[ccp4bb] ccp4-6.0.99d-3, clapham test release
Dear All there is a slim 800 lb tarball at ftp://ftp.ccp4.ac.uk/ccp4/6.1/ccp4-6.0.99d-src.tar.gz this is to test the build and arrangement of files. If you want balbes you will have to manually install PyXML (run the setup.py in PyXML-... using python setup.py build followed by python setup.py install). Further information in the CHANGES file. Feedback (with fixes :-) ) appreciated to determine if there are any major omissions. We are particularly interested in information on the performance of ccp4i. Charles ps - Warning. This is a big one du -sk ccp* 2983368 ccp4-6.0.99d - tarball contents only 819916 ccp4-6.0.99d-src.tar.gz pps - for those of you who checked out d-2, there are minor fixes to refmac5, balbes and crank in this one. pps - System Administration - Database Configuration - checkbox Connect to the database... toggles the use of the new and legacy access to the ccp4 information storage system (network vs. builtin), so if database access is slow, you can compare/rescue the situation by using this and restarting the interface.
[ccp4bb] is it Ok to freeze
Dear Scientists and Friends, I am not sure, whether organic crystals need to be in cryo stream necessarily during data collection from an in house xray machine . How most of the organic crystals have been solved mostly? -- S.Jayashankar (A bit confused new generation researcher). Research Student Institute for Biophysical Chemistry Hannover Medical School Germany
Re: [ccp4bb] is it Ok to freeze
Hi If you mean organic small molecules, then the opinion for the last 15 years at least is probably yes, unless you know you'll have a phase change. Most small molecule crystals don't have the same problems with needing cryoprotectants as macromolecules, due in large part to not having a large proportion of water in the lattice, so the process is somewhat more straightforward. Also, most small molecule crystals can be handled quite happily in the absence of mother liquor, and you don't have to worry about them drying out while transferring to the fibre (rather than loop) which would normally be used for mounting them. Of course, there are numerous exceptions to the most I'm referring to here. In most cases you'll get a substantially better structure at cryo temperatures (of course, what better means may be open to debate). On 19 Jun 2008, at 09:47, Jayashankar wrote: Dear Scientists and Friends, I am not sure, whether organic crystals need to be in cryo stream necessarily during data collection from an in house xray machine . How most of the organic crystals have been solved mostly? -- S.Jayashankar (A bit confused new generation researcher). Research Student Institute for Biophysical Chemistry Hannover Medical School Germany Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 2QH
Re: [ccp4bb] is it Ok to freeze
Harry Can you clarify why you get a substantially better structure at cryo temperatures e.g higher intensity at high resolution due to reduction in B factors, reduction in radiation damage, anything else? Colin -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of harry powell Sent: 19 June 2008 10:12 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] is it Ok to freeze Hi If you mean organic small molecules, then the opinion for the last 15 years at least is probably yes, unless you know you'll have a phase change. Most small molecule crystals don't have the same problems with needing cryoprotectants as macromolecules, due in large part to not having a large proportion of water in the lattice, so the process is somewhat more straightforward. Also, most small molecule crystals can be handled quite happily in the absence of mother liquor, and you don't have to worry about them drying out while transferring to the fibre (rather than loop) which would normally be used for mounting them. Of course, there are numerous exceptions to the most I'm referring to here. In most cases you'll get a substantially better structure at cryo temperatures (of course, what better means may be open to debate). On 19 Jun 2008, at 09:47, Jayashankar wrote: Dear Scientists and Friends, I am not sure, whether organic crystals need to be in cryo stream necessarily during data collection from an in house xray machine . How most of the organic crystals have been solved mostly? -- S.Jayashankar (A bit confused new generation researcher). Research Student Institute for Biophysical Chemistry Hannover Medical School Germany Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 2QH DIVFONT size=1 color=grayThis e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom /FONT/DIV
Re: [ccp4bb] is it Ok to freeze
Hi Colin yes, both of those. Plus freezing out multiple conformations so you can model them properly - bear in mind that a small molecule structure at a resolution worse than 1Å would be challenging to get past the normal criteria of referees, so you should be able to see them at least some of the time (depending on how distinct the multiple conformations are). It may be easier to distinguish the atom type (C,N,O?) if you have a lower temperature dataset - at least 50% of the small molecule structures I did when I was working in that field were _not_ of the compound the chemist thought they had, so working out the atom type was rather important. However, I'm not sure this is a strong reason for doing cryo work on its own - any half decent modern automated small molecule structure solution program could do it with most room temperature datasets. Also, if you have an air-sensitive crystal (chemists say this as a shorthand when they mean more specific things like the chemical is oxygen or moisture-sensitive) you can slow the reactions down enough so that your crystal doesn't decompose because of those. But that's more of a problem with organometallics than organics, except with some of the more exotic organic species... And if your crystal loses solvent (e.g. I used to use CH2Cl2 (methylene chloride to the old hacks here) as a solvent, and that will just evaporate at room temp, leaving you with a powder rather than a beautiful single crystal. Although you can get round air-sensitivity and solvent loss by mounting in a capillary, there are good reasons to avoid that and cryo-cool with a naked (or semi-naked, dressed only in a gossamer- like film of perfluoropolyether oil) crystal if you can, as those of us who have done both regularly know. I'm sure there are other reasons why it would be substantially better, but I also know that there is considerable effort going into high-temperature devices, which will be used to help collect substantially better datasets for the crystals