Re: [ccp4bb] off topic - legacy hardware help needed
It seems like the problem is that the Indigo has an IP address that is not part of the subnet that it is on, so this makes network access impossible. Is this correct? If so, you can just spoof the proper subnet in isolation. You can run dd-wrt on a compatible router and assign any subnet you want (ensuring to disconnect it from the WAN, lest a disgruntled IT guy shows up at your office). Then, just access the SGI via IP as you normally would from another machine on the isolated subnet and edit the config files to change the IP address. This doesn't require tracking down any legacy hardware. James On Jan 23, 2013, at 5:07 PM, Dave Roberts wrote: Hi all, By the way, thanks for all the suggestions on the linux versions. I went against my better judgement and just stuck with Fedora, mainly because I'm familiar with it. I have to admit, I kind of like it. I was able to get it up and running, run nfs to mount local drives, and install all the necessary crystallography software with no hitch - quick. It's kind of nice. And it set up my wireless printer automatically - so all is great. Anyway, we have an old Indigo SGI that runs our NMR. It's a console only system, and we access it via the network from another old SGI (toaster model - blue). The console does not have a video card (nor space for one), so I can't plug in to it and see what's happening. Anyway, our network was recently updated, and in doing so it has made access to our console system unavailable. We can't get there because the IP's that used to be needed are no more. So, I can get the disk out, and I have a variety of unix/linux systems that I could plug it in to. But, alas, I have no motherboards or systems that take SCSI (that I have a sled for or a way to put it in). I need to be able to mount the drive on some sort of system, edit a few config files to fix the network, then plug it all back in. All without messing up boot tables and such (not a big deal, just thought I'd throw that out there). Is there a cable that simply allows me to plug in the back of a SCSI drive then connect to an IDE port on a newer motherboard (or better yet, an external USB port)? Just curious - that would be worth it to me. Any thoughts? Thanks Dave
[ccp4bb] Diamond App for MX
Dear All (apologies for using the bb mailing list for something so specific but we thought it was the best way to get the details to probably all our users) Diamond would like to announce V1.0 of SynchLink, an iPhone/iPad (iOS v6 onwards) app which allows users of Diamond MX beamlines to monitor/re-visit/search information on their data collections and automated data processing results recorded in ISPyB (you will need a fedid login). The app can also be used to check beamline and synchrotron ring status. We encourage you to try it and give feedback - if people find it useful we plan to develop it further and make it available on other platforms. The app is available from the App Store and is free. Please report problems/feedback/suggestions to scisoftj...@diamond.ac.uk The app was developed by Helen Ginn, a very talented Oxford Biochemistry undergraduate during a summer internship. Helen was supervised by Dave Stuart at Oxford and Martin Walsh/Alun Ashton at Diamond. There was also expert input from Ghita Kouadri Mostefaoui and Karl Levik at Diamond who developed the WebServices and integration to ISPyB. Yours Dave and Martin -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
[ccp4bb] refmac5 vs phenix refine mixed up
Dear All, I am working on a perfectly twinned data in space group P31. when I refine this data with phenix refine the R/Rfree is 26.6/29.4 and average B-factor is 38. I did one test now. I used phenix refined pdb and refine with refmac5 and got R/Rfree of 26.2/29.7 and average B-factor is 64. Now I used refmac5 refined pdb and refined with phenix again. Now R/Rfree is 22.1/24.8 and average B-factor is 56. My question is, why B-factor gone up now and R/Rfree reduced. In which refined model should I believe in. If last refined model is true then how should I reduce the B-factor? Thank you Rajesh -- ---x With regards Rajesh K. Harijan Phd Researcher Department of Biochemistry, University of Oulu, Oulu, Finland- 90014 Off Phone: +358 85531174 Mob: +358 400408258
Re: [ccp4bb] refmac5 vs phenix refine mixed up
