Re: [ccp4bb] the structures of Nucleic acid

The phosphorus absorption edge is about 5.8Å. I've had much better luck with 5-Br-U for anomalous phasing. Molecular replacement with sub-structural fragments can also work: <https://scottlab.ucsc.edu/scottlab/reprints/2010_Scott_Methods.pdf> Yours sincerely, William G. Scot

Re: [ccp4bb] Coot installation issue

homebrew heavy-handedly wiped out coocanvas v. 2 when upgrading. I made a temp fix with a sym link as follows: ln -s /usr/local/Cellar/goocanvas/3.0.0/lib/libgoocanvas-3.0.9.dylib /usr/local/lib/libgoocanvas-2.0.9.dylib your path prefix will be different, but you get the idea. > On Sep 30, 2

Re: [ccp4bb] Phasing a difficult RNA heteroduplex structure

ct be solved without resorting to isomorphous replacement, by simply using a small subset of modeled duplexes for molecular replacement. cf: https://doi.org/10.1016/j.ymeth.2010.06.011 It might be worth a try. RNA perhaps inspires hatred because it habitually and bitterly mocks us in silence

Re: [ccp4bb] Coot 0.9.5

I’ve compiled it, but am having trouble with the GUI. This is not a big sur problem per se, but rather is the newer GTK+3 X-windows-independent interface. When we get it working, it will be a much nicer mac interface. Apple threw OpenGL under the bus in the last couple of OS updates. > On

Re: [ccp4bb] Issues in new Mac version 10.15

Which ones? All of the binaries in $CBIN I have say "Mach-O 64-bit executable x86_64” So that is unlikely the issue. I haven’t installed Catalina yet, as I only have one computer that is new enough. But one of the changes is they have locked down much of the file system, and are urging i

Re: [ccp4bb] [OT] Structure-related pun needed urgently

After reflecting on this a bit, I rejected anything dealing with glide planes, and although I initially thought I had something good involving a screw axis of evil, I decided it, too, would probably be lost in translation, not to mention a bit dated. Perhaps something more current, involving e

Re: [ccp4bb] Sir Prof. Aaron Klug 1926 - 2018

, is as much a legacy as his many exceptional contributions to science. Yours sincerely, William G. Scott Professor, Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http://scottlab

Re: [ccp4bb] Asn/Gln - pi-stacking prevalence

positive charge, and O has a partial negative charge. (If you think about it, all pi-stacking interactions, from the point of view of classical electrostatics, would be somewhat repulsive.) Good luck with this, and let us know of the outcome. Bill William G. Scott Director, Program in

Re: [ccp4bb] coot install problems under Mac OS X 11 (El Capitan)

Hi Barry: It is an X11.app bug that has persisted for years now. (It isn’t specific to coot). Briefly, this happens unless you uncheck the checkbox for “Displays have Separate Spaces” in System Preferences>Mission Control William G. Scott Director, Program in Biochemistry and Molecu

Re: [ccp4bb] Coot no GUI

coot --no-graphics William G. Scott http://scottlab.ucsc.edu > On Jul 28, 2017, at 1:34 PM, Reza Khayat wrote: > > Hi, > > Is it possible to run Coot without the use of GUI? We have some Coot scripts > for a pipeline and we’d like to do without the GUI. Thanks. >

[ccp4bb] Abraham Szöke

yed a multitude of fruitful and productive collaborations throughout a period most normal people would consider retirement. He passed away on Thursday at age 87 from an opportunistic infection while combatting lymphoma. William G. Scott Professor, Department of Chemistry and Biochemistry and The Cente

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

benefit to the scientific community. Yours faithfully, William G. Scott Director, Program in Biochemistry and Molecular Biology Professor, Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA

[ccp4bb] just out of totally idle curiosity ...

