Re: [ccp4bb] A photograph of the Arndt-Wonacott rotation camera?
Is the prototype shown Figure 1 from U. W. Arndt, J. N. Champness, R. P. Phizackerley and A. J. Wonacott A single-crystal oscillation camera for large unit cells J. Appl. Cryst. (1973). 6, 457-463 http://dx.doi.org/10.1107/S0021889873009210 http://journals.iucr.org/j/issues/1973/06/00/a10549/a10549.pdf what you are looking for? Regards, Mitch http://journals.iucr.org/services/permissions.html -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gerard Bricogne Sent: Wednesday, October 30, 2013 9:05 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] A photograph of the Arndt-Wonacott rotation camera? Dear all, Apologies for such a retro and non-biological question, but would anyone have a photograph of an Arndt-Wonacott rotation camera that he/she would be willing to share? I collected data on the first two prototypes in the early seventies, then on one of the first commercial models, but I cannot find any images of this ground-breaking piece of equipement on the Web. I found images for the Enraf-Nonius precession camera and the CAD-4 diffractometer, but not for the A-W rotation camera. This would be for use as visual material in presentations, and I would gratefully acknowledge the source of it. Thank you in advance! With fingers crossed ... . Gerard. -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
Re: [ccp4bb] Comparison of Water Positions across PDBs
Hi Elise, Not exactly what you are asking for, but lsqman will compare waters between structures with a cut-off. (However, it will not renumber the waters as you wanted) http://xray.bmc.uu.se/usf/lsqman_man.html#S71 If you want to look at waters related by NCS in a single PDB file with multiple macromolecule chains, then you can use sortwater which will renumber NCS related waters with the same residue number but different chain identifiers. (I think watncs also does a similar thing, but I have not used it). Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dom Bellini Sent: Tuesday, October 29, 2013 3:34 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs Hi Elise, How about taking the homologue structure with highest number of waters and use it to run molecular replacement on all other datasets? Then you could keep only the good waters (manually unfortunately) which will ensure they will all have the same numbers. Probably not the fastest way but it should give what I think you were asking for? HTWorks D From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Swastik Phulera [swastik.phul...@gmail.com] Sent: 29 October 2013 21:16 To: ccp4bb Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs Downloading structures of the same homologous family with blast. Then superimpose them on a reference structure. You may then try to look at over lapping water molecules On 30 Oct 2013 02:23, Elise B ek...@case.edumailto:ek...@case.edu wrote: Hello, I am working on a project with several (separate) structures of the same protein. I would like to be able to compare the solvent molecules between the structures, and it would be best if the waters that exist in roughly the same position in each PDB share the same residue number. Basically, I want to compare solvent molecule coordinates and assign similar locations the same name in each structure. What would be the best strategy for re-numbering the water molecules such that those with similar coordinates in all the structures receive the same residue number? I'd appreciate any suggestions. Elise Blankenship -- 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
Re: [ccp4bb] What kind of reflection data to deposit to PDB
Hi Martyn, I too was puzzled by the statement that unmerged data cannot be handled properly as part of a PDB deposition. We have deposited the unmerged original index intensities for the refinement wavelength (and for additional wavelengths used for phasing in the case of MAD) since 2005. This was based on recommendation #2 from the Report of Task Force on Numerical Criteria in Structural Genomics from the 2001 Airlie meeting (2nd Intl. Struct. Genomics Mtg.). http://www.nigms.nih.gov/NR/rdonlyres/14937E88-B916-4503-A29E-FA11E4B3D445/0/numerical.doc http://www.isgo.org/organization/members07/010410.html Which states that For X-ray data, unmerged integrated intensities (omitting outliers but including systematically-absent axial reflections) should be deposited along with the final, merged intensities and amplitudes for all wavelengths and/or derivatives. We worked the RCSB staff to refine the format of the mmCIF formatted reflection containing multiple data loops for our depositions and this has been used for more than 1300 JCSG depositions and the data is retrievable from all wwPDB partner sites. Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Martyn Symmons Sent: Tuesday, September 17, 2013 3:44 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] What kind of reflection data to deposit to PDB Sorry to contradict, But the mmCIF data model certainly does not seem to require hkl unique within the reflection data. Like CIF the mmCIF formalism has been developed to allow a complete description of a diffraction experiment and the data arising from it. There is a full description at http://mmcif.pdb.org/dictionaries/mmcif_pdbx_v40.dic/Categories/diffrn_refln.html (I am grateful to Rachel Kramer Green at the RCSB for pointing out these links to the dictionary and the papers describing its development). Having chosen mmCIF for the archive and then not using its flexibility seems a bit like having your cake and NOT eating it. It is strange to hear on a discussion board that recently considered the advantages of depositing complete image data, that a case will have to be made for allowing the deposition of full unmerged datasets. ++Martyn On 16/09/2013 14:03, Gerard DVD Kleywegt wrote: Dear all, At present, unmerged data cannot be handled properly as part of a PDB deposition. One reason for this is that changes to the mmCIF/PDBx data model will be required (at the moment, hkl must be unique within the reflection data, which is logical for merged data but precludes handling of unmerged data). There are other (easier to resolve) issues to work out, e.g. having to do with file naming and distribution via the wwPDB ftp archive. The wwPDB partners are presently focusing all efforts on rolling out the new joint deposition and annotation system. Once this system is reasonably stable we will look into accepting/validating/distributing new kinds of data. This concerns not only unmerged Is for X-ray but also unassigned NOE peak lists for NMR. We will seek the advice of the corresponding wwPDB VTFs (Validation Task Forces) to help define the data items that need to be captured, how the data should be processed by wwPDB, and what kind(s) of validation is/are required. --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk On Thu, 5 Sep 2013, Raji Edayathumangalam wrote: Hi Folks, Sorry for the non-ccp4 post. I am trying to determine what is the best form of unmerged reflection data to deposit to the PDB. I have single wavelength anomalous data for my structure and I have two flavors of scaled files from the same exact set of diffraction images: (1) data indexed and scaled in p1, and (2) data indexed in p222, scaled in Scalepack using the no merge original index option and converted to .mtz since the unit cell in the header of the output .sca file was missing. The space group for the dataset is p212121. Please could you let me know what might be the best approach. Many thanks and cheers, Raji -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University 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
Re: [ccp4bb] 3D printing structures?
Hi Ronnie, I have not tried it, but a quick google search for protein ribbon 3d printer turns up the following in the results list-- http://ironchefsynbio.wordpress.com/tag/3d-printer/ http://www.lib.ua.edu/sites/default/files/rodgers/Rodgers%203D%20Printing%20Molecular%20X-ray%20Data_V1.pdf http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-May/008821.html http://www.cgl.ucsf.edu/Outreach/technotes/ModelGallery/index.html Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ronnie Sent: Friday, August 23, 2013 11:16 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] 3D printing structures? An off-topic question-now that 3D printing is becoming more common, has anyone tried to print protein structures other than just the surface representation like in this tutorial? http://www.instructables.com/id/3D-Print-a-Protein-Modeling-a-Molecular-Machine/ Is it possible to print a ribbon representation for example? Thanks! Ronnie
Re: [ccp4bb] Twinning problem
You are welcome. Let me also for the benefit of others who may search the archives in the future, let me correct two errors below - (typo and a miss-recollection). Specially, I was thinking that phenix.refine was now able to refine multiple twin laws, but according to Nat Echols on the phenix mailing list http://phenix-online.org/pipermail/phenixbb/2013-March/019538.html phenix.refine only handles 1 twin law at this time. (My typo was that and our second structure was 3nuz with twin fractions 0.38, 0.32, 0.16 and 0.14 -- not 2nuz). A useful search for deposited structures mentioning tetartohedral http://www.ebi.ac.uk/pdbe-srv/view/search?search_type=all_texttext=TETARTOHEDRALLY+OR+TETARTOHEDRAL Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of herman.schreu...@sanofi.com Sent: Thursday, June 20, 2013 8:04 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] AW: Twinning problem Dear Mitch (and Philip and Phil), It is clear that I should give refmac a go with the non-detwinned F's and just the TWIN command. Thank you for your suggestions, Herman -Ursprüngliche Nachricht- Von: Miller, Mitchell D. [mailto:mmil...