Re: [ccp4bb] density mod., NSC and software..
DM is kind of past tense (unless you are dealing with multicrystal averaging) -- I'd use parrot or shelxe instead (both pretty fast and automated). NCS operators as input do not seem to be in fashion these days, so you might have to put up with heavy atoms or partial MR models... I would not necessarily expect NCS related bits of the density to be fully identical. JED. From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tommi Kajander Sent: 20 December 2011 16:19 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] density mod., NSC and software.. Dear all, Stupid question: if i do density modification (flattening and extension say from 6 to 4Å) w/o averaging on a symmetrical, say dimer, would you expect the thing stays symmetric nevertheless? (in particular if there is a strong peak in the NCS??) (seems to me it doenst necessarily...) favorite programs for NCS averiging?? DM obviously, and solomon doesnt do it. Others that do it (with out a PDB or atoms to derive it from, but rather operators) Thanks, Tommi Tommi Kajander, Ph.D., Docent Structural Biology and Biophysics Institute of Biotechnology University of Helsinki Viikinkaari 1 (P.O. Box 65) 00014 Helsinki Finland p. +358-9-19158903 tommi.kajan...@helsinki.fi -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies.
Re: [ccp4bb] Refmac with TLS terminates early when occupancy changed
Hi Krisztian, I have seen refmac fall over in a similar situation (low-ish res, partially floppy model) during TLS refinement. You could try to rescue it by - using fixed TLS parameters from a previous (successful) refinement - setting initial B-values to a fixed value - including the peptide in one of the larger TLS groups (whichever chain/domain it happens to be bound to) JED. -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Krisztian Fodor Sent: 20 December 2011 13:57 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Refmac with TLS terminates early when occupancy changed Hello Guys, I am trying to refine a 3.2 A complex structure with Refmac using TLS. It seems that I need to decrease the occupancy for a 38 amino acid peptide in the structure. However, after changing the occupancy to 0.50, Refmac terminates after 4 rounds of TLS refinement. The only error message I can see is this towards the end of the log file: Problem xyz 6480 -1.4325285 -0.92473793 etc. And then it says that it is writing out coordinate files etc. which is obviously not happening, because the run was terminated too early. Is this a bug? Any suggestions? Thanks a lot, Krisztian -- Krisztian Fodor, PhD EMBL Hamburg c/o DESY Notkestrasse 85 22603 Hamburg, Germany Email: fo...@embl-hamburg.de Phone: +49 40 89902221 Fax: +49 40 89902149
[ccp4bb] MERGING THREE DATASETS
Hi all, I have three datasets with same space-group and identical cell dimensions which I want to merge together. I remember that this was discussed in the blog some time back. Nevertheless, I can use some help! Thanks in advance, ARKO -- *ARKA CHAKRABORTY* *CAS in Crystallography and Biophysics* *University of Madras* *Chennai,India*
Re: [ccp4bb] MERGING THREE DATASETS
Do you still have the unmerged files? In that case just feed them to pointless and redo scala/etc.. If you only 3 merged data sets, you will have to use combat to convert the mtz files into an fake unmerged format then put them through pointless/scala to get relative scales and merge them.. Eleanor On 12/21/2011 11:15 AM, arka chakraborty wrote: Hi all, I have three datasets with same space-group and identical cell dimensions which I want to merge together. I remember that this was discussed in the blog some time back. Nevertheless, I can use some help! Thanks in advance, ARKO
Re: [ccp4bb] MERGING THREE DATASETS
There are several ways to skin a cat. If you have processed your data with XDS, XSCALE can also do the job (you have to think of the unit cell parameters of the merged data set though - the default may not necessarily what you wish to have), and I am certain other data frame processing suites will have this offered as an option somewhere... (I personally like all the statistics provided by the combat / scala route though). Fred. Eleanor Dodson wrote: Do you still have the unmerged files? In that case just feed them to pointless and redo scala/etc.. If you only 3 merged data sets, you will have to use combat to convert the mtz files into an fake unmerged format then put them through pointless/scala to get relative scales and merge them.. Eleanor On 12/21/2011 11:15 AM, arka chakraborty wrote: Hi all, I have three datasets with same space-group and identical cell dimensions which I want to merge together. I remember that this was discussed in the blog some time back. Nevertheless, I can use some help! Thanks in advance, ARKO