What’s the job situation in Europe looking like for refugee scientists these days? William G. Scott Director, Program in Biochemistry and Molecular Biology Professor, Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz

[ccp4bb] Latest XQuartz upgrade breaks Coot

More regarding" XQuartz upgrade breaks Coot” from people who know more than I do (which admittedly is most everyone, but I digress …): > > Today's Topics: > > 1. Xquartz 2.7.10-rc2 breakage (Jack Howarth) > 2. fink-0.41.0-101 du_sk.t build failure (Patrick Carmack) > > > ---

Re: [ccp4bb] X-rays and matter (the particle-wave picture)

describing this non-classical behavior). BTW that really has to be the ickiest user name alias in the history of the CCP4 BB. William G. Scott http://scottlab.ucsc.edu/~wgscott > On May 21, 2015, at 6:43 PM, Murpholino Peligro wrote: > > Hello Everybody! > I was trying to make som

Re: [ccp4bb] SUMMARY: Equation Editor woes with Office 2011 for Mac

> On May 20, 2015, at 5:38 AM, Randy Read wrote: > > Thanks, as always, to everyone for a thoughtful discussion! Alternatively, as a scientific community, perhaps it is finally time for us to untwist Clippy, bending him backwards and forwards until he snaps at those horrid beady little eyebal

Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac

> On May 18, 2015, at 4:31 AM, Nicolas Soler wrote: > > You just have to learn the (easy) equation syntax or just use this: http://www.macupdate.com/app/mac/18172/tex-fog William G. Scott http://scottlab.ucsc.edu/~wgscott

Re: [ccp4bb] CCP4 and Coot Interface can not maximized to full screen on Macbookpro Yosemite

Glad it works! It sounds like they finally fixed an X11 bug that has been quite problematic these last few years. Bill William G. Scott http://scottlab.ucsc.edu/~wgscott > On May 14, 2015, at 9:06 PM, Xiao Lei wrote: > > Dear William, > > I installed the X11 2.7.8_rc1 a

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

knowledge. All the best, Bill William G. Scott Professor, Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http://scottlab.ucsc.edu/~wgscott > On Apr 24, 2015, at 12:52 AM, Rob

Re: [ccp4bb] PDBcur fails with error message

Hi Jeorge: My Luddite approach to such things: grep -v ANISOU original.pdb > iso_only.pdb HTH, Bill William G. Scott http://scottlab.ucsc.edu/~wgscott > On Apr 24, 2015, at 8:54 AM, jeorgemarley thomas > wrote: > > Dear All, > > Here is the CCP4

[ccp4bb] [OT]: Can anyone recommend a good reference for creating CVs or resumes for US biotech?

sarcasm and strange verb tenses.) If anyone has a good source for successful examples or templates, I would be incredibly grateful. Many thanks in advance. Bill William G. Scott http://scottlab.ucsc.edu/~wgscott

Re: [ccp4bb] OS X yosemite

materialize. YMMV, Bill William G. Scott Professor, Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http://scottlab.ucsc.edu/~wgscott > On Mar 17, 2015, at 4:30 PM, Cygler, Miros

Re: [ccp4bb] CCP4 PATH variable

> On Mar 13, 2015, at 12:42 PM, Petr Leiman wrote: > > this is how we are supposed to use CCP4 today anyway. I’ve never been big on doing what I am told I am supposed to do, so I have been using this: use this to put it at the end of the path: ccp4_first_in_path=0 or this to put it at the b

Re: [ccp4bb] Basic Anomalous Scattering Theory

> On Mar 11, 2015, at 11:13 AM, Keller, Jacob wrote: > > Somebody sent me a pdf with such a mind-picture which describes the origin of > the anomalous effect as arising from broken centrosymmetry of the anomalous > atoms themselves: > > (p. 8) "Under normal conditions, electron distributions w

Re: [ccp4bb] Basic Anomalous Scattering Theory

— enzymology. Hopefully this will be something to get a start with. Bill William G. Scott Director, Program in Biochemistry and Molecular Biology Professor, Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz

Re: [ccp4bb] different Kd and Km value

> On Feb 26, 2015, at 4:51 PM, Srivastava, Dhiraj > wrote: > > Hi > I have a protein with two substrate. when I am doing the binding studies > with the two substrate separately, I am finding one of the substrate to have > similar kd and Km. however the km and kd values are almost 30 fold dif

Re: [ccp4bb] How to rename nucleic acid residues in PDB files

CCP4 has a number of such utilities, such as pdbset. http://www.ccp4.ac.uk/html/pdbset.html You can find others by looking here: http://www.ccp4.ac.uk/html/FUNCTION.html HTH, William G. Scott http://scottlab.ucsc.edu/~wgscott On Oct 7, 2014, at 11:01 AM, Sasha Pausch wrote: > Th

Re: [ccp4bb] How to rename nucleic acid residues in PDB files

> On Oct 6, 2014, at 12:04 PM, Sasha Pausch wrote: > > Hello All, > > I would like to know how to change the nomenclature of bases (for example > from Ad to DA for adenosine triphosphate) in PDB file. perl -pi -e ‘s|Ad|DA|g’ your.pdb