@slac.stanford.edu] Gesendet: Donnerstag, 20. Juni 2013 16:18 An: Schreuder, Herman RD/DE Betreff: RE: Twinning problem Hi Herman, Have you considered the possibility of your crystals being tetartohedral twinned. That is more than one of the twin laws may apply to your crystals. E.g. in P32 it is possible to have tetartohedral twinning which would have 4 twin domains - (h,k,l), (k,h,-l), (-h,-k,l) and (-k,-h,-l). Perfect tetartohedral twinning of P3 would merge in P622 and each twin domain would have a faction of 0.25. We have had 2 cases like this (the first 2PRX was before there was support for this type of twinning except for in shelxl and we ended up with refined twin fractions of 0.38, 0.28, 0.19, 0.15 for the deposited crystal and a 2nd crystal that we did not deposit had twin fractions of 0.25, 0.27, 0.17, 0.31). The 2nd case we had was after support for twining (including tetartohedral twinning) was added to refmac (and I think phenix.refine can also handle this). For 2NUZ, it was P32 with refined twin fractions of 0.25, 0.27, 0.17, 0.31. Pietro Roversi wrote a review of tetartohedral twinning for the CCP4 proceedings issues of acta D http://dx.doi.org/10.1107/S0907444912006737 I would try refinement with refmac using the original (non-detwinned F's) with just the TWIN command to see if it ends up keeping twin fractions for all 3 operators (4 domains) -- especially with crystals 1 and 3 which appear to have the largest estimates of the other twin fractions. Regards, Mitch == Mitchell Miller, Ph.D. Joint Center for Structural Genomics Stanford Synchrotron Radiation Lightsource 2575 Sand Hill Rd -- SLAC MS 99 Menlo Park, CA 94025 Phone: 1-650-926-5036 FAX: 1-650-926-3292 -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of herman.schreu...@sanofi.com Sent: Thursday, June 20, 2013 6:47 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Twinning problem Dear Bulletin Board, Prodded by pdb annotators, which are very hesitant to accept coordinate files when their Rfactor does not correspond with our Rfactor, I had a look again into some old data sets, which I suspect are twinned. Below are the results of some twinning tests with the Detwin program (top value: all reflections, lower value: reflections Nsig*obs (whatever that may mean). The space group is P32, the resolution is 2.3 - 2.6 Å and data are reasonable complete: 95 - 100%. From the Detwin analysis, it seems that the crystals are twinned with twin operator k,h,-l with a twinning fraction of 0.3 for crystal 1, 0.15 for crystal 2 and 0.4 for crystal 3. Crystal 2 can be refined while ignoring twinning to get acceptable but not stellar R and Rfree values. However, when I try to detwin Fobs of e.g. crystal 1 (twinning fraction 0.3), R and Rfree values stay about the same, whatever twinning fraction I try. At the time, I used the CNS detwin_perfect protocol to detwin using Fcalcs, which brought the Rfactors in acceptable range, but I do not feel that was the perfect solution. Ignoring twinning on e.g. crystal 1 produces an Rfactor of 22% and an Rfree of 29% Do you have any idea what could be going on? Thank you for your help! Herman Crystal 1: operator -h,-k,l Suggests Twinning factor (0.5-H):0.113 Suggests Twinning factor (0.5-H):0.147 operator: k,h,-l Suggests Twinning factor (0.5-H):0.277 Suggests Twinning factor (0.5-H):0.323 operator -k,-h,-l Suggests Twinning factor (0.5-H):0.101 Suggests Twinning factor (0.5-H):0.134 Crystal 2: operator -h,-k,l Suggests Twinning factor (0.5-H):0.077 Suggests Twinning factor (0.5-H):0.108 operator: k,h,-l Suggests
Re: [ccp4bb] HETATM automated chain assignment
Have a look at sortwater. http://www.ccp4.ac.uk/html/sortwater.html If you want to use it for non-water ions in addition to waters, you would need to run it a second time for each of the atom types using the water keyword to define the residue type and atom name. Also, it won't work for multi-atom ions, but could work for Na, Cl, K, Mg, Ca etc Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Talon Romain Sent: Friday, February 15, 2013 8:30 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] HETATM automated chain assignment Hello to the CCP4 bulletin board community, I would like to know if I could find a tool to automatically assign HETATM atom (or even, water molecules) to the nearest protein chain ? In my case, I have 4 protein chains in the asymmetric unit : A, B, C and D. I would like to assign each ions and each ligands (which are numerous) with the chain letter of the nearest residue that coordinate them. Usually, I rename everything by hand but as the in-house program of the PDBe AutoDep deposition tool automatically do that... I beg your pardon if this question has just been posted here. I didn't find any tool either in the CCP4 Suite or in the Extensions and Calculate menus of the Coot program (v0.7). Best regards. Romain Talon
Re: [ccp4bb] engh huber
Hi Ed, Chapter 18.3 of international tables vol F includes values designated EH99 which are from a more recent CSD release than the original 1991 Engh Huber paper. R. A. Engh and R. Huber. Structure quality and target parameters. International Tables for Crystallography (2012). Vol. F, ch. 18.3, pp. 474-484 doi: 10.1107/9780955360206857 http://it.iucr.org/Fb/ch18o3v0001/ Also, the Buster groups' Grade server provides dynamic use of the CSD database to derive restraints. http://grade.globalphasing.org And the PURY restraint database has restraints derived from recent CSD releases. I belive it requires a current CSD license is required for use. http://pury.ijs.si/ Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ed Pozharski Sent: Monday, January 14, 2013 9:55 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] engh huber To what extent modern geometric restraints have been upgraded over original EnghHuber? And where I can find a consensus set of values (with variances)? For example, Fisher et al., Acta D68:800 discusses how histidine angles change with protonation, and refers to EnghHuber when it says that ND1-CE1-NE2 goes from 111.2 to 107.5 when histidine acquires positive charge (Fig.6). But angle table (Table 3) in original EnghHuber from 1991 does not have any 107.5 value and seems to suggest that the numbers should rather be 111.7+-1.3 and 108.4+-1.0, respectively. I understand that these values are derived from structural databases and thus can be frequently updated. Is there some resource where most current values would be listed? Cheers, Ed. -- After much deep and profound brain things inside my head, I have decided to thank you for bringing peace to our home. Julian, King of Lemurs
Re: [ccp4bb] refining against weak data and Table I stats
I too like the idea of reporting the table 1 stats vs resolution rather than just the overall values and highest resolution shell. I also wanted to point out an earlier thread from April about the limitations of the PDB's defining the resolution as being that of the highest resolution reflection (even if data is incomplete or weak). https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1204L=ccp4bbD=01=ccp4bb9=AI=-3J=ond=No+Match%3BMatch%3BMatchesz=4P=376289 https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1204L=ccp4bbD=01=ccp4bb9=AI=-3J=ond=No+Match%3BMatch%3BMatchesz=4P=377673 What we have done in the past for cases of low completeness in the outer shell is to define the nominal resolution ala Bart Hazes' method of same number of reflections as a complete data set and use this in the PDB title and describe it in the remark 3 other refinement remarks. There is also the possibility of adding a comment to the PDB remark 2 which we have not used. http://www.wwpdb.org/documentation/format33/remarks1.html#REMARK%202 This should help convince reviewers that you are not trying to mis-represent the resolution of the structure. Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Edward A. Berry Sent: Friday, December 07, 2012 8:43 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] refining against weak data and Table I stats Yes, well, actually i'm only a middle author on that paper for a good reason, but I did encourage Rebecca and Stephan to use all the data. But on a later, much more modest submission, where the outer shell was not only weak but very incomplete (edges of the detector), the reviewers found it difficult to evaluate the quality of the data (we had also excluded a zone with bad ice-ring problems). So we provided a second table, cutting off above the ice ring in the good strong data, which convinced them that at least it is a decent 2A structure. In the PDB it is a 1.6A structure. but there was a lot of good data between the ice ring and 1.6 A. Bart Hazes (I think) suggested a statistic called effective resolution which is the resolution to which a complete dataset would have the number of reflectionin your dataset, and we reported this, which came out to something like 1.75. I do like the idea of reporting in multiple shells, not just overall and highest shell, and the PDB accomodatesthis, even has a GUI to enter it in the ADIT 2.0 software. It could also be used to report two different overall ranges, such as completeness, 25 to 1.6 A, which would be shocking in my case, and 25 to 2.0 which would be more reassuring. eab Douglas Theobald wrote: Hi Ed, Thanks for the comments. So what do you recommend? Refine against weak data, and report all stats in a single Table I? Looking at your latest V-ATPase structure paper, it appears you favor something like that, since you report a high res shell with I/sigI=1.34 and Rsym=1.65. On Dec 6, 2012, at 7:24 PM, Edward A. Berryber...@upstate.edu wrote: Another consideration here is your PDB deposition. If the reason for using weak data is to get a better structure, presumably you are going to deposit the structure using all the data. Then the statistics in the PDB file must reflect the high resolution refinement. There are I think three places in the PDB file where the resolution is stated, but i believe they are all required to be the same and to be equal to the highest resolution data used (even if there were only two reflections in that shell). Rmerge or Rsymm must be reported, and until recently I think they were not allowed to exceed 1.00 (100% error?). What are your reviewers going to think if the title of your paper is structure of protein A at 2.1 A resolution but they check the PDB file and the resolution was really 1.9 A? And Rsymm in the PDB is 0.99 but in your table 1* says 1.3? Douglas Theobald wrote: Hello all, I've followed with interest the discussions here about how we should be refining against weak data, e.g. data with I/sigI 2 (perhaps using all bins that have a significant CC1/2 per Karplus and Diederichs 2012). This all makes statistical sense to me, but now I am wondering how I should report data and model stats in Table I. Here's what I've come up with: report two Table I's. For comparability to legacy structure stats, report a classic Table I, where I call the resolution whatever bin I/sigI=2. Use that as my high res bin, with high res bin stats reported in parentheses after global stats. Then have another Table (maybe Table I* in supplementary material?) where I report stats for the whole dataset, including the weak data I used in refinement. In both tables report CC1/2 and Rmeas. This way, I don't redefine the (mostly) conventional usage of resolution, my Table I can be compared to precedent, I report stats for all the data and for the model against all data, and I take
Re: [ccp4bb] Convention on residue numbering of fusion proteins?
