Re: [ccp4bb] Sokalan cp 42 as a cryoprotectant
Dear Abhimanyu, Sokalan CP42 is a modified polycarboxylate with 'medium' molecular weight. In terms of cryoprotective properties it is likely to behave similar to PEG 2. Try adding 25-35% glycerol as a starting point. Best, Clemens Zitat von abhimanyu singh abhisingh@gmail.com: Dear all, Recently I got couple of crystallization hits in conditions containing 30-40% sokalan cp 42 provided in MIDAS commercial screen from molecular dimensions. I tried to look up for information regarding its probable cryo protection activity but failed to find anything. Could someone have any clue about this ? Thank you. Greetings, -- Abhimanyu Kumar Singh Ph.D. Student Department of Macromolecular Structures National Center for Biotechnology (CNB-CSIC) C/ Darwin 3, Campus de Cantoblanco, 28049 Madrid, Spain. E-Mail: abhimanyu.si...@cnb.csic.es -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 31 84031 -
Re: [ccp4bb] cannot reproduce crystals
'oil separation and light ppt' is not necesserily an indicator that something is wrong with your crystallization condition. Actually, there are quite a few proteins that only crystallize in conditions with oil/water-like phase separation. Some crystals even appear WITHIN the oily drops (e. g. Xylanase). good luck! Clemens Zitat von dusky dew duskyde...@gmail.com: Dear all, I am trying to reproduce some protein crystals. The protein I am getting after cutting the his tag is very pure. I am using the reported protein concentration. The cofactor and EDTA needs to be added externally. The condition has calcium acetate, peg 4k and sodium acetate buffer. Unfortunately I am getting oil separation and light ppt. I have no clue what is wrong. Please help!
Re: [ccp4bb] disulfide engineering
Along these lines, what reagents do people use to promote disuflide bonds, i.e., the anti-DTT? Glutathione (red) + Glutathione (ox), redox potential is adjusted by varying the ratio. Best, Clemens JPK On Thu, Feb 28, 2013 at 2:06 AM, David Briggs drdavidcbri...@gmail.comwrote: You might want to try Disulfide by design http://cptweb.cpt.wayne.edu/DbD2/ Cheers Dave On Feb 28, 2013 6:55 AM, Careina Edgooms careinaedgo...@yahoo.com wrote: Dear CCP4 members I wish to engineer a disulfide bond at the dimer interface of a protein I am working with. Does anyone know of any available software to assist with this? Best Careina -- *** Jacob Pearson Keller, PhD Postdoctoral Associate HHMI Janelia Farms Research Campus email: j-kell...@northwestern.edu *** -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 31 84031 -
Re: [ccp4bb] stereo monitor for DELL T7600
Hi Il, assuming that you work under Linux, be sure to get a Quadro 4000 with a 3-pin stereo connector (this is 'optional' according to Nvidia). The System will then work with the '3D vision System'. All compatible monitors like AcervGD235HZ or ASUS VG236H are listed on the 3D Vision site: http://www.nvidia.de/object/buy-3d-monitors-de.html You will aslo have to get a set of 3d Vision goggles and emitters. BTW, I would strongly suggest to stay away from the 3d Vision *PRO* goggles as we tested six of them and they all failed after less than 3 months of use! Apart from that the stereo quality is excellent compared to all previous stereo systems. Best, Clemens Zitat von jlliu liu jlliu20022...@gmail.com: Hi All, I am ordering a Dell workstation (Dell Precision,T7600n,MT,1300W) with 2GB nVIDIA Quadro 4000. Can anyone recommend to me which stereo monitor would be compatible with this model? I have some stereo models mentioned in previously ccp4bb email: - Zalman ZM-M215W 21.5in - Zalman ZM-M240W 24in - Samsung http://proteincrystallography.org/ccp4bb/message29933.htmlSyncMaster S27A750D 27in - LG D2342P 23in / LG D2542P 25in Any advice will be highly appreciated. Thanks so much in advance! Jl -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 31 84031 -
[ccp4bb] Ferritin crystallisation
Dear all, scanning the literature, it seems that horse spleen Ferritin has so far been crystallised only in presence of Cadmium ions. Is this correct? Does anybody know of conditions lacking Cd? Clemens
Re: [ccp4bb] problem of crystallization
Hi Jennifer, clear drops can still be brought to supersaturation by: -transfer to wells with lower vapour pressure: exchange or add LiCl or other concentrated salt solutions in the reservoir -temperature gradient: place trays on ice/cold surface while hanging drops are at higher temperature, this will draw more water out of the drops. -transient supersaturation might be sufficient to trigger nucleation and subsequent crystal growth: slightly open wells for a few minutes (or longer) and close again. -protein solubility also can strongly depend on temperature: move to 4°C etc. ... and why not using the 100mg/ml stock or concentrate even more? Good luck, Clemens Quoting Jens-Christian Navarro Poulsen [EMAIL PROTECTED]: Hi Jennifer I just want to draw your attention the following paper regarding methylation of Lysines, which reduces the solubility of their test proteins. Walter http://www.ncbi.nlm.nih.gov/pubmed/17098187?ordinalpos=7itool=EntrezSystem 2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum TS, Meier C, Assenberg R, Au KF, Ren J, Verma A, Nettleship JE, Owens RJ, Stuart DI, Grimes JM. http://www.ncbi.nlm.nih.gov/pubmed/17098187?ordinalpos=7itool=EntrezSystem 2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Abstract Lysine methylation as a routine rescue strategy for protein crystallization. Structure. 2006 Nov;14(11):1617-22. PMID: 17098187 [PubMed - indexed for MEDLINE] Best regards, Jens-Christian Navarro Poulsen Dept of Chemistry, KU _ From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Jennifer Han-Chun Tsai Sent: 13. maj 2008 18:17 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] problem of crystallization Hi, This topic is not related to CCP4. I am having problem of crystallizing one protein. It's a pretty small protein with size around 15kDa. I have stock concentration around 100mg/mL. Crystallization plates I set up are with concentration of 10mg/mL, 30mg/mL and 50mg/mL. All the plates had been set up at least one week. Only around 5 wells per plate or less formed precipitation. The rest of wells are pretty clear still. Is there any suggestion for reducing protein solubility or increasing the chance of getting crystals? Thanks for your time, Jennifer
