equation must be written in terms of activities rather than concentrations, otherwise it is totally useless. Nadir Mrabet Selon William G. Scott [EMAIL PROTECTED]: There are 3 pKa's for citric acid: 3.15, 4.77, and 5.19 so it is going to be a lousy buffer at pH 6.7 to 7.25. Also, you need to know what concentration your buffer is, and whether that concentration is with respect to the citrate ion or what. It won't be tribasic with respect to ammonium ion near neutral pH. So if for example you need 1M of this buffer, the simplest thing to do is make up a 1M stock solution of tribasic ammonium citrate and a 1M stock solution of of citric acid and then mix the two together. You can calculate the ratio using the Henderson-Hasselbalch equation or just titrate one into the other while stirring in the presence of a pH electrode. (You'll have to use the pH electrode approach if you took introductory chemistry from anyone other than me at UCSC since my colleagues think that polyprotic acids are too stressful for our undergrads.) William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ On Aug 7, 2008, at 12:42 PM, E rajakumar wrote: Dear All Sorry for non crystallographic query. Can any body mail me how to prepare Ammonium citrate tribasic (citric acid triammonium salt) buffer pH 6.7 to 7.25 and also what is the pKa value. Thanking you in advance Rajakumara E. Rajakumara Postdoctoral Fellow Strcutural Biology Program Memorial Sloan-Kettering Cancer Center New York-10021 NY 001 212 639 7986 (Lab) 001 917 674 6266 (Mobile) Get your new Email address! Grab the Email name you#39;ve always wanted before someone else does! http://mail.promotions.yahoo.com/newdomains/aa/ Pr. Nadir T. Mrabet Cellular Molecular Biochemistry INSERM U-724 UHP - Nancy 1, School of Medicine 54505 Vandoeuvre-les-Nancy Cedex France Tel : +33 (0)3.83.68.32.73 Fax : +33 (0)3.83.68.32.79 E-mail : [EMAIL PROTECTED] - 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] sequential renumbering of a messed up pdb file
They are adjacent. On Jul 31, 2008, at 4:47 PM, Abhinav Kumar wrote: I have a program that can fix it provided the residues with same number are not adjacent in the pdb file. Please let me know and I can send you the program. Thanks Abhinav Abhinav Kumar JCSG @ SSRL, MS 99 2575 Sand Hill Road Menlo Park, CA 945025-7015 Phone: 650 926 2992 Fax: 650 926 3292 On Jul 31, 2008, at 4:09 PM, William Scott wrote: Hi folks: I am hoping there is a simple answer I have overlooked to the following question. I have a pdb file in it that has multiple residues that have the same number and chain ID, and I want to force them to be renumbered sequentially. Is there a simple way to do so (eg, pdbset) or am I doomed to fixing it manually? Thanks. Bill Scott William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
Re: [ccp4bb] Idealizing helix
Refmac should be able to do this without moving stuff too much. CNS (no simulated annealing) also can do this kind of thing. If it becomes problematic, you can restrain the backbone. You can also do this via coot (which uses refmac I am pretty sure). William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ On Jul 30, 2008, at 1:51 PM, Mirek Cygler wrote: I am looking at a protein model (no electron density) that has a highly distorted helix. I would like to idealize this helix in the context of the protein, e.g. do least squares idealization with restrains on the backbone torsion angles, with the smallest possible divergence from the initial structure. Could someone point me to program that can do it? Mirek
Re: [ccp4bb] os x wiki
Hi Patrick: I'm afraid all the insidious stupidness originates from moi. Anyway, the machine hosting this thing has a roached power supply, thanks to the fact that the University electrical supply resembles that produced by, in terms of its stability and reliability, an underfed gerbil- wheel-powered generator in Guatemala. So we ordered a new one from Apple, and hopefully within the next three or four years I will have it back on line. I backed up the mysql database for the wiki every day, but I can't get it to work on any other computer, doubtless due to my complete inability to follow simple instructions or to remember any of the passwords I had used. Hence the first sentence. Sorry 'bout this. Bill William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ On Jul 23, 2008, at 12:27 PM, Patrick Loll wrote: Does anyone know if the Crystallography on OS X Wiki is down? I haven't been able to access the site for a few days, but I don't know if the site is down, or if some new and insidious stupidness has been perpetrated by the rocket scientists who control IT in our institution...thanks. Pat --- Patrick J. Loll, Ph. D. Professor of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 [EMAIL PROTECTED]
Re: [ccp4bb] creat 3D small molecules
My favorite is the elbow builder in phenix. You give it a smiles string and it will build (and optionally, optimize either classically or quantum-mechanically) your small molecule structure. http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification http://www.phenix-online.org/documentation/elbow.htm You can also build one using a smiles string in coot. http://www.msg.ucsf.edu/local/programs/coot/user-manual.html#SEC112 On Jul 22, 2008, at 1:42 PM, Ariel Talavera wrote: Hi all, I need to create the coordinates of a small molecule with no structure yet. Could any one tell me what program can I use to build small molecules? Thanks in advamced. Ariel -- Ariel Talavera, Lic. Dept. of Computational and Structural Biology Center of Molecular Immunology P.O.Box 16040, Havana 11600 Cuba tel: (53-7) 271 7933, ext. 219 fax: (53-7) 272 0644 email: [EMAIL PROTECTED]
[ccp4bb] Fwd: DNA/RNA base stacking restraint add-on to CNS avaliable.
Date: Mon, 14 Jul 2008 15:22:52 -0700 (PDT) From: Martin.Laurberg [EMAIL PROTECTED] To: [EMAIL PROTECTED] Cc: CCP4BB@JISCMAIL.AC.UK Subject: DNA/RNA base stacking restraint add-on to CNS avaliable. Dear all, A DNA/RNA base stacking restraint add-on to CNS version 1.21 is avaliable for download. This may be useful for DNA/RNA-containing structures at lower resolution. http://rna.ucsc.edu/pub/stack.tar -ML -- Martin Laurberg, PhD Noller Laboratory 225 Sinsheimer Laboratories University of California at Santa Cruz CA-95064 Santa Cruz USA Tel +1 (831) 459 35 84 Fax +1 (831) 459 37 37
[ccp4bb] Is there an easy way to down-weight figures of merit?
Hi Citizens: I realize this is one of those warranty-violating questions, but is there a simple way to down-weight figures of merit, or the equivalent in terms of Hendrickson-Lattman coefficients? I'm trying to generalize and automate a procedure for solving RNA structures without heavy-atom phases by feeding phaser random-sequence model A-form RNA helices. It pretty much works, but there comes a point where I want to use the phase probability distribution from the partial/inaccurate model in solvent-flattening while discarding the model, with the hope of minimizing model bias. The problem is that if the refinement of the partial/inaccurate model goes reasonably well, the FOM become inflated to the point where solvent-flattening becomes less effective for improving and correcting phases. Thanks. Bill Scott
[ccp4bb] summary: headhunters [off-topic]
Hi Citizens: I've taken the liberty of summarizing/anonymizing/interpreting a bit with the varied and colo[u]rful responses. They fell into three general categories. Thanks to all who responded and offered sage advice... 1. The unanimous consensus was that headhunters aren't useful for finding consulting gigs (my main purpose for asking is the desire to supplement my current salary, or lack thereof -- the California dollar makes the US dollar look robust). Rather, several replies underscored the importance of connections. Headhunters might be of use for finding (full-time) industrial positions. Several people suggested where to look for possible consulting arrangements (which I believe will be immensely helpful). Some people suggested there might be good money to be made from people willing to pay me not to offer my opinions. 2. There were several trouble in paradise/are you insane/being sarcastic type inquiries. These best answered by the following Woody Guthrie quote (1937): California is a garden of Eden, a paradise to live in or see, But believe it or not, you won't find it so hot If you ain't got the do re mi. 3. By the way, can you fix my computer/update coot/etc? No, but I did find a good motivational poster like the ones you see advertised in magazines on airplanes: http://despair.com/consulting.html Cheers, Bill
Re: [ccp4bb] Reminder - still no 3D stereo under OS X 10.5
Is this true for native aqua gui programs, or just the X11 ones? On Thu, June 26, 2008 1:50 pm, eortlund wrote: Hi Everyone, I am writing everyone just to remind all those who are thinking of upgrading to 10.5 that currently quad-buffered stereo will not work for coot, pymol etc... since Apple has not done a good job with the video drivers in Leopard. So if you would like to use 3D stereo viewing, do not purchase any new Mac hardware since it will not run OS X 10.4. Eric -- Eric Ortlund, Ph.D. Assistant Professor Department of Biochemistry Emory University School of Medicine 1510 Clifton Road, NE, Room G235 Atlanta, GA 30322 Tel 404-727-5014 Fax 404-727-2738 [EMAIL PROTECTED] William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
Re: [ccp4bb] query on DNA-protein complex preparation for crystallization
