Re: [ccp4bb] Poor electron density in some of the chains in an asymmetric unit
Dear All, Thanks for the reply. I will try process and refine the data again, will see if it improves. Thanks again to all. -- Sonali Dhindwal “Live as if you were to die tomorrow. Learn as if you were to live forever.” From: Mark van Raaij mjvanra...@cnb.csic.es To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, 30 April 2013 1:42 AM Subject: Re: [ccp4bb] Poor electron density in some of the chains in an asymmetric unit and 2VAK...average Bs for the twelve, sequence identical, chains vary from 28 to 53. On 29 Apr 2013, at 22:09, David Schuller wrote: On 04/29/13 12:26, Roger Rowlett wrote: FYI, I do know of one example of a solved structure where some of the molecules in the ASU are poorly defined. In 1EKJ, 4 of the 8 molecules in the ASU have low B-factors (mid 30s) and 4 have high B-factors (50s-60s). In the unit cell these layers alternate. It is possible, if everything else has been excluded, that your crystal has a similar crystal-packing issue. Another is 3HDH. Pig short chain L-3-hydroxyacyl-CoA dehydrongenase revisited: sequence analysis and crystal structure determination. Barycki, et al (1999) Protein Science 8: 2010-2018. Examination of the map in the region of subunit C revealed that the electron density was considerably weaker for the third subunit compared to the other subunits... -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] refinement hanging--what am I missing?
What is the relationship between the molecules in the spacegroups - it seems likely that in the bigger cell there is a NC translation of ~(1/2,y,z)? ? (A2 ~ twice a1) That can be checked by the native Patterson.. If so that gives a class of significantly weaker reflections for h odd, and that usually does lead to higher R factors. It also means that the h00 reflections will be weak for h odd, and that the SG assignment could be either P2 2i2i or P21 2i2i - you need to test both.. However that doesnt explain the smaller R factors, unless the packing there also gave rise to a NC translation.. Again checked from the native Patterson.. Eleanor On 29 April 2013 16:14, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Ed, just FYI: while this does not apply in the ccp4/mtz world, the fact you might be missing is that in some refinement environments merging is carried out by the refinement program so that the actual data can be kept unmerged and e.g. the information you refer to does not get lost (although scaling would smoothen it to a certain extent but at least does not erase it as mergin does). In that case you could expand to P1 (as far as I understand). best, Tim On 04/29/2013 04:13 PM, Edward A. Berry wrote: herman.schreu...@sanofi.com wrote: I would process or expand the data to P1, also expand your pdb file to P1 and refine in P1 to see what happens. I would also run Phaser or some other molecular replacement program on the P1 data to see what comes out. process or expand? I don't understand how there can really be a choice here. If the data is expanded from higher symmetry, it will precisely have that higher symmetry, i.e. all reflections that were equivalent in the higher symmetry will be identical. Any information about asymmetry was lost when the data were merged in the higher symmetry space group. Won't refinement by minimizing a target function have exactly the same solution? Or not exactly, because the refinement program can introduce asymmetry by allowing different phases for the equivalent reflections. But where is the information to generate that asymmetry coming from? There is probably something I'm missing here, but i would definitely reprocess in the lower symmetry if the rotation angle was sufficient to give good completeness. eab - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRfo5lUxlJ7aRr7hoRAkHvAJ9VRWDjbH8gcF1OW5vfprehPJDCUwCfTHoA nv3mtZH/Em2VlbDh9IFDvoU= =F/Om -END PGP SIGNATURE-
Re: [ccp4bb] Puzzling Structure
And as a footnote* - * I notice that, following discussion on this bulletin board, the space group of the 2wlv coordinate file has been updated. But at this point did it not occur to the PDB to change the space group in the structure factor file as well? So the coordinates indicate P21 21 2 but the structure factor file still says P21 21 21... Hmm consistency is highly over-rated... Also the author's SF data listing starts with c axis reflections including 0, 0, l odd as well as even, which is sort of a hint here From: MARTYN SYMMONS martainn_oshioma...@btinternet.com To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, 16 April 2013, 14:30 Subject: Re: [ccp4bb] Puzzling Structure Just as a postscript. It has been pointed out to me that the space group was correct in the uploaded PDB and in the mtz reflection file. And there was no editing of this data pre-deposition. I am sort of surprised how quickly people are to beat up on the authors in such cases since we do not have access to the full data and facts. Having the uploaded data available would allow better checking. I'm mainly ignorant of the details, but isn't this the way sequence data is dealt with? - there are the unannotated sequence files which are gradually checked and assimilated (but not over-written). Cheers Martyn From: Michel Fodje michel.fo...@lightsource.ca To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, 15 April 2013, 17:19 Subject: Re: [ccp4bb] Puzzling Structure Just to round up this topic, a bug report was submitted to PDBe concerning entry 2wlv and the PDB has how responded acknowledging the problem. An updated entry will be available in one week. As pointed out by Savvas, it is very likely the CRYST1 record was manually edited prior to deposition resulting in the wrong spacegroup being parsed in by AutoDep and subsequent processing moving the waters around in the wrong space group. Since there is no logical reason for the authors to do this, it was probably inadvertent. I imagine somebody accidentally deleted a space between P 21 21 2 and 18 and tried to fix it by adding it back, between 1 and 8. /Michel -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Edward A. Berry Sent: April-14-13 9:59 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Puzzling Structure Robbie Joosten wrote: Hi Martyn, I think the question is where the error was made - seeing the uploaded file