[ccp4bb] Wanted: Difficult to Crystallize Proteins

known structure 5. the smaller the better, ideally 40 to 100 aa 6. do not oligomerize higher than a dimer Any recommendations will be exceedingly appreciated. James -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com

Re: [ccp4bb] OSX as an NFS server

y run. -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com

Re: [ccp4bb] cannot read mtz file

n the root account, it is OK. Thanks! [广告] 金秋最关注楼盘-房不胜房 -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com

Re: [ccp4bb] buster-tnt on OSX ?

I hope you will take the time to write to either of the mailing lists I indicated above to explain what simplifications you would like to see in our current installation procedures, and look forward to reading them. With best wishes, Gerard. -- On Sun, Oct 26, 2008 at 0

Re: [ccp4bb] buster-tnt on OSX ?

ED] [EMAIL PROTECTED] ********* -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com

Re: [ccp4bb] foam dewar usage ?

- UJF 41, rue Jules Horowitz 38027 Grenoble - France Phone : +33 (0)4 76 20 94 49 Fax : +33 (0)4 76 20 94 80 E-mail : [EMAIL PROTECTED] Web sites : http://www.ibs.fr ; http://psb.esrf.fr ****** -- James Stroud

Re: [ccp4bb] Protein DNA complexes concentration

ed on gel filtration column. I have already tried lyophylisation or amicon method without anty results?? Have you some good idea about this? chaix denis -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com

Re: [ccp4bb] For a laugh..

[flame war snipped] It's usually considered bad manners to publicly post private correspondence without permission, even if it may have some entertainment value. One should consider using plonk instead: http://en.wikipedia.org/wiki/Plonk James -- James Stroud UCLA-DOE Institut

Re: [ccp4bb] DNA building program

storage. Get it now -- James Stroud UCLA-DOE Institute for Genomics and Proteomics 611 Charles E. Young Dr. S. Los Angeles, CA 90095 http://www.jamesstroud.com

Re: [ccp4bb] Pymol movie ration along any axis

s always from Z axis. Does anyone have this experience of rotating molecules along any other specified axis and keeping the same view point as usual? Thanks a lot. Jerry Use video conversation to talk face-to-face with Windows Live Messenger. Get started. -- James Stroud UCLA-DO

Re: [ccp4bb] Pymol movie ration along any axis

When you make movies, Pymol usually allows you rotate molecules along x, y, or z axis. The view point is always from Z axis. Does anyone have this experience of rotating molecules along any other specified axis and keeping the same view point as usual? Thanks a lot. Jerry

Re: [ccp4bb] Reminder - still no 3D stereo under OS X 10.5

e recommending OS X for stereo applications. -ben -- Ben Eisenbraun Structural Biology Grid Harvard Medical School http://sbgrid.org http://hms.harvard.edu -- James Stroud UCLA-DOE Institute for Genomics and Proteomics 611 Charles E

Re: [ccp4bb] Off-topic: Headhunters

s in advance. Bill William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com

Re: [ccp4bb] Maks file in HKL2000

aglines&ei=UTF-8&rd=r1&p=chocolates -- James Stroud UCLA-DOE Institute for Genomics and Proteomics 611 Charles E. Young Dr. S. Los Angeles, CA 90095 http://www.jamesstroud.com

Re: [ccp4bb] HKL2000 and gcc4 - redux

s and limitations of files placed in /usr/lib: "/usr/lib includes object files, libraries, and internal binaries that are not intended to be executed directly by users or shell scripts." If it fulfills the definition and is not expressly forbidden, then its reasonable to assume

Re: [ccp4bb] HKL2000 and gcc4

/ folder, and HKl2000 runs, but our sys-admin refuses to let it stay there. -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com

Re: [ccp4bb] ccp4 install on Leopard

they've got your box and you didn't even know it ever happened. That's one reason off the top of my head. James -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com

