[ccp4bb] Spacegroup choices, reindexing and so on
Hi All, A user question about the xia2 behaviour has opened a pot of worms, and I thought I would ask the community for opinions. If (for example) you are using an automated data processing or analysis tool, and the systematic absences suggest a spacegroup choice, what would you like to do: (1) nothing - just mention this in the output (2) assign the base version of this spacegroup (e.g. P41212 to represent that or it's enantiomorph) (3) create multiple copies of the reflection file with all of the spacegroup options As a further question, if the spacegroup looks like P 2 21 21 (say) would you like this to be reindexed to the standard setting? Now, I suspect that there will be a wide range of opinions on this. Following #1 will give possibly strange effects if truncate tries to inflate systematically absent reflections Following #2 will result in reflections being removed by truncate #3 gives lots of reflection files and lots of mess Currently I follow #2 with reindexing to the standard setting. There have been discussions in the past of being able to flag or enantiomorph in the spacegroup definition in the mtz file. This would be useful here, but would not really help with the reindex or no question... Thanks! Graeme
Re: [ccp4bb] difference between I over sigma_I and I over sd
Hi Lu Yongzhi, It has to be said it is not obvious. However, there are as far as I can see at least three possible definitions of I/sigma, so here we go: (1) I/sigma (calculated, corrected perhaps) for individual observations - sigma based on counting statistics (2) Mean(I) / Sigma(mean) - that is, including the improvement in the measurement by including multiple observations (3) Mean(I) / Spread - that is, the mean I value divided by the spread (standard deviation?) of the observations - which is different to (1) Quoting from pdb pages: Item _reflns_shell.meanI_over_sigI_all Description The ratio of the mean of the intensities of all reflections in this shell to the mean of the standard uncertainties of the intensities of all reflections in this shell. They do not include a definition for the sd version of this. Reading through a handily found scala log file and comparing to the harvesting stats, I find that: meanI_over_sd_all = Mn(I)/sd - (2) above meanI_over_sigmaI_all = I/sigma - (1) above Hope this answers your question. Cheers, Graeme From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Lu Yongzhi Sent: 19 January 2008 09:07 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] difference between I over sigma_I and I over sd Hi everyone, When I scale the data using Scala, I don't know differences between _diffrn_reflns.meanI_over_sigI_all6.5475 _diffrn_reflns.meanI_over_sd_all 21.3013 in the statistics. I think that both sigma and sd have the same meaning--standard deviation. By the way, in the file header of PDB's, what are the meanings of the numbers 5 and 1 in the row HELIX, numbers 0, 1 and -1 in the row SHEET. And in the row SHEET, what's the meaning of the last 6 columns. HELIX1 1 THR A 35 ASP A 37 5 3 HELIX2 2 SER A 41 TYR A 46 1 6 HELIX3 3 GLU A 68 ALA A 82 1 15SHEET1 C 6 GLU A 224 ARG A 232 0 SHEET2 C 6 ILE A 214 GLU A 221 -1 N CYS A 217 O ARG A 229 SHEET3 C 6 PHE A 183 VAL A 189 -1 N PHE A 187 O LEU A 218 SHEET4 C 6 VAL A 302 LEU A 309 -1 O ILE A 306 N LYS A 184 SHEET5 C 6 LYS A 254 HIS A 261 -1 N ILE A 258 O GLY A 305 SHEET6 C 6 GLU A 280 PRO A 288 1 O ASP A 283 N VAL A 257 Thanks Lu Yongzhi
Re: [ccp4bb] Spacegroup choices, reindexing and so on
Dear Graeme, here is what I would do, or what I would like to have. If you are able to identify the Laue group of the data with some degree of certainty, then all of the processing and scaling should be carried out in this Laue group. Then, by looking at systematic absences you may give probabilities for each of the possible space groups, i.e. each of the eight possibilities in P-orthorhombic. Typically one option will have the highest probability and this is the one which should be written out. In a second run, the user should be given the choice of overriding this. Now, for space groups such as P222_1, this should always be reindexed to standard setting, if it turns out to be the one with the highest probability. Hope that helps, Manfred. * * *Dr. Manfred S. Weiss * * * * Team Leader * * * * EMBL Hamburg OutstationFon: +49-40-89902-170 * * c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 * * D-22603 Hamburg Email: [EMAIL PROTECTED] * * GERMANY Web: www.embl-hamburg.de/~msweiss/ * * * On Mon, 21 Jan 2008, Winter, G (Graeme) wrote: Hi All, A user question about the xia2 behaviour has opened a pot of worms, and I thought I would ask the community for opinions. If (for example) you are using an automated data processing or analysis tool, and the systematic absences suggest a spacegroup choice, what would you like to do: (1) nothing - just mention this in the output (2) assign the base version of this spacegroup (e.g. P41212 to