Re: [ccp4bb] xds crashes
Dear Kay, many thanks for your suggestions. We will look into this. best Demetres On 11/29/2022 2:35 PM, Kay Diederichs wrote: Dear Demetres, I googled the Ubuntu 22.04 release notes and found https://discourse.ubuntu.com/t/jammy-jellyfish-release-notes/24668 which says "We’ve enabled the userspace OOMD service and are shipping the systemd-oomd package by default on the “Ubuntu Desktop” flavour, to avoid overloaded systems and the need of the kernel’s OOM killer to kick in. The OOMD status can be checked using oomctl." Then googling "Ubuntu 22.04 oomctl" takes me e.g. to https://askubuntu.com/questions/1405021/firefox-closes-by-itself-in-ubuntu-22-04 and https://bugs.launchpad.net/ubuntu/+source/systemd/+bug/1972159 which confirms that there may be a problem in Ubuntu 22.04 with processes being killed without good reason, and some hints on how to configure your system to avoid that. Maybe the systems-oomd package can simply be removed. Hope that helps, Kay On Tue, 29 Nov 2022 10:25:17 +0200, Demetres D. Leonidas wrote: Dear Kay, you are right and I do apologize for the misunderstanding. Point 1 and 2 are sufficient. best Demetres On 11/29/2022 10:00 AM, Kay Diederichs wrote: Dear Demetres, sounds a bit drastic! The second point alone would certainly suffice, because then no forking is done. What kind of hardware is that? I would expect that on a contemporary workstation you have 8GB of RAM or more; that would allow for 8 or more processes. Do you have a swapfile? If not, create one. Please check out https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Performance Best wishes, Kay On Tue, 29 Nov 2022 09:34:49 +0200, Demetres D. Leonidas wrote: Dear Kay, after some digging and help from Max Nanao we found that the problem was the memory. It was fulling rapidly. The workaround was to: 1. unzip the cbf files prior to processing 2. use maximum number of jobs 1 3. use number of processors 4 4. run xds_par Many thanks for all your help Demetres On 11/29/2022 9:03 AM, Kay Diederichs wrote: Dear Demetres, I agree with what James says: this is the operating system trying to to prevent, in an over-zealous way, the forking of too many or too big (in terms of memory) processes. In other words, XDS hasn't changed, but the operating system changed - it applies different limits to its processes. Your friendly system administrator should try to find out exactly which limit(s) changed, and reset the value(s). Perhaps a hint is in the Release Notes of Ubuntu 22.04 ? Pls report here when you've found it - currently you are the only one reporting it. Best wishes, Kay On Mon, 28 Nov 2022 12:06:43 -0800, James Holton wrote: Sounds like your kernel might think "forkxds" is creating a "fork bomb". Too many sub-processes firing off in too short a time triggers this. On one of my systems, I fixed it by editing /etc/security/limits.d/20-nproc.conf so that users are allowed ~10x more pids than normal. This tends to prevent these mysterious "Killed" errors. HTH? -James Holton MAD Scientist On 11/28/2022 7:44 AM, Demetres D. Leonidas wrote: Dear all, I do not know if this is the right list and I would like to apologize if it is not. We have repeatedly experienced xds crashes in machines running ubuntu 22.04.1 with the following message repeated several times at the INTEGRATE step /usr/local/bin/forkxds: line 60: 3427 Done echo "$itask" 3428 Killed | $amain We are trying to process data from P13 at EMBL-Hamburg. We are running XDS version Jan 10, 2022 BUILT=20220820 Any ideas ? Demetres To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- --- Dr. Demetres D. Leonidas Professor in Biochemistry Department of Biochemistry & Biotechnology University of Thessaly Biopolis 41500 Larissa, Greece - Tel. +302410 565278 Tel. +302410 565297 (Lab) Tel. +304210 565263 (X-ray) Fax. +302410 565290 E-mail: ddleoni...@bio.uth.gr ORCID ID orcid.org/-0002-3874-2523 --- -- Αυ
Re: [ccp4bb] xds crashes
Dear Kay, you are right and I do apologize for the misunderstanding. Point 1 and 2 are sufficient. best Demetres On 11/29/2022 10:00 AM, Kay Diederichs wrote: Dear Demetres, sounds a bit drastic! The second point alone would certainly suffice, because then no forking is done. What kind of hardware is that? I would expect that on a contemporary workstation you have 8GB of RAM or more; that would allow for 8 or more processes. Do you have a swapfile? If not, create one. Please check out https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Performance Best wishes, Kay On Tue, 29 Nov 2022 09:34:49 +0200, Demetres D. Leonidas wrote: Dear Kay, after some digging and help from Max Nanao we found that the problem was the memory. It was fulling rapidly. The workaround was to: 1. unzip the cbf files prior to processing 2. use maximum number of jobs 1 3. use number of processors 4 4. run xds_par Many thanks for all your help Demetres On 11/29/2022 9:03 AM, Kay Diederichs wrote: Dear Demetres, I agree with what James says: this is the operating system trying to to prevent, in an over-zealous way, the forking of too many or too big (in terms of memory) processes. In other words, XDS hasn't changed, but the operating system changed - it applies different limits to its processes. Your friendly system administrator should try to find out exactly which limit(s) changed, and reset the value(s). Perhaps a hint is in the Release Notes of Ubuntu 22.04 ? Pls report here when you've found it - currently you are the only one