[ccp4bb] Coot chain ID
Dear All, I fitted a ligand into a structure along with SO4 and waters (COOT). Then I did the Merge Molecules and did the refinement. In output PDB file the chain ID sequence is showing B, A, C( ligand, protein and SO4 respectively) and the ATOM numbering is starting from ligand (Chain B instead of Chain A). How can I make the sequence A, B and C (Protein, ligand and SO4). Best wishes Dipankar This e-mail and any files transmitted with it are for the sole use of the intended recipient(s) and may contain confidential and privileged information.If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.Any unauthorized review, use, disclosure, dissemination, forwarding,printing or copying of this email or any action taken in reliance on this e-mail is strictly prohibited and may be unlawful. Visit us at http://www.aurigene.com
Re: [ccp4bb] Coot chain ID
Dipankar, A little bit of cut-and-paste in a good text editor will sort that out fairly easily. Tony. Sent from my iPhone On 14 Apr 2012, at 07:54, Dipankar Manna dipanka...@aurigene.commailto:dipanka...@aurigene.com wrote: Dear All, I fitted a ligand into a structure along with SO4 and waters (COOT). Then I did the “Merge Molecules” and did the refinement. In output PDB file the chain ID sequence is showing B, A, C( ligand, protein and SO4 respectively) and the ATOM numbering is starting from ligand (Chain B instead of Chain A). How can I make the sequence A, B and C (Protein, ligand and SO4). Best wishes Dipankar This e-mail and any files transmitted with it are for the sole use of the intended recipient(s) and may contain confidential and privileged information.If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.Any unauthorized review, use, disclosure, dissemination, forwarding,printing or copying of this email or any action taken in reliance on this e-mail is strictly prohibited and may be unlawful. Visit us at http://www.aurigene.com
Re: [ccp4bb] Coot chain ID
In Coot you can use Extensions - Modelling - Reorder Chains Bernahrd -- Bernhard Lechtenberg PhD student Huntington lab University of Cambridge Department of Haematology Cambridge Institute for Medical Research Wellcome Trust/MRC Building, Hills Road Cambridge, CB2 0XY United Kingdom -Original Message- From: Dipankar Manna dipanka...@aurigene.com Reply-to: Dipankar Manna dipanka...@aurigene.com To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Coot chain ID Date: Sat, 14 Apr 2012 06:55:10 + Dear All, I fitted a ligand into a structure along with SO4 and waters (COOT). Then I did the “Merge Molecules” and did the refinement. In output PDB file the chain ID sequence is showing B, A, C( ligand, protein and SO4 respectively) and the ATOM numbering is starting from ligand (Chain B instead of Chain A). How can I make the sequence A, B and C (Protein, ligand and SO4). Best wishes Dipankar This e-mail and any files transmitted with it are for the sole use of the intended recipient(s) and may contain confidential and privileged information.If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.Any unauthorized review, use, disclosure, dissemination, forwarding,printing or copying of this email or any action taken in reliance on this e-mail is strictly prohibited and may be unlawful. Visit us at http://www.aurigene.com
Re: [ccp4bb] Coot chain ID
Edit, or use coot to reorder chains If you read that edited pdb into pdbset pdbset xyzin edited.pdb xyzout edited-and-renumbered.pdb end I think the renumbering happens automatically.. Eleanor On 14 April 2012 09:46, Bernhard Lechtenberg bc...@cam.ac.uk wrote: In Coot you can use Extensions - Modelling - Reorder Chains Bernahrd -- Bernhard Lechtenberg PhD student Huntington lab University of Cambridge Department of Haematology Cambridge Institute for Medical Research Wellcome Trust/MRC Building, Hills Road Cambridge, CB2 0XY United Kingdom -Original Message- From: Dipankar Manna dipanka...@aurigene.com Reply-to: Dipankar Manna dipanka...@aurigene.com To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Coot chain ID Date: Sat, 14 Apr 2012 06:55:10 + Dear All, I fitted a ligand into a structure along with SO4 and waters (COOT). Then I did the “Merge Molecules” and did the refinement. In output PDB file the chain ID sequence is showing B, A, C( ligand, protein and SO4 respectively) and the ATOM numbering is starting from ligand (Chain B instead of Chain A). How can I make the sequence A, B and C (Protein, ligand and SO4). Best wishes Dipankar This e-mail and any files transmitted with it are for the sole use of the intended recipient(s) and may contain confidential and privileged information.If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.Any unauthorized review, use, disclosure, dissemination, forwarding,printing or copying of this email or any action taken in reliance on this e-mail is strictly prohibited and may be unlawful. Visit us at http://www.aurigene.com
