Re: [ccp4bb] ideal bond length and bong angel
Please do NOT use the BB for abuse. Eleanor Gerard DVD Kleywegt wrote: Be care, you insolence might get someone sent disappear. is the chinese secret service editing my incoming mail already, or are you merely using a microsoft grammar checker? --dvd ** Gerard J. Kleywegt [Research Fellow of the Royal Swedish Academy of Sciences] Dept. of Cell Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED] ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. **
Re: [ccp4bb] bond lengths, angles, ideality and refinements
Am 09.01.2008 um 20:48 schrieb Anastassis Perrakis: snip I actually think that inaccurate cells are a big source of misery in many refinements. I have found the idea of WhatCheck to actually check your cell by looking at the projection of bond lengths of certain types along the cell axes most useful. I would hardly advocate to measure your cell that way, but going back to you data and looking at the cell again would be worth it. snip There was a discussion many years ago on this bulletin board about unit cell scaling errors reported by WHAT_CHECK that resulted merely from some different dictionary values used in the refinement program (CNS, if I remember correctly) and in WHAT_CHECK, although both claimed to use the Engh Huber parameters. This difference projected onto the unit cell axes resulted in a reported unit cell scaling error, that could not be fixed by iterative rescaling of the unit cell and refinement, and thus was an artifact. So, I wouldn't even trust the unit cells reported by WHAT_CHECK . . . Best regards, Dirk. *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: [EMAIL PROTECTED] ***
Re: [ccp4bb] unbiased electron density map
Am 10.01.2008 um 01:53 schrieb Dale Tronrud: ... Your quote bring up another matter. An initial map, i.e. before refinement, is unbiased if it is an omit map. If you have done no refinement and you leave the interesting part out of the calculation of Fc there can not be any bias in either the Fo-Fc or the 2Fo-Fc map. This is why an initial map is more reliable for proving binding of a compound, for example, than a bias reduced map after refinement. ... But isn't this only true, if the model that is put in was not refined against a related data set before? If the new Fobs are related to the old Fobs (against which the model was refined before) then you carry any model bias over to the new data, because a simple omit-map using the old data will have model bias. Best regards, Dirk. *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: [EMAIL PROTECTED] ***
Re: [ccp4bb] ideal bond length and bong angel
Please do NOT use the BB for abuse. thank you for your support. although i think some abuse of the english language is unavoidable in an international forum like this --gerard (more important issue: http://www.irrepressible.info/) ** Gerard J. Kleywegt [Research Fellow of the Royal Swedish Academy of Sciences] Dept. of Cell Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED] ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. **
Re: [ccp4bb] crystallization robot
Not to inject a commercial tone, but there seems to be a bias in the posting below. The ceramic tips are breakable, but not all find them incredibly so. And the price is less then $300, not $700. -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Lisa A Nagy Sent: Wednesday, January 09, 2008 11:21 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] crystallization robot We chose the Phoenix crystallization robot because: It has no expensive consumables (tips) intrinsic to the machine. This was also a big item for us because we worry about being able to run the machine for more than 3 years. Would the tips for our 2008 machine be available in 2014? It is easy to program (BIG ITEM) for different tray configurations, and various dispensing methods- even on the same tray. Right now you may not think you'll have to vary drop sizes or add additional components (ligand? detergent?) to your drops, but you probably will. It can draw from 2ml block plates. Reformatting from block plates to your trays is a pain. The nitinol tips won't break (Compared to ~$700 apiece for the incredibly breakable ceramic tips on some other machines). It has cooling blocks for your samples. This is more important than you think. It's fast. It is easily integrated into a fully automated lab system. Right now, though, our humans (including me) are cheaper than rails and robots. It's incredibly accurate, even with 30% PEG 4000 (we tested this ourselves). You can use it for other low volume dispensing applications. -- Lisa Nagy University of Alabama-Birmingham [EMAIL PROTECTED]
Re: [ccp4bb] crystallization robot
