Re: [ccp4bb] Format conversion of Shelx coordinate file
Hello Florian, you can read the .hat-file into coot and save it from there, changing the suggested file-extenstion from .ins to .pdb. In case coot crashes when it reads the .res-file, edit the file and make sure there is only one END-card. Maybe shelxpro would also work. Tim On Mon, Aug 30, 2010 at 05:36:37PM -0400, Florian Schmitzberger wrote: Dear All, What is currently the quickest/easiest way to convert a .hat file with fractional coordinates of heavy atoms generated by ShelxE to PDB format and/or a file format accepted by Sharp? I tried to use coordconv from ccp4, but it failed to make the conversion. Thank you. Regards, Florian --- Florian Schmitzberger Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, SGM 130 Boston, MA 02115, US Tel: 001 617 432 5602 -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] Format conversion of Shelx coordinate file
Hi, What is the motto/slogan of coot? I read so often about it on ccp4bb. If there is not one yet, I propose: coot, the crystallographer's swiss knife :'D Regards, F. Tim Gruene wrote: Hello Florian, you can read the .hat-file into coot and save it from there, changing the suggested file-extenstion from .ins to .pdb. In case coot crashes when it reads the .res-file, edit the file and make sure there is only one END-card. Maybe shelxpro would also work. Tim On Mon, Aug 30, 2010 at 05:36:37PM -0400, Florian Schmitzberger wrote: Dear All, What is currently the quickest/easiest way to convert a .hat file with fractional coordinates of heavy atoms generated by ShelxE to PDB format and/or a file format accepted by Sharp? I tried to use coordconv from ccp4, but it failed to make the conversion. Thank you. Regards, Florian --- Florian Schmitzberger Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, SGM 130 Boston, MA 02115, US Tel: 001 617 432 5602
[ccp4bb] AW: [ccp4bb] Format conversion of Shelx coordinate file
Coot MacGyver -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag von Francois Berenger Gesendet: Dienstag, 31. August 2010 08:15 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Format conversion of Shelx coordinate file Hi, What is the motto/slogan of coot? I read so often about it on ccp4bb. If there is not one yet, I propose: coot, the crystallographer's swiss knife :'D Regards, F. Tim Gruene wrote: Hello Florian, you can read the .hat-file into coot and save it from there, changing the suggested file-extenstion from .ins to .pdb. In case coot crashes when it reads the .res-file, edit the file and make sure there is only one END-card. Maybe shelxpro would also work. Tim On Mon, Aug 30, 2010 at 05:36:37PM -0400, Florian Schmitzberger wrote: Dear All, What is currently the quickest/easiest way to convert a .hat file with fractional coordinates of heavy atoms generated by ShelxE to PDB format and/or a file format accepted by Sharp? I tried to use coordconv from ccp4, but it failed to make the conversion. Thank you. Regards, Florian --- Florian Schmitzberger Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, SGM 130 Boston, MA 02115, US Tel: 001 617 432 5602 attachment: mac-gyver-00_thumb.jpg
[ccp4bb] Postdoctoral position in X-ray crystallography, Montpellier, France
Dear all, Please could you bring this advert to the attention of any potential candidates? With industrialization, the production of chemicals and their introduction into the environment has increased massively. Some of these compounds act as endocrine disrupting chemicals (EDCs) that cause adverse effects in the endocrine system by interfering with hormone signaling. Epidemiological studies suggest a link between the increasing exposure to these chemicals and the development of the main diseases of the industrialized world including reproduction defects, hormone-related cancers, or metabolic disorders. We have launched a research program to elucidate the mechanisms by which EDCs bind to nuclear hormone receptors (NHRs) and in turn improve the predictability of the endocrine-disrupting potential of environmental contaminants. A 3-years postdoctoral research position is open (starting end 2010) at the Center for Structural Biochemistry (CBS) in Montpellier, France. The position requires the applicant to work on structural and biochemical characterization of NHRs including the peroxisome proliferator activated (PPAR), the estrogen (ER) or the androgen (AR) receptors in complex with EDCs. We are looking for highly motivated candidates with experience in protein purification, crystallization, X-ray data collection, structure determination and structural analysis. Applicants should send their CV and the names and contact information of at least three references via email to: William Bourguet Centre de Biochimie Structurale 29 rue de Navacelles 34090 Montpellier, France Tel : +(33) 4 67 41 77 02 Fax : +(33) 4 67 41 79 13 Email : bourg...@cbs.cnrs.fr CBS info : www.cbs.cnrs.fr Best regards, Albane le Maire
Re: [ccp4bb] how to optimize crystallization of a membrane proteinf