Well I am not answering your question. What is the (Wilson) B-factor of the diffraction data ? I would personally compare the average isotropic temperature factor of the model to that of the diffraction data. And further the aim of refinement is not to reduce the B-factor. The aim of refinement is to provide a model that agrees with all data available. There are structures around with very high temperature factors (both for the diffraction data set and for the model). There is nothing wrong with that. Fred. On 24/01/13 11:12, rajesh harijan wrote: Dear All, I am working on a perfectly twinned data in space group P31. when I refine this data with phenix refine the R/Rfree is 26.6/29.4 and average B-factor is 38. I did one test now. I used phenix refined pdb and refine with refmac5 and got R/Rfree of 26.2/29.7 and average B-factor is 64. Now I used refmac5 refined pdb and refined with phenix again. Now R/Rfree is 22.1/24.8 and average B-factor is 56. My question is, why B-factor gone up now and R/Rfree reduced. In which refined model should I believe in. If last refined model is true then how should I reduce the B-factor? Thank you Rajesh -- ---x With regards Rajesh K. Harijan Phd Researcher Department of Biochemistry, University of Oulu, Oulu, Finland- 90014 Off Phone: +358 85531174 Mob: +358 400408258 -- Fred. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494
Re: [ccp4bb] refmac5 vs phenix refine mixed up
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Rajesh, first of all, a model is not true or false, it can only be better or worse. The explanation of what you observe depends on what you did: - - did you use the identical and very same mtz-file as input to all three scenarios? Some people take the output mtz and use it as input to the next refinement cycle, which is a very, very, bad thing to do. - - did you ensure always the same set of reflections was used for Rfree when switching between programs? If not, your R/Rfree are meaningless. It may also be that combining phenix and refmac5 indeed resulted in a better mode - both programs have some substantial differences in how they work. Best, Tim On 01/24/2013 11:12 AM, rajesh harijan wrote: Dear All, I am working on a perfectly twinned data in space group P31. when I refine this data with phenix refine the R/Rfree is 26.6/29.4 and average B-factor is 38. I did one test now. I used phenix refined pdb and refine with refmac5 and got R/Rfree of 26.2/29.7 and average B-factor is 64. Now I used refmac5 refined pdb and refined with phenix again. Now R/Rfree is 22.1/24.8 and average B-factor is 56. My question is, why B-factor gone up now and R/Rfree reduced. In which refined model should I believe in. If last refined model is true then how should I reduce the B-factor? Thank you Rajesh - -- - -- 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/ iD8DBQFRAQ56UxlJ7aRr7hoRAsJmAJ9RcS1Bp7g53LwiTm1ZMAVAICHXAACfdWgD FlLHo/1euT/BIeSW7EhrvHo= =w9IY -END PGP SIGNATURE-
Re: [ccp4bb] refmac5 vs phenix refine mixed up
Yes, the wilson B-factor is comparable which is 53.6. And also same MTZ was used for refmac5 and phenix refine, which is processed one (original one). And also the reflections used in the refinement was: Phenix (46793 reflections) and refmac5 (44431 reflections). I do not know whether I answered you correctly. Thank you Rajesh On Thu, Jan 24, 2013 at 12:12 PM, rajesh harijan rsu.iitku...@gmail.comwrote: Dear All, I am working on a perfectly twinned data in space group P31. when I refine this data with phenix refine the R/Rfree is 26.6/29.4 and average B-factor is 38. I did one test now. I used phenix refined pdb and refine with refmac5 and got R/Rfree of 26.2/29.7 and average B-factor is 64. Now I used refmac5 refined pdb and refined with phenix again. Now R/Rfree is 22.1/24.8 and average B-factor is 56. My question is, why B-factor gone up now and R/Rfree reduced. In which refined model should I believe in. If last refined model is true then how should I reduce the B-factor? Thank you Rajesh -- ---x With regards Rajesh K. Harijan Phd Researcher Department of Biochemistry, University of Oulu, Oulu, Finland- 90014 Off Phone: +358 85531174 Mob: +358 400408258 -- ---x With regards Rajesh K. Harijan Phd Researcher Prof. Rik. K. Wierenga's Group, Department of Biochemistry, University of Oulu, Oulu, Finland- 90014 Off Phone: +358 85531174 Mob: +358 417064469 http://www.biocenter.oulu.fi/projects/wierenga.html
Re: [ccp4bb] refmac5 vs phenix refine mixed up