reporting it. Best wishes, Kay On Mon, 28 Nov 2022 12:06:43 -0800, James Holton wrote: Sounds like your kernel might think "forkxds" is creating a "fork bomb". Too many sub-processes firing off in too short a time triggers this. On one of my systems, I fixed it by editing /etc/security/limits.d/20-nproc.conf so that users are allowed ~10x more pids than normal. This tends to prevent these mysterious "Killed" errors. HTH? -James Holton MAD Scientist On 11/28/2022 7:44 AM, Demetres D. Leonidas wrote: Dear all, I do not know if this is the right list and I would like to apologize if it is not. We have repeatedly experienced xds crashes in machines running ubuntu 22.04.1 with the following message repeated several times at the INTEGRATE step /usr/local/bin/forkxds: line 60: 3427 Done echo "$itask" 3428 Killed | $amain We are trying to process data from P13 at EMBL-Hamburg. We are running XDS version Jan 10, 2022 BUILT=20220820 Any ideas ? Demetres To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- ------- Dr. Demetres D. Leonidas Professor in Biochemistry Department of Biochemistry & Biotechnology University of Thessaly Biopolis 41500 Larissa, Greece - Tel. +302410 565278 Tel. +302410 565297 (Lab) Tel. +304210 565263 (X-ray) Fax. +302410 565290 E-mail: ddleoni...@bio.uth.gr ORCID ID orcid.org/-0002-3874-2523 --- -- Αυτό το email έχει ελεγχθεί για ιούς από το Avast antivirus. www.avast.com To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- ------- Dr. Demetres D. Leonidas Professor in Biochemistry Department of Biochemistry & Biotechnology University of Thessaly Biopolis 41500 Larissa, Greece ---
Re: [ccp4bb] xds crashes
Dear Kay, after some digging and help from Max Nanao we found that the problem was the memory. It was fulling rapidly. The workaround was to: 1. unzip the cbf files prior to processing 2. use maximum number of jobs 1 3. use number of processors 4 4. run xds_par Many thanks for all your help Demetres On 11/29/2022 9:03 AM, Kay Diederichs wrote: Dear Demetres, I agree with what James says: this is the operating system trying to to prevent, in an over-zealous way, the forking of too many or too big (in terms of memory) processes. In other words, XDS hasn't changed, but the operating system changed - it applies different limits to its processes. Your friendly system administrator should try to find out exactly which limit(s) changed, and reset the value(s). Perhaps a hint is in the Release Notes of Ubuntu 22.04 ? Pls report here when you've found it - currently you are the only one reporting it. Best wishes, Kay On Mon, 28 Nov 2022 12:06:43 -0800, James Holton wrote: Sounds like your kernel might think "forkxds" is creating a "fork bomb". Too many sub-processes firing off in too short a time triggers this. On one of my systems, I fixed it by editing /etc/security/limits.d/20-nproc.conf so that users are allowed ~10x more pids than normal. This tends to prevent these mysterious "Killed" errors. HTH? -James Holton MAD Scientist On 11/28/2022 7:44 AM, Demetres D. Leonidas wrote: Dear all, I do not know if this is the right list and I would like to apologize if it is not. We have repeatedly experienced xds crashes in machines running ubuntu 22.04.1 with the following message repeated several times at the INTEGRATE step /usr/local/bin/forkxds: line 60: 3427 Done echo "$itask" 3428 Killed | $amain We are trying to process data from P13 at EMBL-Hamburg. We are running XDS version Jan 10, 2022 BUILT=20220820 Any ideas ? Demetres To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ -- ------- Dr. Demetres D. Leonidas Professor in Biochemistry Department of Biochemistry & Biotechnology University of Thessaly Biopolis 41500 Larissa, Greece - Tel. +302410 565278 Tel. +302410 565297 (Lab) Tel. +304210 565263 (X-ray) Fax. +302410 565290 E-mail: ddleoni...@bio.uth.gr ORCID ID orcid.org/-0002-3874-2523 --- -- Αυτό το email έχει ελεγχθεί για ιούς από το Avast antivirus. www.avast.com To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] xds crashes
Dear all, I do not know if this is the right list and I would like to apologize if it is not. We have repeatedly experienced xds crashes in machines running ubuntu 22.04.1 with the following message repeated several times at the INTEGRATE step /usr/local/bin/forkxds: line 60: 3427 Done echo "$itask" 3428 Killed | $amain We are trying to process data from P13 at EMBL-Hamburg. We are running XDS version Jan 10, 2022 BUILT=20220820 Any ideas ? Demetres -- --- Dr. Demetres D. Leonidas Professor in Biochemistry Department of Biochemistry & Biotechnology University of Thessaly Biopolis 41500 Larissa, Greece - Tel. +302410 565278 Tel. +302410 565297 (Lab) Tel. +304210 565263 (X-ray) Fax. +302410 565290 E-mail: ddleoni...@bio.uth.gr ORCID ID orcid.org/-0002-3874-2523 --- -- Αυτό το email έχει ελεγχθεί για ιούς από το Avast antivirus. www.avast.com To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] CCP4Mg problems