Check the purity of the DNA in solution: A(260 nm)/A(280) = 1.8 for fully deprotected DNA, and you should see a nice clean simple curve with a peak very close to 260 nm. Check it on a denaturing gel. Smearing indicates incomplete deprotection. This is usually the cause of solubility problems. Sometimes resuspending in a strong cationic buffer (say 100 mM Tris pH 8.5) might be required. For crystallization it is probably best to have Na+ or K+ as a counterion, rather than Mg++. So you need to dialize against a high concentration of monovalent salt first, not just deionized water. On Jun 22, 2008, at 9:10 AM, E rajakumar wrote: Hi Artem Evdokimov Thank you for the mail. I have synthesized DMT-on oligos in our laboratory. Deprotection was performed treating with ammonium hydroxide for 15 hours at 55C. Then, DMT-on oligo was separated from off using RPHPLC. DMT was cleaved by treating with 20% glacial acetic acid for one hour. Then, DMT-off DNA was separated from DMT, again using RPHPLC. Lyophilized DMT-off oligos were dissolved in 3 mL of Milli Q water and dialysed against 2 L of milli Q water for 4hrs by changing water 2 times. Then complemntary oligos are concentrated around 1.0 mM and mixed them and concentrated further to 1.5 mM (duplex). 2 mM (final concentration) of Magensium chloride was added to oligos and concentrated to half of the volume. While concentrating oligos become viscos and white precipitate. however, annealing did not help to dissolve the white precipitate. I kept oligos in distilled water, without adusting pH. Please can you mail if I iginite DNA on metal spatual, eiether burns or not, what it indicates? Thanking you Rajakumara [EMAIL PROTECTED] wrote: Hi, How did you synthesize the DNA? I assume external vendor (so few people make their own these days)? How was the DNA purified? Sometimes if only a 'desalting' step is used there may be 'other chemicals' in the mix. Also, what pH was your DNA at, and in what buffer (if any)? If your DNA degraded you may have Pi in solution, which forms insoluble precipitates with many counterions. So, first of all I would check your white precipitate - does it dissolve in anything at all? If it does dissolve, what pH does it have? Does it run on an agarose gel? When you ignite a speck of it on a clean metal spatula - does it burn or does it just sit there (and what color does it become). Normally you can prepare DNA-protein complexes in a variety of ways, including direct addition, concentration, counterdialysis, etc. Regards, Artem -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of E rajakumar Sent: Saturday, June 21, 2008 5:48 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] query on DNA-protein complex preparation for crystallization Dear All Sorry for non-crystallography question. I have synthesized two complementary strands of 16 bases in length for making duplex DNA and co-crystallization with DNA binding protein. I have mixed two complementary strands of 1:1 molar ratio (0.5 mM) in water and concentrated to 1.5 mM (Duplex), while concentrating solution becomes viscous and turned to white precipitate. However, adding 2 mM Magnesium chloride followed by annealing (heating at 90C for 10 minutes and followed by cooling to room temperature) did not help to dissolve the white precipitate. Please can you give me suggestions on following queries? 1.How do I dissolve white precipitate? Is increasing divalent cation or keeping duplex in particular pH could help in dissolving the precipitate? 2.How do I prepare DNA-protein complex? I mean, can I mix diluted DNA and protein in 1:1 molar ratio and concentrate further? Any guidance in this regard will be appreciated. Sorry, foregot to mention that any references in this regards will be great help. Thank you in Advance Rajakumara E. Rajakumara Postdoctoral Fellow Strcutural Biology Program Memorial Sloan-Kettering Cancer Center New York-10021 NY 001 212 639 7986 (Lab) 001 917 674 6266 (Mobile) Send instant messages to your online friends http://uk.messenger.yahoo.com E. Rajakumara Postdoctoral Fellow Strcutural Biology Program Memorial Sloan-Kettering Cancer Center New York-10021 NY 001 212 639 7986 (Lab) 001 917 674 6266 (Mobile) Send instant messages to your online friends http://uk.messenger.yahoo.com
Re: [ccp4bb] environ.def / default.def
Dear Eike: I think I was still asleep when I sent that last email. I am very sorry for writing Eric. Maybe I need to get glasses. tcsh and zsh are both much more user-friendly than bash, and most crystallography programs seem to assume the user is using tcsh, so that might be the best choice. However, if you really want to geek out, zsh is a lot of fun. Bill On May 17, 2008, at 9:45 AM, Eike Schulz wrote: Hello Bill, thanks a lot for making such big effort. It is a real pity but the syntax does not work properly. However, I am more or less convinced now that the whole thing is a bash / (t)csh related problem. It might be the easiest way just to switch to a different sh flavour as login shell. I hope that will settle the issue. Regardless of the success I learned a lot thanks to you and many others. The link you provided seems to be a good compilation of necessary unix knowledge - I will try to circulate it among my colleagues. Thanks again and all the best. Eike On Sat, 2008-05-17 at 08:13 -0700, William Scott wrote: Hi Eric: You shouldn't have to source or do anything with the def files. There seems to be some problems with the ccp4.setup-bash from what I have seen. If it gets sourced more than once, spaces get introduced into the PATH variable, which creates havoc. The file also locally defines setenv to try to use the csh syntax, which may or may not be problematic. I've made one that should avoid these problems and I tried to set it up to what looks like you need for your system. So, please try the following: 1. Eliminate all the directives to source any setup and def files from your shell startup dot files. 2. Put this file somewhere and source it. HTH, Bill PS: The zsh and tcsh shells are both more user-friendly than bash, so you might find those easier (what I sent you should work with zsh, although I have a much better one that makes use of zsh customizable completions and so forth). Here's some more info on unix shells: http://xanana.ucsc.edu/xtal/unix.html On May 17, 2008, at 1:48 AM, Eike Schulz wrote: Hello again, sourcing environ.def or ccp4.setup-bash did not help to make it work. Sourcing default.def results in -- bash: memory: command not found bash: !FITING_NR=50: command not found bash: !TRAING_NR=50: command not found bash: !ROTING_MI=60: command not found bash: !ROTING_MC=290: command not found bash: !TABLING_MI=150: command not found bash: !TABLING_MR=540: command not found --- debugging info: --- echo $CCP4 /usr/local/software/ccp4/ccp4-6.0.2 echo $CCP4I_TOP /usr/local/software/ccp4/ccp4-6.0.2/ccp4i echo $PATH /usr/local/software/ccp4/ccp4-6.0.2/src/phaser/phaser-2.1.1/build/ intel-linux/bin /usr/local/software/ccp4/ccp4-6.0.2/ccp4i/bin /usr/local/software/ccp4/ccp4-6.0.2/etc /home/eschulz1/bin /usr/local/bin /usr/bin:/bin /usr/bin/X11 /usr/X11R6/bin /opt/kde3/bin /usr/lib/jvm/jre/bin /usr/lib/mit/bin /usr/lib/mit/sbin /usr/local/software/XDS-linux_ifc_Intel+AMD /usr/local/software/coot-Linux-i386-redhat-8.0/bin /usr/local/software/ccp4/ccp4-6.0.2/bin /usr/local/software/ccp4/ccp4-6.0.2/include -- I hope this helps you ... Thanks again an best regards Eike On Fri, 2008-05-16 at 20:37 -0700, William Scott wrote: Probably. You should source either the first or the second file depending on your shell (the first for bash, the second for tcsh/csh). That might be the cause of your subsequent problem. For purposes of debugging, can you send us output for the following three commands: echo $PATH echo $CCP4 echo $CCP4I_TOP On Fri, May 16, 2008 5:22 pm, Eike Schulz wrote: Hello again, thanks to some people for their fast and helpfully very detailed advice: Including source /usr/local/software/ccp4/ccp4-6.0.2/include/ccp4.setup-bash source /usr/local/software/ccp4/ccp4-6.0.2/include/ccp4.setup into my .bashrc did indeed solve the problem with MTZDUMP when executed from the shell. Further thanks for some other corrections. But unfortunately the error persists when I try to run refmac from the ccp4i GUI - it complains not to be able to extract data from an .mtz file. Did I miss anything important? Kind regards Eike On Fri, 2008-05-16 at 14:37 -0700, William Scott wrote: On Fri, May 16, 2008 1:06 pm, Eike Schulz wrote: Hello everybody, setenv CCP4_MASTER /usr/local/software/ccp4 setenv CCP4 $CCP4_MASTER/ccp4-6.0.2 For bash, zsh, etc, you need to start with export CCP4_MASTER=/usr/local/software/ccp4
Re: [ccp4bb] No permission to CCP4I_TOP dir
Hi Raja: The root shell isn't inheriting the environment, so to ensure that everything is set up correctly, do this: sudo -s source /sw/bin/init.sh ccp4i The /sw/bin/init.sh will (indirectly) source the whole ccp4 environment setup file. On Fri, May 16, 2008 10:52 am, Raja Dey wrote: Hi Bill, The problem remains. I can use ccp4i before doing sudo -s. See below: anand2:~ rajadey$ sudo -s bash-3.2# ccp4i /sw/share/xtal/ccp4-6.0.2/ccp4i/bin/ccp4i: line 4: /bltwish: No such file or directory /sw/share/xtal/ccp4-6.0.2/ccp4i/bin/ccp4i: line 4: exec: /bltwish: cannot execute: No such file or directory bash-3.2# Raja - Original Message - From: William Scott [EMAIL PROTECTED] Date: Friday, May 16, 2008 10:44 am Subject: Re: No permission to CCP4I_TOP dir To: Raja Dey [EMAIL PROTECTED] The easiest thing is probably to initialize a shell with sudo -s and then start ccp4i and then do it. William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ On May 16, 2008, at 10:41 AM, Raja Dey wrote: Hi Bill, Could you please tell me how I can get permission to the CCP4I_TOP dir? When I am trying to plugg ARP/wARP GUI into the CCP4i interface, after clicking apply it says I have no permission. I am the only user of my macbook with intel core 2 duo (OSX 10.5). Looking forward to hearing from you... Thanks for your help... Raja William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