Re: [ccp4bb] Good way to check ion sites on Coot
And Marjorie Hardings results are nicely tabulated on a web site.. Google for it Eleanor On 13 April 2012 22:08, Marc Kvansakul m.kvansa...@latrobe.edu.au wrote: Hi Andre, Majorie Harding wrote a few nice papers on metal ion binding sites and their associated coordination geometry, examples are: Harding MM (2006) Acta D vol. 62 pp. 678-82 or Harding MM (2004) Acta D vol. 60 pp. 849-59 Best Marc Dr. Marc Kvansakul Laboratory Head, NHMRC CDA Fellow Dept. of Biochemistry| La Trobe University | Bundoora Rm 218, Phys Sci Bld 4, Kingsbury Drive, Melbourne, 3086, Australia T: 03 9479 2263 | F: 03 9479 2467 | E: m.kvansa...@latrobe.edu.au | From: Zhijie Li zhijie...@utoronto.ca Reply-To: Zhijie Li zhijie...@utoronto.ca Date: Fri, 13 Apr 2012 16:37:43 -0400 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Good way to check ion sites on Coot Hi This is what I do: ValidateHighly coordinated waters *From:* Andre Godoy andre_go...@yahoo.com.br *Sent:* Friday, April 13, 2012 3:57 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] Good way to check ion sites on Coot Dear all. can someone tell me what is the best way to check for ion binding sites on my structure? I mean, a text with coordination examples, or maybe a tool on coot for it ... best wishes Andre
Re: [ccp4bb] Disorder or poor phases?
Nothing profound to add to this interesting discussion, but I too would like to plug FobsA - FobsB type maps - when A and B are similar but not quite the same.. It is prudent to omit the interesting parts of model A (or B) - whichever you use to calculate the PHIC and FOM - but the peaks and pits often clear up ambiguity brilliantly. You need to CAD the two data sets together, and make sure both Fobs are on the same scale.. Eleanor On 13 April 2012 19:50, Gloria Borgstahl gborgst...@gmail.com wrote: a recent experience in our lab with molecular replacement (wt and disordered point mutant; same space group and unit cell) was solved with a combination of two methods. 1. We made omit maps in the disordered region at several lower resolutions. The region became interpretable after suffereing through these maps, building residue by residue and refinement. 2. Then we had the bright idea to make Fwt-Fmutant maps to confirm our interpretation. Happily this map did confirm the unexpected large structural changed caused by a point mutant. On Fri, Apr 13, 2012 at 1:31 PM, James Holton jmhol...@lbl.gov wrote: Francis, I think in the cases you describe the region in question is disordered. Time and time again I have users coming to my beamline wanting to clean up a questionable region by getting experimental phases. Ahh! If only I had a nickle for each one. Oh wait, I suppose I kind of do? I take that back! Go MAD everyone! Much as I hate to discourage people from using my favorite technique, Tim is right: phases are not region-specific in electron density maps. Dale does make a good point that there is such a thing as model bias and one can argue that experimental phases don't have it. But, this is only true if you have not yet applied solvent flattening. How long has it been since you looked at a raw experimentally-phased map (before solvent flattening)? I'm willing to bet a while. With very few exceptions, raw experimental phases are lousy. We have actually become quite dependent on density modification to clean them up. In fact, solvent flattening is the only reason why SAD works at all. However, you CAN use anomalous differences to clear up disordered regions in a different way. Something I started calling SeMet scanning a number of years ago. A few of my users have done this, and a good example of it is Figure 3 of Huang et al. 2004 (doi:10.1038/nsmb826). Basically, you mutate residues in the disordered region one at a time to SeMet, and look at phased anomalous difference Fourier (PADF) maps. These maps are surprisingly clear, even when the anomalous difference signal is so weak as to make experimental phasing hopeless. Yes, the best phases to use for PADF maps are model phases, but, as always, it is prudent to refine the model after omitting the thing you are looking for before calculating such