Dear Stuart, I did try to run is as you suggest "ccp4mg -noredirect" and I got the same msg (i.e. "ERROR no status file .CC$MG2/status/last_exit_status.pkl"). The first thing I checked were the write permissions and this was O.K. All other ccp4 programs run smoothly. best Demetres On 9/27/2021 3:37 PM, Stuart McNicholas wrote: Dear Demetres, That message is not actually an error, despite it saying ERROR in big letters. Apologies we should fix this as soon as possible. However, I am guessing that the program is not actually opening? Does anything else happen after that message? One way to possibly help is to run it as follows: ccp4mg -noredirect This way all messages should be sent to the terminal output and we might see something more helpful. Sorry for your difficulties, Stuart On Mon, 27 Sept 2021 at 13:24, Demetres D. Leonidas mailto:ddleoni...@bio.uth.gr>> wrote: Dear all, we have recently installed ccp4 programs in a new box running ubuntu 21.04. Everything works fine except ccp4mg. When we try to run it we get the splash screen and then a message appears at the terminal "ERROR no status file .CC$MG2/status/last_exit_status.pkl". I checked and such a file does not exist but I thought it will be created automatically once you run the program. Any ideas ? Demetres -- ------- Dr. Demetres D. Leonidas Professor in Biochemistry Department of Biochemistry & Biotechnology University of Thessaly Biopolis 41500 Larissa, Greece - Tel. +302410 565278 Tel. +302410 565297 (Lab) Tel. +304210 565263 (X-ray) Fax. +302410 565290 E-mail: ddleoni...@bio.uth.gr <mailto:ddleoni...@bio.uth.gr> ORCID ID orcid.org/-0002-3874-2523 <http://orcid.org/-0002-3874-2523> --- -- Αυτό το e-mail ελέγχθηκε για ιούς από το πρόγραμμα Avast antivirus. https://www.avast.com/antivirus <https://www.avast.com/antivirus> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1> This message was issued to members of www.jiscmail.ac.uk/CCP4BB <http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk <http://www.jiscmail.ac.uk>, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ <https://www.jiscmail.ac.uk/policyandsecurity/> -- --- Dr. Demetres D. Leonidas Professor in Biochemistry Department of Biochemistry & Biotechnology University of Thessaly Biopolis 41500 Larissa, Greece - Tel. +302410 565278 Tel. +302410 565297 (Lab) Tel. +304210 565263 (X-ray) Fax. +302410 565290 E-mail: ddleoni...@bio.uth.gr ORCID ID orcid.org/-0002-3874-2523 --- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] CCP4Mg problems
Dear all, we have recently installed ccp4 programs in a new box running ubuntu 21.04. Everything works fine except ccp4mg. When we try to run it we get the splash screen and then a message appears at the terminal "ERROR no status file .CC$MG2/status/last_exit_status.pkl". I checked and such a file does not exist but I thought it will be created automatically once you run the program. Any ideas ? Demetres -- --- Dr. Demetres D. Leonidas Professor in Biochemistry Department of Biochemistry & Biotechnology University of Thessaly Biopolis 41500 Larissa, Greece - Tel. +302410 565278 Tel. +302410 565297 (Lab) Tel. +304210 565263 (X-ray) Fax. +302410 565290 E-mail: ddleoni...@bio.uth.gr ORCID ID orcid.org/-0002-3874-2523 --- -- Αυτό το e-mail ελέγχθηκε για ιούς από το πρόγραμμα Avast antivirus. https://www.avast.com/antivirus To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Postdoctoral research position
Postdoctoral research position: molecular biologist/bioinformatician A 2-year Post-Doctoral position is available immediately in the Laboratory of Molecular Biology and Genomics in the Department of Biochemistry and Biotechnology of the University of Thessaly, located in the city of Larissa. The selected candidate will work in the framework of a national Research Infrastructure program on Synthetic Biology. Research in the Laboratory of Molecular Biology and Genomics focuses on various aspects of insect olfaction, reproduction and evolution, aiming at the development of new approaches for control of insects of agricultural or medical importance. We are seeking a highly motivated and creative scientist with a track record of successful research. A good bioinformatics background is strongly desired. The ideal candidate should be able to analyze raw sequencing data, perform genome assembly and annotation and have a good understanding of comparative and functional genomics. At the same time, he/she should be able to design and perform experiments in support of the bioinformatics analyses. Candidates should have a PhD and should have training in one or more of the following disciplines: bioinformatics, molecular biology, biochemistry, cell biology, and genome-wide technologies. Familiarity with insect rearing is desirable but not essential. Curriculum Vitae, a brief letter describing interests and prior experience and names of three references should be sent to: kmath...@bio.uth.gr. Research position: MSc Bioinformatician A 2-year position for an MSc Bioinformatician is available immediately in the Laboratory of Molecular Biology and Genomics in the Department of Biochemistry and Biotechnology of the University of Thessaly, located in the city of Larissa. The selected candidate will work in the framework of a national Research Infrastructure program on Synthetic Biology. Research in the Laboratory of Molecular Biology and Genomics focuses on various aspects of insect olfaction, reproduction and evolution, aiming at the development of new approaches for control of insects of agricultural or medical importance. We are seeking a highly motivated individual with a BSc in Biology or related science and an MSc in Bioinformatics. The successful candidate will be involved in raw sequencing data analysis, genome assembly and annotation and comparative and functional genomics studies. His/her research could also lead to a PhD. Curriculum Vitae, a brief letter describing interests and prior experience and names of three references should be sent to: kmath...@bio.uth.gr. -- --- Dr. Demetres D. Leonidas Professor of Biochemistry Department of Biochemistry & Biotechnology University of Thessaly Biopolis 41500 Larissa, Greece - Tel. +302410 565278 Tel. +302410 565297 (Lab) Fax. +302410 565290 E-mail: ddleoni...@bio.uth.gr http://www.bio.uth.gr ORCID ID orcid.org/-0002-3874-2523 --- --- Αυτό το e-mail ελέγχθηκε για ιούς από το πρόγραμμα Avast antivirus. https://www.avast.com/antivirus