Re: [ccp4bb] MERGING THREE DATASETS
Hi I'd have to say that I *really* like using Phil Evan's new program Aimless rather than Scala - not sure if it's in CCP4 yet but it is available from his own ftp site for a number of platforms - ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre (I think). In my hands it's faster and more reliable most of the time. So my route from unmerged files would be pointless then aimless... On 21 Dec 2011, at 11:29, Vellieux Frederic wrote: There are several ways to skin a cat. If you have processed your data with XDS, XSCALE can also do the job (you have to think of the unit cell parameters of the merged data set though - the default may not necessarily what you wish to have), and I am certain other data frame processing suites will have this offered as an option somewhere... (I personally like all the statistics provided by the combat / scala route though). Fred. Eleanor Dodson wrote: Do you still have the unmerged files? In that case just feed them to pointless and redo scala/etc.. If you only 3 merged data sets, you will have to use combat to convert the mtz files into an fake unmerged format then put them through pointless/scala to get relative scales and merge them.. Eleanor On 12/21/2011 11:15 AM, arka chakraborty wrote: Hi all, I have three datasets with same space-group and identical cell dimensions which I want to merge together. I remember that this was discussed in the blog some time back. Nevertheless, I can use some help! Thanks in advance, ARKO Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] density mod., NSC and software..
Thanks judit, well one problem here would be that if you cant feed in operators, that you got say from the map correlations with something like GETAX, and you only have two sites (one per monomer) thats not enough to define a two-fold... same goes of course if you dont have a model (because you would need to get the averaging to work first... ) Tommi Kajander, Ph.D., Docent Structural Biology and Biophysics Institute of Biotechnology University of Helsinki Viikinkaari 1 (P.O. Box 65) 00014 Helsinki Finland p. +358-9-19158903 tommi.kajan...@helsinki.fi On Dec 21, 2011, at 12:56 PM, Debreczeni, Judit wrote: DM is kind of past tense (unless you are dealing with multicrystal averaging) -- I'd use parrot or shelxe instead (both pretty fast and automated). NCS operators as input do not seem to be in fashion these days, so you might have to put up with heavy atoms or partial MR models… I would not necessarily expect NCS related bits of the density to be fully identical. JED. AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking compliance with our Code of Conduct and policies. From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tommi Kajander Sent: 20 December 2011 16:19 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] density mod., NSC and software.. Dear all, Stupid question: if i do density modification (flattening and extension say from 6 to 4Å) w/o averaging on a symmetrical, say dimer, would you expect the thing stays symmetric nevertheless? (in particular if there is a strong peak in the NCS??) (seems to me it doenst necessarily...) favorite programs for NCS averiging?? DM obviously, and solomon doesnt do it. Others that do it (with out a PDB or atoms to derive it from, but rather operators) Thanks, Tommi Tommi Kajander, Ph.D., Docent Structural Biology and Biophysics Institute of Biotechnology University of Helsinki Viikinkaari 1 (P.O. Box 65) 00014 Helsinki Finland p. +358-9-19158903 tommi.kajan...@helsinki.fi
Re: [ccp4bb] bias removal server
Thanks for the clarification. Thanksrajesh From: hofkristall...@gmail.com To: ccp4...@hotmail.com; CCP4BB@JISCMAIL.AC.UK Subject: RE: [ccp4bb] bias removal server Date: Tue, 20 Dec 2011 22:41:10 -0800 I am not sure this service is maintained anymore, but given that with automated model building pretty much the same can be achieved nowadays (pus benefit of a model), the ARP/wARP server in Hamburg is a well-working and up-to-date alternative. BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajesh kumar Sent: Tuesday, December 20, 2011 10:19 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] bias removal server Dear All, Any of you know if the Bias removal server at http://tuna.tamu.edu/ works?My friend says that 'may be the server doesn't exist' as he never heard back from them about login info. ThanksRajesh