Dear Tim Gruene, 2013/1/24 Tim Gruene t...@shelx.uni-ac.gwdg.de -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Rajesh, first of all, a model is not true or false, it can only be better or worse. The explanation of what you observe depends on what you did: - - did you use the identical and very same mtz-file as input to all three scenarios? Some people take the output mtz and use it as input to the next refinement cycle, which is a very, very, bad thing to do. Is the F/SIGF columns of the output mtz of refmac5 still the same as the F/SIGF columns of the input mtz? If they are the same, why cann't I use the F/SIGF columns of the output mtz as input to the next refinement? Thanks for your reply. - - did you ensure always the same set of reflections was used for Rfree when switching between programs? If not, your R/Rfree are meaningless. It may also be that combining phenix and refmac5 indeed resulted in a better mode - both programs have some substantial differences in how they work. Best, Tim On 01/24/2013 11:12 AM, rajesh harijan wrote: Dear All, I am working on a perfectly twinned data in space group P31. when I refine this data with phenix refine the R/Rfree is 26.6/29.4 and average B-factor is 38. I did one test now. I used phenix refined pdb and refine with refmac5 and got R/Rfree of 26.2/29.7 and average B-factor is 64. Now I used refmac5 refined pdb and refined with phenix again. Now R/Rfree is 22.1/24.8 and average B-factor is 56. My question is, why B-factor gone up now and R/Rfree reduced. In which refined model should I believe in. If last refined model is true then how should I reduce the B-factor? Thank you Rajesh - -- - -- 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/ iD8DBQFRAQ56UxlJ7aRr7hoRAsJmAJ9RcS1Bp7g53LwiTm1ZMAVAICHXAACfdWgD FlLHo/1euT/BIeSW7EhrvHo= =w9IY -END PGP SIGNATURE-
Re: [ccp4bb] refmac5 vs phenix refine mixed up
Dear Rajesh, In addition to the R/Rfree, you also need to look at issues like stereochemistry, bad contacts, clashes, the general fit into density, unmodelled ligands/waters, Ramachandran outliers, correct side chain rotamers etc etc. I would advice you to spend (a lot of) time visually inspecting your model and the density, and also make use of servers like MolProbity or WhatIF to examine the quality of your model. Fred is very right that the idea of refinement is to produce a model that agrees with all the data, and not just one with lower R values. cheers Ganesh Le 24/01/13 11:12, rajesh harijan a écrit : Dear All, I am working on a perfectly twinned data in space group P31. when I refine this data with phenix refine the R/Rfree is 26.6/29.4 and average B-factor is 38. I did one test now. I used phenix refined pdb and refine with refmac5 and got R/Rfree of 26.2/29.7 and average B-factor is 64. Now I used refmac5 refined pdb and refined with phenix again. Now R/Rfree is 22.1/24.8 and average B-factor is 56. My question is, why B-factor gone up now and R/Rfree reduced. In which refined model should I believe in. If last refined model is true then how should I reduce the B-factor? Thank you Rajesh -- ---x With regards Rajesh K. Harijan Phd Researcher Department of Biochemistry, University of Oulu, Oulu, Finland- 90014 Off Phone: +358 85531174 Mob: +358 400408258
Re: [ccp4bb] refmac5 vs phenix refine mixed up
if they are the same, there is in principle no problem. (you can quickly check using mtzdump) but, just to make sure, I always use the exact same scaled and truncated mtz-file for all refinements of any particular structure. Then there is no doubt at all...and it is in fact easer, i.e. one less file-name to edit in the GUI or script you use. Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 24 Jan 2013, at 12:03, Qixu Cai wrote: Dear Tim Gruene, 2013/1/24 Tim Gruene t...@shelx.uni-ac.gwdg.de -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Rajesh, first of all, a model is not true or false, it can only be better or worse. The explanation of what you observe depends on what you did: - - did you use the identical and very same mtz-file as input to all three scenarios? Some people take the output mtz and use it as input to the next refinement cycle, which is a very, very, bad thing to do. Is the F/SIGF columns of the output mtz of refmac5 still the same as the F/SIGF columns of the input mtz? If they are the same, why cann't I use the F/SIGF columns of the output mtz as input to the next refinement? Thanks for your reply. - - did you ensure always the same set of reflections was used for Rfree when switching between programs? If not, your R/Rfree are meaningless. It may also be that combining phenix and refmac5 indeed resulted in a better mode - both programs have some substantial differences in how they work. Best, Tim On 01/24/2013 11:12 AM, rajesh harijan wrote: Dear All, I am working on a perfectly twinned data in space group P31. when I refine this data with phenix refine the R/Rfree is 26.6/29.4 and average B-factor is 38. I did one test now. I used phenix refined pdb and refine with refmac5 and got R/Rfree of 26.2/29.7 and average B-factor is 64. Now I used refmac5 refined pdb and refined with phenix again. Now R/Rfree is 22.1/24.8 and average B-factor is 56. My question is, why B-factor gone up now and R/Rfree reduced. In which refined model should I believe in. If last refined model is true then how should I reduce the B-factor? Thank you Rajesh - -- - -- 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/ iD8DBQFRAQ56UxlJ7aRr7hoRAsJmAJ9RcS1Bp7g53LwiTm1ZMAVAICHXAACfdWgD FlLHo/1euT/BIeSW7EhrvHo= =w9IY -END PGP SIGNATURE-