that their developers are interested in. does this help? On 19 Jun 2008, at 10:25, Nave, C (Colin) wrote: Harry Can you clarify why you get a substantially better structure at cryo temperatures e.g higher intensity at high resolution due to reduction in B factors, reduction in radiation damage, anything else? Colin -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of harry powell Sent: 19 June 2008 10:12 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] is it Ok to freeze Hi If you mean organic small molecules, then the opinion for the last 15 years at least is probably yes, unless you know you'll have a phase change. Most small molecule crystals don't have the same problems with needing cryoprotectants as macromolecules, due in large part to not having a large proportion of water in the lattice, so the process is somewhat more straightforward. Also, most small molecule crystals can be handled quite happily in the absence of mother liquor, and you don't have to worry about them drying out while transferring to the fibre (rather than loop) which would normally be used for mounting them. Of course, there are numerous exceptions to the most I'm referring to here. In most cases you'll get a substantially better structure at cryo temperatures (of course, what better means may be open to debate). On 19 Jun 2008, at 09:47, Jayashankar wrote: Dear Scientists and Friends, I am not sure, whether organic crystals need to be in cryo stream necessarily during data collection from an in house xray machine . How most of the organic crystals have been solved mostly? -- S.Jayashankar (A bit confused new generation researcher). Research Student Institute for Biophysical Chemistry Hannover Medical School Germany Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 2QH This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
Re: [ccp4bb] is it Ok to freeze
Hi I just noticed I scrambled that first paragraph. I didn't intend to imply you should be able to see your referees (or their criteria) at least some of the time. It should have read something more like- yes, both of those. Plus freezing out multiple conformations so that you can model them properly; you should be able to see them at least some of the time (depending on how distinct the multiple conformations are). Bear in mind that a small molecule structure at a resolution worse than 1Å would be challenging to get past the normal criteria of referees. On 19 Jun 2008, at 11:05, harry powell wrote: Hi Colin yes, both of those. Plus freezing out multiple conformations so you can model them properly - bear in mind that a small molecule structure at a resolution worse than 1Å would be challenging to get past the normal criteria of referees, so you should be able to see them at least some of the time (depending on how distinct the multiple conformations are). Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 2QH
Re: [ccp4bb] is it Ok to freeze
Typically crystals of small organic compounds do not require freezing as there are no solvent channels. They do in general not suffer from radiation damage at room temperature the way protein crystals do. Occasionally they are mounted in a capillary instead of simply glueing them to a goniometer if they are air sensitive. In principle freezing should not damage the crystals, but one still may have to be carefull if the crystals are large. I think you risk increasing mosiacity, and any manipulation that is not needed will on average only reduce the quality of the specimen rather than improve it Remy Loris Vrije Univesiteit Brussel Jayashankar wrote: Dear Scientists and Friends, I am not sure, whether organic crystals need to be in cryo stream necessarily during data collection from an in house xray machine . How most of the organic crystals have been solved mostly? -- S.Jayashankar (A bit confused new generation researcher). Research Student Institute for Biophysical Chemistry Hannover Medical School Germany
Re: [ccp4bb] is it Ok to freeze
Hi Without wishing to start an argument, I've been checking with some of my colleagues who are chemical crystallographers - the reply I get is that, for routine structural analysis, pretty well all datasets are collected at 100K unless the crystals fall apart at low T, or if the cryostream is broken. I should point out that the first production Cryostream that I came across (serial number 2, which I think may have been the first one sold!) was in the Cambridge Department of Chemistry in about 1985. They didn't become common until the mid-1990's in PX labs, when they were already well-established as a bit of pretty well essential kit for small molecule work. So although what Remy says is true, the practice is to cryocool most of the time. On 19 Jun 2008, at 12:08, Remy Loris wrote: Typically crystals of small organic compounds do not require freezing as there are no solvent channels. They do in general not suffer from radiation damage at room temperature the way protein crystals do. Occasionally they are mounted in a capillary instead of simply glueing them to a goniometer if they are air sensitive. In principle freezing should not damage the crystals, but one still may have to be carefull if the crystals are large. I think you risk increasing mosiacity, and any manipulation that is not needed will on average only reduce the quality of the specimen rather than improve it Remy Loris Vrije Univesiteit Brussel Jayashankar wrote: Dear Scientists and Friends, I am not sure, whether organic crystals need to be in cryo stream necessarily during data collection from an in house xray machine . How most of the organic crystals have been solved mostly? -- S.Jayashankar (A bit confused new generation researcher). Research Student Institute for Biophysical Chemistry Hannover Medical School Germany Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 2QH
Re: [ccp4bb] is it Ok to freeze
This fellow below is presumably and Indian, writing in English at a German University, a very confused new generation researcher, indeed. Maybe this will help: S.Jayashankar (Ein wenig verwirrter Forscher der neuen Generation) Forschungsstudent Institut fuer Biophysikalische Chemie Medizinische Schule, Hannover (where is this?) Deutschland sorry for that :-) Marius Dear Scientists and Friends, I am not sure, whether organic crystals need to be in cryo stream necessarily during data collection from an in house xray machine . How most of the organic crystals have been solved mostly? -- S.Jayashankar (A bit confused new generation researcher). Research Student Institute for Biophysical Chemistry Hannover Medical School Germany
Re: [ccp4bb] How to change R-free set?