phases. Another way to get residue-specific labeling for low-resolution chain tracing is radiation damage. If you expose for the right amount of time, Asp and Glu side chains will be specifically burnt off, but not Asn and Gln. You will also see Met loosing its head, etc. So, as long as you have read Burmeister (2000), an Fo-Fo map of damaged vs undamaged can be used to guide sequence assignment, even at 4.5 A and worse. Anyway, when it comes to the question of is it disordered or is it model bias?, I think it is usually the former. It is very difficult to make model bias suppress a region that is actually well-ordered. Try it! After all, this is the whole reason why we bother looking at fo-fc maps. Then again, it is always possible to have a model so bad that the phase error is enough to squash anything. An excellent example of this can be found in the Book of Fourier. Taking amplitudes from the image of a cat, you can see what happens when you use the phases of a duck: http://www.ysbl.york.ac.uk/~cowtan/fourier/picduckcatfft.gif as opposed to what happens if you use the phases of a manx: http://www.ysbl.york.ac.uk/~cowtan/fourier/piccatmanx2.gif A manx is a species of cat that doesn't have a tail, so no animals were harmed in obtaining these phases. My point here is that the cat's tail can be seen quite readily in the 2fo-fc map if most of the structure is already right, but if your model is completely unrelated to the true structure (fitting a duck into a cat-shaped hole), then everything is in the noise. Real structures are usually somewhere between these two extremes, and I think an important shortcoming in modern crystallography is that we don't have a good quantitative description of this middle-ground. We all like to think we know what model bias is, but we don't exactly have units for it. Should we be using a scale of 0 to 1? Or perhaps duck to cat? Yes, I know we have figure of merit, but FOM is not region-specific. In
Re: [ccp4bb] wwPDB and CCDC
A jolly good thing - congratulations and thanks to the instigators... Eleanor On 13 April 2012 15:40, Gerard DVD Kleywegt ger...@xray.bmc.uu.se wrote: Hi Paul, You saw the wwPDB/CCDC JPG in my PPT at GSK :-) Yes, wwPDB and CCDC have signed an MoU. In pounds and pennies it means, amongst a number of other things, that wwPDB will be allowed to use Mogul in its validation pipeline and that wwPDB will be allowed to incorporate and redistribute CSD coordinates of small molecules that occur in both PDB and CSD. --Gerard (K) On Fri, 13 Apr 2012, Paul Emsley wrote: On 13/04/12 14:30, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Paul, you are not referring to Gerard Bricogne's announcement for the grade-server, are you? http://www.mail-archive.com/**ccp4bb@jiscmail.ac.uk/**msg25770.htmlhttp://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg25770.html :) No. If not - what type of agreement do you have in mind? IIRC, I remember a picture of Gerard (K), Helen, Haruki and a smiling Colin Groom sitting along a table signing something. I was wondering if more details are available on the web. Paul. Best wishes, --Gerard ** Gerard J. Kleywegt http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ** Little known gastromathematical curiosity: let z be the radius and a the thickness of a pizza. Then the volume of that pizza is equal to pi*z*z*a ! **
Re: [ccp4bb] [cnsbb] MTZ label
Dear Sunil, I think you can do this with the ccp4i gui- In the category Reflection Data Utilities select Edit mtz file (sftools) One of the panels is Change column labels and types with options to edit labels or add new label. But Surprise, there are no labels in the list! This is because the list is labels you have selected for the output file. You have to click add another label and you will get to choose from the labels in the input file, and change the labe and/or (probably not a good idea) change its type. However I don't think you need to change labels to run Amore- If you are running amore from the ccp4i gui, start the main amore task, right under the box where you select mtz file with input data,there are two drop-down menus labeled FP and Sigma. The items to select are all the labels in the mtz file, so you select the ones corresponding to FP and Sigma If you still have trouble, I suggest to subscribe to ccp4bb Phaser is another very useful molecular replacement program you should try. You can run it from the CCP4 Gui if it is installed. HTH! sunil wrote: Hi I am facing the problem of putting correct label in the MTZ file. Ctruncate (ccp4 GUI) programme uses some default label which is not sufficient to run AMoRe. Does anyone face this problem of MTZ label? How can we put labels in the MTZ that we want e.g FP or PHIC etc ? If anybody has some clue to this this please help me overcome this problem. I tried to search the google but not able to find any script that can handle the problem of mtz label. I appreciate any help in this regard __._,_.