Unfortunately, some crystals don't diffract at all. You may want to try to 100% verify that it's protein either by SDS-PAGE or mass-spec (100x100x100 micron crystal could contain ~0.5mcg of protein, so you my need to use silver staining). If it is, I'd consider trying to get diffracting crystals by a) dehydration (chances are slim since you have no diffraction at all) b) microseeding c) additive screen (SilverBullets?) d) screening a lot of crystals (how small are the small ones? They may be good enough for microfocus beamlines and yes, smaller crystals generally tend to produce better diffraction quality) e) this one sounds silly, but make sure you are hitting the crystal with the beam (just shift it up and down a notch and take single shot - I've seen this trick actually working several times) The list is not comprehensive. But frankly, having non-diffracting crystals is a poor place to start, these guys waste a lot of time and often still don't diffract no matter what you try. Good luck, Ed. On Mon, 2010-08-30 at 21:24 -0400, qiangm zhang wrote: Hi all, I got a crystal of one membrane protein (~60kD) from Na/K phosphate condition (see getit_4), then I got the improved crystal like getit_5 after trying seeding, different detergents, lipids and additives. But this crystal does not diffract at all, I already tried Izit staining which shows it is protein crystal (detergent crystal?). Does anyone have any good suggestions for the optimization of this membrane protein crystallization? Thank you in advance. Best regards Qiangmin Zhang Biomedical Science Tower 3 Room1034 3501 Fifth Avenue Pittsburgh, PA 15260 -- 张强敏 -- 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 /
[ccp4bb] fail to install ccp4i task for arp warp
Dear All, sorry to bother you with this but I just can't figure out what goes wrong ... I am running the latest version of snow leopard on a MBP unibody with the 64bit kernel. I have an up to date fink installation for native 64bit. With this I have installed ccp4 via fink. I have also installed the latest arp warp version (7.1). Both are running nicely individually ... The thing now is that I cannot install the arp warp task in ccp4i. Neither via the original arp warp installation which says it is successful but no tasks show up nor via the ccp4i interface which always ends up with: UnpackTaskArchive: uncompress failed to create /tmp/install_ARP_wARP_CCP4I6/ARP_wARP_CCP4I6.tar ExamineTaskArchive: failed to unpack temporary copy of /Users/joka/software/arp_warp_7.1/ARP_wARP_CCP4I6.tar.gz Needless to say that the packages unpack just fine when I try this without the interface using the same uncompress binary. It does not make a difference whether I use ccp4i with sudo, su or login as root. I am running out of options here and would really appreciate a hint in the right direction ... I have found this in the ccp4bb http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg10117.html but that does not really help. Cheers, Jochen - Dr. Jochen Kuper Rudolf Virchow Center for Biomedical Research Josef Schneider Strasse 2, Haus D15 97070 Wuerzburg +49 (0) 9313180391 jochen.ku...@virchow.uni-wuerzburg.de
[ccp4bb] Crystallography Position at UCB, Slough, UK
Position Available: Protein Crystallography We have an opening for permanent position in the area of crystallography. The position is at the Slough, UK research hub of UCB, a leader in medicines for epilepsy and inflammatory disease. Applicants are expected to have experience in sub-cloning, protein expression and purification, and crystallization and structure determination of proteins by X-ray crystallography. The individual chosen will provide structural information on compound binding to our molecular targets, to aid Medicinal Chemistry and CADD departments to enable them to work in an information-rich environment. Structural information is also required for NBE projects, both on Fabs and on Fab-antigen complexes. For more information about this post or to apply please contact tom.ce...@ucb.com mailto:tom.ce...@ucb.com or visit our website www.ucb.com http://www.ucb.com/ This position can be found under Job ID: SLO1590 Closing date for applications: 15th October 2010 UCB Celltech is the UK branch of UCB Pharma S.A., a company registered in Belgium with registered offices at Allee de la Recherche 60, 1070 Brussels, Belgium, KBO/BCE nr. 0403.096.168, RPR/RPM Brussels. UCB Celltech's UK branch registration number is BR009137 and its UK representative office is at 208 Bath Road, Slough, Berkshire SL1 3WE. Legal Notice: This electronic mail and its attachments are intended solely for the person(s) to whom they are addressed and contain information which is confidential or otherwise protected from disclosure, except for the purpose for which they are intended. Dissemination, distribution, or reproduction by anyone other than the intended recipients is prohibited and may be illegal. If you are not an intended recipient, please immediately inform the sender and return the electronic mail and its attachments and destroy any copies which may be in your possession. UCB screens electronic mails for viruses but does not warrant that this electronic mail is free of any viruses. UCB accepts no liability for any damage caused by any virus transmitted by this electronic mail. (Ref: #*CUK0308)