represent that or it's enantiomorph) (3) create multiple copies of the reflection file with all of the spacegroup options As a further question, if the spacegroup looks like P 2 21 21 (say) would you like this to be reindexed to the standard setting? Now, I suspect that there will be a wide range of opinions on this. Following #1 will give possibly strange effects if truncate tries to inflate systematically absent reflections Following #2 will result in reflections being removed by truncate #3 gives lots of reflection files and lots of mess Currently I follow #2 with reindexing to the standard setting. There have been discussions in the past of being able to flag or enantiomorph in the spacegroup definition in the mtz file. This would be useful here, but would not really help with the reindex or no question... Thanks! Graeme
Re: [ccp4bb] difference between I over sigma_I and I over sd
Dear all, speaking of I/sigma(I) when you use scalepack, how do you estimate it ? nathalie -- Dr. Nathalie Colloc'h, PhD CI-NAPS, UMR 6232 - UCBN - CNRS GIP Cyceron Bd Becquerel, BP5229 14074 Caen cedex FRANCE Tel. 33.2.31.47.01.32 Fax. 33.2.31.47.02.22 [EMAIL PROTECTED]
[ccp4bb] Swiss Light Source - Beamline Scientist Position
** We are looking for a Beamline Scientist for the Swiss Light Source * * The Paul Scherrer Institut is a centre for multi-disciplinary research and one of the world’s leading user laboratories. With its 1200 employees it belongs as an autonomous institution to the Swiss ETH domain and concentrates its activities on solid-state research and material sciences, elementary particle physics, energy and environmental research as well as on biology and medicine. The Swiss Light Source (SLS) is one of the most advanced radiation sources worldwide. The SLS operates two high performance undulator beam lines for protein crystallography and has recently started the commissioning of a state-of-the-art bending magnet beamline. The Macromolecular Crystallography group is involved in several aspects of protein crystallography including the design and construction of new beamline components as well as various structural biology projects. We are looking for a Beamline Scientist for the Bending Magnet Beamline X06DA /Your tasks/ You will be responsible for the further development and automation of the bending magnet beamline X06DA at the SLS, in close collaboration with the MX-group as well as be involved in the beamline operation. The position offers the opportunity to develop an independent scientific research programme in the field of protein crystallography or protein crystallographic methods development including the supervision of PhD students and postdocs. The infrastructure of the PSI structural biology group will be available for you to pursue your own crystallographic research projects. /Your profile/ You hold a Ph.D. degree in biology or (bio-) chemistry and have several years of experience in either protein crystallography or related beamline instrumentation. Knowledge of high throughput crystallisation techniques would be of advantage. If you are a good team player with fine communication skills and sense of responsibility, this position will offer a great opportunity for you to develop your research career in an exciting and highly multidisciplinary environment. We are looking forward to your application. For further information please contact Dr. Clemens Schulze-Briese, Tel. +41 56 310 45 33, e-Mail [EMAIL PROTECTED] Please send your application to: Paul Scherrer Institut, Human Resources, Mrs. Elke Baumann, ref. code 6112-01, 5232 Villigen PSI, Switzerland. mailto:[EMAIL PROTECTED] -- Dr. Clemens Schulze-Briese - [EMAIL PROTECTED] --- Swiss Light Source at Paul Scherrer Institut CH-5232 Villigen PSI - http://sls.web.psi.ch Phone +41 56 310 4533 - Fax -5292 - Secretary -3178
Re: [ccp4bb] Spacegroup choices, reindexing and so on
Hi Manfred I agree with everything you say except the last bit about re-indexing! For those space groups with alternate settings, e.g. those with standard names C2 or P2221 or P21212, why is it necessary to re-index to the 'standard setting' when the data will have been already indexed correctly by Mosflm or whatever according to the ITC Vol A convention (e.g. a b c for the oI lattice)? It's not clear to me what you gain by re-indexing in that situation (presumably at the heavy-atom solution or translation function stage), and I know from experience that what you lose is the risk of causing endless confusion by having datasets around indexed in both ways. This becomes particularly problematic when the data is stored in some kind of database, because then you really want to have one definitive space group name per crystal which is defined right at the outset and cannot be changed. Changing the space group in mid-stream is then not an option, except by deleting all the database entries for that crystal and starting all over again with the new space group name. Of course if the initial choice of space