[ccp4bb] How to patch CCP4 cif2mtz so it can handle PDB entries with Map Coefficients
Some recently released PDB entries (for instance 3u57) have structure factor files that contain map coefficients. We think this is a really good idea because it means that final maps as interpreted by the crystallographer will then be archived and available. But there is a problem converting such files to mtz with the current cif2mtz program; indeed we raised this on the bb in September: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=CCP4BB;6be4044e.1109 To get around this we produced a quick-fix patch for cif2mtz that is available at: http://www.globalphasing.com/buster/wiki/index.cgi?CCP4cif2mtzPatchToHandleMapCoefficients Regards, Oliver | Dr Oliver Smart | | Global Phasing Ltd., Cambridge UK | | http://www.globalphasing.com/people/osmart/ |
[ccp4bb] Making fixes to cif2mtz easier
The patch in https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=CCP4BB;325e1870.1112 solves the problem with 3u57. A few days ago I read the interesting paper http://journals.iucr.org/d/issues/2011/01/00/dz5216/dz5216bdy.html referring to a crystal structure containing a diselenide bond; I downloaded the model and structure factors for 2xsk, and cif2mtz refused to convert them. This turns out to be because the Bijvoet pairs measured in the header were described as _refln.pdbx_F_meas_plus _refln.pdbx_F_meas_plus_sigma _refln.pdbx_F_meas_minus _refln.pdbx_F_meas_minus_sigma while both the ccp4-6.2.0/lib/data/cif_mm.dic and the http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx_v40.dic dictionaries require these to be _refln.pdbx_F_plus _refln.pdbx_F_plus_sigma _refln.pdbx_F_minus _refln.pdbx_F_minus_sigma It was trivial to fix the problem with a text editor (and this is a case where the right answer is to get wwpdb to fix the sf.cif file at their end), but this led to some discussion at Global Phasing as to what could be done to make cif2mtz handle sf.cif files with unusual data items without requiring modifying and recompiling the source code each time. A summary of where we got to is at http://www.globalphasing.com/buster/wiki/index.cgi?CCP4cif2mtzImproveIdeas I would appreciate any comments on how to proceed in this direction. Tom
Re: [ccp4bb] How to patch CCP4 cif2mtz so it can handle PDB entries with Map Coefficients
Thanks for this. I have recently updated the CCP4-supplied dictionary to include standard mmCIF, exchange dictionary, plus extra CCP4 items. This will be in the next release. I was about to update cif2mtz to recognise these extra columns. Will look at what you have done, may save me a job. cif2mtz is based on the ccif library, which complains if you try to load a cif file which contains a non-dictionary item. I'm sure in the past I tried to find a way round this, and failed. From the user point of view, the mmcif file is ascii and you can hand-edit the column item names. This is the get-out method if cif2mtz fails. Edit the item name to something that is recognised. Cheers Martyn -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk* * Fax: +44 1925 603634Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * *** -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Oliver Smart Sent: 21 December 2011 14:40 To: ccp4bb Subject: [ccp4bb] How to patch CCP4 cif2mtz so it can handle PDB entries with Map Coefficients Some recently released PDB entries (for instance 3u57) have structure factor files that contain map coefficients. We think this is a really good idea because it means that final maps as interpreted by the crystallographer will then be archived and available. But there is a problem converting such files to mtz with the current cif2mtz program; indeed we raised this on the bb in September: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=CCP4BB;6be4044e.1109 To get around this we produced a quick-fix patch for cif2mtz that is available at: http://www.globalphasing.com/buster/wiki/index.cgi?CCP4cif2mtzPatchToHa ndleMapCoefficients Regards, Oliver | Dr Oliver Smart | | Global Phasing Ltd., Cambridge UK | | http://www.globalphasing.com/people/osmart/ |