I am currently refining a high-resolution structure that has many reflections (~180,000). I would like to halve the R-free set from 5% to 2.5%, and am unsure how to do so. Any advice will be greatly appreciated. there is a bunch of commands in dataman to do this (and other things) to your test set - see: http://xray.bmc.uu.se/usf/dataman_man.html#H9 --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] is it Ok to freeze
I would go along with Harry friends, I used crystal cooling when I was at Aafje Vos' Struktuurchemie lab in Groningen in 1972, when the technique had already been in routine use there for at least 10 years, in order to study compounds that are liquid at ambient temp (of course it was custom-built kit using a collection of liq N2 Dewar vessel tubes, nothing as fancy as a Cryostream!). The Groningen group really pioneered the use of low temp for small molecule structures and I don't recall increased mosaicity ever being an issue. Occasionally you would get a compound with a phase transition on the way down and the crystal would literally explode in a puff of powder before your eyes! The motive for using low temp was of course to reduce the thermal motion and libration effects, and thus greatly improve the accuracy of the molecular geometry, and low temp is pretty well essential if you're into valence density deformation maps, again in order the minimise the contribution from thermal motion. -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of harry powell Sent: 19 June 2008 14:05 To: Remy Loris Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] is it Ok to freeze Hi Without wishing to start an argument, I've been checking with some of my colleagues who are chemical crystallographers - the reply I get is that, for routine structural analysis, pretty well all datasets are collected at 100K unless the crystals fall apart at low T, or if the cryostream is broken. I should point out that the first production Cryostream that I came across (serial number 2, which I think may have been the first one sold!) was in the Cambridge Department of Chemistry in about 1985. They didn't become common until the mid-1990's in PX labs, when they were already well-established as a bit of pretty well essential kit for small molecule work. So although what Remy says is true, the practice is to cryocool most of the time. On 19 Jun 2008, at 12:08, Remy Loris wrote: Typically crystals of small organic compounds do not require freezing as there are no solvent channels. They do in general not suffer from radiation damage at room temperature the way protein crystals do. Occasionally they are mounted in a capillary instead of simply glueing them to a goniometer if they are air sensitive. In principle freezing should not damage the crystals, but one still may have to be carefull if the crystals are large. I think you risk increasing mosiacity, and any manipulation that is not needed will on average only reduce the quality of the specimen rather than improve it Remy Loris Vrije Univesiteit Brussel Jayashankar wrote: Dear Scientists and Friends, I am not sure, whether organic crystals need to be in cryo stream necessarily during data collection from an in house xray machine . How most of the organic crystals have been solved mostly? -- S.Jayashankar (A bit confused new generation researcher). Research Student Institute for Biophysical Chemistry Hannover Medical School Germany Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 2QH Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
[ccp4bb] Coot and Hs
Dear all, a problem possibly at the coot/mmdb interface... If one uploads a pdb file (from phenix.refine in the example below) that contains Hs into Coot and then writes it out (with or without any modification done on it) Coot shifts the HG2n of THR on the right by one column space. Because column 17 is kept empty the result is three identical HG2 THR protons. Example: Uploaded: CRYST1 45.460 166.970 167.200 90.00 90.00 90.00 P 21 21 21 SCALE1 0.021997 -0.00 -0.000.0 SCALE2 0.00 0.005989 0.000.0 SCALE3 0.00 0.00 0.0059810.0 ATOM 1 N THR A 2 27.439 61.155 24.800 1.00 70.37 AN ANISOU1 N THR A 2 9721 7539 9478 1186 2103 297 AN ATOM 2 CA THR A 2 26.489 62.215 24.456 1.00 77.21 AC ANISOU2 CA THR A 210790 8621 9925 1145 1971 285 AC ATOM 3 CB THR A 2 26.960 63.618 24.975 1.00 73.93 AC ANISOU3 CB THR A 210519 8251 9322 1244 1638 409 AC ATOM 4 OG1 THR A 2 28.259 63.512 25.579 1.00 73.16 AO ANISOU4 OG1 THR A 210309 7971 9516 1332 1549 489 AO ATOM 5 CG2 THR A 2 25.969 64.197 25.999 1.00 64.65 AC ANISOU5 CG2 THR A 2 9547 7174 7845 1451 1403 582 AC ATOM 6 C THR A 2 26.200 62.288 22.934 1.00 71.92 AC ANISOU6 C THR A 210101 8073 9151869 2179 63 AC ATOM 7 O THR A 2 25.172 61.797 22.455 1.00 64.74 AO ANISOU7 O THR A 2 9210 7258 8131790 2339 -23 AO ATOM 8 HA THR A 2 25.639 62.015 24.900 1.00 71.84 AH ATOM 9 HB THR A 2 27.009 64.232 24.226 1.00 69.26 AH ATOM 10 HG1 THR A 2 28.232 62.991 26.212 1.00 67.50 AH ATOM 11 HG21 THR A 2 26.275 65.055 26.303 1.00 61.19 AH ATOM 12 HG22 THR A 2 25.104 64.300 25.596 1.00 61.19 AH ATOM 13 HG23 THR A 2 25.894 63.607 26.753 1.00 61.19 AH Written: CRYST1 45.460 166.970 167.200 90.00 90.00 90.00 P 21 21 21 SCALE1 0.021997 -0.00 -0.000.0 SCALE2 0.00 0.005989 0.000.0 SCALE3 0.00 0.00 0.0059810.0 ATOM 1 N THR A 2 27.439 61.155 24.800 1.00 70.37 AN ANISOU1 N THR A 2 9721 7539 9478 1186 2103 297 AN ATOM 2 CA THR A 2 26.489 62.215 24.456 1.00 77.21 AC ANISOU2 CA THR A 210790 8621 9925 1145 1971 285 AC ATOM 3 CB THR A 2 26.960 63.618 24.975 1.00 73.93 AC ANISOU3 CB THR A 210519 8251 9322 1244 1638 409 AC ATOM 4 OG1 THR A 2 28.259 63.512 25.579 1.00 73.16 AO ANISOU4 OG1 THR A 210309 7971 9516 1332 1549 489 AO ATOM 5 CG2 THR A 2 25.969 64.197 25.999 1.00 64.65 AC ANISOU5 CG2 THR A 2 9547 7174 7845 1451 1403 582 AC ATOM 6 C THR A 2 26.200 62.288 22.934 1.00 71.92 AC ANISOU6 C THR A 210101 8073 9151869 2179 63 AC ATOM 7 O THR A 2 25.172 61.797 22.455 1.00 64.74 AO ANISOU7 O THR A 2 9210 7258 8131790 2339 -23 AO ATOM 8 HA THR A 2 25.639 62.015 24.900 1.00 71.84 AH ATOM 9 HB THR A 2 27.009 64.232 24.226 1.00 69.26 AH ATOM 10 HG1 THR A 2 28.232 62.991 26.212 1.00 67.50 AH ATOM 11 HG2 THR A 2 26.275 65.055 26.303 1.00 61.19 AH ATOM 12 HG2 THR A 2 25.104 64.300 25.596 1.00 61.19 AH ATOM 13 HG2 THR A 2 25.894 63.607 26.753 1.00 61.19 AH Does anyone know (Paul?) the reason for the above? The only solution right now (that I know of) is to remove all Hs and generate them again (molprobity for example) prior to refinement. Cheers, Roberto --- Roberto Steiner Randall Division of Cell and Molecular Biophysics New Hunt's House King's College London Guy's Campus London, SE1 1UL Phone +44 (0)20-7848-8216 Fax +44 (0)20-7848-6435 e-mail [EMAIL PROTECTED]
Re: [ccp4bb] is it Ok to freeze