Re: [ccp4bb] environ.def / default.def
On Fri, May 16, 2008 1:06 pm, Eike Schulz wrote: Hello everybody, setenv CCP4_MASTER /usr/local/software/ccp4 setenv CCP4 $CCP4_MASTER/ccp4-6.0.2 For bash, zsh, etc, you need to start with export CCP4_MASTER=/usr/local/software/ccp4 export CCP4=$CCP4_MASTER/ccp4-6.0.2 setenv is specific to (t)csh. export is specific to the sh-like shells. --- ... and the .bashrc contains following entries: --- PATH=$PATH:/usr/local/software/ccp4/ccp4-6.0.2/bin/ PATH=$PATH:/usr/local/software/ccp4/ccp4-6.0.2/include/ /usr/local/software/ccp4/ccp4-6.0.2/include/ccp4.setup-bash --- I think that last line would need to be source /usr/local/software/ccp4/ccp4-6.0.2/include/ccp4.setup-bash and you shouldn't need this line: PATH=$PATH:/usr/local/software/ccp4/ccp4-6.0.2/include/ and you should get rid of the trailing slash on this line: PATH=$PATH:/usr/local/software/ccp4/ccp4-6.0.2/bin/ to make it PATH=$PATH:/usr/local/software/ccp4/ccp4-6.0.2/bin but if ccp4.setup-bash works, you shouldn't need to explicitly set any PATH, including the one you missed (for ccp4i). William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
Re: [ccp4bb] My New Address
Can someone delete the old address from the ccp4bb? I've tried emailing but to no avail. On Fri, May 16, 2008 2:28 pm, [EMAIL PROTECTED] wrote: Hello, Your message has been automatically forwarded to my new address which is: sanjukta.aich at usask.ca (replace at with the @ symbol) At your earliest convenience, please update your addressbook/contacts list to reflect my new email address. Note: You will continue to receive this message if you continue to send email to my old account. Thanks, - William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
Re: [ccp4bb] environ.def / default.def
Probably. You should source either the first or the second file depending on your shell (the first for bash, the second for tcsh/csh). That might be the cause of your subsequent problem. For purposes of debugging, can you send us output for the following three commands: echo $PATH echo $CCP4 echo $CCP4I_TOP On Fri, May 16, 2008 5:22 pm, Eike Schulz wrote: Hello again, thanks to some people for their fast and helpfully very detailed advice: Including source /usr/local/software/ccp4/ccp4-6.0.2/include/ccp4.setup-bash source /usr/local/software/ccp4/ccp4-6.0.2/include/ccp4.setup into my .bashrc did indeed solve the problem with MTZDUMP when executed from the shell. Further thanks for some other corrections. But unfortunately the error persists when I try to run refmac from the ccp4i GUI - it complains not to be able to extract data from an .mtz file. Did I miss anything important? Kind regards Eike On Fri, 2008-05-16 at 14:37 -0700, William Scott wrote: On Fri, May 16, 2008 1:06 pm, Eike Schulz wrote: Hello everybody, setenv CCP4_MASTER /usr/local/software/ccp4 setenv CCP4 $CCP4_MASTER/ccp4-6.0.2 For bash, zsh, etc, you need to start with export CCP4_MASTER=/usr/local/software/ccp4 export CCP4=$CCP4_MASTER/ccp4-6.0.2 setenv is specific to (t)csh. export is specific to the sh-like shells. --- ... and the .bashrc contains following entries: --- PATH=$PATH:/usr/local/software/ccp4/ccp4-6.0.2/bin/ PATH=$PATH:/usr/local/software/ccp4/ccp4-6.0.2/include/ /usr/local/software/ccp4/ccp4-6.0.2/include/ccp4.setup-bash --- I think that last line would need to be source /usr/local/software/ccp4/ccp4-6.0.2/include/ccp4.setup-bash and you shouldn't need this line: PATH=$PATH:/usr/local/software/ccp4/ccp4-6.0.2/include/ and you should get rid of the trailing slash on this line: PATH=$PATH:/usr/local/software/ccp4/ccp4-6.0.2/bin/ to make it PATH=$PATH:/usr/local/software/ccp4/ccp4-6.0.2/bin but if ccp4.setup-bash works, you shouldn't need to explicitly set any PATH, including the one you missed (for ccp4i). William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
Re: [ccp4bb] poll: cutoff for high resolution
Actually, if you want to feel really good, I learned (in the context of optics) that you can resolve two points separated by a distance x with a diffraction limit of x/0.7, so this means you can start to see carbon - carbon atomicity at 2.2 Å. On May 15, 2008, at 10:12 AM, Gloria Borgstahl wrote: To me, it seems legal to use the words atomic resolution once we are within the carbon-carbon bond length. So I'm agreeing with Dr. Scott. Otherwise I'll never get to use the words... ** Gloria Borgstahl Eppley Institute for Cancer Research and Allied Diseases 987696 Nebraska Medical Center 10732A Lied Transplant Center Omaha, NE 68198-7696 http://sbl.unmc.edu Office (402) 559-8578 FAX (402) 559-3739 Associate Professor Hobbies: Protein Crystallography, Cancer, Biochemistry, DNA Metabolism, Modulated Crystals, Crystal Perfection, X-ray Topography, Interests: ThimbleTack, skateboarding, RAGBRAI, and rollerskating ** William Scott [EMAIL PROTECTED] Sent by: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK 05/15/2008 12:09 PM Please respond to William Scott [EMAIL PROTECTED] To CCP4BB@JISCMAIL.AC.UK cc Subject Re: [ccp4bb] poll: cutoff for high resolution On May 15, 2008, at 10:01 AM, Ed Pozharski wrote: 1.2A (not surprisingly since this is about the length of covalent bond). A carbon-carbon single bond is about 1.55 Å.
Re: [ccp4bb] poll: cutoff for high resolution
On May 15, 2008, at 12:40 PM, Ed Pozharski wrote: I was just trying to protect poor creatures, after all they [hydrogens] only got one electron to hold on to (:-) Ed. A less radical view (pun intended) suggests two. ;)
Re: [ccp4bb] poll: cutoff for high resolution
On May 14, 2008, at 12:28 PM, Mark Del Campo wrote: At what refinement resolution or resolution ranges would you call a structure high resolution vs. low resolution? I realize that this may boil down to semantics (e.g. some may classify structures as medium resolution), but I wanted to get an opinion from the pros. This really needs to take into account the numerical resolution vs. inherent-coolness-factor tradeoff matrix. For example, if the macromolecule is comprised of 100% amino acids and catalyzes a reaction in the Krebs cycle, high resolution is 0.5*(C=C), the carbon-carbon double-bond length. If it is a snRNP, 7Å is moderate resolution.
Re: [ccp4bb] HKL2000 and gcc4 - redux
mosflm is an incredibly great program, not to mention free as in beer... On May 7, 2008, at 3:07 PM, Chris Waddling wrote: my frustration at HKL2000 not working
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
[ccp4bb] Eden crystallography web site
Hi: If anyone needs EDEN (Abraham and Hanna Szöke's density modification program), the original edencrystallography.org site is gone. As a quick remedy, I've created (with their permission) a google-code page here: http://code.google.com/p/edencrystallography/ The code is GPL-ed, fwiw. All the best, Bill
Re: [ccp4bb] ccp4 install on Leopard
You need to run source /sw/bin/init.sh if you use bash or zsh or source /sw/bin/init.csh if you use tcsh. this will automatically set up the environment variables and then it will do what you want it to (which is to set up the ccp4 environment according to whichever shell you might be using). On Apr 25, 2008, at 1:19 PM, Patrick Loll wrote: Accck! 1. I tried to install Bill Scott's precompiled ccp4 on an intel mac running OS X 10.5. When attempting launch ccp4i, I receive this error message: /sw/share/xtal/ccp4-6.0.2/ccp4i/bin/ccp4i: line 4 /bltwish: no such file or directory Typing which bltwish returns /sw/bin/bltwish, which jibes with the definition of $CCP4I_TCLTK, so I'm not sure where the problem is... 2. Pfui. So next I tried jettisoning the apt-get installation, and instead used the installer downloaded from the ccp4 site (ccp4-6.0.2- osx-i386.dmg.gz). This goes swimmingly, until I actually try to do something. Commands like ccp4i or mtzdump aren't recognized, so I go looking for the ccp4.setup file; but it's not there. Huh? Also, there's no folder named ccp4i, even though this install is supposed to include it... It's Friday, and I'm at the nadir of my weekly brain function, so perhaps some kind soul will tell me where I'm going astray. Thanks, Pat --- Patrick J. Loll, Ph. D. Professor of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 [EMAIL PROTECTED]
Re: [ccp4bb] density_modify.inp is not running in cns1.2 but runs in cns1.1
Could one or both of you try this with the pre-compiled intel version
that comes from the CNS website? If it works on that, it might be
something introduced in the compiling process for the osx-optimized
version made by David.
Thanks.
Bill
On Apr 23, 2008, at 7:26 AM, Sean Johnson wrote:
Raja,
I don't have an answer for you, but I have been experiencing the
same problem. My guess is that a bug was introduced into version
1.2. My workaround is to use DM. I haven't had problems with any
of the other cns scripts in version 1.2.
Sean
Raja Dey wrote:
Hi All,
I am trying to run density_modify.inp in cns 1.2. it stops
with the error enclosed below. But, it runs with cns 1.1 perfectly.
I am using the same two data files(e.g. p65_se_rdey.hkl.cv and
combine.hkl). Does anyone have experience like this? Any solution
is well appreciated. Regards...
Raja
ANOMalous=TRUE {ON}
Program version= 1.2 File version= 1.2
%XMAPASU-AUTOmem: increasing memory allocation to200
Minimum brick that covers asymmetric unit:
A= 0,...,64 B= 0,...,64 C= 0,...,25
Sum of 5287 elements = 5287.
SHOW: average of102400 elements= 0.
ANOMalous=TRUE {ON}
XMPST: average = 0. minimum = 0. maximum = 0.
XMPST: r.m.s. = 0. norm = 0.
XMHISTO: (default from map) RHOMIN and RHOMAX = 0. 0.