would clear this up. But it seems unlikely to me that the depositor saw a huge R factor discrepancy at the end of refinement and just blithely uploaded it. So scenario 3 :- PDB : we cannot reproduce your R factor with our programs Depositor : that's your problem mate - it was fine when it left me...up to you to sort it... Which seems a sort of reasonable attitude to me. Not quite, the depositor has to give, i.e. type, the space group (example depositions: https://www.ebi.ac.uk/pdbe- xdep/autodep/AutoDep?param=QovCsvhNv06Mpnr%2BvIkqqfuqeeBd8leFN AVymZgS%2Fe7mULyfrCaTMN8jsyaGZUTyUDQyN3gMF3o%3D). Don't ask me why, because it is clearly a source of error. In my experience with RCSB autodep2, assuming the information was in the uploaded pdb file, this information is already pre-filled and the depositor just glances over to see it is correct. A missing or extra (1) might not be noticed. So perhaps it is a parsing error, perhaps related to the different ways the space group is represented on the CRYST1 card, and the different stringency of different programs in interpreting the CRYST1 card. But the validation report is included with the approval request letter, and major discrepancies are noted in the text of the validation letter in case the depositor is too busy to actually read the validation report. So if the depositor read more than the first line or two of the letter he should have known there was a problem. Then there is the 2-week default release policy: No major issues were raised during data processing. A summary of some of the key annotations in your entry is shown below. Please verify that these are correct. If we do not hear from you within two weeks, we will consider this entry to have been approved by you. The entry will then be released according to the release/hold instructions you have provided. If this 2-week default release is the rule even when there are issues, the depositor may have put it aside to find the problem when time was available, and waited too long and let the default release kick in. eab
[ccp4bb] Survey on selenium-derivatized nucleic acids for crystallographic applications
Dear Crystallographers, This 10-question survey is conducted on behalf of the NSF-funded program. It is designed to get feedback from the structural biology community on selenium-derivatized nucleic acids for crystallographic applications. Your participation in this survey is greatly appreciated. This survey should take less than 3 minutes to complete. http://www.surveymonkey.com/s/HVKY9T3 Please feel free to forward this invite to any colleagues. We greatly appreciate your time and help with this survey. Sincerely, Sibo Sibo Jiang Georgia State University Department of Chemistry 50 Decatur St. Natural Science Center Rm 548 Atlanta, GA, 30303, USA Phone: 1-404-413-5534 (Lab) 1-404-574-9785 (Cell) Email: sjia...@student.gsu.edumailto:sjia...@student.gsu.edu
[ccp4bb] detectors on home sources
I'm involved in advising my institute on an X-ray home source for a core facility. The vendors are offering some new configurations. Whatever the claimed advantages/disadvantages, I'm hesitant to make a decision without consulting someone with direct experience with them. In particular, has anyone had any experience with using the photon100 CMOS detector being offered by Bruker, or the pilatus 200K detector being offered by Rigaku? I'd also appreciate hearing from anyone with experience with the latest Bruker microfocus rotating anode generator (called the Turbo or TXS)? Many thanks for sharing your experiences. Fareed Aboul-ela Associate Professor Zewail University Zewail City of Science and Technology Giza, Egypt faboul...@zewailcity.edu.eg
Re: [ccp4bb] detectors on home sources
The Excillum MetalJet (TM) source is technically very interesting, with its liquid metal jet anode, but I have no idea how well it works for typical in-house crystallography use. On 04/30/13 15:00, Fareed Aboul-Ela wrote: I'm involved in advising my institute on an X-ray home source for a core facility. The vendors are offering some new configurations. Whatever the claimed advantages/disadvantages, I'm hesitant to make a decision without consulting someone with direct experience with them. In particular, has anyone had any experience with using the photon100 CMOS detector being offered by Bruker, or the pilatus 200K detector being offered by Rigaku? I'd also appreciate hearing from anyone with experience with the latest Bruker microfocus rotating anode generator (called the Turbo or TXS)? Many thanks for sharing your experiences. Fareed Aboul-ela Associate Professor Zewail University Zewail City of Science and Technology Giza, Egypt faboul...@zewailcity.edu.eg mailto:faboul...@zewailcity.edu.eg -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] detectors on home sources
One of the main things (if not THE main thing) to worry about when investing in such expensive equipment is long-time reliability and quality of service in your place. Nothing is more frustrating than seeing your wonderful and expensive equipment standing idle for long periods because of lack of service. This may mean quite often taking compromises and going perhaps not for the front-line state-of-art piece of equipment but rather for the sturdy, hard-working equipment. It worked for us very well. My 2p advice. 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: 972-8-647-2220Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Fareed Aboul-Ela [faboul...@zewailcity.edu.eg] Sent: Tuesday, April 30, 2013 10:00 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] detectors on home sources I'm involved in advising my institute on an X-ray home source for a core facility. The vendors are offering some new configurations. Whatever the claimed advantages/disadvantages, I'm hesitant to make a decision without consulting someone with direct experience with them. In particular, has anyone had any experience with using the photon100 CMOS detector being offered by Bruker, or the pilatus 200K detector being offered by Rigaku? I'd also appreciate hearing from anyone with experience with the latest Bruker microfocus rotating anode generator (called the Turbo or TXS)? Many thanks for sharing your experiences. Fareed Aboul-ela Associate Professor Zewail University Zewail City of Science and Technology Giza, Egypt faboul...@zewailcity.edu.eg