Re: [ccp4bb] how to optimize crystallization of a membrane proteinf
Well said. I've seen three cases by now when switching to a homologue from a different organism led to solving a structure (and way too many cases when crystals just did not diffract, either at all or well enough :). On Tue, 2010-08-31 at 18:48 +0300, Tommi Kajander wrote: Or might be worth going back to the drawing board to design more constructs (and check them around the same conditions), thermostable homologs etc.. what about reductive methylation, anyone had luck with membrane proteins? -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] how to optimize crystallization of a membrane proteinf
I have to say that in my limited experience with membrane protein crystallization, these liquid crystal / spherulite type things are very common, and seldom turn into anything useful. Perhaps others on the list more experienced than I can corroborate or refute this. I just don't want this guy to get misled into perhaps wasting months/years on something not particularly promising. But, as I said, I am happy to be contested/refuted... Jacob On Tue, Aug 31, 2010 at 11:39 AM, Ed Pozharski epozh...@umaryland.eduwrote: Well said. I've seen three cases by now when switching to a homologue from a different organism led to solving a structure (and way too many cases when crystals just did not diffract, either at all or well enough :). On Tue, 2010-08-31 at 18:48 +0300, Tommi Kajander wrote: Or might be worth going back to the drawing board to design more constructs (and check them around the same conditions), thermostable homologs etc.. what about reductive methylation, anyone had luck with membrane proteins? -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] how to optimize crystallization of a membrane proteinf
On Tue, 2010-08-31 at 11:57 -0500, Jacob Keller wrote: I just don't want this guy to get misled into perhaps wasting months/years on something not particularly promising. Trouble is, of course, that one never knows if a particular trick will work this time. We routinely get PEG/fluoride salt crystals, and yet they have to be checked in the beam just in case. I think you touch on a quite difficult question, which is when one has to give up on a crystallization lead as hopeless. Cheers, Ed. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
[ccp4bb] Is the difference between mFo and Fo maps supposed to be very small?
Hi, I want to see how the mFo maps (NOT 2mFo-DFc) compare against Fo maps. In the SIGMAA documentation, it says WCMB is the figure of merit; however, I opened in coot with FP PHIC WCMB combination, and for lots of systems, I didn't see too much difference against FP PHIC maps. Is the difference between mFo and Fo maps supposed to be very small? Best Regards, Hailiang
Re: [ccp4bb] Is the difference between mFo and Fo maps supposed to be very small?
Hi Hailiang, m is typically determined per resolution bin using test reflections and it can range from 0 to 1, so the difference between corresponding mFo and Fo can range accordingly. You can read more on this, for example: Acta Cryst. A42 (1986) 140-149. Acta Cryst. (1995). A51, 880-887. J. Appl. Cryst. (1996). 29, 741-744. and numerous references therein. Pavel. On 8/31/10 10:15 AM, Hailiang Zhang wrote: Hi, I want to see how the mFo maps (NOT 2mFo-DFc) compare against Fo maps. In the SIGMAA documentation, it says WCMB is the figure of merit; however, I opened in coot with FP PHIC WCMB combination, and for lots of systems, I didn't see too much difference against FP PHIC maps. Is the difference between mFo and Fo maps supposed to be very small? Best Regards, Hailiang
Re: [ccp4bb] how to optimize crystallization of a membrane proteinf
Hello Qiangmin, Here are links to a few web resources that have tips for membrane protein crystallization that may help with your optimization strategy: http://kb.psi-structuralgenomics.org/update/2009/06/full/th_psisgkb.2009.25.html http://web.emeraldbiosystems.com/blog/bid/33916/8-Practical-Tips-for-Membrane-Protein-Crystallization http://mcl1.ncifcrf.gov/nihxray/Tips-and-Tricks_Crystallization_Membrane_Protein.pdf good luck, Eric __ Eric Larson, PhD Biomolecular Structure Center Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 On Mon, 30 Aug 2010, qiangm zhang wrote: Hi all, I got a crystal of one membrane protein (~60kD) from Na/K phosphate condition (see getit_4), then I got the improved crystal like getit_5 after trying seeding, different detergents, lipids and additives. But this crystal does not diffract at all, I already tried Izit staining which shows it is protein crystal (detergent crystal?). Does anyone have any good suggestions for the optimization of this membrane protein crystallization? Thank you in advance. Best regards Qiangmin Zhang Biomedical Science Tower 3 Room1034 3501 Fifth Avenue Pittsburgh, PA 15260 -- 张强敏
Re: [ccp4bb] Is the difference between mFo and Fo maps supposed to be very small?