Re: [ccp4bb] pH-ing Jeffamine ED-2001
this is also my experience. However, above pH 8, the buffering effect of the Jeffamines' amino groups starts to be significant and (rough) pre-adjusting of the pH might be necessary. Clemens Quoting Yogesh Gupta PhD [EMAIL PROTECTED]: Hi Amit, Changing the pH of Jeffamine is not so easy . I would keep the pH of Jeffamine constant and rather change the pH of buffer. Anyway if Jeffamine concentration is too low as compare to the buffer you are using, it would not change the final pH much. This is what my experience with Jeffamine is. Cheers, Yogesh On Mon, Apr 21, 2008 at 9:20 AM, amit sharma [EMAIL PROTECTED] wrote: Dear CCP4ers, Apologies for a non-CCP4 query. I intend to set up an optimization grid around one of the crystallization conditions (containing Jeffamine ED-2001pH 7.0 and HEPES pH 7.0) by varying the buffer pH from 5.5 to 7.5. In such a case, is it recommmended that the pH of Jeffamine ED-2001(pH 7.0) also be changed to match the different buffer pHs(5.5-7.5)? Cheers, Amit -- Yogesh K. Gupta, Ph.D. Post Doctoral Fellow Molecular Physiology Biophysics Mount Sinai School of Medicine 1425, Madison Av. (East Bldg. 16-26) Box 1677, New York, NY 10029-6574 Tel:+1 212-659-8639 Fax:+1 212-849-2456 E-mail: [EMAIL PROTECTED] -
[ccp4bb] dry shipper on airplaine
Dear all, I wonder if it would be still/again possible to check in a dry shipper for a flight inside Europe. What is your experience? Cheers, Clemens
Re: [ccp4bb] Arp/warp space group P 21 2 21
seems to be a 'non-standard' setting. Refmac also has problems with this spacegroup, reindexing to P21 21 2 fixed the problem for me. Clemens Quoting PhilEvans [EMAIL PROTECTED]: Is there a reason why Arp/warp doesn't like space group P 21 2 21? Phil
Re: [ccp4bb] Arp/warp space group P 21 2 21
yes, actually my experience with P 21 2 21 dates back to midyear 2007. Retesting with the current refmac version runs fine. Clemens Quoting Ian Tickle [EMAIL PROTECTED]: Victor 'P 21 2 21' *is* the conventional indexing if a = b = c, i.e. it's the setting agreed for deposition of crystal structures by the IUCr and the US National Institute of Standards Technology (NIST) since 1983: it just doesn't seem to have been agreed by a dwindling number of individual program authors. AFAIK Arp/Warp is the only significant program relevant to PX which doesn't recognise the complete set of conventional settings (as defined in $CLIBD/syminfo.lib and symop.lib). In this case, the transformed setting 'P 21 21 2' (corresponding to the unconventional cell a = c = b) is called the 'standard' setting and is the reference symbol used for example as the title of the relevant page in ITC vol A, since for convenience the alternate settings 'P 2 21 21', 'P 21 2 21' and 'P 21 21 2' are all shown on the same page. seems to be a 'non-standard' setting. Refmac also has problems with this spacegroup, reindexing to P21 21 2 fixed the problem for me. Clemens I've not had any trouble with this spacegroup when using a recent version of Refmac/CCP4: are you by any chance using an old version (either of Refmac or CCP4)? If not could you post the relevant error message so the problem can be identified fixed, as it certainly ought to work. Re-indexing is usually not a viable option for us as it causes a lot of pain with our automated processing: if re-indexing really becomes unavoidable then it means we have to delete all the processed data for that crystal and other datasets of the same crystal form, then start all over again from data processing (i.e. from the MOSFLM/D*trek step), so that all datasets co-ordinates associated with a project in the database are indexed the same way. Having datasets around with different indexings (particularly as happened once if 2 of the cell lengths are very similar) is a recipe for chaos! Anyone trying to automate structure solution would likely run into the same problem, unless of course they anticipated this eventuality in the database design. So yes, making all software accept the internationally recognised conventions could save us a lot of work! -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Victor Lamzin Sent: 10 June 2008 16:45 To: PhilEvans Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Arp/warp space group P 21 2 21 Dear Phil, One reason has been simplicity - many ARP/wARP modules operate with space group number only. For space group 18 this would mean P21212. Using space group name might be less robust - I remember some compatibility problems when CCP4 introduced spaces into space group names, this broke some of the parsers, including simple-minded ones from ARP/wARP. If there is, however, a strong wish for ARP/wARP to support 'unconventionally' indexed space groups - then we will certainly try to introduce it. With best regards, Victor PhilEvans wrote: Is there a reason why Arp/warp doesn't like space group P 21 2 21? Phil Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
Re: [ccp4bb] Reducer and crystallization
Hi Sam,
The effect of reducing agents like beta-ME, DTT or TCEP is exactly as you say,
the prevention of disulphide formation or cleavage of existing disulphide
bridges and therefore prevention of aggregation if inter-molecular disulphide
bridges can be formed.
A balancing of reducing power, or better, the redox potential will be
necessary
if you want to reduce certain cystein residues while leaving others
oxidized as
dimers. For example, you have a disulphide containing, secreted protein fused
to a TEV-cleavable tag. The Cystein protease will have to be kept reduced,
while the disulphide bridges of the target protein must be spared. For cases
like that I found it useful to use a mixture of reduced and oxidized
glutathione to adjust the redox potential ('redox buffer').
If the reducing agent is necessary to keep the protein happy, I would not
dialyse it away, at least not for the first screening experiments. For beta-ME
one should keep in mind that it has a certain potential to form adducts with
the proteins cystein residues.
Cheers,
Clemens
Quoting Sam [EMAIL PROTECTED]:
Dear all,
Can anyone enlighten me the effect of reducer in crystallography?