group was really wrong (e.g. the wrong Bravais lattice assignment) then you have no option but to start over and re-process the data. The only other situation where re-indexing may be necessary is where you know the correct Bravais lattice and approximate cell parameters *before* processing the data, e.g. where you have a previously solved isomorphous or near-isomorphous structure, but where the alternate indexings have similar cell parameters so the initial automatic choice of cell orientation may not have been correct. Cheers -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Manfred S. Weiss Sent: 21 January 2008 09:34 To: Winter, G (Graeme) Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Spacegroup choices, reindexing and so on Dear Graeme, here is what I would do, or what I would like to have. If you are able to identify the Laue group of the data with some degree of certainty, then all of the processing and scaling should be carried out in this Laue group. Then, by looking at systematic absences you may give probabilities for each of the possible space groups, i.e. each of the eight possibilities in P-orthorhombic. Typically one option will have the highest probability and this is the one which should be written out. In a second run, the user should be given the choice of overriding this. Now, for space groups such as P222_1, this should always be reindexed to standard setting, if it turns out to be the one with the highest probability. Hope that helps, Manfred. * * *Dr. Manfred S. Weiss * * * * Team Leader * * * * EMBL Hamburg OutstationFon: +49-40-89902-170 * * c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 * * D-22603 Hamburg Email: [EMAIL PROTECTED] * * GERMANY Web: www.embl-hamburg.de/~msweiss/ * * * On Mon, 21 Jan 2008, Winter, G (Graeme) wrote: Hi All, A user question about the xia2 behaviour has opened a pot of worms, and I thought I would ask the community for opinions. If (for example) you are using an automated data processing or analysis tool, and the systematic absences suggest a spacegroup choice, what would you like to do: (1) nothing - just mention this in the output (2) assign the base version of this spacegroup (e.g. P41212 to represent that or it's enantiomorph) (3) create multiple copies of the reflection file with all of the spacegroup options As a further question, if the spacegroup looks like P 2 21 21 (say) would you like this to be reindexed to the standard setting? Now, I suspect that there will be a wide range of opinions on this. Following #1 will give possibly strange effects if truncate tries to inflate systematically absent reflections Following #2 will result in reflections being removed by truncate #3 gives lots of reflection files and lots of mess Currently I follow #2 with reindexing to the standard setting. There have been discussions in the past of being able to flag or enantiomorph in the spacegroup definition in the mtz file. This would be useful here, but would not really help with the reindex or no question... Thanks! Graeme Disclaimer This communication is confidential and may contain privileged
Re: [ccp4bb] Spacegroup choices, reindexing and so on
Dear Ian, I thought that in cases of for instance P-orthorhombic where you can have a screw axis along a, b, or c or any combination of it, the standard is always to make the unique axis the c-axis. I.e. the longest axis in P222, and P2(1)2(1)2(1), but the 2(1)-axis in P222(1) or P2(1)22 or P22(1)2 and the 2-axis in P22(1)2(1) or P2(1)22(1) or P2(1)2(1)2. I am not sure if all programs (even within CCP4) understand any of the non-conventional settings. Best regards, manfred. * * *Dr. Manfred S. Weiss * * * * Team Leader * * * * EMBL Hamburg OutstationFon: +49-40-89902-170 * * c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 * * D-22603 Hamburg Email: [EMAIL PROTECTED] * * GERMANY Web: www.embl-hamburg.de/~msweiss/ * * * On Mon, 21 Jan 2008, Ian Tickle wrote: Hi Manfred I agree with everything you say except the last bit about re-indexing! For those space groups with alternate settings, e.g. those with standard names C2 or P2221 or P21212, why is it necessary to re-index to the 'standard setting' when the data will have been already indexed correctly by Mosflm or whatever according to the ITC Vol A convention (e.g. a b c for the oI lattice)? It's not clear to me what you gain by re-indexing in that situation (presumably at the heavy-atom solution or translation function stage), and I know from experience that what you lose is the risk of causing endless confusion by having datasets around indexed in both ways. This becomes particularly problematic when the data is stored in some kind of database, because then you really want to have one definitive space group name per crystal which is defined right at the outset and cannot be changed. Changing the space group in mid-stream is then not an option, except by deleting all the database entries for that crystal and starting all over again with the new space group name. Of