Re: [ccp4bb] paper

On Sep 2, 2014, at 9:10 PM, Avisek Mondal wrote: > please can you send me this paper... i can not subscribe it from my lab... > Acta Cryst. (2014). F70, 1296-1302[ doi:10.1107/S2053230X14014381 ] No problem: http://tinyurl.com/n3gurpe

Re: [ccp4bb] negative density around disulfide bond

On Jun 1, 2014, at 10:08 PM, Eze Chivi wrote: > Hello, when I refine my structure, I see negative density around the > disulfide bond. I have 7 copies per ASU, and I can see this density in many > of them. In some cases, I see positive density also (negative in the center > of the straight lin

Re: [ccp4bb] crystallographic confusion

in that case would probably be significant. The map image quality, after all, is what we are after, not beautiful Table 1 statistics. Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz

Re: [ccp4bb] install coot in mac through fink

corrupted. Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http://scottlab.ucsc.edu/scottlab/ On Apr 2, 2014, at 8:58 AM, Yamei Yu wrote: > Hi

Re: [ccp4bb] OSX 10.9.2

On Mar 28, 2014, at 10:29 AM, Cygler, Miroslaw wrote: > Hi, > Does the ccp4 suite work with the latest OSX 10.9.2 operating system? Are > there any known problems? > > > Mirek > > > As far as I can tell, it works fine. One problem I have heard (on the ccp4bb) with 10.9.X is that support f

Re: [ccp4bb] largest protein crystal ever grown?

I remember seeing an approx (5mm)^3 haemoglobin crystal in the MRC LMB crystal growing room, and the nucleosome crystals there were almost as big in their longest dimension. Bill On Oct 24, 2013, at 8:33 AM, Tobias Beck wrote: > Dear all, > > I was just wondering if anyone has some informat

Re: [ccp4bb] Only refine "B"s in Refmac?

On Sep 4, 2013, at 2:57 PM, Garib N Murshudov wrote: > You may need to use the latest available version (5.8) from our LMB site Hi Garib: Would it be possible to add a link for the source code, so this could also be used with Coot? Thanks. Bill

Re: [ccp4bb] CCP4 package installation problem in Mac OS

Scroll up to see where it started failing. On Aug 3, 2013, at 11:22 AM, anil kumar wrote: > Dear members, > > I am attempting to install ccp4 package in my mac machine. The download of > the files was directed in a temp folder and done via the package manager > successfully. Upon installatio

Re: [ccp4bb] Harmful effect of X-ray

On Jul 12, 2013, at 12:57 PM, Mark van der Woerd wrote: > I just re-wrote our safety plan because we have to renew our radiation > license for our new in-house instrument. On this plan, they ask you to write > a worst-case scenario. For an in-house sealed tube instrument, producing CuKa > radi

Re: [ccp4bb] RNA for crystallization

the nucleotide resolution you might need. Good luck. 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] delete subject

That last paragraph is great: "Adam is the author of the book Surviving Your Stupid, Stupid Decision to Go to Grad School (Broadway Books, 2010) " -- Bill On Mar 28, 2013, at 9:09 AM, Ian Tickle wrote: > By coincidence this just landed in my Inbox: > > http://membercentral.aaas.org/multimed

Re: [ccp4bb] delete subject

to them not to have to rely only upon my limited abilities and increasingly obsolete knowledge. We should all be able to learn from one anther without fear of reproach. All the best, Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular

Re: [ccp4bb] RNA 3D structure alignment

I find that least-squares fitting of RNA in coot is fairly painless, robust and straightforward. It will move all of the contents of one pdb file, not just the RNA residues you select to align. On Mar 14, 2013, at 1:53 PM, Chen Zhao wrote: > Dear all, > > I am now struggling to align two 3

Re: [ccp4bb] Mac OS 10.8 Mountain Lion and CCP4?

bugs, annoyances and 'features' that have been corrected in 10.8, so I either run 10.8.X or 10.6.8 on my computers in the lab.) Good luck. Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laborato

Re: [ccp4bb] fink problem

It sounds like you have updated the OS system since last updating fink. Easiest thing is to blow it away and start over. I made some tarballs to remove the pain: Or you can just i