Re: [ccp4bb] X-ray pattern has streaks
Dear Krithika, what you probably see is the diffraction pattern of a highly mosaic crystal due to probably internal disordering. cheers Demetres On 3/10/2013 3:40 μμ, Krithika GOkulnath wrote: I introduce myself as Dr.Krithika Gokulnath, CAS in crystallography and Biophysics, UNiversity of Madras. I have been working with a cloned protein and have been successfully able to crystallise it. However data collection done at home source shows a pattern of streaks instead of spots. The crystallization set up contained 12% PEG 8000, 10mM Magnesium chloride, 200mM Potassium chloride in 50 mM Tris pH 7.0. The protein is an enzyme which is also in the buffer containing the above components excepting the precipitant. It is a tetramer at native conditions and molecular weight on SDS-PAGE is 54 Kda. Kindly share your suggestions and speculations on what might be the reason for the streaking. The streaks are many wide spread and there are no high resolution spots or streaks as we might expect in salt crystals. -- --- Dr. Demetres D. Leonidas Associate Professor of Biochemistry Department of Biochemistry Biotechnology University of Thessaly 26 Ploutonos Str. 41221 Larissa, Greece - Tel. +302410 565278 Tel. +302410 565297 (Lab) Fax. +302410 565290 E-mail: ddleoni...@bio.uth.gr http://www.bio.uth.gr ---
Re: [ccp4bb] Off topic: Crystallization screening robot
Hi, to add my thoughts I believe that what your friend is looking for is the OryxNano from Douglas Instruments. We use it for screening, and it is a really trouble free machine. The consumables are not expensive (plates and sealing tape actually) and the price is rather low. I would think that for small crystallization groups (like ours) is the best robot you can buy if you have a small budget. I always thought that the posh mosquito is for big academic labs or companies that can really afford the rather large amount for consumables it requires. best wishes Demetres On 4/9/2013 4:57 ??, Artem Evdokimov wrote: Hi, The most rock-solid robotic screening platform in my experience has been the Mosquito. It has a supply spend of ~$2000/reel of tape which has ~27,000 tips on it so it's roughly 9-9 cents per tip - so per plate with thee proteins on it it's about 3 bucks depending on how you organize the set up. Not to say that other machines are bad, no - there are plenty of good instruments out there but in my opinion Mosquito has unbeatable combination of robust, repeatable set up, disposable tips and accuracy. In my career I've tried or owned about 90% of all devices out there (I guess that's the advantage of having several industrial positions in a row) and so I am fairly confident that this is not a biased comparison. Artem - Cosmic Cats approve of this message P.S. naturally I am not affiliated with TTP in any way. Caveat emptor. On Tue, Sep 3, 2013 at 10:42 AM, Jinyi Zhu jinyi.c...@gmail.com mailto:jinyi.c...@gmail.com wrote: Dear CCP4ers, Sorry for the off topic question. A friend of mine is considering purchasing a crystallization screening robot and would like to know which one would suit his need best. His lab would use the robot occasionally for screening and have a limited budget. He also wants minimum supply purchases for the robot. Could you kindly suggest some models? Thanks! Btw, I have personally used Douglas OryX, ARI crystal Pheonix, Mosquito and Hydra II-Edrop systems. Best, Jinyi -- --- Dr. Demetres D. Leonidas Associate Professor of Biochemistry Department of Biochemistry Biotechnology University of Thessaly 26 Ploutonos Str. 41221 Larissa, Greece - Tel. +302410 565278 Tel. +302410 565297 (Lab) Fax. +302410 565290 E-mail: ddleoni...@bio.uth.gr http://www.bio.uth.gr ---
Re: [ccp4bb] a challenge
Since the discussion for crystallographers is fired up. I want to put on record that I totally agree with Tassos about the profile of a crystallographer. If you take away the crystals, then a crystallographer is no long a crystallographer. Demetres On 13/1/2013 9:52 μμ, Anastassis Perrakis wrote: I think the real challenge (and one that makes for an excellent macromolecular crystallographer) is how well one can interpret a map with poor phases. Let me disagree ... An excellent macromolecular crystallographer, is one that given some crystals can derive the best strategy to collect data, process the data optimally, derive phases using all available information, build a model and refine it in such a way that it best explains both data and geometrical expectations, and do these as efficiently as possible. Efficiency may suggest using one automated suite or another - or indeed may best be achieved by manual labor - be it in the map or in data collection strategy or refinement or another step: and here I am ignoring the art of transforming hair-needle-crystalline-like-dingbits to a diffracting crystal. One that can interpret a map with poor phases can be either a genius in 3d orientation - or a not necessarily too intelligent nor experienced but determined student that can drink and breathe this map for a few weeks in a row until a solution is in place. Neither would make an excellent macromolecular crystallographer by necessity. Tassos -- --- Dr. Demetres D. Leonidas Associate Professor of Biochemistry Department of Biochemistry Biotechnology University of Thessaly 26 Ploutonos Str. 41221 Larissa, Greece - Tel. +302410 565278 Tel. +302410 565297 (Lab) Fax. +302410 565290 E-mail: ddleoni...@bio.uth.gr http://www.bio.uth.gr ---