A little comment on not breakable Phoenix needles. I saw not recoverably bended tips (all 96!) as a result of not very careful operation (done by rep) during presentation of the instrument, I do not know how much is 96 nitinol tips set for replacement Additionally, you hardly can go with 100+100 nl crystallization drops using Phoenix, 200+200 is OK. The speed per triple plate is ca. 12 min, it is long and drops are sitting on shelf open for ~4,5 min. another annoying problems with Phoenix is electrostatic effect and not accurate centering of the drops which both create problems for imagers. Alexey Rak Structural Biology, Chemical Sciences Sanofi-Aventis Centre de Recherche Paris -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Lisa A Nagy Sent: Wednesday, January 09, 2008 5:21 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] crystallization robot We chose the Phoenix crystallization robot because: It has no expensive consumables (tips) intrinsic to the machine. This was also a big item for us because we worry about being able to run the machine for more than 3 years. Would the tips for our 2008 machine be available in 2014? It is easy to program (BIG ITEM) for different tray configurations, and various dispensing methods- even on the same tray. Right now you may not think you'll have to vary drop sizes or add additional components (ligand? detergent?) to your drops, but you probably will. It can draw from 2ml block plates. Reformatting from block plates to your trays is a pain. The nitinol tips won't break (Compared to ~$700 apiece for the incredibly breakable ceramic tips on some other machines). It has cooling blocks for your samples. This is more important than you think. It's fast. It is easily integrated into a fully automated lab system. Right now, though, our humans (including me) are cheaper than rails and robots. It's incredibly accurate, even with 30% PEG 4000 (we tested this ourselves). You can use it for other low volume dispensing applications. -- Lisa Nagy University of Alabama-Birmingham [EMAIL PROTECTED]
Re: [ccp4bb] crystallization robot
I was wrong on the price- yes $300/per, but still, it was a lot of money when we had catastrophic crash several years ago (due to something going haywire- not a script or operator error). I know the nitonol tips are not fool-proof- they just seem a bit more forgiving than the ceramic tips. As far as the length of time plates are on the deck, we have always used humidity chambers. We build them out of lexan. Also, though 100 nl can be dispensed accurately, we prefer to spend the protein and go for larger drops, since it is really nice to be able to harvest from the drop. Our home-built robot can dispense 20nl accurately (although it uses a lot of recoverable protein to do it)- and while pretty crystals form, you can't do much with them. We typically dispense larger drops on that machine as well. -- Lisa Nagy University of Alabama-Birmingham [EMAIL PROTECTED]
Re: [ccp4bb] Gordon conference on membrane protein structure/function
Dear colleagues, We are pleased to announce that the Ligand Recognition and Molecular Gating GRC will be held in Ventura, CA, 2-7 March 2008. This Gordon Research Conference focuses on the structure and function of integral membrane proteins involved in transmembrane signaling (receptors) and transport of ions and small molecules across cell membranes (ion channels and transporters). The emphasis is on combining high resolution structures with functional and theoretical data to probe gating or activation by ligands of these proteins. We have an outstanding group of speakers and topics, including new structures of transporters, ion channels, and G-protein coupled receptors, as well as new functional results in each of these areas. We also have a continued emphasis on methods development. The full program for the 2008 meeting of the Ligand Recognition and Molecular Gating GRC can be found at http://www.grc.org/programs.aspx?year=2008program=ligand http://www.grc.org/programs.aspx?year=2008program=ligand This is really state-of-the-art membrane protein research, and some of the work to be presented was recently highlighted by Nature and Science as breakthroughs of the year. The small size of this meeting provides an ideal forum for students and postdocs to learn about membrane protein structure and function from the experts. Registration closes February 10, 2008. We hope to see you in California in March. Best wishes, Susan Buchanan, Chair (e-mail: [EMAIL PROTECTED]) Carola Hunte, Vice Chair (e-mail: [EMAIL PROTECTED]) -- Susan Buchanan Laboratory of Molecular Biology NIDDK, NIH 50 South Drive, Room 4503 Bethesda, MD 20892-8030 Phone: (+1) 301-594-9222 Fax: (+1) 301-480-0597
Re: [ccp4bb] Zn fingers and Ni columns
Phoebe, We were able to purify the estrogen receptor DNA binding domain with a 6his-tag. After cutting off the tag and re-applying to the Ni-NTA matrix, the protein did not stick to the beads. We had some low resolution crystals that contained a second protein and DNA, which suggests to me that the zinc was bound in the protein, but we did not analyze it further. Kendall -- Kendall W. Nettles, PhD Assistant Professor Department of Cancer Biology The Scripps Research Institute 5353 Parkside Dr. Jupiter Fl 33458 office 561-799-8851 fax 561-799-8805 cell 561-306-7566 On 1/3/08 7:21 PM, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: This has probably been discussed before, so apologies in advance. We're eyeing a protein that has a probable C4 Zn finger in the middle. The collaborators who are nicely going to PCR it up want to know if we'd like it with or without a His tag. Is it a bad idea to co-mingle Zn-binders and Ni columns? Or is it likely to bind the column quite nicely without the tag? thanks, Phoebe -- - Phoebe A. Rice Assoc. Prof., Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 fax 773 702 0439 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabe tically.php?faculty_id=123 http://www.nasa.gov/mission_pages/cassini/multimedia/pia06064.html