I understand that it removes disulphide bond, and prevent protein
aggregation. But how do we find a balance point and must we remove it before
screening crystals?
Thanks for answering first.
Cheers
sam
[ccp4bb] re-indexing, re-orienting and TLS-tensors
Dear all, after re-indexing a dataset I had to re-orient my coordinates accordingly. The model contains some 24 TLS-tensors. Now my question is how to apply the rotation matrix also to the TLS-tensors. What is the mathematical operation and is there a program that can do the job for me? Thanks, Clemens
Re: [ccp4bb] re-indexing, re-orienting and TLS-tensors
this was a difficult case due to poor convergence behaviour during the TLS refinement. At the moment I'm not sure what would be more complicated, re-creating the tensors from scratch or writing a script. What about TLSANL? Is there an (undocumented ?) feature that could be used for things like that? Clemens Quoting Eleanor Dodson [EMAIL PROTECTED]: I would run the TLS again! Eleanor Clemens Grimm wrote: Dear all, after re-indexing a dataset I had to re-orient my coordinates accordingly. The model contains some 24 TLS-tensors. Now my question is how to apply the rotation matrix also to the TLS-tensors. What is the mathematical operation and is there a program that can do the job for me? Thanks, Clemens
Re: [ccp4bb] how to promote folding for an unfolded protein
Hi Jenny, there are probably as many 'folding enhancers' as there are crystallization additives. Arginine might only be the most popular, followed by things like proline and other amino acids. The mode of action of those can partly be explained by their mild chaotropic properties. For a difficult refolding project, the conditions should be screened sytematically. Other things to try would be sucrose, glycerol, PEG in the range of several % etc. with purified chaperones at the end of the row. For initial experiments, I would always go for the quick dilution method! Dialysis is popular in many protocols, however a lot of them were initially developped in / for an industrial context where it makes a big difference if you have a procedure on a 1kg scale needing a 1000 l or a 1000 m3 vessel. In the lab you don't care if you need 10 ul or 10 ml of refoding volume. Other sometimes successful methods are refolding on a column e. g. Ni-NTA, if you have a his-tag, if not, try a gel filtration column. In case you expect disulphide bridges you will have to take care about them during the development of your protocol by adjusting the redox potential (possibly in a stepwise manner). Good luck! Clemens Quoting Jenny [EMAIL PROTECTED]: Dear CCP4 community, Sorry for this off-topic protein purification problem.I'm trying to purify an immunoglobulin-like beta sheet protein with a c-terminus HIS construct. The protein expressed both in the supernat and pellet ( majority ). I purified the supernat and after run gel filtration, it's in the void volume. I also tried to purify from the pellet,and do dialysis refolding ( with and without L-arg ), after overnight dialysis, I run the gel filtration column, the apparent molecular weight looks like dimer/trimer. But when I did a CD scan of the protein, it's showing an unfolded protein profile.I was wondering if there is anyway to promote folding,or if anyway that can make some mutations to make it foldable.Any input would be useful. Thanks a lot. Jenny
[ccp4bb] PhD Position in Structural Biology
A PhD position in structural biology is available in the group of Prof. Utz Fischer at the Institute of Biochemistry, Biocentre of the Julius Maximilans-University, Wuerzburg/Germany. The successful applicant will work on the crystallographic structure determination of the Survival Motor Neuron (SMN) complex, the key player during the pathogenesis of Spinal Muscular Atrophy (SMA). Protocols for bacterial expression and reconstitution of the SMN complex are established and crystals including a first synchrotron dataset are already available. Please send your application including a letter of interest, curriculum vitae, academic certificates and the names and contact details of two referees to: Dr. Clemens Grimm Institute for Biochemistry Biocentre of the University Am Hubland D-97074 Wuerzburg Germany e-mail: [EMAIL PROTECTED]
[ccp4bb] The mystery of the S-tensor WAS: re-indexing, re-orienting and TLS-tensors
Dear all, a few weeks ago I was wondering how to apply a rotation matrix to TLS-tensors and Ian was so kind to supply us with the corresponding formulas. After looking a bit into it, however, the whole matter seems to be complicated by the fact that one value of S is undefined, however, after the transformation it appears within S' at several places. Did we miss something obvious? Or is this actually more complicated than it looked like in the first place? Thanks Clemens Ian Tickle schrieb: Clemens, One thing I should have pointed out, though you may have realised it already: you will most likely want to keep the same relative origins for the new TLS groups so this means that the translational component of the transformation (vector p or matrix P) will always be zero. This is true even if your desired transformation of the co-ordinates contains a non-zero translation component, because this translation is then also applied to the local origin of the TLS group, hence there is no resultant translation *relative* to that origin. In other words the translational component p is only relevant if you want to change the relative origins of the TLS groups (e.g. from COG to COR or vice versa), which is unlikely if all you are doing is re-indexing. Having p=0 (and P=O) of course considerably simplifies the equations, i.e.: T' = RTR~ and the same transformation is applied separately to L and S. Cheers -- Ian -Original Message- From: Clemens Grimm [mailto:[EMAIL PROTECTED] Sent: 09 July 2008 14:20 To: Ian Tickle Subject: RE: [ccp4bb] re-indexing, re-orienting and TLS-tensors Hi Ian, thanks for the formulas! I'll probably give Mthematica a try. Clemens Quoting Ian Tickle [EMAIL PROTECTED]: Hi Clemens The relevant matrix algebra is all there in TLSANL, i.e. you could put some code together based on that to do what you want, however there isn't an option (even an undocumented one!) to do exactly what you want and I don't know of any program which will do that. The math isn't actually all that difficult, all you need is a routine for 3x3 matrix multiplication, or you could use something like R or Mathematica. -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Clemens Grimm Sent: 09 July 2008 12:24 To: [EMAIL PROTECTED]; Eleanor Dodson Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] re-indexing, re-orienting and TLS-tensors this was a difficult case due to poor convergence behaviour during the TLS refinement. At the moment I'm not sure what would be more complicated, re-creating the tensors from scratch or writing a script. What about TLSANL? Is there an (undocumented ?) feature that could be used for things like that? Clemens Quoting Eleanor Dodson [EMAIL PROTECTED]: I would run the TLS again! Eleanor Clemens Grimm wrote: Dear all, after re-indexing a dataset I had to re-orient my coordinates accordingly. The model contains some 24 TLS-tensors. Now my question is how to apply the rotation matrix also to the TLS-tensors. What is the mathematical operation and is there a program that can do the job for me? Thanks, Clemens Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674 Disclaimer This communication