Every small molecule dataset I collected as a graduate student in chemistry back in the mid to late 1980's was at 100K. I never had to worry about crystal slippage during collection, organic solvent evaporation, air oxidation of the sample (organometallic metal clusters) or secondary radiation damage. When I switched to protein crystallography, I was absolutely amazed when told that you can not cool a protein crystal below 4 degrees C for data collection. How times have changed, Diana On Jun 19, 2008, at 9:03 AM, Ian Tickle wrote: I would go along with Harry friends, I used crystal cooling when I was at Aafje Vos' Struktuurchemie lab in Groningen in 1972, when the technique had already been in routine use there for at least 10 years, in order to study compounds that are liquid at ambient temp (of course it was custom-built kit using a collection of liq N2 Dewar vessel tubes, nothing as fancy as a Cryostream!). The Groningen group really pioneered the use of low temp for small molecule structures and I don't recall increased mosaicity ever being an issue. Occasionally you would get a compound with a phase transition on the way down and the crystal would literally explode in a puff of powder before your eyes! The motive for using low temp was of course to reduce the thermal motion and libration effects, and thus greatly improve the accuracy of the molecular geometry, and low temp is pretty well essential if you're into valence density deformation maps, again in order the minimise the contribution from thermal motion. -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of harry powell Sent: 19 June 2008 14:05 To: Remy Loris Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] is it Ok to freeze Hi Without wishing to start an argument, I've been checking with some of my colleagues who are chemical crystallographers - the reply I get is that, for routine structural analysis, pretty well all datasets are collected at 100K unless the crystals fall apart at low T, or if the cryostream is broken. I should point out that the first production Cryostream that I came across (serial number 2, which I think may have been the first one sold!) was in the Cambridge Department of Chemistry in about 1985. They didn't become common until the mid-1990's in PX labs, when they were already well-established as a bit of pretty well essential kit for small molecule work. So although what Remy says is true, the practice is to cryocool most of the time. On 19 Jun 2008, at 12:08, Remy Loris wrote: Typically crystals of small organic compounds do not require freezing as there are no solvent channels. They do in general not suffer from radiation damage at room temperature the way protein crystals do. Occasionally they are mounted in a capillary instead of simply glueing them to a goniometer if they are air sensitive. In principle freezing should not damage the crystals, but one still may have to be carefull if the crystals are large. I think you risk increasing mosiacity, and any manipulation that is not needed will on average only reduce the quality of the specimen rather than improve it Remy Loris Vrije Univesiteit Brussel Jayashankar wrote: Dear Scientists and Friends, I am not sure, whether organic crystals need to be in cryo stream necessarily during data collection from an in house xray machine . How most of the organic crystals have been solved mostly? -- S.Jayashankar (A bit confused new generation researcher). Research Student Institute for Biophysical Chemistry Hannover Medical School Germany Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 2QH Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of
Re: [ccp4bb] is it Ok to freeze
I typically collect data at -50C on all small molecule samples. I've had quite a few cases where there are phase transitions, and you can damage the crystals, especially when the molecules are packed in a pi-pi stacking motif, or I'm dealing with alloy systems. I've also collected data at 16K, so it all depends on your sample. Instead of finding out if there is a phase transition, -50C seems to be a good choice of a temperature to reduce the displacement amplitudes, radiation damage, and solvent loss. Bernie Santarsiero On Thu, June 19, 2008 9:40 am, Diana Tomchick wrote: Every small molecule dataset I collected as a graduate student in chemistry back in the mid to late 1980's was at 100K. I never had to worry about crystal slippage during collection, organic solvent evaporation, air oxidation of the sample (organometallic metal clusters) or secondary radiation damage. When I switched to protein crystallography, I was absolutely amazed when told that you can not cool a protein crystal below 4 degrees C for data collection. How times have changed, Diana On Jun 19, 2008, at 9:03 AM, Ian Tickle wrote: I would go along with Harry friends, I used crystal cooling when I was at Aafje Vos' Struktuurchemie lab in Groningen in 1972, when the technique had already been in routine use there for at least 10 years, in order to study compounds that are liquid at ambient temp (of course it was custom-built kit using a collection of liq N2 Dewar vessel tubes, nothing as fancy as a Cryostream!). The Groningen group really pioneered the use of low temp for small molecule structures and I don't recall increased mosaicity ever being an issue. Occasionally you would get a compound with a phase transition on the way down and the crystal would literally explode in a puff of powder before your eyes! The motive for using low temp was of course to reduce the thermal motion and libration effects, and thus greatly improve the accuracy of the molecular geometry, and low temp is pretty well essential if you're into valence density deformation maps, again in order the minimise the contribution from thermal motion. -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of harry powell Sent: 19 June 2008 14:05 To: Remy Loris Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] is it Ok to freeze Hi Without wishing to start an argument, I've been checking with some of my colleagues who are chemical crystallographers - the reply I get is that, for routine structural analysis, pretty well all datasets are collected at 100K unless the crystals fall apart at low T, or if the cryostream is broken. I should point out that the first production Cryostream that I came across (serial number 2, which I think may have been the first one sold!) was in the Cambridge Department of Chemistry in about 1985. They didn't become common until the mid-1990's in PX labs, when they were already well-established as a bit of pretty well essential kit for small molecule work. So although what Remy says is true, the practice is to cryocool most of the time. On 19 Jun 2008, at 12:08, Remy Loris wrote: Typically crystals of small organic compounds do not require freezing as there are no solvent channels. They do in general not suffer from radiation damage at room temperature the way protein crystals do. Occasionally they are mounted in a capillary instead of simply glueing them to a goniometer if they are air sensitive. In principle freezing should not damage the crystals, but one still may have to be carefull if the crystals are large. I think you risk increasing mosiacity, and any manipulation that is not needed will on average only reduce the quality of the specimen rather than improve it Remy Loris Vrije Univesiteit Brussel Jayashankar wrote: Dear Scientists and Friends, I am not sure, whether organic crystals need to be in cryo stream necessarily during data collection from an in house xray machine . How most of the organic crystals have been solved mostly? -- S.Jayashankar (A bit confused new generation researcher). Research Student Institute for Biophysical Chemistry Hannover Medical School Germany Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 2QH Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL
Re: [ccp4bb] Coot and Hs
Dear Roberto, Roberto Steiner wrote: Dear all, a problem possibly at the coot/mmdb interface... Indeed. If one uploads a pdb file (from phenix.refine in the example below) that contains Hs into Coot and then writes it out (with or without any modification done on it) Coot shifts the HG2n of THR on the right by one column space. Because column 17 is kept empty the result is three identical HG2 THR protons. Technical answer: The current PDB parser in Coot is from mmdb and is for PDB format version 2.3. Phenix.refine and other modern programs use PDB format version 3.0 [1] - released over a year ago. PDB version 3.0 Remediated does not wrap the hydrogen (or other) names and so the hydrogen name unmangler - which is what is tripping you up - need not be executed. I'd like to make Coot compatible with the current PDB standard. If CCP4 were to release a version of mmdb compatible with Coot, I could do that right away [2]. I'm hoping that they will do so today^H^H^H^H^H soon. The only solution right now (that I know of) is to remove all Hs and generate them again (molprobity for example) prior to refinement. Bleugh. Non-optimal (no matter how fine Molprobity is). Paul. [1] or version 3.1? [2] I imagine.