%XMHISTO-ERR: a complete flat map.
XMHISTO: (default from map) SLOT width = 0.00
%XMHISTO-ERR: the SLOT width is too small 0.0
XMHISTO: the number of slots MBINS=1 and width SLOT= 0.
%XDOTYPE-ERR: Variable/type mismatch:
do (masksol=1) (real(automap) = $cutoff)
^
%DO-ERR: Data type mismatch. Selection must be a logical
expression.:
do (masksol=1) (real(automap) = $cutoff)
^
%SHOW error encountered: There were errors in DO expression.
(CNS is in mode: SET ABORT=NORMal END)
*
ABORT mode will terminate program execution.
*
Program will stop immediately.
Maximum dynamic memory allocation:18336916 bytes
Maximum dynamic memory overhead: 360 bytes
Program started at : 18:01:44 on 21-Apr-2008
Program stopped at : 18:01:46 on 21-Apr-2008
CPU time used : 1.9700 seconds
Total runtime : 0. seconds
Program compiled by David Gohara
Regards... Raja
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Utah State University
Department of Chemistry and Biochemistry
0300 Old Main Hill
Logan, UT 84322-0300
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Re: [ccp4bb] problem about coot on MacOSX
I think this version of coot tries to set the DISPLAY variable and that will sabotage launching it in 10.5.2. May I suggest trying this: http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Coot-0.5-pre-1-968_for_Intel_10.5_only On Tue, April 22, 2008 7:53 pm, zhangtao wrote: Dear All: I have a MacOSX (Core Duo model). I need to use Coot on it, I have installed the coot,and installation seems successful. But I can not run it. It give me information following: Gdk-WARNING **: locale not supported by Xlib, locale set to C Gdk-WARNING **: can not set locale modifiers Acquiring application resources from /Applications/coot.app/Contents/coot/share/coot/cootrc _X11TransSocketINETConnect() can't get address for /tmp/launch-gzb6G7/:6000: nodename nor servname provided, or not known Gtk-WARNING **: cannot open display: /tmp/launch-gzb6G7/:0 Gdk-WARNING **: locale not supported by Xlib, locale set to C coot-exe: ./coot-real core: #f No core file found. No debuggingI have updated the OS to 10.5.2 and I have installed X11-2.2.0.1, But there is the same problem.Did anybody encounter the problem.Thank you very much.best wishs Zhang, Tao William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
Re: [ccp4bb] Installing coot on MacOSX 10.5
Dear Chris et al, My guess is something needs ruby built as a build-time dependency, but coot doesn't require it. In any case, I've got the latest version of ruby built and anyone who needs it can download it from one of my servers as described on this page: http://tinyurl.com/h2lzq That saves you the overhead of compiling stuff. You can just download precompiled debian packages and have fink unpack them for you. HTH, Bill William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ On Apr 17, 2008, at 11:51 AM, Chris Richardson wrote: On 17 Apr 2008, at 6:07 PM, Buz Barstow wrote: I'm having trouble installing coot on MacOSX 10.5.2 on my MacBook Pro (Core Duo model). I would like to install coot using fink, but am getting stuck when it comes to installing ruby. Has anyone else experienced this problem? I've spent the afternoon doing a clean rebuild of a fink installation on an iMac (Core 2 Duo) running Tiger 10.4.11, and the process also died at updating ruby. Poking around on Google yields several people with the same problem, but none with a solution. The fink-devel mailing list saw the problem yesterday, so a fix may be forthcoming soon. Regards, Chris The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
Re: [ccp4bb] Installing coot on MacOSX 10.5
I have i librsvg22.9.5-11SAX-based render library for SVG files i librsvg2-gtk2.9.5-11Enable GTK to use SVG data i librsvg2-shlibs 2.9.5-11SAX-based render library for SVG files Do you have all of those installed? If not, the package is missing a dependency and I should fix it. Let me know if that cures the problem. Sorry Bill On Apr 17, 2008, at 2:34 PM, Buz Barstow wrote: Hi Bill, Thanks a lot for your advice. Coot now installs and runs, however, I do get some warnings; ** (coot:20738): WARNING **: Error loading pixmap file: /sw/share/ coot/pixmaps/connect-to-ccp4.svg ** (coot:20738): WARNING **: Error loading pixmap file: /sw/share/ coot/pixmaps/connect-to-oca.svg
Re: [ccp4bb] Installing coot on MacOSX 10.5
Dear Buz: Not sure why you have to install ruby. But if you describe the problem, I might be able to help. Meanwhile you can use what I pre-compiled: http://tinyurl.com/h2lzq This will speed things up by a few orders of magnitude. Bill On Apr 17, 2008, at 10:07 AM, Buz Barstow wrote: Dear All, I'm having trouble installing coot on MacOSX 10.5.2 on my MacBook Pro (Core Duo model). I would like to install coot using fink, but am getting stuck when it comes to installing ruby. Has anyone else experienced this problem? Also, are there any alternative solutions to installing coot? Thanks! and all the best, --Buz
Re: [ccp4bb] upgrade coot via fink on OS X
This is a gtk+2 phenomenon. Same happens with gimp-2. On Apr 14, 2008, at 8:36 AM, Andreas Förster wrote: Hey Klaus, after I installed coot 0.5 via fink for the first time, I encountered stalling during startup as well. However, this resolved itself within a minute. Startup resumed, and the next time around, everything was back to normal. Were you patient enough during startup? Andreas Klaus Futterer wrote: I had previously installed coot 0.3.2 using fink on OS X on MacBook Pro (under Tiger). Trying to update coot using fink proved more difficult. Initially I tried sudo apt-get install coot Coot would install but would not start due to a library version mismatch. Then it got messy. I followed instructions given on Bill Scott's 'Install crystallography using fink' page: fink scanpackages; fink index sudo apt-get update sudo apt-get dist-upgrade The last command stalled - during imagamagick update. Then I just tried again: sudo apt-get install coot Now coot would start, but stall saying: Reading coordinate file: /sw/share/coot/standard-residues.pdb PDB file /sw/share/coot/standard-residues.pdb has been read. Spacegroup: P 1 Cell: 40.631 109.18 93.243 90 90 90 art_render_invoke: no image source given Can anyone suggest to properly update fink and coot? Thanks in advance, Klaus - Klaus Fütterer, Ph.D. School of Biosciences P: +44-(0)-121-414 5895 University of Birmingham F: +44-(0)-121-414 5925 Edgbaston E: [EMAIL PROTECTED] Birmingham, B15 2TT, UK W: www.biochemistry.bham.ac.uk/klaus/ - -- I am not stupid. I have read several books. Salman Rushdie - Midnight's Children
Re: [ccp4bb] Fwd: [ccp4bb] crystallisation robot
Does this include the customary grieving period? On Apr 14, 2008, at 2:10 PM, JOE CRYSTAL wrote: Hi, Does anyone have information about how long it takes to set up a 96- well tray for the crystallization robots available? Besides cost per tray and maintenance cost, another important feature we consider is the time for setting up a 96-well tray. It is an important factor since we are talking about sub-microliter drops. Best, Joe On Fri, Jan 18, 2008 at 12:28 PM, Lisa A Nagy [EMAIL PROTECTED] wrote: Al's Oil on the plates: What a nightmare!!! The oil creeps up the plate and over the sides. It dissolves adhesives. It makes me say bad words in multiple languages. Bigger drops + no oil = fewer bad words. Lisa -- Lisa A. Nagy, Ph.D. University of Alabama-Birmingham [EMAIL PROTECTED] -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Patrick Shaw Stewart Sent: Friday, January 18, 2008 2:20 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Fwd: [ccp4bb] crystallisation robot One thing that people often overlook is that quite a lot of protein can be lost by denaturation on the surface of the drop. This is more significant for smaller drops. Two suggestions: (1) increase the proportion of protein in the - technical term - teeny drop to say two thirds and (2) cover the drops with oil eg Al's oils (silicone/paraffin). You still get vapor diffusion though the oil , and you'd like to slow up equilibration. of course (2) slows up the robotics a little, but both should be trivial to set up..