Re: [ccp4bb] how to update phenix

On Feb 10, 2013, at 8:23 AM, LISA wrote: > Hi all, > My mac has the old version of phenix. How can i update to the new verison? > Should I delete the old version and download the new version to install as > the fist time ? Thanks > > lisa You can delete it and download a new version, or sim

Re: [ccp4bb] off topic:how to prevent DNA tetraplexe forming?

plexes structure? > any suggestion is appreciation. > > > dengzq Unless it has some other, more stable structure to compete it out, you will have this problem persist. Even GTP in solution will do this. Bill William G. Scott Professor Department of Chemistry and Biochemistry and

Re: [ccp4bb] Reading CCP4 maps into PyMol

Give it the suffix .ccp4 On Dec 7, 2012, at 10:52 AM, "Harman, Christine" wrote: > Hi, > Can anyone tell me how to open a CCP4 map in Pymol. > > Thanks, > > Christine > > >

[ccp4bb] Mg++ interactions

Hi folks: Are Mg++ ions ever observed to chelate primary amines? Are there any examples in crystal structures? Thanks. -- Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of

Re: [ccp4bb] hkl2000 install

Make your life easier and use CCP4's imosflm (this is the CCP4 bb after all) On Nov 18, 2012, at 5:48 PM, 王瑞 wrote: > OK,thank you all of you. I have installed one copy of HKL2000 on our > desktop computer. But for my notebook's low 1366*768 resolution, the > HKL2000 can't work ! So what could

[ccp4bb] OT: Has anyone experienced problems with Apple laptop battery expansion?

Hi folks:I'm trying to get a sense for how frequently this sort of thing occurs: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 i

Re: [ccp4bb] Glass Capillaries

On Nov 12, 2012, at 8:13 AM, Michael Roberts wrote: > Dear All, > > I would be interested to learn of other crystallographers' experience in > their use of glass capillaries for protein crystal growth and X-ray > diffraction clarity. > There are many types of glass available - quartz, soda gla

Re: [ccp4bb] CCP4-6.3.0 installtion

On Oct 18, 2012, at 3:39 PM, Kip Guja wrote: > > If the output says: /bin/bash then do > > source /Applications/ccp4-6.3.0/bin/ccp4.setup-sh & ccp4i > > If the output says: /bin/tcsh or /bin/csh then do > > source /Applications/ccp4-6.3.0/bin/ccp4.setup-csh & ccp4i You need to replace "&" wi

Re: [ccp4bb] CCP4 update 6.3.0 006

Dear Ronan et al: I apologize if I have missed it, but is there a simple way to obtain the corresponding changes in the source code for those of us who compile ccp4 ourselves? I looked on the web site and the ftp site but can't seem to find it. Many thanks in advance. Bill On Oct 8, 2012,

Re: [ccp4bb] Off-topic: Best Scripting Language

I'd just use a decent shell scripting language (like zsh) in conjunction with a unix tool like awk. But the gnuplot option sounds ideal. Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laborat

Re: [ccp4bb] CCP4 Update

On Sep 6, 2012, at 9:00 AM, eugene.krissi...@stfc.ac.uk wrote: > If this does not work for you for any reason, please (re-)read update manual > for details. If that does not help as well, please write to us. Dear Eugene: Will there be a way to get the corresponding changes to the source-code?

Re: [ccp4bb] Various OSes and Crystallography

I completely agree with Harry's observation about the glare screen "feature." I find it is quite literally an almost instant headache. There is an option with the macbook pro to pay a ransom to get a usable screen, so my wife did. On my macbook air, I found putting a dull dark grey background

Re: [ccp4bb] Problem with Coot on Mountain Lion

I'm unable to reproduce the error. Can you try it in a temporary new account that doesn't have anything modified, and see if it works? William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories Uni

Re: [ccp4bb] Question on stereo monitor: LG D2342P-PN

;ll bet it will work fine. If you can get it from Best Buy for under $300 and return it within 30 days for a full refund, it might be worth it. Either way, let us know. Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228

Re: [ccp4bb] Nucleophilic attack by the side-chain carboxyl group of Asp?

s, and orbital interactions dominate. So Mg++ prefers oxygen to sulphur, and Hg++ prefers sulphur to oxygen. 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] [COOT] CCP4 6.3.0 released

On Jul 17, 2012, at 6:25 AM, Felix Frolow wrote: > I will wait for fink version if it will be one… :-\ Does anyone use or want this anymore? -- Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laborator