Re: [ccp4bb] unbiased electron density map
Dirk Kostrewa wrote: Am 10.01.2008 um 01:53 schrieb Dale Tronrud: ... Your quote bring up another matter. An initial map, i.e. before refinement, is unbiased if it is an omit map. If you have done no refinement and you leave the interesting part out of the calculation of Fc there can not be any bias in either the Fo-Fc or the 2Fo-Fc map. This is why an initial map is more reliable for proving binding of a compound, for example, than a bias reduced map after refinement. ... But isn't this only true, if the model that is put in was not refined against a related data set before? If the new Fobs are related to the old Fobs (against which the model was refined before) then you carry any model bias over to the new data, because a simple omit-map using the old data will have model bias. Right you are, and it's an important point too. My only defense is that I said If you have done no refinement I don't think of the refinement of several models to data from isomorphous crystals as separate refinements, but sometimes forget to mention this when talking to others. I should be more careful. Dale Tronrud
[ccp4bb] Postdoc positions at Purdue University
Postdoctoral positions in Structural Biology are available immediately in the Chen laboratory at Purdue University. As part of the Markey Center for Structural Biology, the Chen lab integrates X-ray crystallography and biochemical methods to study the mechanism of active transport (See Nature, 450: 515-521; PNAS,102:17969-17974; and Mol. Cell, 12:651-661). For more information please visit our website at http://chen.bio.purdue.edu. Successful candidates should have (or expect) a recent doctoral degree with demonstrated experience in macromolecular crystallography and protein biochemistry. Applicants should send a CV and names of three referees to [EMAIL PROTECTED], or: Jue Chen 915 W. State Street Purdue University West Lafayette, IN 47907
[ccp4bb] ACA 2008 New Structures Session
This is an additional reminder to the community that January 12 (Saturday) is the deadline for abstract submissions for the New Structures session at the 2008 ACA meeting in Knoxville, TN. The session will feature a balance of talks from both the protein and nucleic acid crystallographic communities. Abstract submissions from students interested in the Etter Student Lecturer Award are strongly encouraged. 01.01 New Structures Sunday, June 1st Organizers: David Giedroc and Mark Wilson Description: Recent structures from both the protein and nucleic acid structural communities that are of general interest will be featured, some of which will be discussed prior to publication. In addition to invited talks, some presentations will be chosen from the submitted abstracts. As in previous years, the talks will span a broad range of biological topics and will integrate the discussion of crystallographic methodology with the broader context of biological function Mark A. Wilson Assistant Professor Department of Biochemistry/Redox Biology Center University of Nebraska N164 Beadle Center 1901 Vine Street Lincoln, NE 68588 (402) 472-3626 [EMAIL PROTECTED]
Re: [ccp4bb] crystallization robot
I bought a replacement Cartesian Tip (in Australia) on the 8th of october, 2007 and got charged $660 AUD (of which 60 bucks was the GST tax) - on the 8th of october, the AUD-USD exchange rate was 0.8956, so that would be $537 USD, which is quite a long way from both '$700' and 'under $300'. The tips are quite fragile, and you could guess 10-20% breakage each year of use, gauging from the stories told around here. Janet -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Boutin, Ray Sent: Thursday, 10 January 2008 11:42 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] crystallization robot Not to inject a commercial tone, but there seems to be a bias in the posting below. The ceramic tips are breakable, but not all find them incredibly so. And the price is less then $300, not $700. -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Lisa A Nagy Sent: Wednesday, January 09, 2008 11:21 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] crystallization robot We chose the Phoenix crystallization robot because: It has no expensive consumables (tips) intrinsic to the machine. This was also a big item for us because we worry about being able to run the machine for more than 3 years. Would the tips for our 2008 machine be available in 2014? It is easy to program (BIG ITEM) for different tray configurations, and various dispensing methods- even on the same tray. Right now you may not think you'll have to vary drop sizes or add additional components (ligand? detergent?) to your drops, but you probably will. It can draw from 2ml block plates. Reformatting from block plates to your trays is a pain. The nitinol tips won't break (Compared to ~$700 apiece for the incredibly breakable ceramic tips on some other machines). It has cooling blocks for your samples. This is more important than you think. It's fast. It is easily integrated into a fully automated lab system. Right now, though, our humans (including me) are cheaper than rails and robots. It's incredibly accurate, even with 30% PEG 4000 (we tested this ourselves). You can use it for other low volume dispensing applications. -- Lisa Nagy University of Alabama-Birmingham [EMAIL PROTECTED]