The PDB requires that a single poly peptide have single chain id. See page 5 of the wwPDB annotation / processing procedures guide http://www.wwpdb.org/documentation/wwPDB-A-2012May30.pdf One thing you could do would be to number the second domain starting a 1170 which would sort-of preserve the biological numbering. You could also number domain one as 1200-1300 and the second domain as 2170-2350 if you like. If you use refmac with non-continuous residue numbering, be sure to include a LINKR statement so the peptide bond between the two domains is properly restrained. Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Meindert Lamers Sent: Tuesday, October 23, 2012 9:55 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Convention on residue numbering of fusion proteins? Dear all, Is there any convention on the numbering of residues in a fusion protein? I have a structure of two domains fused together but would like to keep the biological numbering intact. 1st domain: residue 200-300 (protein A). 2nd domain: residue 170-350 (protein B). The fusion is between A300 and B170 Is it OK to label them chain A and B and create a LINK between the two (thus keeping the biological residue number intact). Or do I have to start the 2nd domain with residue number 301 (and loose all biological information). Many thanks, Meindert -- ** Meindert H. Lamers Medical Research Council Laboratory of Molecular Biology Hills Road, Cambridge, CB2 0QH United Kingdom tel +44 (0)1223 402401 fax +44 (0)1223 213556 web: http://www2.mrc-lmb.cam.ac.uk/groups/mlamers/ **
Re: [ccp4bb] Off-topic: PDB deposition of multiple structure factor files
We (JCSG) too have been depositing multiple data sets (including unmerged original index intensities for each wavelength and even for multiple crystals when one was used for phasing and another for refinement, and MAD phases and DM modified map coefficients) since 2004 without problems. These are all in separate data loops of a single structure factor file. Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jens Kaiser Sent: Friday, April 27, 2012 11:54 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Off-topic: PDB deposition of multiple structure factor files It might be a portal issue. But the pdb staff is very helpful in getting this deposited. We deposited data of I think 4 crystals and 3 wavelengths with different phase sets in 2008. (The data was anisotropic, 3.5/4.2 A resolution, model building was not straight forward, so we wanted to preserve as much information as possible. If memory serves right, we have experimental fobs, anisotropy corrected fobs, a derivative and a semet dataset; if you're interested, pdb code is 3dhw, have a look at the sf-file) hth, Jens On Fri, 2012-04-27 at 20:35 +0200, Mark J van Raaij wrote: again, it looks like this is particular to the US portal. We submit via the European www.pdbe.org and can submit multiple datasets. See 2XGF for an example. Note: I think from www.rcsb.org only one file can be downloaded, but www.pdbe.org clearly shows both. Although you are in the US, you can use the pdbe deposition tool AUTODEP - or the Japanese one, if you like. 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 27 Apr 2012, at 20:23, Florian Schmitzberger wrote: Dear All, With my most recent PDBe deposition, in addition to the native data, I had intended to deposit the anomalous data, used for structure determination, and make it available for download. This turned out to be less straightforward than I had anticipated, because the current PDB convention is to only allow a single structure factor file for experimental data (usually the native dataset), available for download from the PDB. In my case, the anomalous data were concatenated with the native data into a single cif file (this worked and made sense, because both for both datasets the unit cell dimensions are virtually identical). I imagine it would be beneficial to be able to make available more than a single structure factor file, including the ones derived from experimental phasing, in the PDB, along with the final coordinates, without concatenating the data into a single file (which may lead to confusion to users when downloaded). Is this anything the PDB is already working to implement in the near future (perhaps via the coming PDBx format)? Best regards, Florian
Re: [ccp4bb] resolution on PDB web page
I too believe that the value is set from the high resolution limit form data collection or refinement. All three numbers (high resolution limit in remark 2, remark 3 and Remark 200) are supposed to be consistent and are defined as the highest resolution reflection used. http://mmcif.rcsb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_reflns.d_resolution_high.html http://mmcif.rcsb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_refine.ls_d_res_high.html Looking at the PDB specification, it shows that there is an option to add a free text comment to the remark 2 resolution -- Additional explanatory text may be included starting with the third line of the REMARK 2 record. For example, depositors may wish to qualify the resolution value provided due to unusual experimental conditions. http://www.wwpdb.org/documentation/format33/remarks1.html We have not done this, but we have in a number of cases qualified the resolution by using a lower resolution in the title of the entry and further detailing this nominal resolution in the remark 3 other refinement remarks. E.g. see http://www.rcsb.org/pdb/explore/explore.do?structureId=1vr0 http://www.rcsb.org/pdb/explore/explore.do?structureId=1vkk Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Edward A. Berry Sent: Wednesday, April 25, 2012 6:55 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] resolution on PDB web page We also use the US portal. Can't speak to the solvent content as we never had a value much over 70%. As for the resolution range, I never saw any place to enter this user-defined resolution of the structure. As far as i know it comes from the record: REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 which should be the high resolution used in refinement. I suppose in an additional remark you could give the optical resolution or the resolution of 90% complete at I/sig=2. Or the title could be The 2.2A resolution structure of protein x, never mind that there were a few reflections used at 1.7A. eab Mark J van Raaij wrote: Phoebe, Jan, PDB, is this something particular to the US portal of the PDB, or general? We always use the European portal pdbe and have not had such problems. Mark 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 25 Apr 2012, at 09:41, Jan Dohnalek wrote: There have been other manipulations with user-input values. We could not input solvent content 83% for 3cg8 (the real value!!!) as being out of the allowed range. The resulting value in the PDB is NULL not showing the actually interesting feature of the structure. I also noticed that the reported resolution values are nonsensically advertised with three decimal positions after the point which is not the way we would put it, is it? Either fight it or live with it ... Jan Dohnalek On Wed, Apr 25, 2012 at 12:23 AM, Phoebe Ricepr...@uchicago.edu wrote: I just noticed that the PDB has changed the stated resolution for one of my old structures! It was refined against a very anisotropic data set that extended to 2.2 in the best direction only. When depositing I called the resolution 2.5 as a rough average of resolution in all 3 directions, but now PDB is advertising it as 2.2, which is misleading. I'm afraid I may not have paid enough attention to the fine print on this issue - is the PDB now automatically advertising the resolution of a structure as that of the outermost flyspeck used in refinement, regardless of more cautious assertions by the authors? If so, I object! = Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 340 Fax: +420 296 809 410
Re: [ccp4bb] mtz2cif capable of handling map coefficients
I have not tried it, but the latest version of the rcsb program sf-convert is supposed to support it (see version 1.2 released March 23) http://sw-tools.pdb.org/apps/SF-CONVERT/index.html http://sw-tools.pdb.org/apps/SF-CONVERT/doc/V1-2-00/documentation.html (Version 1.2 is not yet available as a binary download) Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Francis E Reyes Sent: Thursday, April 05, 2012 8:25 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] mtz2cif capable of handling map coefficients It seems that deposition of map coefficients is a good idea. Does someone have an mtz2cif that can handle this? Thanks! F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder
Re: [ccp4bb] how can merge two PDB
Hi Afshan, in Coot select calculate -- other modeling tools -- find ligands In 0.6.2, there is a message that ligands are limited to 400 atoms or less. Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Afshan Begum Sent: Wednesday, October 19, 2011 8:04 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] how can merge two PDB Dear Juergen Many thank for your response yes you have excatly understand my question we have a MR solution of the rest of our protein and just asking how to make my life easier to not built de novo 45-50 residues. so i could not find the option in coot find ligand so, from where i get it? Best Regards AFSHAN From: Afshan Begum afshan...@yahoo.com To: Bosch, Juergen jubo...@jhsph.edu Sent: Wednesday, October 19, 2011 4:58 PM Subject: Re: [ccp4bb] how can merge two PDB H.EDU To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, October 19, 2011 4:29 PM Subject: Re: [ccp4bb] how can merge two PDB why don't you read in that chain in Coot and run the find ligand option with flexible ligand turned on and select that 6kDa ligand ? You should also choose Fo-Fc map to fit the ligand to maybe at 2.7 sigma. You might have to split up the ligand into pieces, not sure what the limitations in Coot/Find Ligand are. You already have a MR solution of the rest of your protein right ? So you are just asking how to make your life easier to not built de novo 45-50 residues ? Jürgen On Oct 19, 2011, at 10:00 AM, Ed Pozharski wrote: Why not do the molecular replacement - 6kDa is rather small but it most likely will work On Wed, 2011-10-19 at 06:13 -0700, Afshan Begum wrote: Hello CCP4 user I have collected a data set 2.1 for my complex. Actually after first run of Rafmac i can see the density for my inhibitor but the problem is my inhibitor is 6 KDa and i know the sequence of my inhibitor as well this inhibitor already crystallize with other protein molecule present in PDB data bank so how can i put in to that electron density i mean are there any ways to combine two Pdb in one molecule? I would be thankful for your help Best Regards AFSHAN -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs .. 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] TLS and ANISOU/RESIDUAL B-FACTORS - doubt
Hi Catarina , For your final refmac refinement job, you need to include the keyword TLSO ADDU to have the TLS contribution added to the residual B-factors. This keyword can also be set from the recent version of the ccp4i GUI by checking the checkbox for Add TLS contribution to XYZOUT in the TLS section. (This addu output file is needed for deposition but should not be used for further TLS refinement with refmac). Also, depending on the version of refmac you are using, it may also default to adding waters to TLS groups. If it does, then they waters will have ANISOU records after TLS refinement. Note that refmac does not update the TLS range records to reflect this change. If you want to exclude water from TLS assignment, you can also include the TLSD waters exclude keyword. Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Catarina Silva Sent: Wednesday, August 03, 2011 12:47 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] TLS and ANISOU/RESIDUAL B-FACTORS - doubt Dear all, I am trying to deposit a pdb containing TLS groups. PDB instructions states: As we have mentioned on the start page for autodep, entries refined using REFMAC with TLS parameters must now contain the full B-factor in ATOM/HETATM records, with the TLS contribution coded into ANISOU records. I did run Refmac with TLS parameters and, as such, I would expect that all the values necessary to pdb deposition would be on the pdb coming out from refmac. However, when I deposit the pdb a 'serious error' comes up, not allowing me to deposit the coordinates: You will NOT be allowed to proceed for deposition unless these issues are corrected. TLS and ANISOU/RESIDUAL B-FACTORS. As we have mentioned on the start page for autodep, entries refined using REFMAC with TLS parameters must now contain the full B-factor in ATOM/HETATM records, with the TLS contribution coded into ANISOU records.Your entry contains TLS records but no ANISOU records OR Residual B-factors. Please correct this and reupload your structure for validation I don't really understand why these supposed missing values are not already contained in the pdb file, and I can't figure out how to get them. Does anyone knows how to fix this situation? Thanks in advance! Catarina Silva
Re: [ccp4bb] TLS and ANISOU/RESIDUAL B-FACTORS - doubt
Hi Boas, Yes, tlsanal would work but only if the structure was refined with the keyword TLSD waters exclude either by explicitly including the keyword or by using a version that of refmac that defaults to TLSD waters exclude. I believe that recent versions of refmac 5.6 default to tlsd waters exclude but that all refmac 5.5 versions (or at least those after 5.5.0036) default to TLSD water add. If the structure was refined with TLSD waters add, then waters have residual B's but since refmac does not update the TLS ranges to reflect which waters are in which TLS group, tlsanal cannot add the TLS component to the waters and you will end up with a file with full-B on the residues in the TLS range definition and residual B's on the waters. My reason for recommending running another refinement round was that it was less complicated in my mind then trying to explain the nuances of the effect of TLSD waters exclude vs TLSD waters add on determining whether or not tlsanal would be able to properly convert the file. Regards, Mitch -Original Message- From: Boaz Shaanan [mailto:bshaa...@exchange.bgu.ac.il] Sent: Wednesday, August 03, 2011 1:40 PM To: Miller, Mitchell D.; CCP4BB@JISCMAIL.AC.UK Subject: RE: [ccp4bb] TLS and ANISOU/RESIDUAL B-FACTORS - doubt Just wondering: wouldn't running tlsanal on the final refmac output as Catarina has it now put the true aniso record straight? Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Miller, Mitchell D. [mmil...@slac.stanford.edu] Sent: Wednesday, August 03, 2011 11:14 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] TLS and ANISOU/RESIDUAL B-FACTORS - doubt Hi Catarina , For your final refmac refinement job, you need to include the keyword TLSO ADDU to have the TLS contribution added to the residual B-factors. This keyword can also be set from the recent version of the ccp4i GUI by checking the checkbox for Add TLS contribution to XYZOUT in the TLS section. (This addu output file is needed for deposition but should not be used for further TLS refinement with refmac). Also, depending on the version of refmac you are using, it may also default to adding waters to TLS groups. If it does, then they waters will have ANISOU records after TLS refinement. Note that refmac does not update the TLS range records to reflect this change. If you want to exclude water from TLS assignment, you can also include the TLSD waters exclude keyword. Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Catarina Silva Sent: Wednesday, August 03, 2011 12:47 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] TLS and ANISOU/RESIDUAL B-FACTORS - doubt Dear all, I am trying to deposit a pdb containing TLS groups. PDB instructions states: As we have mentioned on the start page for autodep, entries refined using REFMAC with TLS parameters must now contain the full B-factor in ATOM/HETATM records, with the TLS contribution coded into ANISOU records. I did run Refmac with TLS parameters and, as such, I would expect that all the values necessary to pdb deposition would be on the pdb coming out from refmac. However, when I deposit the pdb a 'serious error' comes up, not allowing me to deposit the coordinates: You will NOT be allowed to proceed for deposition unless these issues are corrected. TLS and ANISOU/RESIDUAL B-FACTORS. As we have mentioned on the start page for autodep, entries refined using REFMAC with TLS parameters must now contain the full B-factor in ATOM/HETATM records, with the TLS contribution coded into ANISOU records.Your entry contains TLS records but no ANISOU records OR Residual B-factors. Please correct this and reupload your structure for validation I don't really understand why these supposed missing values are not already contained in the pdb file, and I can't figure out how to get them. Does anyone knows how to fix this situation? Thanks in advance! Catarina Silva
Re: [ccp4bb] Permissions and ownerships in ccp4 6.2.0
Another option is to use the recursive feature of chmod to
change the permissions on the files. E.g.