Re: [ccp4bb] Coot and Hs
Hi Paul, How can I add Hs (hydrogens) stereochemically to protein or peptide using COOT without altering the coordinates of non-hydrogen atoms. Thanks. Sam. Date: Thu, 19 Jun 2008 15:57:46 +0100 From: [EMAIL PROTECTED] Subject: Re: [ccp4bb] Coot and Hs To: CCP4BB@JISCMAIL.AC.UK Dear Roberto, Roberto Steiner wrote: Dear all, a problem possibly at the coot/mmdb interface... Indeed. If one uploads a pdb file (from phenix.refine in the example below) that contains Hs into Coot and then writes it out (with or without any modification done on it) Coot shifts the HG2n of THR on the right by one column space. Because column 17 is kept empty the result is three identical HG2 THR protons. Technical answer: The current PDB parser in Coot is from mmdb and is for PDB format version 2.3. Phenix.refine and other modern programs use PDB format version 3.0 [1] - released over a year ago. PDB version 3.0 Remediated does not wrap the hydrogen (or other) names and so the hydrogen name unmangler - which is what is tripping you up - need not be executed. I'd like to make Coot compatible with the current PDB standard. If CCP4 were to release a version of mmdb compatible with Coot, I could do that right away [2]. I'm hoping that they will do so today^H^H^H^H^H soon. The only solution right now (that I know of) is to remove all Hs and generate them again (molprobity for example) prior to refinement. Bleugh. Non-optimal (no matter how fine Molprobity is). Paul. [1] or version 3.1? [2] I imagine. _ Introducing Live Search cashback . It's search that pays you back! http://search.live.com/cashback/?pkw=form=MIJAAF/publ=HMTGL/crea=introsrchcashback
[ccp4bb] adding hydrogens without altering coordinates of non-hydrogen atoms
Any idea is appreciated how to add Hs (hydrogens) stereochemically to protein or peptide without altering the coordinates of non-hydrogen atoms. Does COOT have any option to do this ? Thanks. Sam. _ Need to know now? Get instant answers with Windows Live Messenger. http://www.windowslive.com/messenger/connect_your_way.html?ocid=TXT_TAGLM_WL_Refresh_messenger_062008
Re: [ccp4bb] Coot and Hs
I think that we will have to 'remediate' Coot (and the whole of CCP4 for good measure). I advise all SHELXL users NEVER to deposit hydrogen atoms, it saves lots of hassle. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Thu, 19 Jun 2008, Edward Snell wrote: It's due to PDB versions 2.3 and 3.0. It's a pain, and Paul is aware of it. The solution you describe works and it's always nice to check with Molprobity. I've tried using the PDB tools to change 3.0 to 2.3 but they also have problems :-( For us poor souls who are suffering with hydrogen any fix would be appreciated. For now, I am pulling the detector back :-) 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 Roberto Steiner Sent: Thursday, June 19, 2008 10:27 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Coot and Hs Dear all, a problem possibly at the coot/mmdb interface... If one uploads a pdb file (from phenix.refine in the example below) that contains Hs into Coot and then writes it out (with or without any modification done on it) Coot shifts the HG2n of THR on the right by one column space. Because column 17 is kept empty the result is three identical HG2 THR protons. Example: Uploaded: CRYST1 45.460 166.970 167.200 90.00 90.00 90.00 P 21 21 21 SCALE1 0.021997 -0.00 -0.000.0 SCALE2 0.00 0.005989 0.000.0 SCALE3 0.00 0.00 0.0059810.0 ATOM 1 N THR A 2 27.439 61.155 24.800 1.00 70.37 AN ANISOU1 N THR A 2 9721 7539 9478 1186 2103297 AN ATOM 2 CA THR A 2 26.489 62.215 24.456 1.00 77.21 AC ANISOU2 CA THR A 210790 8621 9925 1145 1971285 AC ATOM 3 CB THR A 2 26.960 63.618 24.975 1.00 73.93 AC ANISOU3 CB THR A 210519 8251 9322 1244 1638409 AC ATOM 4 OG1 THR A 2 28.259 63.512 25.579 1.00 73.16 AO ANISOU4 OG1 THR A 210309 7971 9516 1332 1549489 AO ATOM 5 CG2 THR A 2 25.969 64.197 25.999 1.00 64.65 AC ANISOU5 CG2 THR A 2 9547 7174 7845 1451 1403582 AC ATOM 6 C THR A 2 26.200 62.288 22.934 1.00 71.92 AC ANISOU6 C THR A 210101 8073 9151869 2179 63 AC ATOM 7 O THR A 2 25.172 61.797 22.455 1.00 64.74 AO ANISOU7 O THR A 2 9210 7258 8131790 2339-23 AO ATOM 8 HA THR A 2 25.639 62.015 24.900 1.00 71.84 AH ATOM 9 HB THR A 2 27.009 64.232 24.226 1.00 69.26 AH ATOM 10 HG1 THR A 2 28.232 62.991 26.212 1.00 67.50 AH ATOM 11 HG21 THR A 2 26.275 65.055 26.303 1.00 61.19 AH ATOM 12 HG22 THR A 2 25.104 64.300 25.596 1.00 61.19 AH ATOM 13 HG23 THR A 2 25.894 63.607 26.753 1.00 61.19 AH Written: CRYST1 45.460 166.970 167.200 90.00 90.00 90.00 P 21 21 21 SCALE1 0.021997 -0.00 -0.000.0 SCALE2 0.00 0.005989 0.000.0 SCALE3 0.00 0.00 0.0059810.0 ATOM 1 N THR A 2 27.439 61.155 24.800 1.00 70.37 AN ANISOU1 N THR A 2 9721 7539 9478 1186 2103297 AN ATOM 2 CA THR A 2 26.489 62.215 24.456 1.00 77.21 AC ANISOU2 CA THR A 210790 8621 9925 1145 1971285 AC ATOM 3 CB THR A 2 26.960 63.618 24.975 1.00 73.93 AC ANISOU3 CB THR A 210519 8251 9322 1244 1638409 AC ATOM 4 OG1 THR A 2 28.259 63.512 25.579 1.00 73.16 AO ANISOU4 OG1 THR A 210309 7971 9516 1332 1549489 AO ATOM 5 CG2 THR A 2 25.969 64.197 25.999 1.00 64.65 AC ANISOU5 CG2 THR A 2 9547 7174 7845 1451 1403582 AC ATOM 6 C THR A 2 26.200 62.288 22.934 1.00 71.92 AC ANISOU6 C THR A 210101 8073 9151869 2179 63 AC ATOM 7 O THR A 2 25.172 61.797 22.455 1.00 64.74 AO ANISOU7 O THR A 2 9210 7258 8131790 2339-23 AO ATOM