course if the initial choice of space group was really wrong (e.g. the wrong Bravais lattice assignment) then you have no option but to start over and re-process the data. The only other situation where re-indexing may be necessary is where you know the correct Bravais lattice and approximate cell parameters *before* processing the data, e.g. where you have a previously solved isomorphous or near-isomorphous structure, but where the alternate indexings have similar cell parameters so the initial automatic choice of cell orientation may not have been correct. Cheers -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Manfred S. Weiss Sent: 21 January 2008 09:34 To: Winter, G (Graeme) Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Spacegroup choices, reindexing and so on Dear Graeme, here is what I would do, or what I would like to have. If you are able to identify the Laue group of the data with some degree of certainty, then all of the processing and scaling should be carried out in this Laue group. Then, by looking at systematic absences you may give probabilities for each of the possible space groups, i.e. each of the eight possibilities in P-orthorhombic. Typically one option will have the highest probability and this is the one which should be written out. In a second run, the user should be given the choice of overriding this. Now, for space groups such as P222_1, this should always be reindexed to standard setting, if it turns out to be the one with the highest probability. Hope that helps, Manfred. * * *Dr. Manfred S. Weiss * * * * Team Leader * * * * EMBL Hamburg OutstationFon: +49-40-89902-170 * * c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 * * D-22603 Hamburg Email: [EMAIL PROTECTED] * * GERMANY Web: www.embl-hamburg.de/~msweiss/ * * * On Mon, 21 Jan 2008, Winter, G (Graeme)
Re: [ccp4bb] difference between I over sigma_I and I over sd
LLI agree the difference between sd and SigI are a bit obscure. One referes to the spread of values about your mean I (The Sd of the reflection distribution) SigI is derived from the SIGI values estimated by the integration. There is some description in the CCP4 study weekend article by Phil Evans /Acta Cryst./ (2006). D*62*, 72-82 [ doi:10.1107/S0907444905036693 ] Scaling and assessment of data quality P. Evans * * http://journals.iucr.org/d/issues/2006/01/00/issconts.html Cant answer the PDB Q - I guess there should be a manual on their web site? Eleanor u Yongzhi wrote: Hi everyone, When I scale the data using Scala, I don't know differences between _diffrn_reflns.meanI_over_sigI_all6.5475 _diffrn_reflns.meanI_over_sd_all 21.3013 in the statistics. I think that both sigma and sd have the same meaning--standard deviation. By the way, in the file header of PDB's, what are the meanings of the numbers 5 and 1 in the row HELIX, numbers 0, 1 and -1 in the row SHEET. And in the row SHEET, what's the meaning of the last 6 columns. HELIX1 1 THR A 35 ASP A 37 5 3 HELIX2 2 SER A 41 TYR A 46 1 6 HELIX3 3 GLU A 68 ALA A 82 1 15 SHEET1 C 6 GLU A 224 ARG A 232 0 SHEET2 C 6 ILE A 214 GLU A 221 -1 N CYS A 217 O ARG A 229 SHEET3 C 6 PHE A 183 VAL A 189 -1 N PHE A 187 O LEU A 218 SHEET4 C 6 VAL A 302 LEU A 309 -1 O ILE A 306 N LYS A 184 SHEET5 C 6 LYS A 254 HIS A 261 -1 N ILE A 258 O GLY A 305 SHEET6 C 6 GLU A 280 PRO A 288 1 O ASP A 283 N VAL A 257 Thanks Lu Yongzhi
[ccp4bb] Announcement - EMBO World Lecture Course
EMBO World Lecture Course on RECENT DEVELOPMENTS IN MACROMOLECULAR CRYSTALLOGRAPHY We would like to announce an EMBO World Lecture Course on RECENT DEVELOPMENTS IN MACROMOLECULAR CRYSTALLOGRAPHY, which will take place from Nov 09-14, 2008 in the town in Pune in India, on the premises of the National Chemical Laboratory NCL. This course consists of various lectures describing recent methodological developments in the field from crystallization, to diffraction data collection, structure determination and function prediction from structure as well as lectures on recent achievements in biology using X-ray diffraction techniques. Pune is located abour 150 km south of Mumbai (Bombay) on the foothills of the Western valley of Maharashtra in Western India. It is a city of great culture and is rich in tradition and history as well as having a balanced climate. Due to space limitations, we can only accommodate up to 100 participants. Preference will be given to applicants who wish to present their own work. From the submitted abstracts a number of short talks will be selected. Also, the three best posters will be awarded a poster price. REGISTRATION for the course is now open. For more information and registration, please check the course homepage http:/cwp.embo.org/wpc08-02/ or contact the organizers Manfred S. Weiss ([EMAIL PROTECTED]) Paul A. Tucker ([EMAIL PROTECTED]) Santosh Panjikar ([EMAIL PROTECTED]) C. G. Suresh ([EMAIL PROTECTED]) Sanjay N. Nene ([EMAIL PROTECTED]) Best regards, Manfred * * *Dr. Manfred S. Weiss * * * * Team Leader * * * * EMBL Hamburg OutstationFon: +49-40-89902-170 * * c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 * * D-22603 Hamburg Email: [EMAIL PROTECTED] * * GERMANY Web: www.embl-hamburg.de/~msweiss/ * * *