Re: [ccp4bb] Procheck fails to run on Mac OS X 10.5

n (Procheck and Sfcheck) without Rampage; Mac OS X 10.5.2. Other ccp4 programs work fine (pdbset, even sfcheck), so I assume it's not a problem with paths, permissions or writing .ps files (I didn't try Amore or Refmac yet). Python is version 2.5, Tcl/Tk 8.4.16. Any help would be

Re: [ccp4bb] into the looking glass

biological molecules would all be racemic. That would be true justice. James -- James Stroud UCLA-DOE Institute for Genomics and Proteomics 611 Charles E. Young Dr. S. Los Angeles, CA 90095 http://www.jamesstroud.com

Re: [ccp4bb] The Lawnmower Man

://www.i-glassesstore.com/ -- David C. Briggs PhD Father & Crystallographer http://www.dbriggs.talktalk.net AIM ID: dbassophile ======== -- James Stroud UCLA-DOE Institute for Genomics and Proteomics 611 Charles E. Young Dr. S. Los Angeles, CA 90095 http://www.jamesstroud.com

Re: [ccp4bb] 3D mouse?

Group phone: +44 1883 722306 (x 305) Marie Curie Research Institute fax : +44 1883 714375 The Chart, Oxted RH8 0TL, UK web : http://mc11.mcri.ac.uk -- James Stroud UCLA-DOE Institute for Genomics and Proteomics 611 Charles E. Young Dr. S. Los Angeles, CA 90095

Re: [ccp4bb] question about processing data

> Melody > -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: [EMAIL PROTECTED] Phone: + 44 208 816 2515 -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com

Re: [ccp4bb] question about processing data

%, should I use merge all the data and call it a 2.15 A dataset or I should cut the data set to say 2.25 A where the highest resolution shell has better completeness (>85%)? What is an acceptable completeness value for the highest resolution shell? Thank you. Best, Melody -- James Str

Re: [ccp4bb] changing names of many files

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. -- James St

Re: [ccp4bb] overlapping DNA in prt-DNA complex structure

? Thanks a lot for your help! Sabine -- James Stroud UCLA-DOE Institute for Genomics and Proteomics 611 Charles E. Young Dr. S. Los Angeles, CA 90095 http://www.jamesstroud.com

Re: [ccp4bb] Merging CCP4i projects from two computers

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 -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com

Re: [ccp4bb] WM_DELETE_WINDOW

or, I expect confirmation if I've made changes. For a crystallography suite, I would err on the side of caution. James -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com

Re: [ccp4bb] WM_DELETE_WINDOW

Maybe it is bound on second look--But it does not confirm exit, which would be handy. On Mar 4, 2008, at 4:46 AM, James Stroud wrote: Who do I contact to spread the news that you can bind the WM_DELETE_WINDOW protocol of the main ccp4i window to the same callback as the "EXIT"

[ccp4bb] WM_DELETE_WINDOW

osing main ccp4i window. -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com

Re: [ccp4bb] finicky protein

room. can any one suggest some solution? Thanks in advance. NSH -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com

Re: [ccp4bb] Tough Low-Res MR

Dear Everyone, Thank you for suggesting phaser. It is king. The problem proved not to be trivial but now appears to be solved with great help from phaser. Time to celebrate. James On Thu, Feb 21, 2008 at 11:48 AM, James Stroud <[EMAIL PROTECTED]> wrote: Hello All, I have a toug

[ccp4bb] Tough Low-Res MR

vances in MR in recent years, but I haven't kept up with all of the software. Does anyone have suggestions for packages to try? James -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com

Re: [ccp4bb] Vista

65-6399 phone: 212- 327-7429 fax: 212-327-7389 -- *:-.,_,.-:*'``'*:-.,_,.-:*'``'*:-.,_,.-:*'``'*:-., Avinash Gill Dartmouth Medical School Biochemistry Dept HB 7200 Vail Bldg Hanover NH 03755 Phone: (O) 603-650-1174 *:-.,_,.-:*'``'*:-.,_,.-:*'``'*:-.,_,.-:*'``&#