Re: [ccp4bb] Reducing Agents and pH
TCEP is often sold as hydrochloride salt and therefore reacts highly acidic. We usually titrate the concentrated solution *before* we add it to our proteins. This can be done within small volumes by dropwise addition of a saturated TRIS solution, check pH by pipetting a drop on a pH test strip. Clemens Zitat von John A. Newitt [EMAIL PROTECTED]: At 5:04 PM -0600 11/25/08, Jacob Keller wrote: Sorry for this very prosaic question: does anybody have a reference describing the mechanisms of reducing agents (TCEP, DTT, BME, etc.), and in particular the effects of the reactions on pH? I think I can draw a convincing reaction mechanism for myself, but I am not sure theoretically why (or even whether) the pH drops in the presence of reducing agents (although I am pretty sure empirically that it does.) I have looked around a bit, but perhaps have not hit on the right google search terms... This doesn't directly address the question I think you are asking, but one obvious way that adding reducing agents could affect the pH is if they contain significant amounts of strong acids. One vendor of TCEP that we used in the past presumably had so much residual HCl in the solid reagent that even when TCEP was added at 1 mM it caused a significant decrease in pH of a buffered solution. It taught us to check the pH after adding reducing agents and also to find another vendor. - John
Re: [ccp4bb] temperature after 30 minutes using microscopes ?
We have tested the Zeiss LED plate with hanging and sitting drop trays and found it it unsuitable for looking at crystals. The reason is the really low contrast with this kind of diffuse illumination. Obviously, contrast is generated by refraction at crystal/mother liquor interfaces and this effect diminishes with diffuse light coming from a range of incidence angles. Clemens Zitat von Jürgen Bosch jubo...@jhsph.edu: Here are some numbers Matthew.Franklin: Okay. Start: 71.9 F Finish: 73.1 F Temperature measured with thermocouple Scotch-taped to the center of the microscope stage, underneath an empty 96-well plate. Room thermostat set to 70. I should have mentioned that I was thinking about fiberoptics and not the halogen light directly under the tray. Still I always had the impression that there's a significant temperature difference when using the fiberoptics for a long time e.g when mounting crystals. The microscope in question is a Zeiss and the $ difference between LED halogen is about 2.5K in favour of the LED system. I have seen the LED version and it seemed good to me - but I have not looked at crystal trays of course. I'll post a summary in a few days. Thanks for all your replies so far, Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Biochemistry and Molecular Biology, W8708 615 North Wolfe Street Baltimore, MD 21205 Phone: +1-410-614-4742 Fax: +1-410-955-3655
Re: [ccp4bb] Lindemann glass
Hilgenberg (Malsfeld, Germany) currently offer their remaining stock. Clemens Zitat von James Holton jmhol...@lbl.gov: Does anyone know the formula or supplier of what was once called Lindemann glass? It is a silicon-free high-boron glass that has no elements in it heavier than oxygen. Used to be used to make clear x-ray windows, but now I can't find anyone who sells it. -James Holton MAD Scientist
[ccp4bb] Ultra-low water B-facors after TLS refinement
LEU A 545 5851 2912 6160 0 0 0 O [.] ATOM721 O HOH Z 26 4.331 15.110 2.443 1.00 2.00 O ATOM722 O HOH Z 27 1.264 -6.899 -12.249 1.00 2.00 O ATOM723 O HOH Z 28 -16.512 7.213 -5.802 1.00 2.00 O ATOM724 O HOH Z 29 10.966 0.572 -2.021 1.00 2.00 O ATOM725 O HOH Z 30 -1.212 -6.621 -13.323 1.00 14.85 O ATOM726 O HOH Z 31 -3.187 -8.577 -15.238 1.00 2.00 O ATOM727 O HOH Z 32 1.541 19.977 -9.823 1.00 2.00 O ATOM728 O HOH Z 33 -18.041 1.731 2.138 1.00 2.00 O ATOM729 O HOH Z 34 -15.674 13.690 -10.888 1.00 10.07 O ATOM730 O HOH Z 35 -6.429 9.025 -15.088 1.00 2.00 O ATOM731 OW0 HOH Z 36 -8.068 11.911 2.520 1.00 2.00 O ATOM732 OW0 HOH Z 37 -8.131 21.050 1.317 1.00 2.94 O ATOM733 OW0 HOH Z 38 7.360 -10.570 -9.323 1.00 2.00 O ATOM734 OW0 HOH Z 39 -3.377 -10.981 -14.550 1.00 2.00 O ATOM735 OW0 HOH Z 40 -10.173 19.052 -0.857 1.00 13.04 O ATOM736 OW0 HOH Z 41 -12.070 1.106 -0.308 1.00 2.00 O ATOM737 OW0 HOH Z 42 -13.008 21.323 -8.964 1.00 2.00 O ATOM738 OW0 HOH Z 43 2.014 -2.216 -18.360 1.00 23.56 O ATOM739 OW0 HOH Z 45 -9.727 -3.842 -8.213 1.00 7.42 O END -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 888 84031 -
[ccp4bb] PhD Student Position
A 3-year PhD student position in protein biochemistry/structural biology is available at the Institute of Biochemistry, Biocenter of the Julius-Maximilians-University, Wuerzburg/Germany. The successful applicant will work on the Survival Motor Neuron (SMN) complex, a key player during the pathogenesis of Spinal Muscular Atrophy (SMA). The work will comprise optimization of protein constructs for crystallization, biochemical characterization, protein purification and crystallographic data collection. In addition, the post offers an excellent opportunity to acquire crystallographic skills, as there are already diffracting protein complex crystals available. The salary level is on grade TV-L E13/2 (? 19.912 ? 28.744 p. a. plus family allowance, if applicable). Please send your application including a letter of interest, curriculum vitae, academic certificates and the names and contact details of two referees to: Dr. Clemens Grimm e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de Institute für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 31 84031 -
Re: [ccp4bb] Phasing at Low Resolution