Re: [ccp4bb] Coot installing problem

If RedHat allows you to install a more current version of glibc, then do that. If not, switch to something like Ubuntu. 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

Re: [ccp4bb] Drawing reaction mechanism

xdrawchem is free and will do this. On May 31, 2012, at 8:01 PM, Appu kumar wrote: > Dear ccp4 user, > Sorry for offset question, Anyone please tell me > the name of programme which can be used to draw enzyme reaction mechanism ( > like Sn1 and Sn2). Your kind hel

Re: [ccp4bb] Sad News

I thought it was some sort of allegory for tenure-track faculty positions. -- Bill On Feb 28, 2012, at 7:16 AM, Gerard Bricogne wrote: > Dear Smita, > > For me, your story mostly illustrates the grave dangers of wanting to > own a BMW while still in high school ... ;-) . > > > Wit

Re: [ccp4bb] All-D World

e for a Ph.D. thesis project (especially when combined with an M.D.), and you, unlike Him, have access to a Sigma catalogue. All the best, Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories Universi

Re: [ccp4bb] DNA length for crystallization

This paper is a favorite:http://www.ncbi.nlm.nih.gov/pubmed/2160019 J Mol Biol. 1990 May 5;213(1):159-66. Crystallization of Escherichia coli catabolite gene activator protein with its DNA binding site. The use of modular DNA. On Feb 15, 2012, at 12:06 AM, LISA wrote: > Hi all, > > I ha

Re: [ccp4bb] 10 mM Na Acetate buffer preparation

http://en.wikipedia.org/wiki/Henderson–Hasselbalch_equation or any intro chemistry text 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

Re: [ccp4bb] Coot on an SGI

monitor attached to a $600 mac mini. I'm sorry this doesn't answer your question, but I think an ancient version of coot on an ancient computer will just be a world of hurt. -- Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology

Re: [ccp4bb] image compression

that would be the best way to handle it from a central repository, allowing the end-user to decide on the fly. The lossless files could somehow be tagged as such, to avoid confusion. Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular

Re: [ccp4bb] not so good news (Steve Jobs RIP)

On Oct 5, 2011, at 5:52 PM, Bosch, Juergen wrote: > http://www.apple.com/stevejobs/ > > May innovation continue to lead the future. > > Jürgen I've been quite saddened about this all evening. Even though we knew it was coming, it is still incredibly sad, especially at his age (only 56). Alth

Re: [ccp4bb] Linux vs MacOS for crystallographic software

On Sep 28, 2011, at 5:26 PM, Jacqueline Vitali wrote: > Dear colleagues, > > I need some advice for a new computer. > > (1) I have the option of an HP Z210 8 GB with a low end Quadro Nvidia 400 > 512 MB. > > --How does Coot run with this card? > OK > --I am happy with any Linux. However,

[ccp4bb] Rigaku high voltage tank

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

Re: [ccp4bb] Desmond 3.0 Tutorial, Oct 5 in Boston, MA

On Sep 22, 2011, at 9:29 AM, Ben Eisenbraun wrote: > Desmond 3.0 Tutorial 2.2 was quite impressive. (sorry.)

Re: [ccp4bb] Mac OSX 10.7 Lion

an inconvenient vista. Peace and joy, Bill On Sep 16, 2011, at 6:33 AM, William G. Scott wrote: > Dear Phil (and everyone): > > 1. I've now got automated build systems for coot for 10.7.1 and 10.6.8. I > just haven't had a chance to get the 10.6.8 one on line. I'

Re: [ccp4bb] more Computer encryption matters

OS X 10.7 enables you to do whole-drive encryption. Here is a description from Arse Technica: http://arstechnica.com/apple/reviews/2011/07/mac-os-x-10-7.ars/13 I ain't never tried it myself. 10.7 seems to run slow enough as it is. -- Bill On Aug 18, 2011, at 5:34 AM, Andreas Förster wrote:

Re: [ccp4bb] OSX Lion

On Jul 27, 2011, at 6:45 AM, Bosch, Juergen wrote: > But Bill has updated his webpage

Re: [ccp4bb] fink unofficial fix for OSX 10.7 (Lion)

On Jul 22, 2011, at 4:24 AM, Xiaoguang Xue wrote: > I noticed that the Fink repository will not run on the Lion system All the debian utilities work (as does the crystallography software), so it is just the fink perl wrapper script itself that doesn't work. Here is a cheap and easy, but unoffic