[ccp4bb] HHMI Post-doc Job opening
All, I am posting on behalf of Dr. Karolin Luger. Dr. Luger has a job opening for a post-doctoral researcher. Job Summary: Looking for a highly motivated individual with a strong interest in integrated approaches to problems in structural biology. The lab has extensive crystallographic and spectroscopic resources, and is part of the W.M. Keck Center for Chromatin Structure and Function. Please look at the following web site for additional information and for guidelines how to apply. http://www.hhmi.org/jobs/main?action=jobjob_id=548 Please DO NOT RESPOND to me. Thank you. Mark Mark van der Woerd, PhD Research Scientist II Dept. of Biochemistry and Molecular Biology Colorado State University Fort Collins, CO 80523 Phone (970) 491-0469 More new features than ever. Check out the new AIM(R) Mail ! - http://webmail.aim.com
[ccp4bb] FW: [ccp4bb] crystallization robot
What a great time in crystallization; lots of options, lots of choices. After reviewing the automation available for crystallization and our unique needs we decided on the Phoenix. We have used the Phoenix from Art Robbins Instruments with excellent results since installation October 2006. Each lab has a unique set of needs when it comes to automating crystallization. We've found it very useful to identify those needs, prioritize those needs and then compare them to the capabilities of the automation and the company behind the automation. Needs are unique, so if anyone has any specific questions about our use and experience with the Phoenix, please feel free to ask. Kind Regards, Bob Cudney - Hampton Research [EMAIL PROTECTED]
[ccp4bb] scale data with multiple MTZ files
I tried to scale, using SCALA through CCP4i GUI, three blocks of data collected with one crystal (3 mtz files output from MOSFLM). The GUI has only one MTZ input slot. Which program can be used to combine the 3 unmerged mtz files together? CAD refused to handle these raw mtz files. Thanks in advance for any help. Huiying -- Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: [EMAIL PROTECTED]
[ccp4bb] crystallization robot
We have been quite happy with our crystallization robot from Innovadyne. It transfers from deep well blocks to crystallization plates, and very reliably sets up 200nl + 200nl drops. We have tried smaller drops with decent success, which works better with certain plates. It can be easily programmed, has good support from the company, and has very inexpensive tips. I¹ve also used the Cartesian Honeybee extensively, which I found worked well, but required much more work in cleaning and daily maintenance, and did not do the large volume transfers. Kendall -- Kendall W. Nettles, PhD Assistant Professor Department of Cancer Biology The Scripps Research Institute 5353 Parkside Dr. Jupiter Fl 33458 office 561-799-8851 fax 561-799-8805 cell 561-306-7566
Re: [ccp4bb] scale data with multiple MTZ files
Huiying Li wrote: I tried to scale, using SCALA through CCP4i GUI, three blocks of data collected with one crystal (3 mtz files output from MOSFLM). The GUI has only one MTZ input slot. Which program can be used to combine the 3 unmerged mtz files together? CAD refused to handle these raw mtz files. Thanks in advance for any help. Huiying Using the CCP4 GUI, employ the following steps: 1. Open a Sort/Modify/Combine job and renumber your data sets (reset batch numbers option). A simple method is to add 1000 to the batch numbers for one data set and 2000 to the batch numbers for the second data set (assuming you have less than 999 frames of data output from MOSFLM.) 2. Open another Sort/Modify/Combine job and combine the renumbered MTZ files into one merged file. Click on Add File to add additional renumbered batches from step 1. Each batch of reflections will now have unique batch numbers. 3. Open a Scale and Merge Intensities task window. Select as your input the sorted and combined file output from step 2. In the Define Datasets section, choose Combine All Input Datasets into a Single Output Dataset. You can convert the scaled intensities to structure factors by checking the appropriate box. The combined datasets will not have monotonically varying R(merge) values across batches (1-1000, 1001-2000, 2001-3000) becuase of discontinuities in the data. However the merged datasets should have good overall statistics if appropriate for merging. Cheers, -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [EMAIL PROTECTED]