OK, here's a concrete case: A 150kDa protein complex, the plate-like crystals can be produced in sufficient number; Se-Met derivatives available, total number of Met around 20, subunits could be marked and combined individually. Diffraction is highly anisotropic, in certain directions up to 3.8A,while in others only 5A. Similarly, the spot quality is very dependent on orientation. Space group I222, a=75 b=150 c=250. Datsets scale well with 3-4% Rsym up to 12 A resolution. At 4.5A Rsym rises above 50% (I/sigma is still at 2.0). The 'sweet' slices of the dataset scale significantly better, but give only 70% (non-anomalous) completness. We hope to improve datasets slightly by orienting the crystals. 65% of the structure would be available as coordinate building blocks from the PDB, however, MR with these components so far did not yield a clear solution. Any suggestions or experiences with similar cases are welcome. Cheers, Clemens Zitat von Clemens Vonrhein vonrh...@globalphasing.com: [Show Quoted Text - 64 lines][Zitattext verstecken] Hi Clemens, maybe re-phrasing your question: What would be the best technique/strategy to phase crystals that [ ] diffract to maximal ___ A [ ] typical diffraction to __ A [ ] are radiation sensitive [ ] easily reproducable [ ] large crystals (up to ___ um) [ ] long needles [ ] thin plates [ ] have ___ mol/asu [ ] spacegroup ___ [ ] nice diffraction pattern [ ] poor diffraction pattern (reason: ___) [ ] anisotropic diffraction (resolution in poorest direction: ___ A) [ ] cell dimensions of roughly ___ ___ ___ ___ ___ ___ [ ] purified from native source [ ] expressed in expression system ___ [ ] anything else: ___ Tick the appropriate boxes and fill out the blanks as much as possible - that should give more important and necessary information. There are consequences to consider for all of those points that would then give some rough guidelines for your particular project/problem. Maybe CCP4 should have an online form to describe a particular crystallographic problem? Cheers Clemens On Thu, May 14, 2009 at 09:35:28AM +0200, Clemens Grimm wrote: Dear all, after the SeMet phasing discussion, what would be -in general- the best technique to phase low resolution data (=4A) of large complexes (=150 kDA) - in terms of - derivatization compounds (is there something like the 'golden five' HA compounds for these cases), - data collection techniques and - phasing methods? Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
[ccp4bb] crystool
Dear all, is the Rupp Segelke CRYSTOOL still accessible somewhere? The old link http://www-structure.llnl.gov/crystool/crystool.htm seems not to work anymore. Or are there alternatives? Thanks Clemens
Re: [ccp4bb] Phantom Crystals
Zitat von George DeTitta deti...@hwi.buffalo.edu: I'd appreciate it if people could tell me their experiences with what I would call phantom crystals, or ghost crystals. These are objects that display the seeming morphology of crystals (clear facets, sharp edges) ... There is also a second type of ghost crystals, those which do not have edges at all, with a ball- or egg-like apearance and which diffract perfectly well! but do not diffract X-rays AT ALL. I would not count objects that diffract to 30 A in this category. I mean objects that don't show a single Bragg spot. George T. DeTitta, Ph.D. Principal Research Scientist Hauptman-Woodward Institute Professor and Chairman Department of Structural Biology SUNY at Buffalo 700 Ellicott Street Buffalo NY 14203-1102 USA (716) 898-8600 (voice) (716) 898-8660 (fax) www.hwi.buffalo.edu http://www.hwi.buffalo.edu
[ccp4bb] PhD Position in Structural Biology, Wuerzburg, Germany
A PhD position in structural biology is available in the group of Prof. Utz Fischer at the Institute of Biochemistry, Biocentre of the Julius Maximilans-University, Wuerzburg/Germany. The successful applicant will work on the crystallographic structure determination of the Survival Motor Neuron (SMN) complex, the key player during the pathogenesis of Spinal Muscular Atrophy (SMA). Protocols for bacterial expression and reconstitution of the SMN complex are established and first crystals are already available. Please send your application including a letter of interest, curriculum vitae, academic certificates and the names and contact details of two referees to: Dr. Clemens Grimm e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany web: www.biozentrum.de
Re: [ccp4bb] Test of cryoconditions without X-rays or cryostream
Checking Cryo-Conditions under the microscope can actually be very useful. Even if you have access to a X-ray beam, simple pre-tests can be very informative. This can be done as follows: A 24well plate cover is placed on a stereo microscope open side down, a second one on top of it the other way around. Carefully pour lN2 into it (might make a crackling noise, however the plastic should stand it). A 1 mm loop is placed on top of a 'crystal wand' tool, dipped first into the cryo buffer under investigation and then quickly into the lN2 on the microscope. Hold the loop right under the lN2 surface and focus. Vitrification of the shock-cooled buffer can now be assesed. I usually check a series with increasing concentrations of cryo-protectant to determine the critical point for successful vitrification. To the final buffer I then add a certain safety margin to avoid unpleasant surprises during the synchrotron trip, if an X-ray test is not possible. Clemens Zitat von Karthik S biokart...@gmail.com: I have not heard of anyone checking for suitable cryo in that fashion how fast can you do it before it is affected by room temp and how would you know about the ice rings, but when you have crystal(s) and not crystal you can freeze different ones in several different cryos (sugars, glycerol etc) and take them with you to the trip. good luck! -- Karthik Graduate Student-Biophysics University of Michigan Ann Arbor, MI 48109 karth...@umich.edu 734-763-3384 On Tue, Sep 22, 2009 at 4:24 AM, Claudia Scotti claudiasco...@hotmail.comwrote: Dear List, Sorry for the probably silly question. Any suggestions to test cryoconditions without X-rays or cryostream? I'd need to freeze crystals before going to ESRF and I'm a bit anxious. Is it enough to try to freeze the cryoconditions in liquid nitrogen checking under the microscope (or by eye) or is this still risky? Thanks, Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 -- With Windows Live, you can organize, edit, and share your photos.http://www.microsoft.com/middleeast/windows/windowslive/products/photo-gallery-edit.aspx
[ccp4bb] PhD Position in Structural Biology, Wuerzburg, Germany