Re: [ccp4bb] Low resol structure
On Apr 11, 2008, at 3:04 AM, Jim Naismith wrote: However, does anyone know how to convince editors and non- xtallographers that 3.45A is valid? You have to introduce them to the resolution vs. biological interest trade-off matrix, and how it ought to be diagonaliz(s)ed. Bill
Re: [ccp4bb] Off topic: Real funny until someone loses a Happy Meal
As opposed to putting McDonald's food into their stomachs? On Apr 4, 2008, at 9:33 AM, Ezra Peisach wrote: I saw that toy - Personally, I do not like the idea of encouraging children to aim a light (low powered led) directly at one's eye... Ezra P Hubbard wrote: I took my 5 year old niece to a McDonald's (in England) for a happy meal today - Spiderwick Chronicles promotion. The toy's light effect reminded me of a visual aid I saw to help introduce X-ray diffraction and the crystal lattice to students. My niece was more interested in using the visual effect to see if her toy was a goodie or baddie. Cheers! Going green? See the top 12 foods to eat organic. http://green.msn.com/galleries/photos/photos.aspx?gid=164ocid=T003MSN51N1653A
Re: [ccp4bb] Mg++ binding to N7 of G
Sorry, I should have been less cryptic: On Apr 2, 2008, at 2:13 PM, Jacob Keller wrote: Forgive the naive questions: To what do the terms hard and soft refer here? In inorganic chemistry, hard refers to bonding where the Coulomb potential dominates, and soft where orbital terms dominate. If one partner prefers electrostatic interactions and the other more covalent- like interactions, the interaction is less probable. So Mg++ likes oxygen, Mn++ likes Nitrogen. And G, I assume, is glycine, Guanine but what is N7? Purine numbering... JPK *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: [EMAIL PROTECTED] *** - Original Message - From: William G. Scott [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, April 02, 2008 3:58 PM Subject: [ccp4bb] Mg++ binding to N7 of G Howdie folks: I've got what appears to be an inner-sphere interaction between Mg++ and the N7 of a G. The mode of binding is the same as what is observed at this site for Mn++, confirmed with anomalous data. Our resolution is 1.6 Å, so I am reasonably confident this is right. However, my chemist's viewpoint is that Mg++ is too hard and N is too soft for this to happen. I looked in a database called http://merna.lbl.gov for Mg++ binding sites, and a bunch pop up for inner-sphere N7 interactions with Mg++. However, if I restrict the search to structures having 1.8 Å resolution or better, the number goes to zero. Since Mg++ has the same number of electrons as water and no useful absorbance, it seems assigning them based on hydration geometry and bond distances is the only hope. Does anyone have anything more definitive I can refer to? Thanks. Bill Scott
Re: [ccp4bb] advice regarding computer hardware purchase
Hi Chu-Young: I would recommend either a PC running Ubuntu Linux (my personal favorite distribution -- they are all more or less the same thing) or else Apple Mac OS X, depending upon your other needs, budget, etc. I've got a lot of propaganda for OS X here: http://xanana.ucsc.edu/xtal and a little bit for Ubuntu Linux here: http://xanana.ucsc.edu/linux/debian_linux.html Welcome back. Bill William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ On Apr 1, 2008, at 1:04 PM, Chu-Young Kim wrote: Hello everyone, I have not done much crystallography in the past five years but I'm trying to get back into it now because we stumbled upon a very interesting enzyme. It seems a lot has changed in the computer hardware world. I was trained on an SGI back in graduate school. What kind of hardware should I purchase to run all the popular crystallography software? Also, which operating system will give me the least headache? We are basically starting from scratch. Our department has a new Bruker machine and an older Rigaku we can use. Any advice you may have will be greatly appreciated. Thanks in advance for your comments. Chu-Young Kim
Re: [ccp4bb] Coot problems on mac...
HI Simon: The X11 guy at Apple is very interested in trying to help. If you could join the Apple X11 mailing list and document this as carefully as possible, it would be a real benefit. He's out of town for a few days but is interested in dealing with this as soon as he returns. There is a rc for v. 2.2.0 that I installed a couple of days ago. It isn't a magic bullet, but between that and the very latest coot from the pre-release, I was able to get a couple of hours of work done without interruption (well, from the X-server). Bill On Mar 25, 2008, at 5:35 AM, Simon Kolstoe wrote: Has anyone found a solution to the X window problem on macs running 10.5.2? Both Coot and pymol are becoming almost unusable by freezing frequently because of X11 not responding. I've upgraded my X11 to 2.1.4 from the webpage http://trac.macosforge.org/projects/xquartz/wiki/ but the problem still persists. I know a couple others have commented on this problem, but have yet to see an answer. Simon
Re: [ccp4bb] ccp4i - Directories Project Directory Error
In both cases, you have to make sure you are setting up the environment appropriately for ccp4, unique to the unix shell you are using. In the case of the ccp4 package you compile with the aid of the fink script, at the start of a shell session, you, or your dot file, needs to issue source /sw/bin/init.sh or source /sw/bin/init.csh for bash and zsh or tcsh, respectively. That in turn sources the appropriate environment setup file in $CCP4/include. On Mar 25, 2008, at 7:47 AM, Kurt Padilla wrote: William, Thanks for your advice. I intend to give it a try in the next few days. Hopefully, I will have some positive results to share. Anastassis, I tried using the binary from the link you provided, but I was unable to get the program to run even though Installer said that the installation was successful. I don't remember the details, but the installation did not produce an executable .app file and typing ccp4i into Terminal didn't launch the program either. Kurt On Tue, Mar 25, 2008 at 10:35 AM, Anastassis Perrakis [EMAIL PROTECTED] wrote: Hi - I am sure that its not a fink problem really, but why not try the CCP4 distribution? http://www.ccp4.ac.uk/download/ A. On Mar 22, 2008, at 5:34, Kurt Padilla wrote: Hello, When I click on 'Apply' in the Directories Project Directory window, I get the following error: ERROR saving parameters to file /Users/Kat/.CCP4/unix/ directories.def Has anyone else encountered this error? I installed CCP4 on a MacBook Pro running Leopard using fink. This error always occurs, except in one mysterious instance today, but only to hang in refmac. I checked, but there is no .CCP4 folder in '/Users/Kat/'. When I tried to create one myself, OS X wouldn't allow me to do so according to some rule that folder names can't begin with periods. I am getting the impression that CCP4 is buggy on OS X. Any information on avoiding these problems and getting CCP4 to work? Thank You, Kurt Padilla on the behalf of: Kathleen Frey Amy Anderson Lab Dept. of Pharmaceutical Science University of Connecticut
Re: [ccp4bb] ccp4i - Directories Project Directory Error
That is exactly how it is supposed to work with 10.5. No need to use an xterm, and it sets the DISPLAY variable automatically. I assume you have write-permissions in the directory it is trying to make the .CCP4 directory? On Mar 25, 2008, at 9:32 AM, Kurt Padilla wrote: Sue, Currently, when I type in ccp4i into Terminal, X11 launches and then CCP4 does too. I am running OS X 10.5 with a fink installation. Kurt On Tue, Mar 25, 2008 at 12:04 PM, Sue Roberts [EMAIL PROTECTED] wrote: I also thought the problem was using the Terminal window and not the X11 window, but, interestingly, typing ccp4i in a Terminal window, not an X11 window does work. X11 does need to be installed and running, -- that could be the problem. (Caveat, this is in 10.4, not 10.5 - I have 10.5 but haven't installed it yet because of the coot discussions) Sue On Mar 25, 2008, at 8:37 AM, Anastassis Perrakis wrote: Hi - You need to add to your .chrc, or type in an ***X11*** window (and not in the Terminal). source /usr/local/ccp4-6.0.2//bin/ccp4.setup-csh then it will work. it does not really install a real application in the OSX sense. A. On Mar 25, 2008, at 15:47, Kurt Padilla wrote: William, Thanks for your advice. I intend to give it a try in the next few days. Hopefully, I will have some positive results to share. Anastassis, I tried using the binary from the link you provided, but I was unable to get the program to run even though Installer said that the installation was successful. I don't remember the details, but the installation did not produce an executable .app file and typing ccp4i into Terminal didn't launch the program either. Kurt On Tue, Mar 25, 2008 at 10:35 AM, Anastassis Perrakis [EMAIL PROTECTED] wrote: Hi - I am sure that its not a fink problem really, but why not try the CCP4 distribution? http://www.ccp4.ac.uk/download/ A. On Mar 22, 2008, at 5:34, Kurt Padilla wrote: Hello, When I click on 'Apply' in the Directories Project Directory window, I get the following error: ERROR saving parameters to file /Users/Kat/.CCP4/unix/ directories.def Has anyone else encountered this error? I installed CCP4 on a MacBook Pro running Leopard using fink. This error always occurs, except in one mysterious instance today, but only to hang in refmac. I checked, but there is no .CCP4 folder in '/Users/Kat/'. When I tried to create one myself, OS X wouldn't allow me to do so according to some rule that folder names can't begin with periods. I am getting the impression that CCP4 is buggy on OS X. Any information on avoiding these problems and getting CCP4 to work? Thank You, Kurt Padilla on the behalf of: Kathleen Frey Amy Anderson Lab Dept. of Pharmaceutical Science University of Connecticut Sue Roberts Biochemistry Biophysics University of Arizona [EMAIL PROTECTED]
Re: [ccp4bb] ccp4i - Directories Project Directory Error
If I move my .CCP4 directory out of the way and start ccp4i, it makes a new one: zsh-% ccp4i 22:14:16 Creating a home directory for CCP4 at /Users/wgscott/.CCP4 22:14:16 Creating CCP4i shadow area at /Users/wgscott/.CCP4/CCP4I_TOP 22:14:16 Creating shadow subdirectory /Users/wgscott/.CCP4/CCP4I_TOP/bin 22:14:16 Creating shadow subdirectory /Users/wgscott/.CCP4/CCP4I_TOP/src 22:14:16 Creating shadow subdirectory /Users/wgscott/.CCP4/CCP4I_TOP/etc Are you sure it isn't there? What do you get for ls ~/.CCP4 By the way the unix command for making a directory like this is mkdir ~/.CCP4 but the GUI appears to do that automatically. Maybe you are trying to make the thing with the Finder (Apple's file browser)? Best to avoid it for anything unixy. It is a carbon-based relic of pre-osx days. On Mar 21, 2008, at 9:34 PM, Kurt Padilla wrote: Hello, When I click on 'Apply' in the Directories Project Directory window, I get the following error: ERROR saving parameters to file /Users/Kat/.CCP4/unix/directories.def Has anyone else encountered this error? I installed CCP4 on a MacBook Pro running Leopard using fink. This error always occurs, except in one mysterious instance today, but only to hang in refmac. I checked, but there is no .CCP4 folder in '/Users/Kat/'. When I tried to create one myself, OS X wouldn't allow me to do so according to some rule that folder names can't begin with periods. I am getting the impression that CCP4 is buggy on OS X. Any information on avoiding these problems and getting CCP4 to work? Thank You, Kurt Padilla on the behalf of: Kathleen Frey Amy Anderson Lab Dept. of Pharmaceutical Science University of Connecticut
Re: [ccp4bb] Crystal scoring sheets for iPhones/Pocket-PCs
Sounds great. You can jailbreak an iPhone/iPod touch and install a whole BSD subsystem on it. So printing should be possible at some point... This of course also suggests that iPod touch is a valid research expense ... William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ On Mar 19, 2008, at 8:59 AM, P Hubbard wrote: Hi, I could be wrong, but I’m not aware of any servers that have tray inspection web pages designed for iPhones and Pocket-PCs, so I thought I’d try and make a web page with simple scoring sheets for such devices. I don’t own an iPhone myself, but the following web page seems to work well on a phone I tried out at an O2 store. Hope it’s of use to people who don't have a computer by their microscope. http://www.pageforaday.com/xtalwizard/fixed_order-i.html In response to a request, I’ve also allowed an option to include your custom screens. I’ve designed it so that you don’t need an account. P.S: I’ve read that you can’t print directly from an iPhone (though I assume you can either e-mail the data URL, or plug the phone into a computer with a printer). I’ve not tried the page out on a Pocket- PC, but I expect it will display reasonably well on these screens too (with JavaScript enabled), and I believe many of the newer Pocket-PCs allow wireless printing. Maybe Apple will release an appropriate iPhone update soon. Thanks _ Climb to the top of the charts! Play the word scramble challenge with star power. http://club.live.com/star_shuffle.aspx?icid=starshuffle_wlmailtextlink_jan
Re: [ccp4bb] changing names of many files
Install zsh. Then invoke it. Then issue: autoload -U zmv alias mmv='noglob zmv -W' Then you are ready for some fun: mmv 1105\ A*.osc A*.osc Then if you decide to make your default shell zsh, you can put that in your .zshrc file and all you have to remember in the future is mmv Raja Dey wrote: Hi, How I can change names of many files keeping the extension same. My files are like this 1105 A0176.osc 1105 A0177.osc 1105 A0178.osc 1105 A0179.osc 1105 A0180.osc I want to change them as A0176.osc A0177.osc A0178.osc A0179.osc A0180.osc I am using ubuntu linux. Thanks... RD Raja Dey, Ph.D. Research Associate Molecular and Computational Biology University of Southern California 1050 Childs Way, Los Angeles, CA 90089 - Chat on a cool, new interface. No download required. Click here.