[ccp4bb] Post-Doctoral position in Molecular Biology
Dear all, I am posting this on behalf of a colleague, so please do not reply to this msg. Instead send any mail to kmath...@bio.uth.gr many thanks Demetres Post-Doctoral position in Molecular Biology Department: Biochemistry and Biotechnology, University of Thessaly, Greece Closing date: December 12, 2012 Anticipated start date: January 1, 2013 A postdoctoral position is available at the Laboratory of Molecular Biology and Genomics in the Department of Biochemistry and Biotechnology of the University of Thessaly, Greece. The Department of Biochemistry and Biotechnology is located in the city of Larissa, in the center of Greece, 380 km north of Athens and 250 km south of Salonika. The DBB offers high level training for biochemists, molecular biologists and biotechnologists. The three main directions of Department’s research activities are: (i) Functional genomics, (ii) Bioactive molecules and (iii) Biodiversity. The main focus of the Laboratory of Molecular Biology and Genomics regards crucial questions of the biology, ecology and sex differentiation of the major olive pest, the olive fly, in an effort to develop novel, environmentally friendly methods to control this insect. The post-doctoral position concerns the analysis of the olfactory system of the olive fly. The entire transcriptome of the olfactory system will be sequenced and olfactory and gustatory genes will be identified. Subsequently, functional analysis of selected loci will be performed via RNAi-mediated transient inhibition in adult flies. Finally, efforts should be initiated for generation of transgenic lines in which selected loci are stably inhibited or impaired. The length of the appointment will be until August 31, 2015. Candidates are expected to have a PhD in molecular biology, biochemistry, biotechnology or related areas. Experience in insect rearing and insectary maintenance will be an asset. Good knowledge of English language is expected (CAE or equivalent certificate is an advantage). He/she is contributing to research and teaching activities performed by given workplace. Postdoc is responsible for self-educating and for sharing the obtained knowledge with other team members. The salary is 1800€/month. Required documents (to be sent to kmath...@bio.uth.gr) are: full CV including list of publications, motivation letter / research statement (no more than 2 pages), names of 2 experts in the field who can provide recommendation letters. Electronic applications are strongly preferred. This position is financed by the European Union and the Greek Ministry of Education (project OLFLY SMELL SEX / 2002). -- --- Dr. Demetres D. Leonidas Associate Professor of Biochemistry Department of Biochemistry Biotechnology University of Thessaly 26 Ploutonos Str. 41221 Larissa, Greece - Tel. +302410 565278 Tel. +302410 565297 (Lab) Fax. +302410 565290 E-mail: ddleoni...@bio.uth.gr http://www.bio.uth.gr ---
[ccp4bb] Unusually low B factors with phenix
Hello, I am experiencing a weird problem with B factor refinement (individual, isotropic) in phenix.refine (1.8.1.-1168) and a structure at 1.9 A resolution. The ADP values after the refinement are very very low, less than 2 and sometimes 0. I am getting the same result with and without optimization of the X-ray/ADP weight. Has anyone else noticed that and is there a workaround ? Demetres -- --- Dr. Demetres D. Leonidas Associate Professor of Biochemistry Department of Biochemistry Biotechnology University of Thessaly 26 Ploutonos Str. 41221 Larissa, Greece - Tel. +302410 565278 Tel. +302410 565297 (Lab) Fax. +302410 565290 E-mail: ddleoni...@bio.uth.gr http://www.bio.uth.gr ---
Re: [ccp4bb] Unusually low B factors with phenix
Dear Tim, this affects all atoms and yes I did reset the B-factors to 20.00 prior to refinement. I have not tried REFMAC but now I will give it a try since phenix does not seem to do the job. best Demetres On 2/11/2012 1:34 μμ, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Demetres, does this affect all atoms, or only a few selected ones? Did you compare with refmac5 (for e.g. input script errors), or did you reset the B-factors to a reasonable value (e.g. 20-30) prior to refinement? pdbset can do this conveniently. Best, Tim On 11/02/2012 11:06 AM, Demetres D. Leonidas wrote: Hello, I am experiencing a weird problem with B factor refinement (individual, isotropic) in phenix.refine (1.8.1.-1168) and a structure at 1.9 A resolution. The ADP values after the refinement are very very low, less than 2 and sometimes 0. I am getting the same result with and without optimization of the X-ray/ADP weight. Has anyone else noticed that and is there a workaround ? Demetres - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQk6+vUxlJ7aRr7hoRAvCZAKDxzmLYV74HKanTuoNiqLEu6AmlRwCgkVQs Q+SZVN6ISb0X38ZekG119/s= =xKhB -END PGP SIGNATURE- -- --- Dr. Demetres D. Leonidas Associate Professor of Biochemistry Department of Biochemistry Biotechnology University of Thessaly 26 Ploutonos Str. 41221 Larissa, Greece - Tel. +302410 565278 Tel. +302410 565297 (Lab) Fax. +302410 565290 E-mail: ddleoni...@bio.uth.gr http://www.bio.uth.gr ---