Re: [ccp4bb] MERGING THREE DATASETS
Hi, The solution provided by Mr. Dodson worked out well! Also it was nice to learn about the other options available. Thanks a lot! ARKO On Wed, Dec 21, 2011 at 5:13 PM, harry powell ha...@mrc-lmb.cam.ac.ukwrote: Hi I'd have to say that I *really* like using Phil Evan's new program Aimless rather than Scala - not sure if it's in CCP4 yet but it is available from his own ftp site for a number of platforms - ftp://ftp.mrc-lmb.cam.ac.uk/**pub/preftp://ftp.mrc-lmb.cam.ac.uk/pub/pre (I think). In my hands it's faster and more reliable most of the time. So my route from unmerged files would be pointless then aimless... On 21 Dec 2011, at 11:29, Vellieux Frederic wrote: There are several ways to skin a cat. If you have processed your data with XDS, XSCALE can also do the job (you have to think of the unit cell parameters of the merged data set though - the default may not necessarily what you wish to have), and I am certain other data frame processing suites will have this offered as an option somewhere... (I personally like all the statistics provided by the combat / scala route though). Fred. Eleanor Dodson wrote: Do you still have the unmerged files? In that case just feed them to pointless and redo scala/etc.. If you only 3 merged data sets, you will have to use combat to convert the mtz files into an fake unmerged format then put them through pointless/scala to get relative scales and merge them.. Eleanor On 12/21/2011 11:15 AM, arka chakraborty wrote: Hi all, I have three datasets with same space-group and identical cell dimensions which I want to merge together. I remember that this was discussed in the blog some time back. Nevertheless, I can use some help! Thanks in advance, ARKO Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH -- *ARKA CHAKRABORTY* *CAS in Crystallography and Biophysics* *University of Madras* *Chennai,India*
Re: [ccp4bb] MERGING THREE DATASETS
Hi, would like to apologize for addressing Dr. Dodson incorrrectly...it was purely unintentional... regards. ARKO On Wed, Dec 21, 2011 at 5:13 PM, harry powell ha...@mrc-lmb.cam.ac.ukwrote: Hi I'd have to say that I *really* like using Phil Evan's new program Aimless rather than Scala - not sure if it's in CCP4 yet but it is available from his own ftp site for a number of platforms - ftp://ftp.mrc-lmb.cam.ac.uk/**pub/preftp://ftp.mrc-lmb.cam.ac.uk/pub/pre (I think). In my hands it's faster and more reliable most of the time. So my route from unmerged files would be pointless then aimless... On 21 Dec 2011, at 11:29, Vellieux Frederic wrote: There are several ways to skin a cat. If you have processed your data with XDS, XSCALE can also do the job (you have to think of the unit cell parameters of the merged data set though - the default may not necessarily what you wish to have), and I am certain other data frame processing suites will have this offered as an option somewhere... (I personally like all the statistics provided by the combat / scala route though). Fred. Eleanor Dodson wrote: Do you still have the unmerged files? In that case just feed them to pointless and redo scala/etc.. If you only 3 merged data sets, you will have to use combat to convert the mtz files into an fake unmerged format then put them through pointless/scala to get relative scales and merge them.. Eleanor On 12/21/2011 11:15 AM, arka chakraborty wrote: Hi all, I have three datasets with same space-group and identical cell dimensions which I want to merge together. I remember that this was discussed in the blog some time back. Nevertheless, I can use some help! Thanks in advance, ARKO Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH -- *ARKA CHAKRABORTY* *CAS in Crystallography and Biophysics* *University of Madras* *Chennai,India* -- *ARKA CHAKRABORTY* *CAS in Crystallography and Biophysics* *University of Madras* *Chennai,India*
[ccp4bb] linux upgrade preferences for CCP4
hello, I'm considering upgrading my linux software from CENTOS5 to perhaps Fedora or UBUNTO. Does anyone have an opinion about the best linux version to upgrade to for not only CCP4 but also for general robustness and for the best standard apps..Thanks Paul Dr. Paul Kraft Structural Biologist cell 586-596-2770 email: haresea...@yahoo.com email: kraft_proteome_resea...@yahoo.com This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so.