chmod -R a+rX .
which will recursively add read for all users to files (and directories) and
will
also add execute if the file is a directory or if it already has at least one
execute
bit set.
Regards,
Mitch
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dirk Kostrewa
[kostr...@genzentrum.lmu.de]
Sent: Tuesday, July 19, 2011 6:14 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Permissions and ownerships in ccp4 6.2.0
Dear all,
or use a modified version of Clemens's commands for that:
find . -perm 700 -exec chmod 755 {} \;
find . -perm 750 -exec chmod 755 {} \;
find . -perm 600 -exec chmod 644 {} \;
find . -perm 640 -exec chmod 644 {} \;
Best regards,
Dirk.
Am 19.07.11 14:34, schrieb Clemens Vonrhein:
Dear all,
ideally, permissions should be either
rw-r--r-- (0644)
or (for files that need to be executed as well as directories)
rwxr-xr-x (0755)
One quick fix:
find . -type d -exec chmod -v 0755 {} ;
find . -type f -exec chmod -v 0755 {} ;
but that last command makes every single file executable, which is
rather ugly (but doing a selective chmod 0755/0644 is a bit tricky
with all those script files - some need to be executed but others
arent). I don't see a need to have read-only files like all the CIF
dictionaries with permission 0755.
The correct permissions can only be set during packaging
unfortunately.
Cheers
Clemens
--
***
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone: +49-89-2180-76845
Fax:+49-89-2180-76999
E-mail: kostr...@genzentrum.lmu.de
WWW:www.genzentrum.lmu.de
***
Re: [ccp4bb] methods to capture proteins from cell culture medium
Hi Bei, For the extracellular protein I worked on in graduate school, I typically purified it from 4 L preps in LB media. The standard protocol was to do a crude low cut with ammonium sulfate cut followed by precipitation of the protein with a high cut. The pellet was then resuspended, dialyzed and loaded on an S-sepharose column. I experimented with taking the media (after spinning out the cells) and diluting 1:1 with a low ionic strength buffer and loading directly onto the S-sepharose column. This worked, but the loading time for 8 L was so long it was not worth it. Another option might have been to use bulk media to bind the protein in a batch step. I never tested this. A final option that we explored was Expanded-Bed Adsorption Chromatography. This would allow us to get rid of the initial centrifugation step to remove the cells from the media and would allow fast loading with a high speed pump. We priced out the media, column and pump from Pharmacia at the time, but never ended up purchasing the system. The technology looked promising and should have worked well for our system, but we decided that we did not need to do too many more preps for the project and just used the standard protocol. Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of joybeiyang Sent: Tuesday, April 12, 2011 2:14 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] methods to capture proteins from cell culture medium Dear all, My protein of interest was expressed as secreted protein, so I have to collect the medium and change the buffer with sortorius Jet before I load the sample onto a IMAC, the buffer change step in my current protocol can last for 12hrs (I have to concentrate 4L to 200ml, then dilute it with lysis buffer and concentrate it again, then dilute and concentrate repeatedly) and is really boring and troublesome, besides I always observe protein loss during this step and the detergent in the medium usually concentrate as well in this step which would interfere with subsequent purification process. I am wondering if there are more convenient ways to capture the target protein from medium? How about the following: 1. directly load the medium onto a ion exchange column? 2. Amonium sulfate precipitation? 3. anyother thoughts? Thank you very much in advance! Best, Bei 2011-04-12 joybeiyang
Re: [ccp4bb] .pir file
Hi Careina, There are several places on the web that describe the PIR format (also called NBRF) E.g. http://www.ebi.ac.uk/help/formats.html#pir http://www.bioinformatics.nl/tools/crab_pir.html etc. The program readseq -- either via command line or webserver -- e.g. http://www.ebi.ac.uk/cgi-bin/readseq.cgi http://iubio.bio.indiana.edu/cgi-bin/readseq.cgi http://iubio.bio.indiana.edu/soft/molbio/readseq/java can convert from many formats into PIR format (called NBRF for output choice). Or you can convert from fasta to pir pretty easy with a text editor if it is just something you do occasionally. However, since you mentioned that you wanted a pir format file for use with arp/warp. I should mention that arp/warp will only accept .pir files with a blank comment line (i.e. the line after the 1st line (which starts P1;) must be blank rather than containing a free text description of the sequence). Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Careina Edgooms Sent: Thursday, February 17, 2011 9:57 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] .pir file Dear CCP4 mailing list I have a relatively simple question. How do I get sequence file in .pir format which is required for many programs? I normally use fasta format but some programs eg arpwarp do not allow me to use that Thanks for your help Careina
Re: [ccp4bb] reindexing
I find the phenix.explore_metric_symmetry utility to be useful for cases like this. phenix.explore_metric_symmetry --unit_cell=50.48 74.14 149.51 90. 94.16 90. --space_group=p2 \ --other_unit_cell=96.792 74.052 154.271 90. 90.060 90. --other_space_group=p2 It shows that the volume ratio between target and lego cell is 1.98. When it tries to transform the smaller cell into the larger cell, it gives the following result - Target unit cell : 74.1 96.8 154.3 90.1 90.0 90.0 Lego cell : 50.5 74.1 149.5 90.0 94.2 90.0 / 200 \ matrix : M = | 010 | \ 001 / Additional Niggli transform: -y,-x,-z Additional similarity transform: x,y,z Resulting unit cell : 74.1 101.0 149.5 94.2 90.0 90.0 Deviations :-0.1 -4.3 3.1 -4.1 0.0 0.0 Deviations for unit cell lengths are listed in %. Angular deviations are listed in degrees. - So, with a 3-4% difference in length for 2 unit cell edges and a 4 degree difference on the one angle, they do not quite align. Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Wang, Xiaoqiang Sent: Friday, February 11, 2011 6:04 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] reindexing Hi everyone, We collected several derivative data sets which have different cell parameters: (1) 50.480 74.140 149.510 90.000 94.160 90.000 p2 (2) 96.792 74.052 154.271 90.000 90.060 90.000 p2 For one of data sets, HKL2000 and Mosflm gave (1) and (2) as autoindex solution, respectively. Is it possible to convert (1) to (2) by reindexing? Thanks, Xiaoqiang
Re: [ccp4bb] CCP4 SW Web Broadcast
I had good audio for the Buster talk. However, early during Jeff Headd's talk, the audio level dropped to a level that with maximum amplification could still not really be understood- sort of like the wrong microphone was turned on. Later near the end of the talk and during the question/answer session, the audio was back to normal. Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Francis E Reyes Sent: Thursday, January 06, 2011 10:10 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] CCP4 SW Web Broadcast Video is fine.. Anyone getting audio (or is it my realplayer setup? ) ... F On Jan 6, 2011, at 10:04 AM, ronan.kee...@stfc.ac.uk wrote: Dear all, The web stream is now working and can be accessed from: http://extrplay.dl.ac.uk/ There will be full coverage tomorrow (Friday). Apologies again for the delay. Best wishes, Ronan -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of ronan.kee...@stfc.ac.uk Sent: 06 January 2011 08:50 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] CCP4 SW Web Broadcast Dear All, For those of you hoping to view the CCP4 Study Weekend online, we're experiencing some technical difficulties with the webcast equipment. Unfortunately the live stream won't be available for the first part of the meeting. We're hoping to fix it as soon as possible and we'll send an update as soon as it's available. Our apologies for the inconvenience. Best wishes, Ronan Ronan Keegan CCP4 Group - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
Re: [ccp4bb] How to add methyl group on the NZ atom of lysine
Hi Peter, If the lysine is dimethylated, the monomer code needed is MLY. By mass spec we found most sites to be dimethylated. However, looking at the structures we found a few sites to be protected from methylation. These had clear density for the NZ atom, no density for methyl groups and a hydrogen bonding network that could explain protection from the dimethylaminoborane reagent. Regards, Mitch P.S. Note that some older versions of the monomer library have a MLY.cif file that libcheck expands to give a planer arrangement of NZ and CE, CH1, CH2 instead of the proper tetrahedral arrangement. Looking at the CVS log - http://www.ccp4.ac.uk/ccp4bin/viewcvs/ccp4/lib/data/monomers/m/MLY.cif the CCP4 distributed version of MLY was corrected 9/16/2010 for release-6_1_24. So if you have an older version of the library -- e.g. the one distributed with CCP4 release 5.0 - 6.1.12, you will want to update your MLY.cif restraint file. Either from the ccp4 CVS, and the one Phil Evans distributed list in 2009 https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0904L=CCP4BBP=R599391=CCP4BB or the one from the current library on Garib's site -- see https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0904L=CCP4BBP=R602311=CCP4BB or you can use the one I generated http://smb.slac.stanford.edu/~mmiller/MLY_mon_lib-mm2.cif which was used for refining 3MC3 3LN3 3IUZ 3HSA 3GS9 2QJV 2I6G 2FTZ 2FCL 2F4I and 2ETV. While some programs need the link records to display the bonds, refmac doesn't need them if you have the monomer defined as an L-peptide in the restraint file. The PDB will generate the necessary LINK records on deposition if they are missing. -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Robbie Joosten Sent: Thursday, November 04, 2010 6:27 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] How to add methyl group on the NZ atom of lysine Hi Peter, Iff you are sure you are dealing with methyl-lysine, you can get it into your structure by using Get monomer to get the compound MLZ. Position it correctly and then merge it into the structure. I prefer using a text editor to do this. Make sure you put the ATOM records at the right position in the file (otherwise real-space refinement won't work). You probably also need to make LINK records, which you can copy from an existing PDB file (1xer has the links you need). Helix-Turn-Helix, Robbie Joosten Date: Thu, 4 Nov 2010 09:04:53 -0400 From: yoge...@scripps.edu Subject: Re: [ccp4bb] How to add methyl group on the NZ atom of lysine To: CCP4BB@JISCMAIL.AC.UK Dear All and Peter, In one of my structure, I find similar positive density though my protein was not methylated. Are there are any other reasons for appearance of such positive density next to Lysine. Thanking you Yogi From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of peter66 wright Sent: Thursday, November 04, 2010 7:26 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] How to add methyl group on the NZ atom of lysine Dear All, Could anyone please tell me how to add methyl group in COOT on the NZ atom of lysine that has been methylated before crystallisation? The density map is attached to this mail from which you can clearly see the methyl group should be there, but I do not know how to add. Many thanks for help. Peter