___ Reply to sender mailto:sktewarybt1...@yahoo.co.in?subject=Re%3A%20MTZ%20label | Reply to group mailto:cn...@yahoogroups.com?subject=Re%3A%20MTZ%20label | Reply via web post http://groups.yahoo.com/group/cnsbb/post;_ylc=X3oDMTJwdjMxbmFkBF9TAzk3MzU5NzE0BGdycElkAzMwMzA4MTAEZ3Jwc3BJZAMxNzA1MDgyOTQ2BG1zZ0lkAzIxNjQEc2VjA2Z0cgRzbGsDcnBseQRzdGltZQMxMzM0NDA5OTUy?act=replymessageNum=2164 | Start a New Topic http://groups.yahoo.com/group/cnsbb/post;_ylc=X3oDMTJla2FldDJjBF9TAzk3MzU5NzE0BGdycElkAzMwMzA4MTAEZ3Jwc3BJZAMxNzA1MDgyOTQ2BHNlYwNmdHIEc2xrA250cGMEc3RpbWUDMTMzNDQwOTk1Mg-- Messages in this topic http://groups.yahoo.com/group/cnsbb/message/2164;_ylc=X3oDMTM0aDVnOTE2BF9TAzk3MzU5NzE0BGdycElkAzMwMzA4MTAEZ3Jwc3BJZAMxNzA1MDgyOTQ2BG1zZ0lkAzIxNjQEc2VjA2Z0cgRzbGsDdnRwYwRzdGltZQMxMzM0NDA5OTUyBHRwY0lkAzIxNjQ- (1) Recent Activity: Visit Your Group http://groups.yahoo.com/group/cnsbb;_ylc=X3oDMTJlZXFvdGNtBF9TAzk3MzU5NzE0BGdycElkAzMwMzA4MTAEZ3Jwc3BJZAMxNzA1MDgyOTQ2BHNlYwN2dGwEc2xrA3ZnaHAEc3RpbWUDMTMzNDQwOTk1Mg-- List information at http://groups.yahoo.com/group/cnsbb. Posting is only allowed for members of this list. Yahoo! Groups http://groups.yahoo.com/;_ylc=X3oDMTJkaXBkdXF2BF9TAzk3MzU5NzE0BGdycElkAzMwMzA4MTAEZ3Jwc3BJZAMxNzA1MDgyOTQ2BHNlYwNmdHIEc2xrA2dmcARzdGltZQMxMzM0NDA5OTUy Switch to: Text-Only mailto:cnsbb-traditio...@yahoogroups.com?subject=Change Delivery Format: Traditional, Daily Digest mailto:cnsbb-dig...@yahoogroups.com?subject=Email Delivery: Digest • Unsubscribe mailto:cnsbb-unsubscr...@yahoogroups.com?subject=Unsubscribe • Terms of Use http://docs.yahoo.com/info/terms/ . __,_._,___
[ccp4bb] Anybody knows why SSRL is unaccessible ?
neither the websites nor ssh works to any of the machines. Did they fall into a black hole ? e.g. http://www-ssrl.slac.stanford.edu Jürgen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://web.mac.com/bosch_lab/
Re: [ccp4bb] Anybody knows why SSRL is unaccessible ?
I guess I must have missed this, glad we collected our data yesterday at ALS (shameless advertisement). Hopefully things will be restored soon though. Jürgen On Apr 14, 2012, at 12:33 PM, Richard Gildea wrote: They were hit by a lightning strike on Thursday evening which took out their power: https://slacportal.slac.stanford.edu/sites/esh/emergency/Pages/default.aspx Cheers, Richard On Apr 14, 2012 9:28 AM, Bosch, Juergen jubo...@jhsph.edumailto:jubo...@jhsph.edu wrote: neither the websites nor ssh works to any of the machines. Did they fall into a black hole ? e.g. http://www-ssrl.slac.stanford.eduhttp://www-ssrl.slac.stanford.edu/ Jürgen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742tel:%2B1-410-614-4742 Lab: +1-410-614-4894tel:%2B1-410-614-4894 Fax: +1-410-955-2926tel:%2B1-410-955-2926 http://web.mac.com/bosch_lab/ .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://web.mac.com/bosch_lab/
Re: [ccp4bb] Anybody knows why SSRL is unaccessible ?
They were hit by a lightning strike on Thursday evening which took out their power: https://slacportal.slac.stanford.edu/sites/esh/emergency/Pages/default.aspx Cheers, Richard On Apr 14, 2012 9:28 AM, Bosch, Juergen jubo...@jhsph.edu wrote: neither the websites nor ssh works to any of the machines. Did they fall into a black hole ? e.g. http://www-ssrl.slac.stanford.edu Jürgen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://web.mac.com/bosch_lab/
Re: [ccp4bb] Rigaku R-axis IIC X-ray diffraction system
The first Rigaku R-AXIS IIC in North America were installed in late 1990 at Yale University and McMaster University. That's the same year the Hubble Telescope went into space and the first search engine Archie was released. The last R-AXIS IIC shipped in 1994. So these are really vintage systems if anyone is still using them. Jim From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Ng Chyan Leong [c...@mrc-lmb.cam.ac.uk] Sent: Friday, April 13, 2012 11:48 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Rigaku R-axis IIC X-ray diffraction system Dear all, Do you know is anyone still using Rigaku R-axis IIC X-ray diffraction system with support services? It seems Rigaku no longer support this systems. Thank you in advance. Best Regards, Leong