On Tue, 2010-08-31 at 13:15 -0400, Hailiang Zhang wrote: Is the difference between mFo and Fo maps supposed to be very small? For an essentially correct model, yes. The major advantage of (2mFo-DFc) maps is suppression of model bias, so if you don't see much difference then your model is very well refined. For illustration, introduce a systematic error on purpose and see which map gives you better result. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] Is the difference between mFo and Fo maps supposed to be very small?
Actually I cut a small domain from the well-defined structure (just for a test). The missing part showed in 2mFo-DFc map but not in both mFo and Fo maps, and the mFo and Fo maps are so close so that I wonder whether figure of merit generated by SIGMAA helps or not in this situation... Best Regards, Hailiang On Tue, 2010-08-31 at 13:15 -0400, Hailiang Zhang wrote: Is the difference between mFo and Fo maps supposed to be very small? For an essentially correct model, yes. The major advantage of (2mFo-DFc) maps is suppression of model bias, so if you don't see much difference then your model is very well refined. For illustration, introduce a systematic error on purpose and see which map gives you better result. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] how to optimize crystallization of a membrane proteinf
Hi, The picture looks like detergent crystals, specially DDM crystals. I have same crystals in many conditions. With regards, Parveen
Re: [ccp4bb] how to optimize crystallization of a membrane proteinf
Yea, Parveen has actually asked about this here a year ago and I found this discussion quite useful indeed: www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg11717.html and I think we all get tons of these crystals especially in conditions with PEGs. There are lots of things you can try and have been suggested, but I found this reference most helpful by far: A general protocol for the crystallization of membrane proteins for X-ray structural investigation. http://www.ncbi.nlm.nih.gov/pubmed/19360018 (this is actually the paper in the link that Eric posted: http://kb.psi-structuralgenomics.org/update/2009/06/full/th_psisgkb.2009.25.html) Best, Matt On Tue, Aug 31, 2010 at 12:53 PM, Parveen Goyal parveen...@gmail.comwrote: Hi, The picture looks like detergent crystals, specially DDM crystals. I have same crystals in many conditions. With regards, Parveen -- Matthew L.H. Chu, PhD Postdoctoral Scholar - Weis Lab Department of Structural Biology Fairchild D143, MC 5126 Stanford School of Medicine Stanford, CA 94305-5432 Lab: 650-724-3306 Alternative Email: matt...@stanford.edu
Re: [ccp4bb] Is the difference between mFo and Fo maps supposed to be very small?
If I understand correctly, the only difference between mFo and Fo map will be weighting in different resolution shells according to figure-of-merit. While this will presumably downweigh the less reliable resolution shells, it will hardly make up for the heavy model bias. The reason you see the missing region in (2mFo-DFc) map is because it is effectively the sum of model map (mFo) which shows you the parts of the model you have already placed and difference map (mFo-DFc) which shows you the regions which are still missing. On Tue, 2010-08-31 at 15:20 -0400, zhan...@umbc.edu wrote: Actually I cut a small domain from the well-defined structure (just for a test). The missing part showed in 2mFo-DFc map but not in both mFo and Fo maps, and the mFo and Fo maps are so close so that I wonder whether figure of merit generated by SIGMAA helps or not in this situation... Best Regards, Hailiang On Tue, 2010-08-31 at 13:15 -0400, Hailiang Zhang wrote: Is the difference between mFo and Fo maps supposed to be very small? For an essentially correct model, yes. The major advantage of (2mFo-DFc) maps is suppression of model bias, so if you don't see much difference then your model is very well refined. For illustration, introduce a systematic error on purpose and see which map gives you better result. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] how to optimize crystallization of a membrane proteinf
I have had a lot of problems of my own with poorly diffracting (or not at all) membrane protein crystals. After a previous discussion here, I summarised the suggestions I got in this ccp4 user wiki; http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Improving_crystal_quality There are a few ideas there that have already been put forward. My personal opinion is that (assuming your crystals are protein) detergent is the deciding factor. I second the suggestion for shorter chain detergents, but also suggest that you carefully consider your detergent concentration. While you want it to be above cmc, I have found excessive concentration to be bad for crystallisation. If you are going back to the drawing board, I can highly recommend the MemGold and MemStart/Sys screens developed by the lab of So Iwata at the Imperial College, and sold by Molecular Dimensions (in the UK). It has given me a lot of success in getting initial hits for various membrane proteins. MemGold has been designed to specifically target alpha-helical membrane proteins, as described in this paper; http://onlinelibrary.wiley.com/doi/10.1110/ps.073263108/full Hope you find something useful here. Good luck. Damon.