Re: [ccp4bb] is it Ok to freeze
Ha, everyone seems to be bragging about how far back cryo- crystallography really goes. In that vain, I'd like to mention that, in Martinsried, we had a room that was lined with insulated steel walls and that could be flushed with liquid nitrogen. It was requested (demanded, really...) by Robert Huber when the Max-Planck Institute was finalized in 1972 (I hope I got my history right). That room contained an entire diffraction system. Talk about crystal cooling... bah, way too dinky. Cool the entire room! Of course, it was a hazard to work in that room, and so - as far as I know - there was only one post-doc from India how ever used it. That room had an ante-room with two more generators plus detectors that could be cooled down to -20°C! Ah, the good old Wild West times of macromolecular crystallography... Cheers - MM On Jun 19, 2008, at 11:48 AM, Pietro Roversi wrote: Well everyone, talking of early applications of cryocooling to X-ray crystallography, what about Sten Samson's marvellous helium cryostat which was operational at Caltech since the end of the 1970s and used to reach temperatures around 20 K routinely , see for example: Proc Natl Acad Sci U S A. 1982 Jul;79(13):4040-4. Structure of a B-DNA dodecamer at 16 K. Drew HR, Samson S, Dickerson RE. That instrument (and its twin) are now both with Riccardo Destro in Milano. Ciao! Pietro -- Pietro Roversi Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3RE, England UK Tel. 0044-1865-275385 Mischa Machius, PhD Associate Professor Department of Biochemistry 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
Re: [ccp4bb] is it Ok to freeze
... room that was lined with insulated steel walls and that could be flushed with liquid nitrogen. I'm trying to picture this ... did you guys have some kind of LN2- proof SCUBA diving equipment to work in there? 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/ - On 19 Jun 2008, at 18:04, Mischa Machius wrote: Ha, everyone seems to be bragging about how far back cryo- crystallography really goes. In that vain, I'd like to mention that, in Martinsried, we had a room that was lined with insulated steel walls and that could be flushed with liquid nitrogen. It was requested (demanded, really...) by Robert Huber when the Max-Planck Institute was finalized in 1972 (I hope I got my history right). That room contained an entire diffraction system. Talk about crystal cooling... bah, way too dinky. Cool the entire room! Of course, it was a hazard to work in that room, and so - as far as I know - there was only one post-doc from India how ever used it. That room had an ante-room with two more generators plus detectors that could be cooled down to -20°C! Ah, the good old Wild West times of macromolecular crystallography... Cheers - MM On Jun 19, 2008, at 11:48 AM, Pietro Roversi wrote: Well everyone, talking of early applications of cryocooling to X-ray crystallography, what about Sten Samson's marvellous helium cryostat which was operational at Caltech since the end of the 1970s and used to reach temperatures around 20 K routinely , see for example: Proc Natl Acad Sci U S A. 1982 Jul;79(13):4040-4. Structure of a B-DNA dodecamer at 16 K. Drew HR, Samson S, Dickerson RE. That instrument (and its twin) are now both with Riccardo Destro in Milano. Ciao! Pietro -- Pietro Roversi Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3RE, England UK Tel. 0044-1865-275385 -- -- Mischa Machius, PhD Associate Professor Department of Biochemistry 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
Re: [ccp4bb] is it Ok to freeze
Sadly, I have never seen the room being used. Perhaps one of the 'older' Martinsrieder on the forum has seen it. MM On Jun 19, 2008, at 12:11 PM, Klaus Futterer wrote: ... room that was lined with insulated steel walls and that could be flushed with liquid nitrogen. I'm trying to picture this ... did you guys have some kind of LN2- proof SCUBA diving equipment to work in there? 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/ - On 19 Jun 2008, at 18:04, Mischa Machius wrote: Ha, everyone seems to be bragging about how far back cryo- crystallography really goes. In that vain, I'd like to mention that, in Martinsried, we had a room that was lined with insulated steel walls and that could be flushed with liquid nitrogen. It was requested (demanded, really...) by Robert Huber when the Max-Planck Institute was finalized in 1972 (I hope I got my history right). That room contained an entire diffraction system. Talk about crystal cooling... bah, way too dinky. Cool the entire room! Of course, it was a hazard to work in that room, and so - as far as I know - there was only one post-doc from India how ever used it. That room had an ante-room with two more generators plus detectors that could be cooled down to -20°C! Ah, the good old Wild West times of macromolecular crystallography... Cheers - MM On Jun 19, 2008, at 11:48 AM, Pietro Roversi wrote: Well everyone, talking of early applications of cryocooling to X-ray crystallography, what about Sten Samson's marvellous helium cryostat which was operational at Caltech since the end of the 1970s and used to reach temperatures around 20 K routinely , see for example: Proc Natl Acad Sci U S A. 1982 Jul;79(13):4040-4. Structure of a B-DNA dodecamer at 16 K. Drew HR, Samson S, Dickerson RE. That instrument (and its twin) are now both with Riccardo Destro in Milano. Ciao! Pietro -- Pietro Roversi Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3RE, England UK Tel. 0044-1865-275385 Mischa Machius, PhD Associate Professor Department of Biochemistry 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 Mischa Machius, PhD Associate Professor Department of Biochemistry 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
Re: [ccp4bb] is it Ok to freeze
I've been in that cold room / hutch. I never heard of it being flushed with LN2. I think that is just to make the room sound cooler. Jim On Thu, 19 Jun 2008, Mischa Machius wrote: Sadly, I have never seen the room being used. Perhaps one of the 'older' Martinsrieder on the forum has seen it. MM On Jun 19, 2008, at 12:11 PM, Klaus Futterer wrote: ... room that was lined with insulated steel walls and that could be flushed with liquid nitrogen. I'm trying to picture this ... did you guys have some kind of LN2-proof SCUBA diving equipment to work in there? Klaus
Re: [ccp4bb] Coot and Hs
Roberto, An also less than optimal work around might be to take your refined .pdb from PHENIX or CCP4 and run it through the downgrade utility on MolProbity to change to PDBv2.3 format before working in Coot. I don't think it is necessary to convert back to PDBv3.0 for phenix.refine, but MolProbity will do this automatically if you upload a PDBv2.3 file. The workhorse of the conversion is a program called the Remediator, which is available for download here: http://kinemage.biochem.duke.edu/software/remediator.php It certainly is a pain to have to be switching back and forth, but this should allow you to keep your refined hydrogen positions. Good Luck, -bob On Thu, Jun 19, 2008 at 7:26 AM, Roberto Steiner [EMAIL PROTECTED] wrote: Dear all, a problem possibly at the coot/mmdb interface... If one uploads a pdb file (from phenix.refine in the example below) that contains Hs into Coot and then writes it out (with or without any modification done on it) Coot shifts the HG2n of THR on the right by one column space. Because column 17 is kept empty the result is three identical HG2 THR protons. Example: Uploaded: CRYST1 45.460 166.970 167.200 90.00 90.00 90.00 P 21 21 21 SCALE1 0.021997 -0.00 -0.000.0 SCALE2 0.00 0.005989 0.000.0 SCALE3 0.00 0.00 0.0059810.0 ATOM 1 N THR A 2 27.439 61.155 24.800 1.00 70.37 A N ANISOU1 N THR A 2 9721 7539 9478 1186 2103297 A N ATOM 2 CA THR A 2 26.489 62.215 24.456 1.00 77.21 A C ANISOU2 CA THR A 210790 8621 9925 1145 1971285 A C ATOM 3 CB THR A 2 26.960 63.618 24.975 1.00 73.93 A C ANISOU3 CB THR A 210519 8251 9322 1244 1638409 A C ATOM 4 OG1 THR A 2 28.259 63.512 25.579 1.00 73.16 A O ANISOU4 OG1 THR A 210309 7971 9516 1332 1549489 A O ATOM 5 CG2 THR A 2 25.969 64.197 25.999 1.00 64.65 A C ANISOU5 CG2 THR A 2 9547 7174 7845 1451 1403582 A C ATOM 6 C THR A 2 26.200 62.288 22.934 1.00 71.92 A C ANISOU6 C THR A 210101 8073 9151869 2179 63 A C ATOM 7 O THR A 2 25.172 61.797 22.455 1.00 64.74 A O ANISOU7 O THR A 2 9210 7258 8131790 2339-23 A O ATOM 8 HA THR A 2 25.639 62.015 24.900 1.00 71.84 A H ATOM 9 HB THR A 2 27.009 64.232 24.226 1.00 69.26 A H ATOM 10 HG1 THR A 2 28.232 62.991 26.212 1.00 67.50 A H ATOM 11 HG21 THR A 2 26.275 65.055 26.303 1.00 61.19 A H ATOM 12 HG22 THR A 2 25.104 64.300 25.596 1.00 61.19 A H ATOM 13 HG23 THR A 2 25.894 63.607 26.753 1.00 61.19 A H Written: CRYST1 45.460 166.970 167.200 90.00 90.00 90.00 P 21 21 21 SCALE1 0.021997 -0.00 -0.000.0 SCALE2 0.00 0.005989 0.000.0 SCALE3 0.00 0.00 0.0059810.0 ATOM 1 N THR A 2 27.439 61.155 24.800 1.00 70.37 A N ANISOU1 N THR A 2 9721 7539 9478 1186 2103297 A N ATOM 2 CA THR A 2 26.489 62.215 24.456 1.00 77.21 A C ANISOU2 CA THR A 210790 8621 9925 1145 1971285 A C ATOM 3 CB THR A 2 26.960 63.618 24.975 1.00 73.93 A C ANISOU3 CB THR A 210519 8251 9322 1244 1638409 A C ATOM 4 OG1 THR A 2 28.259 63.512 25.579 1.00 73.16 A O ANISOU4 OG1 THR A 210309 7971 9516 1332 1549489 A O ATOM 5 CG2 THR A 2 25.969 64.197 25.999 1.00 64.65 A C ANISOU5 CG2 THR A 2 9547 7174 7845 1451 1403582 A C ATOM 6 C THR A 2 26.200 62.288 22.934 1.00 71.92 A C ANISOU6 C THR A 210101 8073 9151869 2179 63 A C ATOM 7 O THR A 2 25.172 61.797 22.455 1.00 64.74 A O ANISOU7 O THR A 2 9210 7258 8131790 2339-23 A O ATOM 8 HA THR A 2 25.639 62.015 24.900 1.00 71.84 A H ATOM 9 HB THR A 2 27.009 64.232 24.226 1.00 69.26 A H ATOM 10 HG1 THR A 2 28.232 62.991 26.212 1.00 67.50 A H ATOM 11 HG2 THR A 2 26.275 65.055 26.303 1.00 61.19 A H ATOM 12 HG2 THR A 2 25.104 64.300 25.596 1.00 61.19 A H ATOM 13 HG2 THR A 2 25.894 63.607 26.753 1.00 61.19 A H Does anyone know (Paul?) the reason for the above? The only solution right now (that I know of) is to remove all Hs and generate them again (molprobity for example) prior to refinement. Cheers, Roberto ---