A PhD position in structural biology is available in the group of Prof. Utz Fischer at the Institute of Biochemistry, Biocentre of the Julius Maximilans-University, Wuerzburg/Germany. The successful applicant will work on the crystallographic structure determination of the Survival Motor Neuron (SMN) complex, the key player during the pathogenesis of Spinal Muscular Atrophy (SMA). Protocols for bacterial expression and reconstitution of the SMN complex are established and first crystals are already available. Please send your application including a letter of interest, curriculum vitae, academic certificates and the names and contact details of two referees to: Dr. Clemens Grimm e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany web: www.biozentrum.de
[ccp4bb] Batch Queing of ccp4i Jobs
Dear all, has anybody set up successfully a batch queue for ccp4i under SUSE linux? Regards, Clemens
Re: [ccp4bb] units of the B factor
Zitat von marc.schi...@epfl.ch: Dale Tronrud wrote: While it is true that angles are defined by ratios which result in their values being independent of the units those lengths were measured, common sense says that a number is an insufficient description of an angle. If I tell you I measured an angle and its value is 1.5 you cannot perform any useful calculation with that knowledge. I disagree: you can, for instance, put this number x = 1.5 (without units) into the series expansion for sin X : x - x^3/(3!) + x^5/(5!) - x^7/(7!) + ... and compute the value of sin(1.5) to any desired degree of accuracy (four terms will be enough to get an accuracy of 0.0001). Note that the x in the series expansion is just a real number (no dimension, no unit). ... However you get this Taylor expansion under the assumption that sin'(0)=1 sin''(0)=0, sin'''(0)=-1, ... this only holds true under the assumption that the sin function has a period of 2pi and this 'angle' is treated as unitless. Taking e. g. the sine function with a 'degree' argument treated properly as 'unit' will result in a Taylor expansion showing terms with this unit sticking to them. Clemens
[ccp4bb] setting cell/spacegroup in imosflm
Dear all, I would like to set manually cell and SG in the iMosflm interface - is this possible? Thanks Clemens -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 888 84031 -
[ccp4bb] Postdoctoral Position at the University of Wuerzburg
A postdoctoral position in Structural Biology of the Spliceosomal Assembly Machinery is available at the Biocenter of the University of Wuerzburg, Germany, within the department of Biochemistry. The successful candidate will participate in all stages of crystallographic structure determination from cloning, protein expression and purification to synchrotron data collection, processing and model building. The following qualifications will be required: - a PhD degree - experience in protein expression and purification - experience in data collection and processing - cumputing skills (scripting languages, linux system administration) would be an advantage. We offer an initial 2 year contract, extendable depending on project success. Payment will be in accordance with German public service positions (TVöD E13), including extensive social security plans. More information about the department and the biocenter is available on the respective web sites at: www.biozentrum.de Please send your application including a letter of interest, a CV and names of two references to: clemens.gr...@biozentrum.uni-wuerzburg.de The University of Wuerzburg is an equal opportunity employer with an affirmative action program for the disabled. -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 888 84031 -
[ccp4bb] Vapor diffusion calculator
regardless of what such a (kinetic) calculator will calculate at the end - we will have to feed it with data of the type vapour pressure vs. concentration and temperature of substance X. Even without a whole simulation tool for the kinetics of a vapour diffusion experiment this will already enable us to tell what the equilibrium state/endpoint of the experiment will be. As the substances we are interested in are typically stuff like PEGs and at very high concentration (non-ideal behaviour!), we will need experimental data. For some salts there are tables. But for PEGs etc. this has to be generated. I feel that only having this kind of data at hand would already be tremendously useful! Clemens Zitat von Jacob Keller j-kell...@md.northwestern.edu: Dear Crystallographers, Is anybody aware of a calculator for vapor diffusion experiments to plot concentrations of various solvent components as a function of time? For a simple example, what happens when I mix a protein solution containing 50mM NaCl 1:1 with a reservoir containing 50% MPD but no salt? Where is the vapor diffusion equilibrium, and how does the drop composition change as a function of time? More complicated would be experiments involving volatile components other than water, as I think, for example, ethanol would almost instantly equilibrate, then the water diffusion would kick in over a longer time scale. Even more complicated would be pH-dependent volatilities such as acetate. I don't think this would be impossible to figure out, but it would be nice if there were a pre-existing tool/server to do such. Regards, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 888 84031 -
Re: [ccp4bb] Vapor diffusion calculator
Zitat von Imre Toeroe t...@embl.de: Hi, this might be relevant here: http://scripts.iucr.org/cgi-bin/paper?S0907444995000436 Yes! thanks for the link. Imre Clemens Grimm wrote: regardless of what such a (kinetic) calculator will calculate at the end - we will have to feed it with data of the type vapour pressure vs. concentration and temperature of substance X. Even without a whole simulation tool for the kinetics of a vapour diffusion experiment this will already enable us to tell what the equilibrium state/endpoint of the experiment will be. As the substances we are interested in are typically stuff like PEGs and at very high concentration (non-ideal behaviour!), we will need experimental data. For some salts there are tables. But for PEGs etc. this has to be generated. I feel that only having this kind of data at hand would already be tremendously useful! Clemens Zitat von Jacob Keller j-kell...@md.northwestern.edu: Dear Crystallographers, Is anybody aware of a calculator for vapor diffusion experiments to plot concentrations of various solvent components as a function of time? For a simple example, what happens when I mix a protein solution containing 50mM NaCl 1:1 with a reservoir containing 50% MPD but no salt? Where is the vapor diffusion equilibrium, and how does the drop composition change as a function of time? More complicated would be experiments involving volatile components other than water, as I think, for example, ethanol would almost instantly equilibrate, then the water diffusion would kick in over a longer time scale. Even more complicated would be pH-dependent volatilities such as acetate. I don't think this would be impossible to figure out, but it would be nice if there were a pre-existing tool/server to do such. Regards, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 888 84031 - -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 888 84031 -