Re: [ccp4bb] Coot "Bad magic number" errors

Sorry about this. Issue the command sudo perl -pi -e 's|/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6\:/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5\:||g' /Library/Coot/bin/coot and that will fix it. I'll make a new one. Bill On Mar 10, 20

Re: [ccp4bb] Detaching crystals from glass cover slides

Hi Wataru: I hope all is well. For the ones you already have grown, try very gently prying them off with a wedge-shaped needle. If you can grow more, try using a very thin smooth layer of vacuum grease, and apply the drop to that. I managed to get RNA crystals to grow that way that otherwise

Re: [ccp4bb] Mg2+ or water

On Dec 20, 2010, at 1:16 PM, jlliu liu wrote: > it is also within hydrogen bonding distance to the main > chain N of another protein residue. This also strongly suggests it is not Mg2+, which prefers hard ligands such as charged oxygen, rather than softer ligands like uncharged backbone nitroge

Re: [ccp4bb] CCP4 hey

On Dec 3, 2010, at 3:11 AM, U US wrote: > Hello CCP4, long time no see! I wanted to show you this article. I've made > over $2k in the past month and I barely work 4 hours a day. Grad school was the best 13 years of my life, too.

Re: [ccp4bb] vector and scalars

> As usual, the Omniscient Wikipedia does a pretty good job of giving the > standard mathematical definition of a "vector": > > http://en.wikipedia.org/wiki/Vector_space#Definition > > If the thing fulfills the axioms, it's a vector. Complex numbers do, as well > as scalars. It is a bit mo

Re: [ccp4bb] [QUAR] Re: [ccp4bb] embarrassingly simple MAD phasing question (another)

On Oct 14, 2010, at 2:28 PM, Jacob Keller wrote: > I have always found this angle independence difficult. Why, if the anomalous > scattering is truly angle-independent, don't we just put the detector at 90 > or 180deg and solve the HA substructure by Patterson or direct methods using > the pure

Re: [ccp4bb] embarrassingly simple MAD phasing question (another)

On Oct 14, 2010, at 2:31 PM, Tim Gruene wrote: > I would like to understand how the notion of a photon being scattered from all > electrons in the crystal lattice explains the observation that radiation > damage > is localised to the size of the beam so that we can move the crystal along and > sh

Re: [ccp4bb] embarrassingly simple MAD phasing question (another)

On Oct 14, 2010, at 7:40 AM, Ed Pozharski wrote: > On Thu, 2010-10-14 at 08:41 +0200, Tim Gruene wrote: >> This sounds as though you are saying that a single photon interacts >> with several >> electrons to give rise to a reflection. > > Not only with several - it shouldn't be much of an exagger

Re: [ccp4bb] Summary : [ccp4bb] embarrassingly simple MAD phasing question

On Oct 13, 2010, at 3:09 PM, Tim Gruene wrote: > Dear Bill, > > The discussion is becoming complicated because of the mixing of notations. > There is a theory or model which describes the atomic scattering factor as >f = f0 + f' +if" > from which the structure factor is calculated. That right

Re: [ccp4bb] embarrassingly simple MAD phasing question (another)

On Oct 13, 2010, at 4:21 PM, Jacob Keller wrote: > While we are on embarrassingly simple questions, I have wondered for a long > time what is the reference phase for reflections? I.e. a given phase of say > 45deg is 45deg relative to what? Is it the centrosymmetric phases? Or a > theoretical wav

Re: [ccp4bb] Whither pymol?

be happy > about > this ...) > > Tim > > On Tue, Sep 21, 2010 at 07:10:56PM -0700, William G. Scott wrote: Thanks, Tim. Several people have pointed out I missed the sourceforge svn repository. Considering I use this to make the fink package tarball, I am suitably emba

Re: [ccp4bb] OSX 10.6, Fink CCP4 install problem

Hi David: I think you need to start with the pure 64-bit fink from cvs in order to get this to work. All the errors are a consequence of using the 32-bit version. You can't mix them. I have no idea why they still don't have a binary installer, but they don't. Email me directly if you need more

Re: [ccp4bb] imosflm conflict with mosflm (OS X/fink 32-bit)

, > in combination with either the fink or the system wish, gives a nicely > working imosflm. And thanks for the fink packages... > > Engin > > On 7/6/10 6:36 AM, William G. Scott wrote: >> Remove both. >> >> On OS X, 10.6, imosflm uses the tcl/tk supplied