Re: [ccp4bb] refmac5 vs phenix refine mixed up
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear, of course you could ask Garib whether or not the output data were modified by refmac5 - often they are, at least linearly scaled (which would certainly do no harm), and unless you have read the refmac5 code or Garib assures you I would not rely on it. Further trouble is that by using the output mtz-file, which contains more data columns like the sigma-weighted coefficients for map calculations, the e.g. GUI might accidentally pick the wrong one overlooked by the user, especially if the user is less experienced. To always use the same input mtz-file you avoid such possibilities and it also points a novice user to what refinement is actually doing. Best, Tim On 01/24/2013 12:03 PM, Qixu Cai wrote: Dear Tim Gruene, 2013/1/24 Tim Gruene t...@shelx.uni-ac.gwdg.de Dear Rajesh, first of all, a model is not true or false, it can only be better or worse. The explanation of what you observe depends on what you did: - did you use the identical and very same mtz-file as input to all three scenarios? Some people take the output mtz and use it as input to the next refinement cycle, which is a very, very, bad thing to do. Is the F/SIGF columns of the output mtz of refmac5 still the same as the F/SIGF columns of the input mtz? If they are the same, why cann't I use the F/SIGF columns of the output mtz as input to the next refinement? Thanks for your reply. - did you ensure always the same set of reflections was used for Rfree when switching between programs? If not, your R/Rfree are meaningless. It may also be that combining phenix and refmac5 indeed resulted in a better mode - both programs have some substantial differences in how they work. Best, Tim On 01/24/2013 11:12 AM, rajesh harijan wrote: Dear All, I am working on a perfectly twinned data in space group P31. when I refine this data with phenix refine the R/Rfree is 26.6/29.4 and average B-factor is 38. I did one test now. I used phenix refined pdb and refine with refmac5 and got R/Rfree of 26.2/29.7 and average B-factor is 64. Now I used refmac5 refined pdb and refined with phenix again. Now R/Rfree is 22.1/24.8 and average B-factor is 56. My question is, why B-factor gone up now and R/Rfree reduced. In which refined model should I believe in. If last refined model is true then how should I reduce the B-factor? Thank you Rajesh - -- - -- 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/ iD8DBQFRARtHUxlJ7aRr7hoRAnvXAKCqUV5IHvKJShQHrN8/cCGmC4DDrACgw9gL 6MGqgIDK4DJ2vcHtuzdWPBc= =Pl4P -END PGP SIGNATURE-
Re: [ccp4bb] refmac5 vs phenix refine mixed up
PS just checked an example, and the the refmac input and output F and SIGF are in fact NOT the same and have been subjected to something more than linear scaling. This was using refmac version 5.5.0109, admittedly not the newest one. So using the refmac output mtz as input for the next run is wrong as Tim states, although it is probable that in practice the resulting differences may not be noticeable. Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 24 Jan 2013, at 12:03, Qixu Cai wrote: Dear Tim Gruene, 2013/1/24 Tim Gruene t...@shelx.uni-ac.gwdg.de -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Rajesh, first of all, a model is not true or false, it can only be better or worse. The explanation of what you observe depends on what you did: - - did you use the identical and very same mtz-file as input to all three scenarios? Some people take the output mtz and use it as input to the next refinement cycle, which is a very, very, bad thing to do. Is the F/SIGF columns of the output mtz of refmac5 still the same as the F/SIGF columns of the input mtz? If they are the same, why cann't I use the F/SIGF columns of the output mtz as input to the next refinement? Thanks for your reply. - - did you ensure always the same set of reflections