Re: [ccp4bb] Sftools and Phaser compatibility issues - continued
FYI -- The :h suffix for R3 is described in the IUCr symmetry cif (intl tables vol G chapter 4.7) under _space_group.reference_setting where it states For the space groups where more than one setting is given in International Tables, the following choices have been made. For monoclinic space groups: unique axis b and cell choice 1. For space groups with two origins: origin choice 2 (origin at inversion centre, indicated by adding :2 to the Hermann-Mauguin symbol in the enumeration list). For rhombohedral space groups: hexagonal axes (indicated by adding :h to the Hermann-Mauguin symbol in the enumeration list). http://it.iucr.org/Ga/ch4o7v0001/ch4o7.pdf http://www.iucr.org/resources/cif/dictionaries/cif_sym The H3 / H32 designations are PDB conventions/standards. In the PDB format description it states that For a rhombohedral space group in the hexagonal setting, the lattice type symbol used is H. From an archive of the PDB documentation at the University of Washington, there is list of changes by PDB version that suggests that the PDB introduced the H designation with the release of PDB format v2.0 (sometime around March 1997) see http://www.bmsc.washington.edu/CrystaLinks/man/pdb/guide2.2_frame.html http://www.bmsc.washington.edu/CrystaLinks/man/pdb/part_6.html The RCSB's archive of the 2.2 format gives a file not found error. http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html Regards, Mitch -Original Message-- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Nat Echols Sent: Thursday, September 02, 2010 8:06 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Sftools and Phaser compatibility issues - continued On Thu, Sep 2, 2010 at 5:31 AM, herman.schreu...@sanofi-aventis.com wrote: The other question is: why does phaser write 'R 3 :H' in the mtz? When the problem with the P21221 space group first popped up last year, Randy told me that space group numbers like 2018 are non-standard, and that space group 18 with the name P21221 was the way to go. This is fair enough, but 'R 3 :H' is neither PDB nor ccp4 standard and I did not find it in the international tables. Is it maybe a phenix standard? No, it pre-dates Phenix - it's the extended Hermann Mauguin symbol, whatever that means: http://www.ccp4.ac.uk/html/symmetry.html I don't know why it's used preferentially in Phenix, but in theory it's supported by CCP4 programs, except those which are still using the older symmetry information. syminfo.lib has the correct information (space group number 146), symop.lib does not. As previously noted the last time this discussion came up (December, if memory serves), Coot also uses this notation: http://www.biop.ox.ac.uk/coot/doc/coot/Reading-coordinates.html -Nat
Re: [ccp4bb] TLSANL total B factor question
Hi Shiva, Not directly related to the problem you reported, but I wanted to warn you that in refmac 5.5.0072 the default is for the keyword TLSD WATERS ADD to be applied. This keyword tells refmac to assign all of your water molecules to existing TLS groups. (It does this quietly without any notice as to which waters are assigned to which groups in the TLS header of the pdb, TLSOUT or to the log file and no listing of the default setting of this keyword in the logfile.) So unless you included the non-default keyword TLSD WATERS EXCLUDE then your waters have residual B's as well in your pdb file and TLSANL cannot convert them to full B's since it has no record of which waters belong to which TLS groups. Thus the output from TLSANL will be a file with mixed full (on protein atoms) and residual (on water atoms) B-factors. If you did not give the keyword TLSD WATERS EXCLUDE, then the only method I know to ensure that the B-factors on the waters are properly converted to full-B is to re-run your last refmac job and add the keyword TLSO ADDU which will give you full B's on your output. (Note that you should not use this file for input into another round of refmac refinement -- unless you do a B-factor reset first). Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Shiva Kumar Sent: Thursday, May 20, 2010 8:46 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] TLSANL total B factor question Dear Crystallographers I am trying to print out my total B factors using TLSANL (version: 6.1) in CCP4- 6.1.1. My TLSANL’s input file.pdb is coming from refmac (version: 5.5.0072) using the TLS restraint refinement option and isotropic B factors. The TLSANL’s output file.pdb contains the following ATOM and ANISOU records as an example. REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS :2 REMARK 3 ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS REMARK 3 ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS ATOM 88 C ASN A 14 0.748 -5.841 -6.258 1.00 35.84 C ANISOU 88 C ASN A 14 5335 4549 3734 0 0 0 C ATOM 89 O ASN A 14 0.807 -6.941 -6.845 1.00 35.04 O ANISOU 89 O ASN A 14 5229 4375 3709 0 0 0 O I am not able to understand why my ANISOU record contains ‘0 0 0’ for the anisotropic component. Something is not correct and I'm not sure why I am not able to print out my total B factors. I would appreciate it if someone could tell me what is going wrong and how can I print my total B factors. Thanks Regards Shiva Kumar
Re: [ccp4bb] updated mtz file or original one in refmac5
The decrease in missing reflections are due to the fact that the output file does not include the missing reflections that are lower resolution than the lowest resolution observed reflection. Thus, this file is no longer uniqueified and then refmac reports a higher completeness since it no longer counts the missing low resolution reflections as missing. In addition, if you are using experimental phase restraints, these data columns are not included in the output. I would recommend always using the same input data file for each round of refinement. Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ed Pozharski Sent: Tuesday, May 18, 2010 6:47 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] updated mtz file or original one in refmac5 I just checked a recent refmac job and it seems that in the output mtz the Fobs has indeed changed. what's more interesting, the number of missing reflections has changed too (disturbingly, it decreased so that the dataset looks more complete 97.07% to 97.17% in this case). But if the same overall anisotropic B scaling is done every time, there seems to be no harm, right? Ed. On Tue, 2010-05-18 at 05:10 +0100, Frank von Delft wrote: Hi Jay No, don't use the new one: the F's in there have been scaled by the overall anisotropic B-factors. (At least, they used to be, a few years ago.) Definitely go with the old one, every time. The output mtz has the coefficients for the maps, that's all. Cheers phx. On 17/05/2010 18:26, Ian Tickle wrote: Hi Jay I always use the original, I only use the new one for maps deposition of Fcalc etc. But I don't think it does any harm to use the new one, all the info is copied over. HTH. Cheers -- Ian On Mon, May 17, 2010 at 5:25 PM, Jay Panccp4p...@gmail.com wrote: Hello every one, I am just starting to use refmac to do refinement. There is an mtz output file each time. Should I use this one for further refinement or should I use the original mtz file (the one after scaling)? Thanks. Jay -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse /
Re: [ccp4bb] Unusually low B factors after refinement
Hi Kyle, Are you refining with TLS? If so, then the default output will be the residual B-factors. To get the full B-factors you need to add the TLS component to the residual B's. This can be done by re-running your refmac job with the keyword TLSO ADDU Note that this version of refmac will also add your waters to TLS groups by default unless you give it the keyword TLSD waters Exclude So unless you included this keyword, then re-running refmac with your same input file and the TLSO ADDU keyword is the only way to ensure that your waters are converted to full B's as the CCP4 program TLSANL cannot do this since the TLS definitions in TLSOUT and the PDB header are not updated with regards to which waters were assigned to different TLS groups. Also, if you use the keyword TLSO ADDU, you should not use this PDB file as input to your next round of refinement unless you also use reset the B factors with the BFACtor SET ## keyword since refmac expects residual B's on the input file. I am not sure how many of these keywords are accessible via the ccp4i interface or if you have to add them via the run and view command file option if you use ccp4i. Regards, Mitch --- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Kyle Dolan Sent: Friday, May 07, 2010 3:12 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Unusually low B factors after refinement Hello, I am trying to run restrained refinement with Refmac5 (version 5.5.0109), including refinement of isotropic temperature factors, and I am seeing some very unusual behavior by the program. In the output pdb file, nearly all of the individual atomic B factors have a value of 2.0! My data is only to 2.9 Angstrom so I've been told to expect much larger atomic B factors. I am using anisotropy-corrected data (I ran my original data through the ellipsoidal truncation anisotropy correction server from UCLA), but when I repeated the run using the original uncorrected mtz file I still saw an average atomic B around 10. I also looked back at the output pdbs from some previous rigid-body refinements (using the same anisotropy-corrected data) and there the B factors are much higher, 50-100. I'm not sure how to prevent Refmac from making this mistake--can anyone offer a suggestion? Thanks, Kyle Kyle T. Dolan Department of Biochemistry and Molecular Biology The University of Chicago k...@uchicago.edu