Re: [ccp4bb] Micro-g Crystal Growth and the literature
(and other researchers, for that matter) could grow crystals in space, and extract critical data from the x-ray diffraction of these space-grown crystals (in space); AND if costs could be reduced by 30-50%; AND if the end-product is the data, not the crystals . . . do you still think (profit) margins would be nominal? Is your assessment of very low margins based on assumed very high costs? Jack -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 888 84031 -
Re: [ccp4bb] Micro-g Crystal Growth and the literature
wouldn't offer crystal growth, I would offer access to the data from x-ray diffraction of space-grown crystals. Is the data from significantly improved crystals not a valuable commodity? If the pharmaceutical industry (and other researchers, for that matter) could grow crystals in space, and extract critical data from the x-ray diffraction of these space-grown crystals (in space); AND if costs could be reduced by 30-50%; AND if the end-product is the data, not the crystals . . . do you still think (profit) margins would be nominal? Is your assessment of very low margins based on assumed very high costs? Jack -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 888 84031 -
Re: [ccp4bb] cryo condition
Hi Faisal, Did you try to simply raise the Sokalan CP7 percentage? Additives like Glycerol can increase the solubility of proteins, in that case you have to counteract by increasing also the precipitant concentration. If your crystals crack, a likely reason is osmotic shock. Particularly large crystals tend to be problematic. It is in general advisable to transfer the cryo protectant onto the crystal within the mother liquor rather than fishing the crystal out with a loop. In addition, it might be necessary to prepare intermediate concentration of the cryo protectant by mixing with reservoir solution and do a stepwise increase. I had several projects with very large crystals that definitely needed at least five gradual steps over a time span of more than half an hour to extract datasets with reasonable mosaicity. Sokalan CP7 is an acrylate copolymer. Therefore, low molecular weight sodium polycralyte as a cryo protectant (e. g. Aldrich #420344) might be worth a try, possibly also in combination with some amount of good old glycerol, PEG, Trehalose, TMAO etc. Best wishes, Clemens Zitat von Faisal Tarique faisaltari...@gmail.com: Hello everyone Can anybody suggest me a cryo condition for a crystal obtained in MIDAS screen of Molecular Dimension: G1 0.1MTris8.0G10.1Mpotassium chloride25% v/vSOKALAN®CP7 0.1MHEPES7.0 G20.3Mammonium formate20% v/vSOKALAN® CP 5 0.1MHEPES7.0 Crystals are in beautiful cuboid shaped but all sorts of PEG combinations and Glycerol formulation failed to prevent it from cracking and dissolving. Has anybody faced a similar situation as mentioned above and what precaution was taken to prevent it from cracking or dissolving. Your suggestions will be of immense help Thanks in advance -- Regards Faisal School of Life Sciences JNU -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 31 84031 -
Re: [ccp4bb] AW: [ccp4bb] Phenix: heavy atoms
herman.schreu...@sanofi.com wrote: Polar space groups have none or a single rotation axis, e.g. P1, P2x, P3x, P4x, P6x. Otherwise Tims argument is valid. Dear Herman, Is there really a general definition what a 'polar space group' is? For example, SG P321 would have more than a single rotation axis but it would be polar along its twofolds, wouldn't it? Best, Clemens In coot, I would switch on symmetry and use a fairly large box and see whether symmetry atoms match your built molecule. In that case, coot has options to write out the symmetry molecule. If not, different origins might have been used, or a polar shift has to be applied. In this case, you might try to manually superimpose your Selenium coordinate using to Rotate Translate Zone option. By careful only to translate, not to rotate. Best, Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Tim Gruene Gesendet: Mittwoch, 15. April 2015 09:58 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Phenix: heavy atoms Dear Natalia, you can use Coot to generate the symmetry related molecules and see if the substructure matches your model. If your space group is polar, as in e.g. P2(1) or P2(1)2(1)2(1), your coordinates may float freely along the polar axis and looking the the symmetry related atoms would not help. I am not sure Coot has a feature to drag the coordinates along the polar axis. Best, Tim On 04/15/2015 05:24 AM, Natalia O wrote: Dear All, I am new to the crystallography and I am seeking for an advice considering data processing. I have a dataset with 2.8 A resolution. I used hybrid substructure search program in phenix, I got the heavy atom sites (selenium), and then I submitted the site to the autosol. With autosol half of the residues were positioned and there are some loops missing, and a part of structure was built as a chain of alanines. Importantly only half of the methionines was built. Now I am trying to build loops manually in Coot. I was able to build one of the loops, and this loop has a methionine residue, so I wanted to check if one of the heavy atom sites agrees with the self-built methionine position. And here I got completely confused, because if I open a pdb file containing my heavy atom sites and at the same time I open the model - the coordinates, they are not placed in one asymmetric unit. I expected that heavy atoms were found, and then basically “on top of them” the model was built. But that’s not what I see. I am missing something basic and important here and I am completely clueless. What is the relation between the origin of coordinates in the file with heavy atoms and the origin of coordinates of the molecular model? Thank you! Natalia - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 31 84031 -
[ccp4bb] PhD and Postdoc Position in Structural Biology (Cryo Electron Microscopy and X-ray Crystallography)