was used for Rfree when switching between programs? If not, your R/Rfree are meaningless. It may also be that combining phenix and refmac5 indeed resulted in a better mode - both programs have some substantial differences in how they work. Best, Tim On 01/24/2013 11:12 AM, rajesh harijan wrote: Dear All, I am working on a perfectly twinned data in space group P31. when I refine this data with phenix refine the R/Rfree is 26.6/29.4 and average B-factor is 38. I did one test now. I used phenix refined pdb and refine with refmac5 and got R/Rfree of 26.2/29.7 and average B-factor is 64. Now I used refmac5 refined pdb and refined with phenix again. Now R/Rfree is 22.1/24.8 and average B-factor is 56. My question is, why B-factor gone up now and R/Rfree reduced. In which refined model should I believe in. If last refined model is true then how should I reduce the B-factor? Thank you Rajesh - -- - -- 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/ iD8DBQFRAQ56UxlJ7aRr7hoRAsJmAJ9RcS1Bp7g53LwiTm1ZMAVAICHXAACfdWgD FlLHo/1euT/BIeSW7EhrvHo= =w9IY -END PGP SIGNATURE-
Re: [ccp4bb] refmac5 vs phenix refine mixed up
Dear all As it was already stated it is essential to use the same input file (after scaling and trancating) for all refinement sessions. Output mtz file in the absence of twinning has been scaled to account for anisotropic overall B values. It is modification of the data. In the twinning case output contains detwinned data. It is serious modification of the data and should not be used as input file for next refinement session. Output file in general is representation of the model and useful for model building but not for further refinement cycles. Regards Garib On 24 Jan 2013, at 11:30, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear, of course you could ask Garib whether or not the output data were modified by refmac5 - often they are, at least linearly scaled (which would certainly do no harm), and unless you have read the refmac5 code or Garib assures you I would not rely on it. Further trouble is that by using the output mtz-file, which contains more data columns like the sigma-weighted coefficients for map calculations, the e.g. GUI might accidentally pick the wrong one overlooked by the user, especially if the user is less experienced. To always use the same input mtz-file you avoid such possibilities and it also points a novice user to what refinement is actually doing. Best, Tim On 01/24/2013 12:03 PM, Qixu Cai wrote: Dear Tim Gruene, 2013/1/24 Tim Gruene t...@shelx.uni-ac.gwdg.de Dear Rajesh, first of all, a model is not true or false, it can only be better or worse. The explanation of what you observe depends on what you did: - did you use the identical and very same mtz-file as input to all three scenarios? Some people take the output mtz and use it as input to the next refinement cycle, which is a very, very, bad thing to do. Is the F/SIGF columns of the output mtz of refmac5 still the same as the F/SIGF columns of the input mtz? If they are the same, why cann't I use the F/SIGF columns of the output mtz as input to the next refinement? Thanks for your reply. - did you ensure always the same set of reflections was used for Rfree when switching between programs? If not, your R/Rfree are meaningless. It may also be that combining phenix and refmac5 indeed resulted in a better mode - both programs have some substantial differences in how they work. Best, Tim On 01/24/2013 11:12 AM, rajesh harijan wrote: Dear All, I am working on a perfectly twinned data in space group P31. when I refine this data with phenix refine the R/Rfree is 26.6/29.4 and average B-factor is 38. I did one test now. I used phenix refined pdb and refine with refmac5 and got R/Rfree of 26.2/29.7 and average B-factor is 64. Now I used refmac5 refined pdb and refined with phenix again. Now R/Rfree is 22.1/24.8 and average B-factor is 56. My question is, why B-factor gone up now and R/Rfree reduced. In which refined model should I believe in. If last refined model is true then how should I reduce the B-factor? Thank you Rajesh - -- - -- 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/ iD8DBQFRARtHUxlJ7aRr7hoRAnvXAKCqUV5IHvKJShQHrN8/cCGmC4DDrACgw9gL 6MGqgIDK4DJ2vcHtuzdWPBc= =Pl4P -END PGP SIGNATURE- Dr Garib N Murshudov Group Leader, MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
Re: [ccp4bb] off topic - legacy hardware help needed