Re: [ccp4bb] Vista

must I still avoid it? Thanks, Deena Deena Abells Oren, PhD Manager, Structural Biology Resource Center Rockefeller University 1230 York Avenue New York, NY 10065-6399 phone: 212- 327-7429 fax: 212-327-7389 -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles

Re: [ccp4bb] Codon Optimized Expression

principle express identically. I have no idea what the mechanism for this differential expression could be. -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com

Re: [ccp4bb] Python 3.0 breakage

On Feb 2, 2008, at 1:36 AM, Gerard DVD Kleywegt wrote: Do you mind if we call you Bruce, just to keep it clear? No need for the formalities, Lenny will be fine. -- Sig wisely sitting this one out.

Re: [ccp4bb] Python 3.0 breakage

priate name would be "Benny Hill" or "Chris Rock". James -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com

Re: [ccp4bb] Python 3.0 breakage

"Pretty much every program will need changes," Baxter said, but he stressed that the shift would be some time in coming..." -- James Stroud UCLA-DOE Institute for Genomics and Proteomics 611 Charles E. Young Dr. S. Los Angeles, CA 90095 http://www.jamesstroud.com

Re: [ccp4bb] Web site GOOD, Attachment BAD (was: salt sensitive complex)

nice weekend. > > Jerry > Helping your favorite cause is as easy as instant messaging. You IM, we give. Learn more. <http://im.live.com/Messenger/IM/Home/?source=text_hotmail_join>

Re: [ccp4bb] microsoft 3-button wheel mouse with OS X 10.5

. 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 -- James Stroud UCLA-DOE Institute for Genomics and Proteomics 611 Charles E. Young Dr. S. Los Angeles, CA 90095 http://www.jamesstroud.com

Re: [ccp4bb] microsoft 3-button wheel mouse with OS X 10.5

Give it a shot. Don't forget that you paid for *both* the M$ mice and the mighty mice, so you should experiment to see which one you like better. James -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com

Re: [ccp4bb] Principal axes and moment of inertia matrix

ition gets the principle axes, so this becomes a 1-op with numpy. Please let me know if you find errors. James #! /usr/bin/env python """ moi.py (c) 2008, James Stroud This module is released under the GN

Re: [ccp4bb] ideal bond length and bong angel

ls cannot be used to their full extent i'm not so sure anymore Be care, you insolence might get someone sent disappear. -- James Stroud UCLA-DOE Institute for Genomics and Proteomics 611 Charles E. Young Dr. S. Los Angeles, CA 90095 http://www.jamesstroud.com

Re: [ccp4bb] Annoying coot issue

I finked the 0.4 pre-release. It seems to work. I think the binaries are broken, so don't waste your time with them. James On Nov 26, 2007, at 1:38 AM, James Stroud wrote: Anyone have undefined symbols (referenced from ImageIO) in the libjpeg provided by coot 0.3.2? Running OS X 10

[ccp4bb] Annoying coot issue

Maybe I'll try to build from source... James -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com

[ccp4bb] PDB Crazy or Me?

reads here with PDB in the title recently, but didn't read them because I thought they discussed esoteric and philosophical issues that do not affect us common folk. James -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com

Re: [ccp4bb] The importance of USING our validation tools

Could such solvent ordering be a byproduct of unusually low solvent content as both of the structures seem to have (1h6w & 1ocy)? Perhaps cryoprotectant did not penetrate the solvent channels, but the crystal maintained its integrity nevertheless? On Aug 28, 2007, at 1:14 AM, Kevin Cowtan

Re: [ccp4bb] Questions about diffraction

On Fri, 24 Aug 2007 4:54:53 pm CDT James Stroud wrote: Here's a fun way to think of it: A photon hits a crystal and will diffract off in a certain direction with the same energy as the original photon. The direction is subject to a probability distribution based on the lattice, with a