Re: [ccp4bb] Spacegroup choices, reindexing and so on
I meant to post this response to Pietro's reply to the BB: I agree that bugs in software are an ever-present source of annoyance, but the only software in general use that I'm aware of that can't cope with the conventional ITC-A settings is Arp/Warp (and even this was definitely true only for the previous versions and may have been fixed in the current one which I don't currently have access to). I'm not aware of any other popular software in general use (this includes all CCP4 software that I'm aware of, and certainly includes Shel-X, CNS Phenix) that can't cope with the ITC-A settings? It seems to me that the solution is to fix the bug in the software - I can't believe it can be that hard to sort it out (or alternatively of course use different software without that bug, though of course the alternatives may well have different bugs!). Cheers -- Ian -Original Message- From: Pietro Roversi [mailto:[EMAIL PROTECTED] Sent: 21 January 2008 11:10 To: Ian Tickle Subject: Re: [ccp4bb] Spacegroup choices, reindexing and so on Dear Ian, I would agree with everyhting you say but as luck had it I have been unfortunate enough to get P21212 and P2221 crystals lately and you'd be surprised to find out how many pieces of software could not cope with non-standard settings - at the end I had to give up and conform to the norm out of bug exhaustion ... Regards Pietro -- Pietro Roversi Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3ER, England UK Tel. 0044-1865-275385 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] Crystal Imaging Systems - possibilities and recommendations
Dear Colleagues, We are currently contemplating the acquisition of an automated imaging system for crystallization screen plates (96-well). I am aware that Molecular Dimensions sells these systems ranging in price between 47 and 71 k and I am inviting your opinions, comments and advice on these and other commercially available systems, in particular regarding price, reliability and ease of use. Thanks in advance, Pedro Matias Industry and Medicine Applied Crystallography Macromolecular Crystallography Unit ___ Phones : (351-21) 446-9100 Ext. 1669 (351-21) 446-9669 (direct) Fax : (351-21) 441-1277 or 443-3644 email : [EMAIL PROTECTED] Mailing address : Instituto de Tecnologia Quimica e Biologica Apartado 127 2781-901 OEIRAS Portugal
Re: [ccp4bb] Spacegroup choices, reindexing and so on
On Jan 21, 2008, at 14:08, Ian Tickle wrote: I meant to post this response to Pietro's reply to the BB: I agree that bugs in software are an ever-present source of annoyance, but the only software in general use that I'm aware of that can't cope with the conventional ITC-A settings is Arp/Warp (and even this was definitely true only for the previous versions and may have been fixed in the current one which I don't currently have access to). Despite the very many reasons to upgrade to the latest ARP/wARP, which I would very highly recommend to do for every user (*) unfortunately support for the conventional ITC-A settings is not one of the reasons to upgrade ... Sorry Ian (and Eleanor ... et al) Tassos (*) especially for the ones that have to pay, like Astex ;-) I'm not aware of any other popular software in general use (this includes all CCP4 software that I'm aware of, and certainly includes Shel-X, CNS Phenix) that can't cope with the ITC-A settings? It seems to me that the solution is to fix the bug in the software - I can't believe it can be that hard to sort it out (or alternatively of course use different software without that bug, though of course the alternatives may well have different bugs!). Cheers -- Ian -Original Message- From: Pietro Roversi [mailto:[EMAIL PROTECTED] Sent: 21 January 2008 11:10 To: Ian Tickle Subject: Re: [ccp4bb] Spacegroup choices, reindexing and so on Dear Ian, I would agree with everyhting you say but as luck had it I have been unfortunate enough to get P21212 and P2221 crystals lately and you'd be surprised to find out how many pieces of software could not cope with non-standard settings - at the end I had to give up and conform to the norm out of bug exhaustion ... Regards Pietro -- Pietro Roversi Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3ER, England UK Tel. 0044-1865-275385 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] Dual Head Stereo On FireGL
Hello all, I have 2 21inch CRTs connected to a stereo capable firegl card and I am hoping to enable the active stereo on the extended desktop. Stereo works on a single screen setup but does not on the extended desktop on 2 monitors. I have a similar setup on an nvidia quadro card using xinerama that everything works fine. Does anyone have a working xorg.conf on the ati setup? I am beginning to suspect that the ati driver does not support dual monitor with stereo flipping. Any comment is appreciated. Thanks in advance. Ray Cornell University