Re: [ccp4bb] Somewhat OT: question of professional courtesy
I think that people who do this are not really crystallographers (at least to me) since they do not give credit to the effort that produces a structure. That is why that I always insist on proper refereeing when I review a manuscript. Maybe it is time for this community to ask journals to put it on their requirement rules for publishing. Otherwise only the PDB takes credit (I think is like mentioning just the journal but not the authors when reference to a paper). Demetres On 25/7/2012 3:33 ??, Radisky, Evette S., Ph.D. wrote: Somewhat OT: question of professional courtesy Dear bb, This morning as I scanned an accepted manuscript from a well-respected-but-not-particularly-glamorous journalthat publishes manymacromolecularstructures, I came across a briefmention of homologyand rmsdwith a published structure listed by PDB accession number, but no citation of theprimary reference for this structure. (OK, so I wouldn't have noticed or cared had it not been one of mine.) The paper did not have a lot of references, so it was not due to limitation in the number of refs permitted. I havealwaysthoughtit a matter of professional courtesyto cite the appropriate reference when one uses and mentionsastructure from the PDB, but as I think back, I realize no oneexplicitly told me this--it is just an assumption that I made. Maybe I am the one with unrealistic expectations here? Is there ageneralconsensusamong crystallographerson thispractice? Thanks! Evette Evette S. Radisky, Ph.D. Assistant Professor Mayo Clinic Cancer Center Griffin Cancer Research Building, Rm 310 4500 San Pablo Road Jacksonville, FL 32224 (904) 953-6372 -- --- Dr. Demetres D. Leonidas Associate Professor of Biochemistry Department of Biochemistry Biotechnology University of Thessaly 26 Ploutonos Str. 41221 Larissa, Greece - Tel. +302410 565278 Tel. +302410 565297 (Lab) Fax. +302410 565290 E-mail: ddleoni...@bio.uth.gr http://www.bio.uth.gr ---
[ccp4bb] Postdoctoral Position in synthesis of glucopyranonucleosides
Dear all, please follow the link http://www.hecra.gr/vacancies/21_6.pdf for a posdoctoral position in Organic Synthesis at the Department of Biochemistry and Biotechnology, University of Thessaly. Demetres -- --- Dr. Demetres D. Leonidas Associate Professor of Biochemistry Department of Biochemistry Biotechnology University of Thessaly 26 Ploutonos Str. 41221 Larissa, Greece - Tel. +302410 565278 Tel. +302410 565297 (Lab) Fax. +302410 565290 E-mail: ddleoni...@bio.uth.gr http://www.bio.uth.gr ---
Re: [ccp4bb] Devices Suitable to Concentrate Protein Solutions in Liter Scale
Dear Xuan Yang, for such large volumes we use a Pellicon type system. The one we have in the lab is a polyethersulfone PTJK prep/Scale TFF 2.5 FT2 High flux 10 k from Millipore. good luck Demetres Xuan Yang wrote: Dear All, I am working on protein refolding via dialysis in large volumn (typically 2~4 litters). It was problematic when I wanted to concentrate the solution to at least less than 500ml. If you know any device appropriate for such task, please help me out:) Thanks in advance! Sincerely, Xuan Yang -- Demetres D. Leonidas, Ph.D. Senior Researcher Structural Biology Chemistry Group Institute of Organic and Pharmaceutical Chemistry The National Hellenic Research Foundation 48, Vassileos Constantinou Avenue Athens 116 35, Greece == Tel. +30 210 7273841 (office) +30 210 7273895 (lab) Fax. +30 210 7273831 E-mail: d...@eie.gr URL: http://athena.eie.gr ==
[ccp4bb] Marie Curie Fellowship
Please find attached an advert for a short Marie-Curie fellowship at the National Hellenic Research Foundation, Athens, Greece. We seek to recruit a biology/biochemistry graduate, with not more than 4 years of research experience at post-graduate or equivalent level, who will be trained by research in the Molecular Endocrinology Laboratory of the National Hellenic Research Foundation: http://www.eie.gr/nhrf/institutes/ibrb/programmes/molendocrinology-en.html in the context of the EURODESY project: http://www.eie.gr/nhrf/institutes/iopc/eu-projects/eurodesy/index-en.html Familiarity with cell culture and molecular cell biology and pharmacology methodologies will be considered an asset. The position will be available from March 2009. The duration of the fellowship will be 6 months. Eligibility criteria and reimbursement rates for Marie Curie Fellows are described in the handbook at: http://ec.europa.eu/research/fp6/mariecurie-actions/action/stage_en.html Applications should be e-mailed to Dr. MN Alexis (mnale...@eie.gr) till 1st of March 2009 and should include a full CV and the names and addresses of 1-2 referees. -- Demetres D. Leonidas, Ph.D. Senior Researcher Structural Biology Chemistry Group Institute of Organic and Pharmaceutical Chemistry The National Hellenic Research Foundation 48, Vassileos Constantinou Avenue Athens 116 35, Greece == Tel. +30 210 7273841 (office) +30 210 7273895 (lab) Fax. +30 210 7273831 E-mail: d...@eie.gr URL: http://athena.eie.gr ==
[ccp4bb] Nikos Oikonomakos
Dear all, it is with great sadness that we announce the passing of Nikos Oikonomakos yesterday. Nikos was a dear friend, a passionate researcher and an innovative teacher. We will all miss him . -- Dr. Demetres D. Leonidas Senior Researcher Structural Biology and Chemistry Group Institute of Organic Pharmaceutical Chemistry National Hellenic Research Foundation 48, Vassileos Constantinou Avenue Athens 116 35, Greece Tel. +30210-7273841 (Office) +30210-7273895 (Lab) Fax. +30210-7273831 E-mail: [EMAIL PROTECTED] URL: http://athena.eie.gr