Re: [ccp4bb] I/sigma continued
If you want even more confusion on the labeling -- take a look at the PDB to mmCIF correspondence mappings for conversion between PDB and mmCIF format. In the PDB file format under REMARK 200 http://www.wwpdb.org/documentation/format32/remarks1.html#REMARK%20200 there is a line written as REMARK 200 I/SIGMA(I) FOR THE DATA SET : and REMARK 200 I/SIGMA(I) FOR SHELL : I/SIGMA(I) is not defined, but I always read it as the mean of [I/sigma(I)] and not the mean of I / mean of sigma(I). However, using the pdb to mmCIF correspondence guide. http://mmcif.pdb.org/dictionaries/pdb-correspondence/pdb2mmcif.html#REMARK200 This I/SIGMA(I) FOR THE DATA SET is linked to the pdb mmCIF dictionary token _reflns.pdbx_netI_over_av_sigmaI http://mmcif.pdb.org/dictionaries/mmcif_pdbx.dic/Items/_reflns.pdbx_netI_over_av_sigmaI.html this is defined as The ratio of the average intensity to the average uncertainty, /. which sounds like I/sigma(I) and not I/sigma(I). Likewise, the REMARK 200 I/SIGMA(I) FOR SHELL : shell value is linked to the mmCIF token _reflns_shell.meanI_over_sigI_obs using the PDB exchange dictionary give the definition The ratio of the mean of the intensities of the reflections classified as 'observed' (see _reflns.observed_criterion) in this shell to the mean of the standard uncertainties of the intensities of the 'observed' reflections in this shell. There is a separate pdb mmCIF dictionary token _reflns.pdbx_netI_over_sigmaI http://mmcif.pdb.org/dictionaries/mmcif_pdbx.dic/Items/_reflns.pdbx_netI_over_av_sigmaI.html Which is defined as The mean of the ratio of the intensities to their standard uncertainties, or I/SIGMA(I) So I have never understood why the PDB to mmCIF correspondence maps I/SIGMA(I) FOR THE DATA SET to _reflns.pdbx_netI_over_av_sigmaI and not to _reflns.pdbx_netI_over_sigmaI. Or if the PDB file format is supposed to have the mean of I / mean sigI then why is it written as I/SIGMA(I) in the header and not as I/SIGMA(I)? I never got a satisfactory answer when I asked the deposition staff. I haven't checked the latest version of pdb_extract, but in one of the previous versions, depending on which scaling program you used it would extract either mean (I) / mean (sigmaI) or mean (I/sigmaI) and assign it to the same _reflns.pdbx_netI_over_av_sigmaI token. Regards, Mitch (P.S. There are other strange mappings in the conversion between PDB and mmCIF formats but that is for another day...) -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Anastassis Perrakis Sent: Monday, March 30, 2009 11:40 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] I/sigma continued On 30 Mar 2009, at 20:30, James Holton wrote: Frank von Delft wrote: So, what statistic do we want to look at? That depends on what you are trying to do with the data. There is no way for Phil to know this, so it is good that he prints out lots of different statistics. That said, when talking about the data quality requirements for structure solution by MAD/SAD, I suggest looking at I/sigma(I) where: I - merged intensity (proportional to photons) assigned to a reciprocal lattice point (hkl index) Does ANY program print this out...? SCALA calls this Mn(I/sd). Sounds like d*TREK calls it I/sig avg. That is my understanding as well. With HKL you compute it by hand from the average I and average error. hmmm ... from error or from stat.? Should chi^2 be 1 first? Not sure about XDS... Confusingly, XDS calls that I/SIGMA from what I understand (which as I said before is NOT what SCALA calls I/sigma) Since we only use XDS and (mostly) SCALA in the lab, that is very confusing. I am pretty sure btw that I have myself -wrongly- quoted I/sigma as being I/sigma(I) in at least 3-4 papers. And I can bet I am not the only one that did so. I/sigmaI and I/sigma(I) are in my view more deterministic labels and will get safer on their way to Table 1. Tassos -James Holton MAD Scientist
Re: [ccp4bb] O/T: can a protein which dimerizes in solution crystallize as a monomer?
Hi Bernie, We had a case recently which was a dimer in the crystal (with 2 Ca binding sites in the symmetric dimer interface) but anSEC gave monomer under standard conditions ( 20mM Tris, 200mM NaCl, 0.5mM TCEP at pH7.5, Temperature at 8C ). The crystals had 0.2 M Ca Acetate. We had a little protein left over and tried running anSEC+SLS after adding Ca2+ to the protein sample and using a mobile phase of 20 mM Tris pH 7.5, 200 mM NaCl, 0.2 M CaCl2. It then ran as a dimer. See comments in remark 300 for pdb id 3DB7 http://www.pdb.org/pdb/explore/explore.do?structureId=3DB7 and the related TOPSAN page for this protein -- http://www.topsan.org/explore?pdbId=3db7 This supports Pat Loll Ethan Merritt's comments about the conditions (crystal and anSEC) influencing on the oligomerizaiton state. Neither of these conditions are what we expect the protein sees in the periplasm and we did not any protein left to investigate the concentration of Ca needed to shift the distribution from monomer to dimer, so it is hard to say for sure how it functions physiologically. Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Ethan A Merritt Sent: Thursday, December 11, 2008 8:34 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] O/T: can a protein which dimerizes in solution crystallize as a monomer? On Thursday 11 December 2008, Santarsiero, Bernard D. wrote: In parallel with the discussion around this off-CCP4-topic, are they any good examples of the opposite case, where the protein is a monomer in solution (as evident from light scattering, MW determination through centrifugation, EPR, etc.) but crystallizes as a dimer or higher multimer? I don't think such a question is entirely well-defined, for two reasons. 1) The monomer/dimer equilibrium in solution may well depend on the specific conditions (pH, concentration, presence of ligands, temperature, etc). Unless these conditions are replicated in your crystallization medium, it is uncertain to what extent the solution measurement is relevant. 2) How extensive an interface is required in order for it to be considered a dimer/multimer interaction? In the limiting case of very small interfaces, the entire crystal might be consider a single oligomer, with each lattice-packing contact constituting a monomer:monomer interaction. That's not a very useful place to set the threshold, but where do you set it - 100 A^2 ? 500 A^2 ? 1000 A^2? Some definition other than surface area? That said, I have some interest in the question as a practical matter. We have a new structure that is obviously, but totally unexpectedly, a tetramer in the crystal. In this case the monomer:monomer interaction surface is 1500 A^2. But exactly what criteria would I use to argue that this is a real tetramer? What criteria would I use to argue that it is a crystal artifact? Yes, of course ideally one would go back to the lab and survey for solution measurements that are consistent with tetramerization, but that is not always practical, and may lead right back to your original question. -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742
Re: [ccp4bb] Foam Dewars Part II
Hi Alun, The material we use is cross linked polyethylene/EVA foam. We use the 4 PCF (pounds per cubic foot) variety it has tradenames of youngboard, artilon and epilon. (see http://smb.slac.stanford.edu/facilities/hardware/cassette_kit/dewar_schematics.pdf and http://smb.slac.stanford.edu/facilities/hardware/cassette_kit/FabricationDewarAndLid.pdf for how we have the large dewars for the SSRL cassette Clyde described fabricated. ) Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Alun R. Coker Sent: Thursday, October 09, 2008 6:51 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Foam Dewars Part II Hi All, I think the foam from these dewars would make excellent flooring in LN2 working areas (where most other flooring cracks). I have seen Judo mats made out of a foam that looks similar. Can anyone tell me what this foam is? Alun. -- Alun R. Coker University College London Division of Medicine, Royal Free Campus Centre for Amyloidosis and Acute Phase Proteins Rowland Hill Street London NW32PF Tel: +44(0)207 433 2764
Re: [ccp4bb] to extract protein sequence from a rebuilt pdb file
Hi Jane, Qingping Xu wrote a python script that will extract the sequence from the PDB file and align it with a fasta file. The script depends on biopython and clustalw. Regards, Mitch -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Miller, Mitchell D. Sent: Tuesday, October 03, 2006 1:57 PM To: Bottomley, Matthew; [EMAIL PROTECTED] Subject: RE: [ccp4bb]: PDB to 1 letter code *** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** Hi Matt, Qingping Xu wrote a python script that will compare a PDB file with a fasta file and corrects ala/gly to the correct amino acid on output. The script depends on biopython and clustalw. If you are interested I made a copy available, http://smb.slac.stanford.edu/~mmiller/seqcheck.py http://biopython.org/ http://www.ebi.ac.uk/clustalw/ Regards, Mitch From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Jane Bailey Sent: Wednesday, October 01, 2008 1:40 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] to extract protein sequence from a rebuilt pdb file Hi, all I am currently rebuilting my structure in coot, and the protein sequence is around 98% rebuilt yet. I am looking for a way to extract protein sequence from the rebuilt.pdb so that I could see clearly which part need to be rebuilt by sequence alignment. Any ideas about this? thanks Best Jane
Re: [ccp4bb] Refmac out-put file header information