Re: [ccp4bb] is it Ok to freeze
Dick Dickerson tried to do the same thing at Caltech around the same time. The major problem with cooling equipment was that the Picker goniometer had lots of metal in it, and each of the metal pieces cooled and contracted differently, so the alignment was always off. Nice idea, but not useful. That's when they got the idea to just cool the sample. Yes, Sten Samson's device was elegant in a number of ways, and we could collect 16-20K data for weeks on it. Bernie Santarsiero On Thu, June 19, 2008 12:04 pm, Mischa Machius wrote: Ha, everyone seems to be bragging about how far back cryo- crystallography really goes. In that vain, I'd like to mention that, in Martinsried, we had a room that was lined with insulated steel walls and that could be flushed with liquid nitrogen. It was requested (demanded, really...) by Robert Huber when the Max-Planck Institute was finalized in 1972 (I hope I got my history right). That room contained an entire diffraction system. Talk about crystal cooling... bah, way too dinky. Cool the entire room! Of course, it was a hazard to work in that room, and so - as far as I know - there was only one post-doc from India how ever used it. That room had an ante-room with two more generators plus detectors that could be cooled down to -20°C! Ah, the good old Wild West times of macromolecular crystallography... Cheers - MM On Jun 19, 2008, at 11:48 AM, Pietro Roversi wrote: Well everyone, talking of early applications of cryocooling to X-ray crystallography, what about Sten Samson's marvellous helium cryostat which was operational at Caltech since the end of the 1970s and used to reach temperatures around 20 K routinely , see for example: Proc Natl Acad Sci U S A. 1982 Jul;79(13):4040-4. Structure of a B-DNA dodecamer at 16 K. Drew HR, Samson S, Dickerson RE. That instrument (and its twin) are now both with Riccardo Destro in Milano. Ciao! Pietro -- Pietro Roversi Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3RE, England UK Tel. 0044-1865-275385 Mischa Machius, PhD Associate Professor Department of Biochemistry 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
[ccp4bb] PhD Scholarship opportunity
Structure-Function Studies of Protein Trafficking The Role: A PhD scholarship is available immediately in the lab of Dr. Brett Collins at the Institute for Molecular Bioscience, University of Queensland, Brisbane (Australia). The successful applicant will join a team using multidisciplinary approaches to study intracellular membrane trafficking in the human cell. The student will use X-ray crystallography to determine structures of membrane coat proteins, biochemical and biophysical methods to probe protein-protein and protein-lipid interactions and cell biology experiments to study protein localisation in vivo. Students with skills in molecular biology, protein chemistry or cell biology but with an interest in structural biology are encouraged to apply. The Person: Prospective candidates will be expected to have graduated recently with Honours Class I or IIA (or the equivalent such as MSc) in biochemistry, bioinformatics, cell biology or related disciplines. Remuneration: The stipend will be in the range $20,007-$25,007 per annum for 3 years. Both Australian national and international students are encouraged to apply. Opportunities: The position offered is part of an ARC Discovery Project Grant “From structures to systems: A hierarchical approach to understanding sub-cellular components” awarded to Dr. Collins and Prof. Alan Mark (School of Molecular and Microbial Sciences). The Structural Biology group of Dr. Collins has close ties with several structural biology and cell biology labs studying membrane trafficking in Australia and internationally. Students will be encouraged to attend national and international conferences to present their work and to publish their research in high quality journals. Application Details: Applicants should provide a full CV, a summary of their academic record and research interests as well as the names and contact details (address, telephone, fax and e-mail) of two academic referees. The Institute: The Institute for Molecular Bioscience (www.imb.uq.edu.au) is a national research and development initiative at the University of Queensland. The IMB is staffed by approximately 400 research scientists and students working in research divisions encompassing genomics and bioinformatics, genetics and developmental biology, cell biology, structural biology and biological chemistry and molecular design. Contacts: Dr. Brett Collins ([EMAIL PROTECTED]). http:// www.imb.uq.edu.au/index.html?page=82433. Closing Date For Applications: 25th July 2008 (or until filled). Brett Collins, PhD Group leader Institute for Molecular Bioscience Level 3 North Queensland Bioscience Precinct The University of Queensland St. Lucia, 4072, Qld, AUSTRALIA e-mail: [EMAIL PROTECTED] phone: 61-7-3346-2043 FAX:61-7-3346-2101 Courier address: Institute for Molecular Bioscience Queensland Bioscience Precinct Building 80, Services Road University of Queensland St. Lucia, Brisbane Queensland, Australia 4072