Re: [ccp4bb] Merging CCP4i projects from two computers
Syncing directories with unison (use the same version of the program on all computers) or rsync can help. Lately I've been using svn, which is I think the best way to deal with this. Setting up a server on linux is probably easiest. You can do this with any type of file, by the way, it doesn't have to be ascii. William G. Scott contact info: http://chemistry.ucsc.edu/~wgscott On Mar 7, 2008, at 3:57 AM, Derek Logan wrote: Hi everyone, I've been working on a project using CCP4i on two separate computers in parallel and now unfortunately have jobs spread over the two locations. I would now like to consolidate these. Some of the new jobs on one computer will have the same run number as different ones on the other. Is there any convenient way to merge the projects? I guess the answer is no, or else the question would have been asked and answered already ;-) Thanks Derek -- Derek Logan tel: +46 46 222 1443 Molecular Biophysicsfax: +46 46 222 4692 Lund University mob: +46 76 8585 707 Box 124, Lund, Sweden
Re: [ccp4bb] Merging CCP4i projects from two computers
NFS is alive and well (even on OS X 10.5), but having separate copies on different computers and/or an svn server has the additional merits of being a backup system and one you can use with computers that don't have static IPs. David J. Schuller wrote: Back in the good old days, we were able to share disks between computers with something called NFS, and even further back, file versioning in VMS might have been relevant and useful. But I am wandering.
Re: [ccp4bb] phenix.refine and refmac
phenix.refine also produces an mtz file by default, and that can be auto-opened with coot, along with the coordinates. On Mar 4, 2008, at 7:27 AM, yang li wrote: Since the map from phenix couldnot be opened by coot directly--or I donnot know how to--I used refmac to get a mtz map file.
Re: [ccp4bb] seeing if this list can be put on gmane
Here is an example: http://news.gmane.org/gmane.editors.textmate.general Charles Ballard wrote: Dear Mark gmane has an obscure e-mail address function. We would use that. Charles On 26 Feb 2008, at 16:58, Mark J. van Raaij wrote: Dear Charles, it would perhaps be good to make sure email addresses are not publicly visible on gmane, to avoid spamming. greetings, Mark J. van Raaij Dpto de Bioquímica, Facultad de Farmacia Universidad de Santiago 15782 Santiago de Compostela Spain http://web.usc.es/~vanraaij/ On 26 Feb 2008, at 17:25, Charles Ballard wrote: Right, if CCP4BB is to be archived on gmane, the list owner must agree (and as that is me, it seems OK), and the list users must be informed. If there is any reason not to gmane this list, please let me know. Note, I do not plan to allow posting from gmane, as this defeats the purpose of having to get people to register. Charles Ballard CCP4
Re: [ccp4bb] suggestion: CCP4BB on gmane.org
I agree! I suggested this about a year ago too. All they need is permission from ccp4. The current system of archives is hard to use (and for mentally deficient people like me, impossible). Bill Kay Diederichs wrote: Dear all, I love CCP4BB, but I hate going on holidays because when I come back my Inbox is usually full with CCP4BB messages. The way out of this misery would be to have a mailing list archive which is presented such that it can be read with a newsreader. news.gmane.org offers this service. For all those who don't know this: it lets you read mailing lists without having subscribed to them. Currently there are almost 14.000 mailing lists hosted by gmane.org . To read one of this, you use your email client (e.g. thunderbird), - open an new account in the file menu - choose newsgroup account - enter the information about yourself - enter news.gmane.org as newsgroups server - later choose the mailinglists/newsgroups you want to subscribe to - read these in your email client as usual One can also post messages, but that needs an additional step, with confirmation emails going back and forth. May I suggest that the people who run the CCP4BB please consider this, and fill out the form at http://gmane.org/subscribe.php ? thank you, Kay -- Kay Diederichshttp://strucbio.biologie.uni-konstanz.de email: [EMAIL PROTECTED]Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz
[ccp4bb] Citations in supplementary information are invisible
Hi Citizenry: This is worth reading: http://www.nature.com/nature/journal/v451/n7181/full/451887d.html Without knowingly doing so, I've short-cited coot and probably other crystallographic software in this way. I hope one day to redeem myself. Bill
Re: [ccp4bb] cns and refmac refinement
Then I used CNS to do annealing, then use refmac to do rigid body refinement. That can be why the R-factors went up. Rigid-body subsequent to simulated annealing will (if anything) undo the refinement ... Anastassis Perrakis wrote: Just to point out that I have missed the NCS presence; Lijun is *perfectly* correct; even more I should emphasize the point and say that at 3.0 A, Thou Must Use NCS (if I say again anything about Gospels and Kleywegt we end up with more facebook groups ...) I think there is no reason at this resolution edge (~3A), making bonds possibly resolvable, that NCS should not be used, By the way, it is a dimer and I didnot use NCS restarin during refinement. Below is from refmac log: I would however disagree with Lijun thats its instability. Of course the 180 cycles are of no use at all (10 cycles in Refmac are more than enough in 99% of cases), but Rfree shoots up from 32.6 to 36.2 in 12 cycles, which is clearly an indication of some sort of pathology, and not instability. Well, tight NCS is the best starting point in this case. Tassos
Re: [ccp4bb] microsoft 3-button wheel mouse with OS X 10.5
Yes, thanks, that does it for the Terminal.app, but not for any of the rest. It would be great to have such a feature globally. mb1pja wrote: Dear Bill William Scott wrote Aqua simply behaves by slightly different rules. Although I am a slobbering OS X fan, this lack of customizability to me, as well as a lack of focus-follows-mouse, it a negative. To get focus-follows-mouse in Aqua, type the following in your Terminal window: defaults write com.apple.Terminal FocusFollowsMouse -string YES and then logout and log in again or quit and restart Terminal. I had thought I originally got that useful hint from your own fabulous PX on OSX pages but clearly not. best wishes Pete Artymiuk On 20 Jan 2008, at 15:39, William Scott wrote: Hi David: david lawson (JIC) wrote: Dear All, Sorry for the slightly off-topic subject. We have recently bought a few iMacs for crystallography. I'm not keen on the supplied mighty mouse May I have them? so I have switched to using a microsoft 3-button wheel mouse. I would like to configure it so that it behaves as it would with other unix systems such as RH Linux. You managed to use Microsoft, behaved and Linux (albeit RH) all in one sentence without a hint of irony. i.e. (1) double-clicking with LH button on a file name selects ALL of the file name, not just up to the first full stop. Although your choice of Microsoft products shows dedication to a company with a firm reputation for placing the customizability needs of its customers ahead of its own desire to make profits, the first thing to realize is that you should never ever ever install their drivers. Ever. So if you did, take them out, now, and reboot. I'll wait. It is still early Sunday morning here. (2) clicking the scroll wheel pastes the selected text AND it can be done multiple times without re-selecting. When you've gotten rid of the drivers, this should now work. In Apple's Terminal program (as of 10.5) and iTerm (as of 1215), you just set the preference to do middle-button-paste and left-button select, and Blair's your uncle. Unfortunately, in pretty much every other application I can think of on OS X, this, sadly, does not work, and there is nothing Steve Gates will let you do about it. (2) I would like these functions to work in terminal windows, the ccp4i gui and web pages (and probably a few other things I haven't thought of yet!) AND be able to transfer the selected text between applications. I'd like to be at my ideal high-school weight, be paid more than a postdoc, and, well ... Getting the OS X gui to play nice with X11 is sometimes challenging. With the exception of Terminal and iTerm, you have to explicitly put stuff in the copy/paste buffer (command-C) before it is in the system clipboard. Then you can paste to X11 programs with a middle-button click, but this only works if you uninstalled that viral driver. Going from X11 to aqua programs requires selecting the text in the usual X11 manner but explicitly issuing the paste command (command- p). If you are using KDE X11 applications, you are really in for headaches. To get whole-string selection in iTerm or Terminal, there is a preference setting that allows you to input which characters you want to have considered parts of a word for click-to-select purposes. Unfortunately, pretty much every other application lacks this customizability, and I know of no system-wide preference setting that would enable you to do this globally. Aqua simply behaves by slightly different rules. Although I am a slobbering OS X fan, this lack of customizability to me, as well as a lack of focus-follows-mouse, it a negative. If you really need the canonical linux behavior, you can install gnome, xfce4, KDE, enlightenment, or any number of other window managers via fink. I've found KDE buggy and the XFCE4 is way out of date. Gnome is probably the best bet, and there is a major effort now to bring it completely up to date in fink. I have installed the microsoft intellipoint drivers that seem to give more control over configuring the various buttons through system preferences, but I still can't get what I want. Therein lies the problem, I am afraid. OS X will behave better using the default settings. It may be possible to tinker around with the driver, including separate settings in X11, to recover canonical behavior, but for purposes of sanity, uninstall them first, get everything working as best as possible, verify middle-button-paste works in X11, verify X11 coot and pymol do the right thing, and then if you need additional functionality, reinstall the drivers, verify things like coot and pymol still use the middle button correctly, or adjust until they do, and only then try customizing. Best of luck! Bill Any help would be much appreciated. Many thanks Dave Lawson --- Dr. David M
Re: [ccp4bb] antibody crystallization
I want to thank the very many people who responded to my inquiry. I'm overwhelmed and really appreciative. I've still got to read through it all, but a clear (near-unanimous) consensus is emerging. All the best, and again thanks very much for the help. I really appreciate it. Bill