[ccp4bb] ccp4mg doesn't start in windows error in startup script
Dear CCP4rs This morning we encountered a problem with ccp4mg in windows. It does not start and a window entitled error in startup script pops in with several lines referring to the code. Uninstalling and reinstallation of the program did not help. Has anyone else encountered this ? Demetres -- Demetres D. Leonidas, Ph.D. Structural Biology Chemistry Group Institute of Organic and Pharmaceutical Chemistry The National Hellenic Research Foundation 48, Vassileos Constantinou Avenue Athens 116 35, Greece == Tel. +30 210 7273841 (office) +30 210 7273895 (lab) Fax. +30 210 7273831 E-mail: [EMAIL PROTECTED] URL: http://athena.eie.gr ==
Re: [ccp4bb] crystallization incubators
Dear Alexandra, we are using the VELP FOC incubators (http://www.velp.com/en/product/5/Environment_line/101/Refrigerated_incubators/143/FOC_225I/) around 2000 Euros. Demetres Alexandra Deaconescu wrote: Hello everyone: I know this question has been posted before, but what models of crystal growth incubators do you recommend? I was thinking of a smaller benchtop incubator. I have found this from Torrey Pines Scientific, EchoTherm Chilling Incubator, Digital, Bench Top, Programmable, 115VAC, 50/60 Hz, 2 amp. 55 liter capacity. 4 racks provided. Positions for 6. UL, CSA and CE approved. *Price: $3380.00* I was wondering if anyone else knows of something better... Many thanks, Alex Alexandra M. Deaconescu Postdoctoral Fellow Grigorieff Laboratory Brandeis University Rosenstiel Center MS 029 415 South St. Waltham, MA 02454 USA For deliveries: Brandeis University Kalman Dock 415 South St. Waltham, MA 02454 USA -- Demetres D. Leonidas, Ph.D. Structural Biology Chemistry Group Institute of Organic and Pharmaceutical Chemistry The National Hellenic Research Foundation 48, Vassileos Constantinou Avenue Athens 116 35, Greece == Tel. +30 210 7273841 (office) +30 210 7273895 (lab) Fax. +30 210 7273831 E-mail: [EMAIL PROTECTED] URL: http://athena.eie.gr ==
Re: [ccp4bb] crystallisation robot
Oryxnano 50+50 nL Demetres David Briggs wrote: I'll defend the honour of the phoenix... (again) Bernhard Rupp 100+100 nl Dave Briggs (and all users at Univ of Manchester, UK) 100+100nl Others.. Only time we have ANY problems is when the nano dispensing tip gets clogged. Often a good wash whilst still on the machine will clear the blockage. Dave -- David C. Briggs PhD Father Crystallographer http://www.dbriggs.talktalk.net http://www.dbriggs.talktalk.net AIM ID: dbassophile -- Demetres D. Leonidas, Ph.D. Structural Biology Chemistry Group Institute of Organic and Pharmaceutical Chemistry The National Hellenic Research Foundation 48, Vassileos Constantinou Avenue Athens 116 35, Greece == Tel. +30 210 7273841 (office) +30 210 7273895 (lab) Fax. +30 210 7273831 E-mail: [EMAIL PROTECTED] URL: http://athena.eie.gr ==
[ccp4bb] Postdoc protein crystallographer in Greece
Dear all, the following is been sent on behalf of Prof. Tzartos and all inquiries should be send to him. Postdoc protein crystallographer in Greece A postdoctoral position for a protein crystallographer is immediately available at the Laboratory of Molecular Neurobiology and Immunology, Department of Biochemistry of the Hellenic Pasteur Institute, Athens, Greece (www.pasteur.gr). The major part of the activities of the lab involves the expression of extracellular domains (210-220 amino acids long) of several subunits of human nicotinic acetylcholine receptors in eukaryotic expression systems, construction of mutant forms, purification and, recently, crystallization and co-crystallization efforts. The lab has some past expertise in protein crystallography (2 Fab fragments) but the new post-doc will be now the main crystallographer of the group. The new post-doc should have extensive expertise in protein crystallization and considerable expertise in crystallographic analysis. Expertise in molecular biology approaches is useful but not necessary. S/he will collaborate closely with members of the lab (mostly with expertise in molecular biology biochemistry) who currently produce sufficient amounts of wt and mutant forms of the AChR domains in various expression systems, and with collaborating excellent crystallographers in neighbouring labs. The main task of the post-doc will be to obtain diffraction quality crystals of these domains and their subsequent structure determination (of fundamental importance for subsequent drug design). S/he may also be involved with new expressions. The lab is supported by several international grants (3 EC grants, 2 MDA, 1 AFM etc) and has (or has access to) all needed equipment. The post will be supported by an EC grant. Please send a preliminary request with a CV and a summary of research experience and interests to Prof. Socrates Tzartos, emails: [EMAIL PROTECTED] and [EMAIL PROTECTED] -- Demetres D. Leonidas, Ph.D. Structural Biology Chemistry Group Institute of Organic and Pharmaceutical Chemistry The National Hellenic Research Foundation 48, Vassileos Constantinou Avenue Athens 116 35, Greece == Tel. +30 210 7273841 (office) +30 210 7273895 (lab) Fax. +30 210 7273831 E-mail: [EMAIL PROTECTED] URL: http://athena.eie.gr ==
Re: [ccp4bb] Twinning in C2 ?