Hi Yusuf, You need to run the uniqueify script to expand the input file to include all possible reflections (observed and missing from your data set). I have not run xdsconv with the GENERATE_FRACTION_OF_TEST_REFLECTIONS=0.05 However, generally after running xdsconv without that command, it is necessary to run f2mtz, cad and uniqueify to prepare the input file for refmac. You can do a quick test like mtzdump test.mtz if it reports that your Fobs are 100% complete, then you need to run uniqueify to expand the file to contain all possible reflections up to the highest resolution in your input file. Without this, then the statistics will not be reported correctly in refmac and many other programs. see http://www.ccp4.ac.uk/dist/html/refmac5/files/log.html#pobs Percentage observed Fraction of the observed reflections in %. If uniqueify has been run before using REFMAC, this value will be calculated correctly. Otherwise it will be 100.0%. If your free flag column label is FreeRflag, then you can run the uniqueify script from the command line like: uniqueify -p 0.05 -f FreeRflag test.mtz if your input file is test.mtz the output from the script will be test-unique.mtz. or you can use the ccp4i task merge mtz files (CAD) by inputting your existing .mtz file and checking the box to complete the reflection list and extend your input freeR set. Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Yusuf Akhter Sent: Friday, August 08, 2008 2:20 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Refmac out-put file header information Dear Mitch, I did not run uniqueify but i have added free-R flags by running xdsconv with extra command line in in-put file GENERATE_FRACTION_OF_TEST_REFLECTIONS=0.05 Dear Leo, This 94.5% is total completeness of the data. I am pasting below the header information in that PDB file. REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.74 REMARK 3 DATA CUTOFF(SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE(%) : 100.00 REMARK 3 NUMBER OF REFLECTIONS : 12072 Have anybody some suggestions?? Thanks, yusuf -- Yusuf Akhter EMBL Hamburg c/o DESY, Notkestraße 85, 22603 Hamburg, Germany Thank you very much to Artem, Lijun, Dale and Paul for giving me great suggestions regarding my earlier query on D to L amino acid residues. Now one more problem is in same 3 A structure refinement. For those who not remembered my case. I have processed a diffraction data-set at 3 A using XDS. I am using Refmac for refinement. My data is 95.4% of completeness at Signal/noise =-3. I noticed that in the header of out-put PDB file from Refmac shows 100% completeness. Is it a bug?? May somebody tell me where the problem is? Thanks in advance. yusuf -- Yusuf Akhter EMBL Hamburg c/o DESY, Notkestraße 85, 22603 Hamburg, Germany Quoting Yusuf Akhter [EMAIL PROTECTED]: Hi Everybody, I am refining structure of a protein at 3 Angstrom. I am doing model building in Coot. After several rounds of refinement using Refmac when I tried to run PROCHECK on my partially build model I found that some of the residues are D-amino acids. How to change these D-amino acids to L-amino acids?? Is there any option in Coot for that?? Thanks in advance, yusuf - This mail sent through IMP: http://horde.org/imp/
Re: [ccp4bb] quote source
Hi Bernhard, Google books is your friend... It returns 2 hits for Although the hydrogen bond is not strong it has great significance in determining the properties of substances. Because of its small bond energy Both are essays / chapters by Max Perutz I Wish I'd Made You Angry Earlier: Essays on Science, Scientists, and Humanity - Page 166 has the quote attributed to Pauling but without reference. http://books.google.com/books?id=GkODMkCWndQCpg=PA166dq=%22Although+the+hydrogen+bond+is+not+strong+it+has+great+significance+in+determining+the+properties+of+substances.+Because+of+its+small+bond+energy%22sig=ACfU3U0HC6n1toHJgD9Z-bedRSs7eVvz8Q And Pioneering Ideas for the Physical and Chemical Sciences: Josef Loschmidt's ... - Page 1 by W. Fleischhacker, Thomas Schönfeld has a chapter titled The significance of the hydrogen bond for physiology by Max Perutz where the quote is attributed to being from Pauling's newly published Nature of the Chemical Bond which Perutz obtained with a Christmas 1939 book token so I presume it was the 1940 version. http://books.google.com/books?id=cMc9BHNyIWsCpg=PA1lpg=PA1dq=%22Although+the+hydrogen+bond+is+not+strong+it+has+great+significance+in+determining+the+properties+of+substances.+Because+of+its+small+bond+energy%22source=webots=sU9k_3dU9wsig=3ZCCE8u8ZpLBa-ycU2v0eT1s4oghl=ensa=Xoi=book_resultresnum=2ct=result The 1960 version of Pauling's book is on Google books and it has a similar but not identical statement. see pp. 449-450. http://books.google.com/books?id=L-1K9HmKmUUCprintsec=titlepagedq=Nature+of+the+Chemical+Bond+Paulingsource=gbs_toc_scad=1#PPA449,M1 Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Bernhard Rupp Sent: Wednesday, July 23, 2008 10:26 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] quote source Dear All, does someone know the proper reference of this L. Pauling statement? Although the hydrogen bond is not strong it has great significance in determining the properties of substances. Because of its small bond energy and the small activation energy involved in its formation and rupture, the hydrogen bond is especially suited to play a part in reactions occurring at normal temperatures. It has been recognised that hydrogen bonds restrain protein molecules to their native configurations, and I believe that as the methods of structural chemistry are further applied to physiological problems it will be found that the significance of the hydrogen bond for physiology is greater than that of any other single structural feature. It is quoted by Perutz but no ref Thx, br - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 [EMAIL PROTECTED] [EMAIL PROTECTED] http://www.ruppweb.org/ - The hard part about playing chicken is to know when to flinch -
Re: [ccp4bb] Expression vector with NdeI-ClaI sites
Another new school cloning reference: Klock, H.E., Koesema, E.J., Knuth, M.W. Lesley, S.A. Combining the polymerase incomplete primer extension method for cloning and mutagenesis with microscreening to accelerate structural genomics efforts. Proteins (2008) 71, 982-994. published online 14 November 2007 (doi:10.1002/prot.21786). http://dx.doi.org/10.1002/prot.21786 Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Mark Collins Sent: Monday, July 21, 2008 9:48 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Expression vector with NdeI-ClaI sites Or do the new school cloning, SLIC (Sequence Ligation Independent Cloning) and subclone into any position in a vector. This method uses a PCR product and vector, the PCR primers have 20-40bp overlap with a region in the vector. Mix cut and purified vector with PCR product. Digest with T4 polymerase, quench, and transform. When I do the PCR in the morning I have clonies the next day. REF: Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC Mamie Z Li Stephen J Elledge Nat Meth V4(3) pp 251 Mark -- Mark Collins Columbia University Biochemistry Molecular Biophysics Black Building 259/201 Office/Lab 212 305 1951 (work) [EMAIL PROTECTED]
Re: [ccp4bb] Parameter MAXSAVE exceeded
You could also try cns2mtz? http://www.ysbl.york.ac.uk/~cowtan/cns2mtz/cns2mtz.html Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Ezra Peisach Sent: Thursday, July 03, 2008 11:28 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Parameter MAXSAVE exceeded I do not know off hand what a .cv file is - unless it is a cns/xplor reflection file. Instead of using f2mtz - try sftools. Ezra Jayashankar wrote: Dear scientists and friends, When I try to convert a .cv file to .mtz by f2mtz I got the following error,what it means ans what should I do to get rid of it. ''Parameter MAXSAVE exceeded'' -- S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany
Re: [ccp4bb] JCSG dataset archive
I would like to also add that depending on what you want to use the test data for, you may find that the data JCSG has deposited with the PDB is sufficient. The JCSG crystal structures include the following data sections in the structure factor file deposited with the PDB (since spring 2004). 1. First section -- loop over merged Fobs, (or Iobs), sigF (or sigI), Fcalc, Phicalc, FreeR-flag (status) 2. For each wavelength of data used in phasing there is a separate loop over the scaled, unmerged, original index intensities and sigI. 3. Then there is a data loop for the experimental phasing results listing the HL-coefficients from the phasing program (usually autoSHARP or solve). 4. The last loop is over fom, pdbx_fom_weighted_fmap and phase from density modification. The Fmap coefficient and the DM phase is the starting map used for automated model building. (For MR structures, the just the first 2 data sections are present). If you are interested in testing MAD or SAD phasing, DM or autobuilding, algorithms etc, then the data deposited with the PDB is probably sufficient for your needs. http://www.pdb.org/pdb/search/navbarsearch.do?newSearch=yesisAuthorSearch=noradioset=AllinputQuickSearch=JCSG%20crystal If you wanted to reintegrate the data from the diffraction images or if you wanted to compare your autotraced model with the autotraced model we obtained, then these additional data (as well as log files) are only available through the JCSG dataset archive. So as Ashley mentioned, please request access to the archive if you are still interested in this additional data. Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Deacon, Ashley Sent: Thursday, June 12, 2008 9:41 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] JCSG dataset archive All, Thanks to everyone who has recently requested access to the JCSG dataset archive. We have a large and growing number of users. Your requests will be handled shortly and you will receive notification via e-mail. Our registered users fall into 3 main classes: 1) Methods developers who want access to a wide array of test data. 2) Students and postdocs who want datasets for training purposes. 3) Researchers interested in one of our structures, who want access To all the data we have available, including datasets from different constructs or crystal forms that didn't necessarily make it into our final PDB deposition. For those who may still be interested, the dataset archive can be accessed through our structure gallery page: http://www.jcsg.org/prod/scripts/structure_gallery/gallery.shtml The datasets are available without restriction, most of them are Se MAD/SAD or distant homology MR. We do ask you to register and explain why you want access. This is largely for tracking/statistics purposes (we won't be sending you a lot of junk mail). Hopefully in the future we can improve the system to better serve our users. Soon we will be adding diffraction image datasets for *all* our structures as Soon as they are deposited. In the meantime, if there is a dataset you would like that is not currently available through the archive just drop me an e-mail. Suggestions are always welcome. Sincerely, Ashley Deacon Joint Center for Structural Genomics.