[ccp4bb] SUMMARY: [ccp4bb] microsoft 3-button wheel mouse with OS X 10.5
Dear All, Thanks to Bill Scott, James Stroud and Jürgen Bosch for their responses. Here is the original email: We have recently bought a few iMacs for crystallography. I'm not keen on the supplied mighty mouse so I have switched to using a microsoft 3-button wheel mouse. I would like to configure it so that it behaves as it would with other unix systems such as RH Linux. i.e. (1) double-clicking with LH button on a file name selects ALL of the file name, not just up to the first full stop. (2) clicking the scroll wheel pastes the selected text AND it can be done multiple times without re-selecting. (2) I would like these functions to work in terminal windows, the ccp4i gui and web pages (and probably a few other things I haven't thought of yet!) AND be able to transfer the selected text between applications. I have installed the microsoft intellipoint drivers that seem to give more control over configuring the various buttons through system preferences, but I still can't get what I want. Any help would be much appreciated. Many thanks Dave Lawson --- Here are the responses: -- Bill: -- Hi David: david lawson (JIC) wrote: Dear All, Sorry for the slightly off-topic subject. We have recently bought a few iMacs for crystallography. I'm not keen on the supplied mighty mouse May I have them? so I have switched to using a microsoft 3-button wheel mouse. I would like to configure it so that it behaves as it would with other unix systems such as RH Linux. You managed to use Microsoft, behaved and Linux (albeit RH) all in one sentence without a hint of irony. i.e. (1) double-clicking with LH button on a file name selects ALL of the file name, not just up to the first full stop. Although your choice of Microsoft products shows dedication to a company with a firm reputation for placing the customizability needs of its customers ahead of its own desire to make profits, the first thing to realize is that you should never ever ever install their drivers. Ever. So if you did, take them out, now, and reboot. I'll wait. It is still early Sunday morning here. (2) clicking the scroll wheel pastes the selected text AND it can be done multiple times without re-selecting. When you've gotten rid of the drivers, this should now work. In Apple's Terminal program (as of 10.5) and iTerm (as of 1215), you just set the preference to do middle-button-paste and left-button select, and Blair's your uncle. Unfortunately, in pretty much every other application I can think of on OS X, this, sadly, does not work, and there is nothing Steve Gates will let you do about it. (2) I would like these functions to work in terminal windows, the ccp4i gui and web pages (and probably a few other things I haven't thought of yet!) AND be able to transfer the selected text between applications. I'd like to be at my ideal high-school weight, be paid more than a postdoc, and, well ... Getting the OS X gui to play nice with X11 is sometimes challenging. With the exception of Terminal and iTerm, you have to explicitly put stuff in the copy/paste buffer (command-C) before it is in the system clipboard. Then you can paste to X11 programs with a middle-button click, but this only works if you uninstalled that viral driver. Going from X11 to aqua programs requires selecting the text in the usual X11 manner but explicitly issuing the paste command (command-p). If you are using KDE X11 applications, you are really in for headaches. To get whole-string selection in iTerm or Terminal, there is a preference setting that allows you to input which characters you want to have considered parts of a word for click-to-select purposes. Unfortunately, pretty much every other application lacks this customizability, and I know of no system-wide preference setting that would enable you to do this globally. Aqua simply behaves by slightly different rules. Although I am a slobbering OS X fan, this lack of customizability to me, as well as a lack of focus-follows-mouse, it a negative. If you really need the canonical linux behavior, you can install gnome, xfce4, KDE, enlightenment, or any number of other window managers via fink. I've found KDE buggy and the XFCE4 is way out of date. Gnome is probably the best bet, and there is a major effort now to bring it completely up to date in fink. I have installed the microsoft intellipoint drivers that seem to give more control over configuring the various buttons through system preferences, but I still can't get what I want. Therein lies the problem, I am afraid. OS X will behave better using the default settings. It may be possible to tinker around with the driver, including separate settings in X11, to recover canonical behavior, but for purposes of sanity, uninstall them first, get everything working as best as possible, verify middle-button-paste
[ccp4bb] Help Superposition programmes!