Re: [ccp4bb] linux upgrade preferences for CCP4
On Wed, Dec 21, 2011 at 2:29 PM, Paul Kraft haresea...@yahoo.com wrote: hello, I'm considering upgrading my linux software from CENTOS5 to perhaps Fedora or UBUNTO. Does anyone have an opinion about the best linux version to centos 6
Re: [ccp4bb] linux upgrade preferences for CCP4
Opinions? You want opinions? On this mailing list? This one ought to keep us going until the new year. As for Fedora v. Ubuntu, my opinion is that Fedora is better for a centrally managed system, whereas Ubuntu is perhaps more convenient for a single owner-operator. Fedora uses the RPM system for software distribution. and it's easy to install a lot of pre-packaged libraries and applications, including Coot and Pymol. If you do stereo, installation of the nVidia proprietary drivers is easy enough using the RPMFusion repository. The akmod-nvidia module rebuilds the driver automatically for a kernel upgrade. But as for robustness? Ha ha ha ha ha ha ha. I can't use that word in the same sentence as Fedora. It is Red Hat's bleeding edge product, where they introduce all the latest, greatest bugs. Fedora 15 and 16 do not have a graphical application for managing system services, because they just switched to systemctl and do not have all the details worked out yet. A current issue in the Linux community is desktops. Fedora switched from Gnome 2 to Gnome 3 in their previous release (15). G3 has a whole bushel of bugs and some nonintuitive features. Ubuntu switched from Gnome to their own Unity desktop, which has sent some users fleeing to the Mint distribution. I am just now contemplating a switch in the opposite direction, from Fedora to Scientific Linux 6. Like CENTOS, SL is a repackaging based on the Red Hat Enterprise source code, and is FREE. It has backing from some of the big physics labs, including CERN and Fermilab. The price of stability is that you don't get all the latest stuff. In SL6.1, the current version of Firefox is 3.6.24, and the image rendering is SLOW. I am wondering if I want to go back that far in time. Also, SL does not have their own bugzilla. If you encounter a bug, they tell you to take it to RedHat. You can imagine the finger-pointing circles that is going to lead to. On 12/21/2011 03:29 PM, Paul Kraft wrote: hello, I'm considering upgrading my linux software from CENTOS5 to perhaps Fedora or UBUNTO. Does anyone have an opinion about the best linux version to upgrade to for not only CCP4 but also for general robustness and for the best standard apps..Thanks Paul Dr. Paul Kraft Structural Biologist cell 586-596-2770 email: haresea...@yahoo.com email: kraft_proteome_resea...@yahoo.com This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] linux upgrade preferences for CCP4
On Wednesday, 21 December 2011, Paul Kraft wrote: hello, I'm considering upgrading my linux software from CENTOS5 to perhaps Fedora or UBUNTO. Does anyone have an opinion about the best linux version to upgrade to for not only CCP4 but also for general robustness and for the best standard apps..Thanks Well, since you ask... My preference is for Mandriva, followed by Suse. IMHO neither Fedora nor RHEL (of which CENTOS is a clone) are as suitable right out of the box for use either at home or in the lab. We (lab scientists) are just not in their target audience, so their packaging and configuration defaults are not the best for our use. Oh, and I much prefer a KDE desktop, which is only an afterthought at best in the distros you mention. Ethan
Re: [ccp4bb] linux upgrade preferences for CCP4
Paul, Wait a while, and then CENTOS 6 (or not wait a while). In my opinion neither of your choices are as stable as CENTOS. The big drawback is that CENTOS does not have the latest gadgets - but gadgets and stability are mutually exclusive, by definition. I have lately been annoyed because I obtained a program that needs C-libraries that are not available in CENTOS5, so I can appreciate your thinking, but I am not planning on moving away from CENTOS. It is completely maintenance-free nothing ever crashes and all standard programs work on it. Uh-oh, I think I just heard a breaking-sound in the computer room. :-) Mark -Original Message- From: Paul Kraft haresea...@yahoo.com To: CCP4BB CCP4BB@JISCMAIL.AC.UK Sent: Wed, Dec 21, 2011 1:29 pm Subject: [ccp4bb] linux upgrade preferences for CCP4 hello, I'm considering upgrading my linux software from CENTOS5 to perhaps Fedora or UBUNTO. Does anyone have an opinion about the best linux version to upgrade to for not only CCP4 but also for general robustness and for the best standard apps..Thanks Paul Dr. Paul Kraft Structural Biologist cell 586-596-2770 email: haresea...@yahoo.com email: kraft_proteome_resea...@yahoo.com This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so.