Re: [ccp4bb] phases origin shift
There is a resolve script that will allow you to shift the origin of phases to match another set --- http://solve.lanl.gov/Resolve/html_resolve_manual/resolve_sample_scripts.htm#offset_phases Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Jianghai Zhu Sent: Friday, June 06, 2008 9:02 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] phases origin shift Hi All, I have a data set with experimental phases. I would like to shift the origin of the phases so that it matches the origin of another data set and phases, which has different cell constants. Any suggestion of what tools has the ability to do this? i.e. shift the origin by (0.0, 0.0, 0.5). Thanks. -- Jianghai
Re: [ccp4bb] Summary: Calculating R-factor and maps from a Refmac model containing TLS downloaded from the PDB
Hi Martyn, When the rcsb processes files, that line is stripped form the PDB file. We have taken an effort in the last few years to copy it into the REMARK 3 OTHER REFINEMENT REMARKS: field so that it is retained in the PDB file. Sometimes you can find out if that line was in the original PDB file header that was deposited by checking the mmCIF formatted file in the loop over the _database_PDB_remark.id _database_PDB_remark.text In the case of 2qua, the text for pdb_remark id 3 contains the line ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY http://www.pdb.org/pdb/files/2qua.cif Since I don't deposit with EBI / pdbJ, I am not sure if they also strip this record from the PDB formatted header or not. Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Winn, MD (Martyn) Sent: Tuesday, March 18, 2008 7:04 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Summary: Calculating R-factor and maps from a Refmac model containing TLS downloaded from the PDB Refmac (at least 5.2) and TLSANL write a line into the PDB header specifying what is in the B column: REMARK 3 ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY Looking at 2qua which used Refmac 5.3, that line isn't there. I don't know at what stage it has been lost. Of course, it would be nice if all the TLS stuff was in dedicated header records. Note that you can use TLSANL to recover residual B from combined B (given TLS parameters), see keywords BRESID and ISOOUT. Note also you would need ANISOU records to reproduce R factors - combined B would not be enough. Cheers Martyn -Original Message- From: CCP4 bulletin board on behalf of Pavel Afonine Sent: Tue 3/18/2008 1:25 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Summary: Calculating R-factor and maps from a Refmac model containing TLS downloaded from the PDB 2) Some files list in the ATOM B column the residual B after TLS has been accounted for while others list the total B (TLS and residual). There is no clear indication in the PDB file which interpretation is being used. That is a fundamental deficiency in the existing PDB standard. It simply doesn't specify how to present this critical information. A draft change covering this was circulated at the PDB get-together of last summer's ACA meeting, and I discussed with Garib and Eleanor that we should as a community decide how we would like it handled. The consensus as I understand it is that people would prefer that the B field of individual ATOM records contain the *net* B rather than the residual B, so that old programs will continue to work as expected. However, this puts even more importance on the TLS description in the header being correct, since the information is otherwise not recoverable. We were going to circulate a letter, but I plead guilty to letting the matter slide. This is exactly what phenix.refine does (since 2005, I guess): it always prints out the total B-factor for each atom (Bindividual+Btls+Boverall). The TLS information (TLS matrices, origin coordinates and TLS group selections) are reported as well in PDB file header, so if necessary one can always extract the information about individual contributions. This makes it more straightforward to reproduce the R-factor statistics without any prior manipulations with the model. Another notable omission is the lack of scattering factors. If you have refined a SAS data set, e.g. a Se-edge dataset of a SeMet metallo-protein, then the R factors may vary by 1% just because of incorrectly reproduced f' terms for the Se and metal atoms. Ethan Merritt phenix.refine also always reports f' and f'' in output PDB file if they were used in refinement. I hope they don't get stripped off when deposited with PDB. Pavel.
Re: [ccp4bb] Webcast of the CCP4 study weekend ?
Hi Juergen, I found that if I follow the link for the Jan 4 talks on the http://extrplay.dl.ac.uk/ http://extrplay.dl.ac.uk/CCP4/20080104-1/ It appears that they did not update the link page and are using the same URL for the streaming today that they used yesterday Regards, Mitch P.S. I was using IE v 6 on XP. -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Juergen Bosch Sent: Friday, January 04, 2008 9:35 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Webcast of the CCP4 study weekend ? Rajesh Ponnusamy wrote: Do the webcast is working in this link ? http://extrplay.dl.ac.uk/ Thank you Rajesh Ponnusamy Except of the archived lectures nothing works for me, (OS X Safari, Firefox, Linux, Mozilla) I was ready to watch Piet at 6 am PST, but then decided to have another cup of tea instead hitting reload. So I guess they have some sort of problems. Juergen -- Jürgen Bosch University of Washington Dept. of Biochemistry, K-426 1705 NE Pacific Street Seattle, WA 98195 Box 357742 Phone: +1-206-616-4510 FAX: +1-206-685-7002 Web: http://faculty.washington.edu/jbosch
Re: [ccp4bb] Webcast of the CCP4 study weekend ?
I was using real player v 8 with Ie v 6 and I also tried it with IE 6 and real player v 10.5 on another system and it worked. Currently the site gives me the error file not found for rtsp://extrplay.dl.ac.uk/broadcast/CCP4.rm but this is only since the live streaming session ended. I did not get up early enough to watch all of the talks, but was able to see from Florian Brückner's talk at ~15:00 Leeds time until the end of Axel Brunger's talk at the end of session 3. Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Kay Diederichs Sent: Friday, January 04, 2008 10:42 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Webcast of the CCP4 study weekend ? The error message is that it cannot find rtsp://extrplay.dl.ac.uk/CCP4/20080104-083503-1.rm
Re: [ccp4bb] FreeR flag value swap
Hi Petra, You can use sftools, to set the FreeR_flag column to be the old ((FreeR_flag - 1)*-1 ) e.g. sftoos eof read myfile.mtz calc col FreeR_flag = col FreeR_flag 1 - -1 * write free-R-swap-1-0.mtz quit eof Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Petra Lukacik Sent: Thursday, September 27, 2007 12:03 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] FreeR flag value swap I have a mtz file (output from phenix AutoSol and AutoBuild) where the FreeR flag for the test set has a value of 1 and and the working set has value 0. This is opposite to the ccp4 default where the FreeR set used within refinement is flagged as 0. Is there a way to swap the two around so that my file has the ccp4 default arrangement? Preferably I would like to avoid conversion to ASCII reflection file formats (and back to mtz). Many thanks Petra -- Dr Petra Lukacik NIDDK, NIH Building 50, Room 4507 50 South Drive Bethesda MD 20892 USA Tel: 301 594 9231 -
Re: [ccp4bb] small molecule refinement GUI for Mac
What about Ton Spek's Platon / System-S package? http://www.cryst.chem.uu.nl/platon/pl00.html It does not have precompiled mac OSX binaries (only linux and windows), but it does have source code and instructions for compiling under unix and states that it will compile without changes under macOSX. It is free for academics. Regards, Mitch From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Kristof Van Hecke Sent: Friday, August 31, 2007 5:16 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] small molecule refinement GUI for Mac Dear all, I'm looking for a small molecule refinement GUI for shelxl under Mac OSX (commercially or non-commercially available). Any suggestions are very welcome! Many thanks Sincerely Kristof -- Kristof Van Hecke, PhD Biomoleculaire Architectuur Celestijnenlaan 200 F B-3001 Heverlee (Leuven) Tel: +32(0)16327468 -- Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm for more information.
Re: [ccp4bb] SAD: Refine against anomalous data
Hi Ethan, I have been wanting a way to instruct refmac to accept a user-defined f' term since about forever. According to Garib's latest release notes, a command was added to refmac 5.3.0015 and later to allow f' to be specified. I have not tried it myself yet.. see http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_news.html Anomolous form factors anom formfactor [Name] [f'] [f''] It will modify form factor of the given atom and use f' part only Regards, -Mitch -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Ethan Merritt Sent: Friday, August 10, 2007 9:20 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] SAD: Refine against anomalous data On Friday 10 August 2007 04:53, Clemens Vonrhein wrote: It should be trivial to put this into REFMAC too (Garib!): just add cards like FPRIme atom-type f'-value so that a user can do FPRIme Se -4.5 REFMAC then corrects C by the difference f'(CuKa)-(-4.5) (after reading the f'(CuKa) from atomsf.lib). And suddenly all those partially substituted Se-MET are becoming 100% substituted again ... a kind of 'in-silico expression system'. I heartily endorse this suggestion. I have been wanting a way to instruct refmac to accept a user-defined f' term since about forever. Failing that, it would be nice if the ccp4i interface to refmac had a slot for specifying an alternative ATOMSF file. As it is one has to edit the command script by hand in order to change ATOMSF. A follow-on request is that the entire scattering factor table, including such user-specified values, be dumped in the output cif and pdb files. -- Ethan A MerrittCourier Deliveries: 1959 NE Pacific Dept of Biochemistry Health Sciences Building University of Washington - Seattle WA 98195-7742
Re: [ccp4bb] Double conformations of cysteine !
The SSBOND record does not allow the specification of an alternate location indicator. The PDB practice is to list the SSBOND record if any confirmation is in an SS-bond. I think that refmac has problems with this since it will try to apply the SSBOND patch to both confirmations. The workaround is to use the LINK record in refmac for the SS-bonded A confirmation (which allows alternate atoms to be specified) and use a link_id of SS. Refmac should then generate the correct restraints for the conformer involved in the disulfide bond. Note that this should probably be listed as SSBOND in the header for the deposited PDB file. Regards, Mitch See http://www.wwpdb.org/documentation/format23/sect6.html http://www.ccp4.ac.uk/html/refmac5/files/coordinates.html#pdb_ssbond -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Prasenjit Bhaumik Sent: Friday, July 06, 2007 10:46 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Double conformations of cysteine ! Hello, We are trying to refine a structure using REFMAC and we are facing problem in refining the double conformations of a cysteine residue. One conformation is involved in formation of a disulfide linkage and other conformation is free. Is there any way to define the restraints so that both the conformations can be refined. With kind regards, Prasenjit -- Prasenjit Bhaumik, Ph.D. Protein Structure Section Macromolecular Crystallography Laboratory National Cancer Institute at Frederick 1050 Boyles Street, Building-539, Room-145 P.O. Box B, Frederick, MD-21702, USA Phone: 301-846-1974, Fax: 301-846-7101 E-mail: [EMAIL PROTECTED] -