Dear Eleanor, many thanks for all your help and suggestions. We finally have solved the mutant structure. The trick was to use the pseudo translation (there was not any 2 fold axis in the self rotation) with MOLREP which found two molecules and then applied the pseudo translation to provide us with the other two molecules yielding a tetramer. I think that initially the programs and also ourselves missed the pseudo translation because it is very close to the crystallographic one (0.49 0 0.48). Many thanks to Peter Zwart who also advised us to follow the same procedure. Demetres Eleanor Dodson wrote: Oh dear - this is tricky! You could have a dimer in the asymmetric unit, or two monomers in the asymm unit which generate dimers using the crystallographic 2 folds. Things worth checking - What does the self rotation show? Is there a clear 2 fold axis which is different from the crystallographic one? If so you can use all of MOLREPs cleverness to use the self rotation definition and the pseudo translation. (Under search parameters you can give the self rotation list of solutions - just use self rotation with 1 or 2 solutions and edit out the top one which will be the crystallographic 2 fold) It will find the pseudo trans vector automatically. If the only 2 fold is the cryst one then you need to search for 2 molecules with the pseudo translation. Eleanor What is the solvent content of the native - the mutant has a smaller volume so less solvent - is that feasible? I think I would generate P1 data Demetres D. Leonidas wrote: Dear Eleanor, Yes the native is a dimer and we did the search using the dimer as a model but we had similar results (i.e. all programs find one molecule). The graphs from TRUNCATE show rather normal and I am attaching a gif file with the plot for the cumulative intensity. As for pseudo-translation running the Analyse Data for MR option in ccp4 in the patterson map we are getting a significant peak at fractional coordinates 0.4897 0.0 0.4767. How this can help ? Do we need to apply this pseudo translation to the solution we are getting from molrep ? many thanks Demetres P.S. I will summarize for the members of the list all the suggestions I will get at the end Eleanor Dodson wrote: You dont say whether the molecules in the native cell form a dimer - if so I would search with that (you may need to turn off the packing search) Or whether there is a pseudo translation vector in the mutant form.. Or what the data analysis graphs from TRUNCATE show - are they normal? Eleanor Demetres D. Leonidas wrote: Dear all, we have encountered a problem in solving one mutant structure. The mutant protein crystallizes in the same space group as the native (C2) but the unit cell dimensions are different. These for the native structure are 101.2 33.1 73.4 90 90.3 90 and for the mutant 160.4 32.3 107.0 90 125.7 90. As a result the mutant structure has four molecules in the asymmetric unit while the native had two. When we run molecular replacement all programs (CNS, molrep, and amore) find only two molecules. Phaser finds four but when we try to refine the Rfree does not drop below 0.44 if we use four molecules and 0.53 if we only use two no matter how well we built the molecule and regardless of any addition of water molecules (the resolution of the data is 2.1). The interesting thing is that in the electron density map we can clearly see density for a substrate analog that was included in the crystallization media. Do you thing that we have a case of twinning here ? We have to mention that Tod Yates served did not indicate any perfect merohedral twinning (partial merohedral twinning for this space group is not possible). We would appreciate any comments Many thanks Demetres -- Demetres D. Leonidas, Ph.D. Structural Biology Chemistry Group Institute of Organic and Pharmaceutical Chemistry The National Hellenic Research Foundation 48, Vassileos Constantinou Avenue Athens 116 35, Greece == Tel. +30 210 7273841 (office) +30 210 7273895 (lab) Fax. +30 210 7273831 E-mail: [EMAIL PROTECTED] URL: http://athena.eie.gr ==
Re: [ccp4bb] Twinning in C2 ?
Dear Eleanor, Yes the native is a dimer and we did the search using the dimer as a model but we had similar results (i.e. all programs find one molecule). The graphs from TRUNCATE show rather normal and I am attaching a gif file with the plot for the cumulative intensity. As for pseudo-translation running the Analyse Data for MR option in ccp4 in the patterson map we are getting a significant peak at fractional coordinates 0.4897 0.0 0.4767. How this can help ? Do we need to apply this pseudo translation to the solution we are getting from molrep ? many thanks Demetres P.S. I will summarize for the members of the list all the suggestions I will get at the end Eleanor Dodson wrote: You dont say whether the molecules in the native cell form a dimer - if so I would search with that (you may need to turn off the packing search) Or whether there is a pseudo translation vector in the mutant form.. Or what the data analysis graphs from TRUNCATE show - are they normal? Eleanor Demetres D. Leonidas wrote: Dear all, we have encountered a problem in solving one mutant structure. The mutant protein crystallizes in the same space group as the native (C2) but the unit cell dimensions are different. These for the native structure are 101.2 33.1 73.4 90 90.3 90 and for the mutant 160.4 32.3 107.0 90 125.7 90. As a result the mutant structure has four molecules in the asymmetric unit while the native had two. When we run molecular replacement all programs (CNS, molrep, and amore) find only two molecules. Phaser finds four but when we try to refine the Rfree does not drop below 0.44 if we use four molecules and 0.53 if we only use two no matter how well we built the molecule and regardless of any addition of water molecules (the resolution of the data is 2.1). The interesting thing is that in the electron density map we can clearly see density for a substrate analog that was included in the crystallization media. Do you thing that we have a case of twinning here ? We have to mention that Tod Yates served did not indicate any perfect merohedral twinning (partial merohedral twinning for this space group is not possible). We would appreciate any comments Many thanks Demetres -- Demetres D. Leonidas, Ph.D. Structural Biology Chemistry Group Institute of Organic and Pharmaceutical Chemistry The National Hellenic Research Foundation 48, Vassileos Constantinou Avenue Athens 116 35, Greece == Tel. +30 210 7273841 (office) +30 210 7273895 (lab) Fax. +30 210 7273831 E-mail: [EMAIL PROTECTED] URL: http://athena.eie.gr == inline: cumulative.gif