On 01/24/2013 03:19 AM, James Stroud wrote: It seems like the problem is that the Indigo has an IP address that is not part of the subnet that it is on, so this makes network access impossible. Is this correct? If so, you can just spoof the proper subnet in isolation. You can run dd-wrt on a compatible router and assign any subnet you want (ensuring to disconnect it from the WAN, lest a disgruntled IT guy shows up at your office). Then, just access the SGI via IP as you normally would from another machine on the isolated subnet and edit the config files to change the IP address. This doesn't require tracking down any legacy hardware. Yes, something like that. I don't think you even need to involve a router, just find a computer with an extra ethernet port, configure it with an address compatible with that on the old SGI, and plug both into a switch. SSH or telnet across and configure a new address on the SGI, then reboot and replug. On Jan 23, 2013, at 5:07 PM, Dave Roberts wrote: Hi all, By the way, thanks for all the suggestions on the linux versions. I went against my better judgement and just stuck with Fedora, mainly because I'm familiar with it. I have to admit, I kind of like it. I was able to get it up and running, run nfs to mount local drives, and install all the necessary crystallography software with no hitch - quick. It's kind of nice. And it set up my wireless printer automatically - so all is great. Anyway, we have an old Indigo SGI that runs our NMR. It's a console only system, and we access it via the network from another old SGI (toaster model - blue). The console does not have a video card (nor space for one), so I can't plug in to it and see what's happening. Anyway, our network was recently updated, and in doing so it has made access to our console system unavailable. We can't get there because the IP's that used to be needed are no more. So, I can get the disk out, and I have a variety of unix/linux systems that I could plug it in to. But, alas, I have no motherboards or systems that take SCSI (that I have a sled for or a way to put it in). I need to be able to mount the drive on some sort of system, edit a few config files to fix the network, then plug it all back in. All without messing up boot tables and such (not a big deal, just thought I'd throw that out there). Is there a cable that simply allows me to plug in the back of a SCSI drive then connect to an IDE port on a newer motherboard (or better yet, an external USB port)? Just curious - that would be worth it to me. Any thoughts? Thanks Dave -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
[ccp4bb] STOE for macromolecular xtallography
Hi All, does anyone in macromolecular crystallography have any experience with STOE apparatus and in particular with their STADI VARI goniometer and PILATUS 100K detetor? Thank you Kyriacos This message was sent using IMBB - WebMail.
[ccp4bb] 3D Monitors
Hello everyone, I know there already has been discussion about 3D monitors on the Coot/CCP4bb. However since there are a few more out there now and I am currently thinking about buying one, I thought to get a few opinions from crystallographers would be nice! Especially if there are people happily model building with the cheaper LG 3D monitors? :-) So I am looking at the moment at: - Zalman ZM-M215W 21,5in - Zalman ZM-M240W 24in - Samsung SyncMaster S27A750D 27in - LG D2342P 23in / LG D2542P 25in Thanks a lot! Sabine
Re: [ccp4bb] 3D Monitors
Hi Sabine, We are absolutely happy with our LG D2342P. The major advantages include the simplicity in setting up and the light weight of the glasses. For more information, please read this thread: http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg27816.html Zhijie -- From: Sabine Schneider sabine.schnei...@cup.uni-muenchen.de Sent: Thursday, January 24, 2013 11:13 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] 3D Monitors Hello everyone, I know there already has been discussion about 3D monitors on the Coot/CCP4bb. However since there are a few more out there now and I am currently thinking about buying one, I thought to get a few opinions from crystallographers would be nice! Especially if there are people happily model building with the cheaper LG 3D monitors? :-) So I am looking at the moment at: - Zalman ZM-M215W 21,5in - Zalman ZM-M240W 24in - Samsung SyncMaster S27A750D 27in - LG D2342P 23in / LG D2542P 25in Thanks a lot! Sabine
Re: [ccp4bb] refmac5 vs phenix refine mixed up
Most likely scenario is that Phenix by default assigns Rfree flag as 1, while ccp4/refmac - as 0. That would explain your Rfree going down - because your Rfree reflections were refined by refmac. It would be nice if default setting was the same in different suites. Best wishes.