Re: [ccp4bb] imosflm conflict with mosflm (OS X/fink 32-bit)

Dear Harry et al: I'm sorry, I've been immersed in grant renewal/resubmission hell. I obviously screwed something up in a rush. Briefly, if you have 10.6.X, ccp4 and OS X have everything you need for a nice, fully-functioning OS X aqua imosflm gui. Bill PS: The 64-bit ccp4 and mosflm work gr

Re: [ccp4bb] imosflm conflict with mosflm (OS X/fink 32-bit)

Remove both. On OS X, 10.6, imosflm uses the tcl/tk supplied with OS X, and the latest mosflm is in ccp4, so there is no need for any of that. Just use what is in ccp4. Sorry for this. On Jul 5, 2010, at 4:34 PM, Engin Özkan wrote: > Hi everybody, > > I was doing a regular fink update (OS X

Re: [ccp4bb] Cryo tongs/manipulator

When searching, avoid the almost overwhelming temptation to spell it as "vile manipulator" or you will just wind up with a listing of university administrators. Bandaranayake, Rajintha wrote: > Hello all, > Does anyone know where one could purchase cryo-vial tongs/manipulatos with > the plastic

[ccp4bb] Off-topic: Univ California boycott of Nature publishing group

Hi folks: Sorry about the off-topic nature (so to speak) of this post, especially given that it is not yet Friday, but I am interested what our community thinks of this: http://library.ucsc.edu/sites/default/files/Nature_Faculty_Letter.pdf Something similar happened with UC and Cell Press a fe

Re: [ccp4bb] Should I be worried about negative electron density?

On May 18, 2010, at 4:13 PM, Jay Pan wrote: Hello Everyone, I have a reasonably well fitted electron density map through molecular replacement. However, there is always some red region left no matter how hard I tried when the mtz file is loaded into Coot. Is this because my model is still

Re: [ccp4bb] Please remove me from this list

Although not as dramatic, there is a simple, private, method one can use to unsubscribe, and it possesses the additional merit of actually doing what you want: http://www.ccp4.ac.uk/ccp4bb.php Colapietro, Anne-Marie wrote: > Please remove me from this list. > Thank you, > Anne-Marie > > -

Re: [ccp4bb] Rejected posting to CCP4BB@JISCMAIL.AC.UK

Yo Hari: The symbolic link won't solve the problem. I managed to scrape together a blt for tcltk 8.5 on OSX, so it is possible. Most of the hacks in turn came from a different Linux distro (gentoo) so it should be possible on ubuntu. Here by the way is the patch: http://fink.cvs.sourceforge.n

Re: [ccp4bb] how to refine RNA with two phosphate at 5' by phenix

Lisa Wang wrote: > hi all, > I have one structure contains dsRNA with two phosphate group at 5'.. I > named > the first residue GDP and got a cif file by running phenix.elbow. Then I > refine my structure by running phenix.refine my.pdb my.cif. But the fist > and > the second residue do not link wi

Re: [ccp4bb] Extra density near serine residue?

Knowing the distances and angles to the nearest neighbors might help us guess. If it is extra density contiguous with the SER, it might indicate a mutation (or sequence error). On Mar 9, 2010, at 8:38 PM, Jeremiah Farelli wrote: > I am currently wrapping up a structure, and I have a bit of wei

Re: [ccp4bb] low resolution phasing protocols

This was done in total despair: http://sage.ucsc.edu/scottlab/reprints/2008_Scott_ActaCrystD.pdf Francis E Reyes wrote: > Hi all > > I'm in search of literature *detailing* low resolution [4-5A] phasing > protocols. Heck I'll take detailed thesis chapters (since they tend to be > more detailed

Re: [ccp4bb] linux question

On Feb 27, 2010, at 7:10 PM, David Roberts wrote: > I have a quick question about linux for all. Is there anybody running a > windows pc with linux on a bootable cd or bootable drive/flash drive/??? that > works for crystallography apps? I have a colleague who does molecular > dynamics calcul

Re: [ccp4bb] linux question

On Feb 28, 2010, at 5:11 PM, Damon Colbert wrote: > I have a persistent Kubuntu 8.10 .. it took a week to work out some > problems. The main one being that with limited space on the thumb drive, > one cannot do a complete update of Kubuntu. Therefore many libraries are > missing and dependancy e

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