Dear CCP4-programmers, I have recently installed CCP4 6.0.2 on a Mac G5 running (still) under OS 10.4. So far it was running OK - until tonight. When using superposition programmes (TOPP or Superpose) via the CCP4i I get the following message: Information from CCP4Interface script *** The program run with command: topp has failed with error message Last system error message: No such file or directory TOP: Open failed: File: /Users/anita/work/Integ/models/ASVcc.pdb The file exists and I can run e.g. coordconv on it. I did try TOPP using online commands - the same error occurs. Is that a bug or something else going wrong? Thanks for any suggestion! Anita
Re: [ccp4bb] Help Superposition programmes!
Yes - you are right! It doesnt work on my PC either.. I dont understand the code at all. Did it work on an older version of CCP4? Eleanor Anita Bentley wrote: Dear CCP4-programmers, I have recently installed CCP4 6.0.2 on a Mac G5 running (still) under OS 10.4. So far it was running OK - until tonight. When using superposition programmes (TOPP or Superpose) via the CCP4i I get the following message: Information from CCP4Interface script *** The program run with command: topp has failed with error message Last system error message: No such file or directory TOP: Open failed: File: /Users/anita/work/Integ/models/ASVcc.pdb The file exists and I can run e.g. coordconv on it. I did try TOPP using online commands - the same error occurs. Is that a bug or something else going wrong? Thanks for any suggestion! Anita
Re: [ccp4bb] Help Superposition programmes!
On Mon, Jan 21, 2008 at 06:28:58PM +0100, Anita Bentley wrote: I have recently installed CCP4 6.0.2 on a Mac G5 running (still) under OS 10.4. So far it was running OK - until tonight. When using superposition programmes (TOPP or Superpose) via the CCP4i I get the following message: Information from CCP4Interface script *** The program run with command: topp has failed with error message Last system error message: No such file or directory TOP: Open failed: File: /Users/anita/work/Integ/models/ASVcc.pdb The file exists and I can run e.g. coordconv on it. This could be a known problem. From: http://www.ccp4.ac.uk/problems.php#6.0.2-programs Topp claims it cannot find the input files corresponding to keywords MOL1 and MOL2, even though the files exist. This can be fixed by applying the patch topp.f-r1.16.2.5-r1.16.2.6.diff (also available from ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/patches) to $CCP4/src/topp_/topp.f and remaking topp. -ben -- Ben Eisenbraun Structural Biology Grid http://sbgrid.org/
Re: [ccp4bb] Crystal Imaging Systems - possibilities and recommendations
Do you want an imager, or a more sophisticated system that will store plates and image them according to a schedule? With imaging, it is important to think about what you want out of the system, as it is easy to be disappointed with them. The images you get will not be as good as what you see down a microscope (imagine if you set the microscope up to have drop A1 in focus and well lit, and after that you only translated the plate). Do you want to be able to find an xtal in an image, and then immediately know what was in the drop, reservoir, temperature of setup etc? In which case, you should look at the crystallisation database which is behind the imager - all software requires that you put information into it before you can retrieve it, so how easy is it to get information into your database? Janet -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Pedro M. Matias Sent: Tuesday, 22 January 2008 12:38 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Crystal Imaging Systems - possibilities and recommendations Dear Colleagues, We are currently contemplating the acquisition of an automated imaging system for crystallization screen plates (96-well). I am aware that Molecular Dimensions sells these systems ranging in price between 47 and 71 k€ and I am inviting your opinions, comments and advice on these and other commercially available systems, in particular regarding price, reliability and ease of use. Thanks in advance, Pedro Matias Industry and Medicine Applied Crystallography Macromolecular Crystallography Unit ___ Phones : (351-21) 446-9100 Ext. 1669 (351-21) 446-9669 (direct) Fax : (351-21) 441-1277 or 443-3644 email : [EMAIL PROTECTED] Mailing address : Instituto de Tecnologia Quimica e Biologica Apartado 127 2781-901 OEIRAS Portugal
[ccp4bb] CCP4 for bioinformatics?
Dear Crystallographers, Does anyone know of a bioinformatics counterpart of ccp4? It seems like there should really be such an entity, so that folks would not have to write scripts, reinventing the wheel all of the time. I am trying right now to manipulate some sequences into various forms, and I was imagining a moleman homolog for bioinformatics (perhaps seqman?). Regards, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: [EMAIL PROTECTED] ***
Re: [ccp4bb] CCP4 for bioinformatics?