[ccp4bb] antibody crystallization
Hi folks: A colleague has an antibody they would like a crystal structure of, bound to a peptide. Currently it is a whole antibody. From my superficial search of the literature, it looks like everyone uses Fab fragments in such cases. Is this true, and is it stupid to try the whole thing? If anyone would be kind enough to point me to a good methodological overview for crystallizing these things in the literature, I would be exceptionally grateful. Many thanks. Bill William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
Re: [ccp4bb] differences between Rsym and Rmerge
I had learned that Rsym compared symmetry-related reflections within an image or film (in the context of a rotation exposure), and Rmerge compared symmetry-related reflections on different images or films with one another. Is that wrong? Bill Manfred S. Weiss wrote: Dear Mohd and all others, Well, I guess it is time again to define and talk about R-factors. The term R_sym goes back to the times, when X-ray data were recorded by precession photography on film. Except for the central cone, each reflection was observed only once and R_sym described the agreement strictly between symetry-related reflections, hence R_sym. In diffractometer times, when reflections were measured one by one, only for a subset of reflections (typically a plane in reciprocal space) were symmetry-related reflections measured two times. R_sym became R_int, where int stands for internal agreement. These additional reflections were just measured to calculate R_int, later on they were discarded. Nowadays, where a diffraction data set typically consists of dozens or hundreds of images recorded from some sort of an area detector, multiple measurements of the same reflection AND symmetry-related reflections are merged together to calculate the mean intensity for a given reflection. Hence, the agreement factor becomes R_merge or merging R-factor. As you can see, R_merge is more general than R_sym, and is (as Kay pointed out) the preferred term. However, when talking about R-factor I can never refrain from mentioning that R_merge should actually NEVER EVER be used, because it is inherently flawed. As the redundancy or the multiplicity of the data increases, R_merge will also increase, although the mean intensity will be more precisely determined. As was postulated by Kay and myself about 10 years ago, R_merge should be replaced by a redundancy-independent merging R-factor (termed R_rim or R_meas). Unfortunately, only SCALA and XDS produce this R-factor, SCALEPACK does not (not yet, I hope -- pun to Dallas). If you want to calculate R_rim or R_meas based on scaled but unmerged data, I have my own program, which you can download from my web site, as does Kay. I hope this clarifies things. Cheers, Manfred. * * *Dr. Manfred S. Weiss * * * * Team Leader * * * * EMBL Hamburg OutstationFon: +49-40-89902-170 * * c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 * * D-22603 Hamburg Email: [EMAIL PROTECTED] * * GERMANY Web: www.embl-hamburg.de/~msweiss/ * * * On Fri, 18 Jan 2008, Salameh, Mohd A., Ph.D. wrote: Hi everybody! I will appreciate it if anybody can clarify to me the differences between Rmerge and Rsym. Many thanks, M Mohammed A. Salameh, Ph.D. Mayo Clinic Cancer Center Griffin Cancer Research Building 4500 San Pablo Road Jacksonville, FL 32224 Tel:(904) 953-0046 Fax:(904) 953-0277 [EMAIL PROTECTED]
Re: [ccp4bb] PERL system call to CCP4
This looks promising: http://www.ccp4.ac.uk/newsletters/newsletter36/13_perl.html Ezra Peisach wrote: You may wish to look at the occp4-pm perl package by E. Courcelle and J.P. Samama (formerly available from ftp://ftp.ipbs.fr/pub/occp4 - but this no longer works...) I no longer have a copy but someone might... Ezra [EMAIL PROTECTED] wrote: Dear CCP4 users, I am writing a PERL script to execute a number of CCP4 commands (ncsmask, pdbset, and dm) in succession. I have tried using system call or PIPE command, neither of which work. The ccp4 scripts generated work independently on the command line. Any suggestions? Thank you in advance!
Re: [ccp4bb] ideal bond length and bong angel
Hi Yang Li: Macromolecular crystal refinement programs use ideal bond lengths and angles. The simplest ones just assume any carbon-carbon single bond (C-C) is the same as any other, and use one average value, and any carbon-carbon double bond (C=C) is the same as any other, and use another average value, and so on for all possible linkages. Better ones treat individual cases differently, so that the Calpha-Cbeta bond in amino acids is compared only to other Calpha-Cbeta bond lengths, for example. The best ones will have a specific average value for each Calpha-Cbeta bond length for each amino acid that has this bond. Similarly for angles. The standard value is usually established from very high resolution crystal structures of (for example) individual amino acids, and/or quantum chemistry calculations. Various different methods are employed to penalize deviation from ideality in a refinement. It is common to use a simple quadratic penalty, which can be characterized by a Hook's Law spring constant, and this is justified where the harmonic approximation for bond potentials is valid (and it should be in crystal structures). Each refinement program has its own way of implementing the above, so the best thing to do is to look at the bond parameter dictionaries that your program uses. I hope that comes closer to answering your question. All the best, Bill Scott yang li wrote: By the way, I think my bad english embarrassed my meaning. What I want to say is which bond length is used as the standard? the C=N or Ca-N or even the side chains? Or all of them?Which angel is used to compare, the Ca-C'-N or C'-N-Ca or others. At first I suppose the bond length only calculate the C=N bond, and donnot know which one is used as the aggel. It should be a quite stupid question for whom knows it. Just forget it.
Re: [ccp4bb] apologize
Dear Yang Li: Happy New Year to you, too, (ahead of Feb. 7th). You certainly owe us no apology; the reverse may not be true. Your question is an important one, as is what you have written below. I'm not certain I have a completely satisfactory answer. The reason is that ideal bond lengths may or may not be true in the sense that the value is established by social consensus, and is thus guaranteed to be perfectly accurate, even though it may be quite precise. Because of this, and because of natural deviations from ideality (which really only become trustworthy observations at extremely high resolution), a certain amount of wiggle room is typically allowed in terms of rmsd. The more conservative the refinement, the smaller the rmsd from ideality will be. Some people believe 0.02 Å deviation from ideality is reasonable, based on the accuracy of the dictionary values of bond lengths and angles; others consider that to be too sloppy and a way to artificially deflate Rfactors. I seem to have detected a tendency in the literature to aim for about 0.01 Å deviation. The new refinement program phenix.refine, which is supposed to optimize weighting between X-ray terms and stereochemical constraints automatically, seems to settle in at quite conservative values, such as 0.005 Å, whereas with refmac, I can't seem to get the geometry any more ideal than 0.005 Å even if I try to idealize a structure in the absence of X-ray data. So, like you, I am a bit confused, and wouldn't mind hearing more from the experts. All the best, Bill yang li wrote: Dear All, I am very sorry to involve you into such insignificance discussion, I have reached agreement with Prof Gerard, please stop talking about things beyond science, thanks! I read a book today, which said A refined model should exhibit rms deviations of no more than 0.02A for bond length and 4 for bond angels, I just wonder about the standard of the bond length and the bond angel. I think most of you have read similar words! But maybe I didnot express clearly and made some phrasal mistakes. At last, happy new year to you all--though very late! Sincerely! Yang Li
Re: [ccp4bb] bond lengths, angles, ideality and refinements
Sorry, that should have read because the value is established by social consensus, it is thus NOT guaranteed to be perfectly accurate, ... In other words, one can imagine some source of systematic error in establishing an ideal bond length. For example, the crystal packing environment of small molecules might tend to distort a bond by a couple hundredths of an Ångstrom. William Scott wrote: Dear Yang Li: Happy New Year to you, too, (ahead of Feb. 7th). You certainly owe us no apology; the reverse may not be true. Your question is an important one, as is what you have written below. I'm not certain I have a completely satisfactory answer. The reason is that ideal bond lengths may or may not be true in the sense that the value is established by social consensus, and is thus guaranteed to be perfectly accurate, even though it may be quite precise. Because of this, and because of natural deviations from ideality (which really only become trustworthy observations at extremely high resolution), a certain amount of wiggle room is typically allowed in terms of rmsd. The more conservative the refinement, the smaller the rmsd from ideality will be. Some people believe 0.02 Å deviation from ideality is reasonable, based on the accuracy of the dictionary values of bond lengths and angles; others consider that to be too sloppy and a way to artificially deflate Rfactors. I seem to have detected a tendency in the literature to aim for about 0.01 Å deviation. The new refinement program phenix.refine, which is supposed to optimize weighting between X-ray terms and stereochemical constraints automatically, seems to settle in at quite conservative values, such as 0.005 Å, whereas with refmac, I can't seem to get the geometry any more ideal than 0.005 Å even if I try to idealize a structure in the absence of X-ray data. So, like you, I am a bit confused, and wouldn't mind hearing more from the experts. All the best, Bill yang li wrote: Dear All, I am very sorry to involve you into such insignificance discussion, I have reached agreement with Prof Gerard, please stop talking about things beyond science, thanks! I read a book today, which said A refined model should exhibit rms deviations of no more than 0.02A for bond length and 4 for bond angels, I just wonder about the standard of the bond length and the bond angel. I think most of you have read similar words! But maybe I didnot express clearly and made some phrasal mistakes. At last, happy new year to you all--though very late! Sincerely! Yang Li
Re: [ccp4bb] Malic Acid interferes heavy metal binding?