Re: [ccp4bb] Questions about diffraction

Jacob Keller Northwestern University 6541 N. Francisco #3 Chicago IL 60645 (847)467-4049 [EMAIL PROTECTED] *** -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com/

Re: [ccp4bb] The importance of USING our validation tools

dhere to these ideals. -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com/

Re: [ccp4bb] CCP4 Wiki

ack on. When you make an announcement, I'll add the "Unit Cell Volumes" page. James -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com

Re: [ccp4bb] CCP4 Wiki

ar site, but your incorrect equation is a liability to everyone who tries to use it--I did try real hard to help. -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com

Re: [ccp4bb] CCP4 Wiki

t; be definitely appreciated. -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com

Re: [ccp4bb] Off topic summary: where to buy just spin column without kits

istributed by various > companies in the US and Europe. > Others mentioned that you can buy them from Qiagen directly with some > sweet talking, but I'm not sure how the prices compare. > > Merry nucleic acid purification! > > Eric -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com

Re: [ccp4bb] how to convert matrix to angle

Knee-jerk answer: The magnitude of the rotation component of the transformation yielded from the optimal least squared superposition of the two domains. Implicit is the ability to generate said least squared superposition. On Jul 7, 2007, at 8:21 PM, Bernhard Rupp wrote: Not that I want t

[ccp4bb] [FIXED] Kay Diederichs Email

n only partially intended) in Macs. James On Jul 7, 2007, at 9:38 AM, James Stroud wrote: Hello All, I'm not trying to pick on Kay Diederichs here, but is anyone else having trouble with Kay's email? I am using Mac Mail and it seems to be crashing as a result of his cryptographic sig

Re: [ccp4bb] Kay Diederichs Email

On Jul 7, 2007, at 3:09 PM, Robert Sweet wrote: Oh, go ahead. Religious analogies are appropriate for Apple users, aren't they? Well, with the introduction of the iphone, we mac devotees are presently devolving to something more akin to idolatry than actual religion.

[ccp4bb] Kay Diederichs Email

Hello All, I'm not trying to pick on Kay Diederichs here, but is anyone else having trouble with Kay's email? I am using Mac Mail and it seems to be crashing as a result of his cryptographic signature file. This effect is not isolated as it crashes on both of my intel Macs. I am running O

Re: [ccp4bb] ccp4mg povray rendering

input files, does ccp4mg output the background as the alpha channel > or do I need to go about this a different way? > > Thanks, > > Ray -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com

Re: [ccp4bb] Swiss humour - no laughing matter? (Re: [ccp4bb] process SeMet labelled data)

I have found in my usenet adventures that usenet mavens often point to this link before trying to sort out among themselves exactly what level of humor to take with dubious posts: http://www.catb.org/~esr/faqs/smart-questions.html Of course usenet mavens also complain a little too m

Re: [ccp4bb] Good NMR Board

There is an NMR Board. Problem is that you have to abide by its Rules: First Rule: You do not talk about the NMR board. Second Rule: You DO NOT talk about the NMR board. James Justin Schmitz wrote: Morning every body! Does anybody know a board for NMR releated questions which has a qualit

Re: [ccp4bb] Removal of cold gas layer for cryocooling

I propose a simple contraption to minimize the vapor layer in cryocrystallography, using freezing in the liquid phase. This idea is based on the findings in the citation below. It is modified from designs used in the pet feeding industry. The novel aspect is that liquid nitrogen is used rat

Re: nucleic acid helices

On Monday 22 January 2007 00:35, james whisstock wrote: > Quanta (accelrys) had a feature for this. Its so expensive, they don't even tell you the price. -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com

Re: nucleic acid helices

For a quick dna or rna: http://structure.usc.edu/make-na Its super easy. James On Jan 22, 2007, at 12:11 AM, Florian Brückner wrote: Dear all, I am looking for a program or webtool that can create canonical nucleic acid helices (like B-form, A-form...) as well as a program that can calcu

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