Re: [ccp4bb] refmac5 vs phenix refine mixed up
On Thu, Jan 24, 2013 at 10:34 AM, Leonid Sazanov saza...@mrc-mbu.cam.ac.uk wrote: Most likely scenario is that Phenix by default assigns Rfree flag as 1, while ccp4/refmac - as 0. That would explain your Rfree going down - because your Rfree reflections were refined by refmac. According to Garib, the current version of Refmac will automatically switch to the proper flags, so this problem should go away. -Nat
Re: [ccp4bb] refmac5 vs phenix refine mixed up
Hi, It would be nice if default setting was the same in different suites. it's a nice idea of course, but I feel it is impractical as it would require changing a lot of software, both modern and legacy. However, given array of flags it is algorithmically trivial to figure out what is test and work flags. That's what phenix.refine have been doing since its beginning (2005). And my understanding is that Refmac does this too. As always, there are corner cases here, but it's better than nothing. Plus, programs (at least phenix.refine, can't speak for others) tell which flag was actually used, and they provide option to define the flag value to use. Pavel
Re: [ccp4bb] refmac5 vs phenix refine mixed up
Yes, Nat is right. Starting with the latest version 5.7 (that is part of ccp4) refmac makes sure that it uses correct set for free reflections. Hopefully it will remove some of the confusions when switching from one software to another. refmac 5.8 version should definitely have this feature. This version with some bug fixes and feature additions can be found from this page; http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ This version should be available from the next ccp4 update. Garib On 24 Jan 2013, at 18:36, Nat Echols wrote: On Thu, Jan 24, 2013 at 10:34 AM, Leonid Sazanov saza...@mrc-mbu.cam.ac.uk wrote: Most likely scenario is that Phenix by default assigns Rfree flag as 1, while ccp4/refmac - as 0. That would explain your Rfree going down - because your Rfree reflections were refined by refmac. According to Garib, the current version of Refmac will automatically switch to the proper flags, so this problem should go away. -Nat Dr Garib N Murshudov Group Leader, MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
[ccp4bb] render.exe in COOT
What is render.exe in COOT? Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com
Re: [ccp4bb] render.exe in COOT
On 24/01/13 22:16, Rex Palmer wrote: What is render.exe in COOT? I suspect you are referring to the the Raster3D program (which coot uses to generate a ray-traced image).
[ccp4bb] B-factors
Hi all, I have been refining twinned data (at 3.1 A resolution) using refmac. My R and Rfree values are 19.6 and 26.2 respectively with NCS restraints and isotropic B-factor refinement.. I am not sure weather it is a good idea to refine individual B-factors at this resolution. I have also tried refining the same model in phenix but this time not refining the Bfactors. My Rfactor and Rfree are 25 and 32 respectively. Refining with TLS in Phenix drops R factors to 23 and 29. Then I used the output PDB from phenix and refined it in CCP4 (selecting overall B-factor refinement option instead of Isotropic) and my R factors are R work=16 and Rfree =21. If Rfree reflections are refined my refmac upon switching from phenix to refmac then does this contaminate the Rfree set ? Should swiching between refinement programs Phenix and Refmac be avoided? Urmi Dhagat
Re: [ccp4bb] B-factors
On Thu, Jan 24, 2013 at 3:52 PM, Urmi Dhagat udha...@svi.edu.au wrote: If Rfree reflections are refined my refmac upon switching from phenix to refmac then does this contaminate the Rfree set ? Should swiching between refinement programs Phenix and Refmac be avoided? Repeating what was said earlier today: if you use the newest version of Refmac, either in CCP4 6.3 or downloaded from Garib's homepage, you will not have any problem switching back and forth with Phenix (any version). -Nat
Re: [ccp4bb] B-factors