Re: [ccp4bb] linux upgrade preferences for CCP4
The price of stability is that you don't get all the latest stuff. In SL6.1, the current version of Firefox is 3.6.24, and the image rendering is SLOW. I am wondering if I want to go back that far in time. Not out of the box, but the latest ffx works in centos6. I think there are third party repos for ffx, but I just download and maintain that separately (e.g. in /opt or /usr/local ), which basically amounts to clicking update in the about box of ffx. Also, SL does not have their own bugzilla. If you encounter a bug, they tell you to take it to RedHat. You can imagine the finger-pointing circles that is going to lead to. Centos 6 does but it's really not that big of a help either and neither is RHAT's bugzilla unless it's something that effects the majority of servers that RHAT gets paid to support (e.g. some bug in NFS, the filesystem, or kernel)
[ccp4bb] OT: LN2 autofill
Hi Fellows, I am looking for some advice re LN2 autofill. I want to automatically refill an open special-use foam Dewar on the crystal harvesting robot from an unpressurized secondary storage Dewar. We found this system http://www.norhof.com/fillingexample.html and it seems to do what we need and also seems reasonably priced (little more than 5k) plus shipping from Europe. I wonder if someone has experience with US available alternatives or finds some gotcha I missed... Maybe off-board if considered mission creep... Best regards, BR - Scientists are there to find the laws of nature. Engineers are there to work around them. -
[ccp4bb] Post-doctoral position in Pfizer (Groton, CT, USA)
Dear all, A post-doctoral position is available in the Structural Biology and Biophysics group at Pfizer's research labs in Groton, Connecticut (USA). To apply, please go to www.pfizer.com/careers and search for job ID 959727. Job Focus The successful candidate for this position will join Groton Structural Biology and Biophysics (SBB), a multi-disciplinary group with well-established expertise in molecular biology, protein biochemistry, biological mass spectrometry, NMR, biophysics, crystallography computational sciences. Our mission is to provide integrated molecular insights into drug target mechanism and target-ligand interactions to impact discovery efforts across important therapeutic areas, such as Immunology Autoimmune Diseases, Inflammation Remodeling, Neuroscience, Cardiovascular, Metabolic Endocrine Diseases and Oncology. As a Postdoctoral Scientist - Protein Crystallography, you will be able to use your creativity, energy and expertise to contribute to cutting edge science and drug discovery through structural studies of a few novel multi-domain proteins from our rich portfolio of exciting therapeutic targets. You will drive the progression of these projects through protein expression, purification, characterization, crystallization and structural analysis in collaboration with other scientists in our multidisciplinary teams. You will have the opportunity to explore a wide range of biophysical techniques to solve your scientific problems, and learn from scientific experts in these areas. You will also have the opportunity to develop a broad understanding of other disciplines involved in drug discovery. You will be highly encouraged publish in peer reviewed journals and present your results at international conferences. Responsibilities - Design and execute experiments in construct design, protein expression, purification, characterization, crystallization, structural solution using de novo methods. - Analysis of relevant data and literature to extract novel structural insights and experimental design ideas - Collaborative efforts with academic labs will be considered as well Qualifications - Doctoral degree in Biochemistry, Molecular Biology, Chemistry or related field - Established track record applying innovative methods to drive project success throughout the gene-to-structure process Prior Experience: - 0-2 years of postdoctoral experience - Knowledge of crystallography theories and applications - Breadth of knowledge in related fields - Strong oral and written presentation skills - Proven ability to design and conduct experiments from protein expression to structure solution, leading to publication in reputable journals - Familiar with protein characterization, biophysical, computational techniques and has a passion for solving tough scientific problems using broad and creative thinking and experiments - Strong interpersonal and communication skills