Dear Jinjin: Malic acid, a diprotic acid, has a pKa of about 3.4 for the first dissociation and a second at about 5.1. So it is best as a buffer within a pH range of about 2.4 to 6.1, and it at its best around best in the range of 3.4 to 5.1. If the pH of your solution is indeed 7, then it is doing little to buffer it (but the small amount of tris might). Many diprotic and polyprotic organic acids chelate metal ions. If you could substitute a different dianionic salt in the mother liquor, like a sulphate, it might help. Bill On Wed, 9 Jan 2008 18:42:06 -0500 JINJIN ZHANG [EMAIL PROTECTED] wrote: Dear All, I have got large and nice crystals in a condition that contains 40% glycerol, 75 mM DL-Malic Acid pH7.0, and that's it! No precipitant?! No buffer?! I'm so comfused. As far as from the product website, the Malic Acid has no buffering function. I don't know whether it's a precipitant. The protein itself was stored in a buffer contains 20mM Tris pH7.5, 150mM NaCl and 10% glycerol. I'm having difficulties in getting heavy metal bound derivatives. I was wondering whether the Malic Acid interferes heavy metal binding? Does anyone has any success with crystals grow with similar conditions? Any comment and suggestion is highly appreciated. Regards, Jinjin Zhang
Re: [ccp4bb] Any programs other than GRASP have a surface scribing function?
Just to add to that, on OS X, if you install the apbs and pymol packages via fink, everything will be set up for you. I think this is also true of at least Ubuntu and other debian linux varieties. As far as I am aware, the plugin is not compatible with the non-X-windows PyMOL on OS X. On Tue, 8 Jan 2008 20:30:50 + hua jing [EMAIL PROTECTED] wrote: You can use APBS plugin in PyMol. See installation instruction at http://www-personal.umich.edu/~mlerner/PyMOL/ or http://www.pymolwiki.org/index.php/APBS Holly Date: Tue, 8 Jan 2008 14:01:02 -0600 From: [EMAIL PROTECTED] Subject: [ccp4bb] Any programs other than GRASP have a surface scribing function? To: CCP4BB@JISCMAIL.AC.UK Dear CCP4'ers, Any Windows/Linux/OS X programs have a surface scribing function similar to that found in GRASP, to quickly draw the border of a surface selection (or subset) and calculate or display local features of the molecular surface? I have no access to SGIs now. I have a memory of similar function elsewhere but am not finding the ability within GRASP2, DINO, CHIMERA, etc. Perhaps I'm thinking of Setor which was also IRIX, and perhaps this memory is suspect... Other selection methods for a molecular surface require more of my time to define the subset. Many thanks, Jim James R. Thompson Assistant Professor of Biophysics Mayo Clinic College of Medicine Department of Physiology and Biomedical Engineering Mayo Proteomics Research Center Office 507-538-3891 Fax 507-538-3954 E-mail [EMAIL PROTECTED] _ Watch “Cause Effect,” a show about real people making a real difference. http://im.live.com/Messenger/IM/MTV/?source=text_watchcause
Re: [ccp4bb] Gastroeneterology position, Metro Tennessee area.
Hi Jessica: Thanks for posting these gastroeneterology and dermatology adverts to the CCP4 bulletin board. Many of in macromolecular X-ray crystallography are contemplating just such a career change, and although the retraining procedure may take 7 to 10 years, I am sure you would be willing to hold the position open given the flood of applications you will doubtless receive to your thoughtful and well-targetted email. The gastroeneterology position is one that is truly near and dear to my heart right now, and as an extra bonus, my whole family, including the dog, appear to have live cultures of norovirus at the moment. This has made me rue the decision to install a white carpet several years ago, which now possesses an interesting patina. Please let me know if I should post pictures. If, on the other hand, you were to decide that advertising for physician positions on a macromolecular crystallography email list was not an efficient means of getting the word out on behalf of your clients, I am sure those of us receiving these emails and contemplating just such a lucrative career change, complete with an endoscopy chamber in Tennesee, would somehow endure the trauma. Peace and joy in a prosperous new year, Bill On Mon, 7 Jan 2008 09:27:21 -0500 Jessica Martin [EMAIL PROTECTED] wrote: To all those interested, We have a 2 current openings in the same facility for a Gastroenterology specialist in Tennessee. Consultation status with the health system and will follow up with patients in the hospital after they are admitted. ? Benefits include NO call Endoscopy procedure lab (suite) available Highly competitive salary Excellent benefits, CME, Malpractice Moving expenses provided ? Please fax CV/Resume attention: Jessica Martin to fax number 206-666-4501. Any questions may be directed [EMAIL PROTECTED] Thank you! ?Jessica Martin Deb Bailey Recruiting 206-666-4501 203 Red Fern Pl Hot Springs, AR 71901 More new features than ever. Check out the new AOL Mail ! - http://webmail.aol.com
Re: [ccp4bb] Protein DNA complex refinement
Also, the PDB now uses prime (') instead of asterisk (*) for the ribose
numberings, and uses OP1 instead of O1P, and so forth.
Do the new refmac dictionaries have that (I haven't been able to get it to
work in the context of coot).
Garib Murshudov wrote:
If you take new dictionary with new refmac it may solve this and some
other naming problems.
Try from the website:
www.ysbl.york.ac.uk/YSBLPrograms/index.jsp
Garib
On 3 Jan 2008, at 16:53, Daouda TRAORE wrote:
Hi all,
I'm trying to refine a protein DNA complex using Refmac.
Unfortunately the job fails because of the definition of nucleosides :
In the pdb file I use for molecular replacement (and it's the same
for all protein-DNA complex I found in the PDB) nucleosides are
labelled DG, DT, DA , DC. In the monomer libraries for Refmac these
are labelled GD, TD, AD, CD.
The jobs fails also if I replace the DG, DT, DA , DC by GD, TD,
AD, CD in the coordinate file prior to refinement.
Could someone help me.
--
Daouda A.K. TRAORE, PhD Student
Laboratoire de Cristallographie et Cristallogenèse des Protéines
Institut de Biologie Structurale de Grenoble
41 rue Jules Horowitz
38027 Grenoble Cedex 1 - France
Phone: @IBS: +33 4 38 78 95 96 @ESRF/FIP: +33 4 76 88 27 89
Fax: +33 4 38 78 51 22
Laboratoire Chimie et Biologie des Metaux
CEA Grenoble iRTSV / LCBM / PMB
17 Avenue des Martyrs
38054 Grenoble Cedex 9 - France
Phone : +33 4 38 78 38 75
Fax : +33 4 38 78 34 62
E-mail: [EMAIL PROTECTED]
Re: [ccp4bb] Difference Map in COOT - Possible lignad but clash with structure?
On Fri, 28 Dec 2007 15:55:39 + Brenda Patterson [EMAIL PROTECTED] wrote: Hello, I am fairly new to this lark No problem. With a name like Patterson, your future is guaranteed (unless of course you see everything in the world with intensity but no phase). I have a density in my difference map which resembles my ligand. The thing is, it overlaps the density map of my structure and if I were to place the ligand in that map, then there would be a steric clash. ... how to proceed? The best thing to do at this point is to refine your structure while omitting the residues involved in the potential steric clash. The ligand may bind by induced fit -- i.e., changing the conformation at the binding site from that of the original structure. When you do that, the density that comes back will be less biased, and the answer to how it fits together may be apparent at that point.
Re: [ccp4bb] Coot 0.4 on Mac OS X 10.4
Yes, Virginia, there is a Santa Coot: http://tinyurl.com/24mchk This one will work on intel, both 10.4 and 10.5. If there are any problems let me know. PPC version to follow in the next few days. It is designed to be stand-alone, and to inflexibly install into /usr/local/coot I used a gtk+2 theme to make it look almost OS X native. On Thu, 20 Dec 2007 09:40:41 -0600 Mischa Machius [EMAIL PROTECTED] wrote: Y'all - I was wondering if anyone had a precompiled, stand-alone binary (Universal or Intel) of coot 0.4 for Mac OS X 10.4 that is not dependent on Fink (or anything else, for that matter)? Thanks so much. Best - MM Mischa Machius, PhD Associate Professor UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Dallas, TX 75390-8816; U.S.A. Tel: +1 214 645 6381 Fax: +1 214 645 6353