On Thursday, January 24, 2013 03:52:12 pm Urmi Dhagat wrote: Hi all, I have been refining twinned data (at 3.1 A resolution) using refmac. My R and Rfree values are 19.6 and 26.2 respectively with NCS restraints and isotropic B-factor refinement.. I am not sure weather it is a good idea to refine individual B-factors at this resolution. I have also tried refining the same model in phenix but this time not refining the Bfactors. My Rfactor and Rfree are 25 and 32 respectively. Refining with TLS in Phenix drops R factors to 23 and 29. I would suspect it is possible to do better than that. My thoughts on how to approach it were written up for a past CCP4 Study Weekend and appeared in Acta D last year: To B or not to B Acta D 68:468 (2012). You can find a link to the PDF on the TLSMD web site http://skuld.bmsc.washington.edu/~tlsmd/references.html Ethan Then I used the output PDB from phenix and refined it in CCP4 (selecting overall B-factor refinement option instead of Isotropic) and my R factors are R work=16 and Rfree =21. If Rfree reflections are refined my refmac upon switching from phenix to refmac then does this contaminate the Rfree set ? Should swiching between refinement programs Phenix and Refmac be avoided? Urmi Dhagat -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] off topic - legacy hardware help needed
Note that you'll need a crossover rather than a straight through serial cable and probably a DB25 to DS9 adaptor, but once you get your hands on the cable this is a straightforward solution. kmj On Wed, Jan 23, 2013 at 5:49 PM, Johan Hattne jhat...@lbl.gov wrote: On 23 Jan 2013, at 16:07, Dave Roberts drobe...@depauw.edu wrote: Anyway, we have an old Indigo SGI that runs our NMR. It's a console only system, and we access it via the network from another old SGI (toaster model - blue). The console does not have a video card (nor space for one), so I can't plug in to it and see what's happening. Anyway, our network was recently updated, and in doing so it has made access to our console system unavailable. We can't get there because the IP's that used to be needed are no more. I'm not familiar with the Indigo, but I presume it has a serial port over which you could log in to the machine. Connect the Indigo to an accessible machine with a serial cable (you can even get serial/USB adapters that sort-of work, too) and run something like minicom or screen. // Cheers; Johan Postdoctoral Fellow @ Physical Biosciences Division ___ Lawrence Berkeley National Laboratory * 1 Cyclotron Rd. Mail Stop 64R0121 * Berkeley, CA 94720-8118 * +1 (510) 495-8055
Re: [ccp4bb] B-factors
Dear Urmi, The way you switched from Phenix to Refmac may not have resulted in the flat B-factor model in Ethan's paper. You should really do a thorough test in which you reset the B-factors before you start refinement. Shameless plug: PDB_REDO will do this automatically and has a few fallback options for cases in which the Hamilton test is inconclusive. Your R-factors a quite low for your resolution which suggests that you may have been a bit too conservative when picking your resolution cut-off. If you have more data you can try using that as well. This may also help your choice of B-factor model. It will improve your data/parameter ratio. HTH, Robbie Netherlands Cancer Institute www.cmbi.ru.nl/pdb_redo Sent from my Windows Phone From: Ethan Merritt Sent: 2013-01-25 01:36 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] B-factors On Thursday, January 24, 2013 03:52:12 pm Urmi Dhagat wrote: Hi all, I have been refining twinned data (at 3.1 A resolution) using refmac. My R and Rfree values are 19.6 and 26.2 respectively with NCS restraints and isotropic B-factor refinement.. I am not sure weather it is a good idea to refine individual B-factors at this resolution. I have also tried refining the same model in phenix but this time not refining the Bfactors. My Rfactor and Rfree are 25 and 32 respectively. Refining with TLS in Phenix drops R factors to 23 and 29. I would suspect it is possible to do better than that. My thoughts on how to approach it were written up for a past CCP4 Study Weekend and appeared in Acta D last year: To B or not to B Acta D 68:468 (2012). You can find a link to the PDF on the TLSMD web site http://skuld.bmsc.washington.edu/~tlsmd/references.html Ethan Then I used the output PDB from phenix and refined it in CCP4 (selecting overall B-factor refinement option instead of Isotropic) and my R factors are R work=16 and Rfree =21. If Rfree reflections are refined my refmac upon switching from phenix to refmac then does this contaminate the Rfree set ? Should swiching between refinement programs Phenix and Refmac be avoided? Urmi Dhagat -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