Re: [ccp4bb] linux upgrade preferences for CCP4
On Wed, 2011-12-21 at 15:40 -0500, Sabuj Pattanayek wrote: On Wed, Dec 21, 2011 at 2:29 PM, Paul Kraft haresea...@yahoo.com wrote: hello, I'm considering upgrading my linux software from CENTOS5 to perhaps Fedora or UBUNTO. Does anyone have an opinion about the best linux version to centos 6 FWIW, I use RHEL 5 = CentOS 5 and recently upgraded to 6. Everything I use (not crystallographic software) works fine except vmware workstation currently does not work on it, so if you use vmware (I use it to run Windows inside Linux) you have to wait a while. Best to all from an old lurker, George Reeke
Re: [ccp4bb] linux upgrade preferences for CCP4
FWIW, I use RHEL 5 = CentOS 5 and recently upgraded to 6. Everything I use (not crystallographic software) works fine except vmware workstation currently does not work on it, Tried upgrading to vmware workstation v8? Compat guide : http://www.vmware.com/resources/compatibility/search.php?deviceCategory=softwaretestConfig=17 says that v8 works with RHEL6/CENTOS6 as the host OS. VirtualBox is a decent alternative if you don't want to pay.
Re: [ccp4bb] linux upgrade preferences for CCP4
Fedora releases are supported for about a year from initial release. Red Hat Enterprise, Centos and Scientific Linux are all supported for about 5 years. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] [off topic] Control of crystals' direction and position in the drop.
I tried the bookend drop method. It didn't work for me but hopefully it will benefit other people. There is only one thing I need to add to the detailed protocol from Martyn. I had trouble not cutting through the plastic slides. Even I could do it, it was impossible to peel a layer up. So in the end, it became much easier for me by just cutting a cross in the middle of the coverslip, raising up one corner of the cross, and sealing it with a clear tape. Hopefully it can help. Nian On Tue, Nov 15, 2011 at 3:32 PM, MARTYN SYMMONS martainn_oshioma...@btinternet.com wrote: Attached is a picture of making the bookend setup - step b. shows the razor levering up the flap from the plastic coverslip - be careful not to cut right through (I have done that and the drop dries extra quick in such a case) also be careful to apply the protein/well droplet as shown with to the shiny side of the lifted flap. (Apologies for the attachment). hope your crystals go well. Martyn -- *From:* Nian Huang huangn...@gmail.com *To:* CCP4BB@JISCMAIL.AC.UK *Sent:* Tuesday, 15 November 2011, 17:44 *Subject:* Re: [ccp4bb] [off topic] Control of crystals' direction and position in the drop. Thank you guys. I basically tried almost everything that I can find in the hampton catalogue and in this bulletin, seeding, hanging, sitting, sandwitch drops (which made things worse), temperature, gel, oil batch, and additive screens. Manipulating the crystal with fiber increases the chance to make it grow twin. The book end coverslip sounds a fantasic idea. It might be just going to work. Best, Nian
Re: [ccp4bb] linux upgrade preferences for CCP4
On 12/22/2011 06:56 AM, David Schuller wrote: Fedora releases are supported for about a year from initial release. Red Hat Enterprise, Centos and Scientific Linux are all supported for about 5 years. Ubuntu has long term support distributions as well: Starting with Ubuntu 12.04 LTS [...] versions will receive 5 years support Previous versions were 3 years for desktop and 5 years for server. cf. https://wiki.ubuntu.com/LTS Regards, F.
[ccp4bb] bug in Coot when saving coordinates
I am adding solvent molecules into unmodelled blobs of density in Coot. When I am finished, I merge molecules, then save my coordinates. For some reason Coot is saving two copies of each molecule that I have modelled and assigns them different chain ID's. I notice this when I open it in PyMol and when I open the coot pdb file using a text editor. Is there a reason why Coot does this?, or a way that I can save my work in the same state that I prepared it in?