On Monday 21 January 2008 15:33, Jacob Keller wrote: Dear Crystallographers, Does anyone know of a bioinformatics counterpart of ccp4? It seems like there should really be such an entity, so that folks would not have to write scripts, reinventing the wheel all of the time. I am trying right now to manipulate some sequences into various forms, and I was imagining a moleman homolog for bioinformatics (perhaps seqman?). BioPython http://biopython.org/wiki/Main_Page There is also BioPerl http://www.bioperl.org/wiki/Main_Page I worked with that for a while. From my limited contact with the project, they seemed strangely uninterested in 3D structure. But for sequence-based work it was a useful toolkit. -- Ethan A Merritt
Re: [ccp4bb] CCP4 for bioinformatics?
manipulate some sequences into various forms, and I was imagining a moleman homolog for bioinformatics (perhaps seqman?). as a matter of fact, i did write exactly that program nine years ago - http://xray.bmc.uu.se/usf/seqman_man.html :-) - not quite a 'ccp4 for bioinformatics' but indeed a simple sequence-homolog of moleman it's very limited, though. i mostly use it for generating exam questions for my bioinformatics courses. many of the ideas (and then some) i had for a suite of sequence/structure-oriented programs (initially called SEQSYST but subsequently renamed to SBIN - http://xray.bmc.uu.se/usf/sbin.html) were later implemented in a much better program called indonesia (see manual at http://xray.bmc.uu.se/dennis/ - this program used to be called FarOut in an earlier incarnation) by dennis madsen, patrik johansson, mark harris, susan arent, and others. since these are all smart kids who know java that program even has a nice gooey. it is maintained by dennis ([EMAIL PROTECTED]) --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. **
[ccp4bb] protein expression problem
Hi, I have been trying to express a rat protein in bacteria. The MBP-fusion expressed at very high level (~ 40 mg/L) while the GST-fusion and His-tag only gave inclusion bodies. The problem is that all protein runs in the void volume on a size-exclusion column (s-200, hepes, pH 7.4, 200 mM NaCl), no matter it is the intact MBP-fusion or cleaved sample. There is no Cys on this protein so there is unlikely any disulfide bond related problem. Anything I can do before I throw away this construct and try insect or mammalian cells? Thanks. Best, Chen - Never miss a thing. Make Yahoo your homepage.
Re: [ccp4bb] protein expression problem
Hi Chen, You could try adding some detergent or other solubilising agent (eg NDSBs) to your buffer. Have you tried other pHs? If you are sat near to or on the pI of your protein, it will be at its least soluble and more likely to aggregate. I've had protein behave like yours at pH 7.5 but behave perfectly (i.e. monodisperse) at pH 5.5. As you can get you protein in inclusion bodies, have you considered doing an inclusion body prep (using 'bugbuster' or something similar) and then trying some refolding protocols? Jungbauer A, Kaar W. Current status of technical protein refolding.J Biotechnol. 2007 Feb 20;128(3):587-96. Some people have had success with SUMO tags as well. HTH, Cheers, David On 22/01/2008, Daniel Jin [EMAIL PROTECTED] wrote: Hi, I have been trying to express a rat protein in bacteria. The MBP-fusion expressed at very high level (~ 40 mg/L) while the GST-fusion and His-tag only gave inclusion bodies. The problem is that all protein runs in the void volume on a size-exclusion column (s-200, hepes, pH 7.4, 200 mM NaCl), no matter it is the intact MBP-fusion or cleaved sample. There is no Cys on this protein so there is unlikely any disulfide bond related problem. Anything I can do before I throw away this construct and try insect or mammalian cells? Thanks. Best, Chen Never miss a thing. Make Yahoo your homepage. -- David C. Briggs PhD Father Crystallographer http://www.dbriggs.talktalk.net AIM ID: dbassophile
Re: [ccp4bb] CCP4 for bioinformatics?
BioPython There is also BioPerl And BioJava too, http://biojava.org/wiki/Main_Page Depend of your computing preference, and the size of your project... Regards, -- Watier Yves PhD Student, European Synchrotron Radiation Facility (ESRF) Experiments Division / Materials Science Group ID31 high resolution powder diffraction beamline. 6 Rue Jules Horowitz, BP 220, 38043 Grenoble, Cedex 9, France. Office: 10.01.06 Tel. (+)33(0)4.76.88.29.67 Fax. (+)33(0)4.76.88.27.07 http://www.esrf.fr/UsersAndScience/Experiments/MaterialsScience/ID31/