A PhD and a postdoc position in structural biology is available at the department of biochemistry at the Biocentre (head Prof. Utz Fischer) of the Julius Maximilans University, Wuerzburg/Germany. The successful applicant will work interdisciplinary on the fields of biochemistry, cryo-electron microscopy and x-ray crystallography to elucidate the molecular mechanisms of the Vaccinia Virus gene expression. Please send your application including a letter of interest, curriculum vitae, academic certificates and the name and contact detail of one referee to Prof. Utz Fischer/Dr. Clemens Grimm e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de Lehrstuhl für Biochemie Biozentrum der Universitaet Wuerzburg Am Hubland D-97074 Wuerzburg -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 31 84031 -
[ccp4bb] PhD position at the University of Wuerzburg
A PhD position in structural biology is available at the department of biochemistry of the Biocenter of the Julius Maximilians University, Wuerzburg/Germany. The topic of the work will be the structural organization of the SMN complex. This megadalton-sized molecular machine assembles U snRNP particles, the basic building blocks of the spliceosome. Genetic defects of its name-giving core component, the SMN protein, are the cause of the devastating neuromuscular disease spinal muscular atrophy (SMA). Our group has recently solved the structure of key components of the SMN complex bound to substrate Sm proteins (Grimm et al., Mol Cell. 2013 49(4):692-703). The planned work will continue these efforts and characterize large entities of the SMN complex. The successful candidate will work mainly in the field of crystallography and optimize, express and purify protein constructs and complexes for structural studies. Please send your application including a letter of interest, curriculum vitae and academic certificates to: Dr. Clemens Grimm e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de Lehrstuhl für Biochemie Biozentrum der Universitaet Wuerzburg Am Hubland D-97074 Wuerzburg -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 31 84031 -
[ccp4bb] PhD and Postdoc Positions in Structural Biology
A PhD and a postdoc position in structural biology is available at the department of biochemistry at the Biocentre (head Prof. Utz Fischer) of the Julius Maximilians University, Wuerzburg/Germany in the field of RNP biochemistry. The successful applicant will establish protocols for the isolation and reconstitution of preparative amounts of RNP complexes, which will then be characterized by cryo-electron microscopy and x-ray crystallography. We are looking for candidates with expertise in protein expression and purification and a strong interest in structural biochemistry. Prior knowledge of cryo electron microscopy, protein crystallography or biophysical methods is a plus. Please send your application including a letter of interest, curriculum vitae, academic certificates and the name and contact detail of at least one referee to Prof. Utz Fischer/Dr. Clemens Grimm e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de Lehrstuhl für Biochemie Biozentrum der Universitaet Wuerzburg Am Hubland D-97074 Wuerzburg -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 31 84031 - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] PhD and Postdoc Positions in Structural Biology
A PhD and a postdoc position in structural biology is available at the department of biochemistry at the Biocentre (head Prof. Utz Fischer) of the Julius Maximilians University, Wuerzburg/Germany in the field of RNP biochemistry. The successful applicant will establish protocols for the isolation and reconstitution of preparative amounts of RNP complexes, which will then be characterized by cryo-electron microscopy and x-ray crystallography. We are looking for candidates with expertise in protein expression and purification and a strong interest in structural biochemistry. Prior knowledge of cryo electron microscopy, protein crystallography or biophysical methods is a plus. Please send your application including a letter of interest, curriculum vitae, academic certificates and the name and contact detail of at least one referee to Prof. Utz Fischer/Dr. Clemens Grimm e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de Lehrstuhl für Biochemie Biozentrum der Universitaet Wuerzburg Am Hubland D-97074 Wuerzburg -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 31 84031 -
[ccp4bb] EMAN e2proc2d mrcs conversion issue
Dear All, we are experiencing a problem when trying to convert a 2D stack to single images: e2proc2d.py --unstacking stack.mrcs frame.mrc 76 images, processing 0-75 stepping by 1 1 images according to the manual this should output a a series of numbered single image files, however, it writes only a single 3D image: e2iminfo.py frame.mrc frame.mrc1 images in MRC format 2048 x 2048 x 76 representing 0 particles The input file is reported to be a 2D stack: e2iminfo.py stack.mrcs stack.mrcs 76 images in MRC format2048 x 2048 76 total images representing 0 particles Versions tested are EMAN 2.21a final and EMAN 2.2 final. Are we doing something wrong or is this a bug? Any help appreciated. Clemens -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 31 84031 - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Phenix: No reference model matches
Dear All, I am not getting any reference model matches in Phenix: Reference Model Matching Summary: reference file: reference.pdb Model: Reference: Total # of matched residue pairs: 0 Total # of reference model restraints: 0 working model and reference are exactly identical. I suspect that this has to do with some specificities of the PDB files (below). Has anybody else encountered such a problem? Thanks, Clemens ATOM 1 N ASP I 2 265.380 222.283 314.077 1.00121.12 N ATOM 2 CA ASP I 2 266.526 221.945 313.241 1.00121.12 C ATOM 3 C ASP I 2 266.172 222.082 311.764 1.00121.12 C ATOM 4 O ASP I 2 266.687 222.959 311.071 1.00121.12 O ATOM 5 CB ASP I 2 267.014 220.523 313.548 1.00121.12 C ATOM 6 CG ASP I 2 268.389 220.226 312.962 1.00121.12 C ATOM 7 OD1 ASP I 2 268.514 220.091 311.725 1.00121.12 O ATOM 8 OD2 ASP I 2 269.356 220.128 313.748 1.00121.12 O ATOM 9 N SER I 3 265.292 221.202 311.291 1.00116.78 N ATOM 10 CA SER I 3 264.929 221.164 309.884 1.00116.78 C ATOM 11 C SER I 3 264.010 222.332 309.531 1.00116.78 C ATOM 12 O SER I 3 263.497 223.041 310.397 1.00116.78 O ATOM 13 CB SER I 3 264.250 219.839 309.548 1.00116.78 C ATOM 14 OG SER I 3 265.045 218.745 309.967 1.00116.78 O ATOM 6438 N ASN I 795 197.555 302.028 252.461 1.00 91.20 N ATOM 6439 CA ASN I 795 196.094 301.970 252.599 1.00 91.20 C ATOM 6440 C ASN I 795 195.641 301.634 254.015 1.00 91.20 C ATOM 6441 O ASN I 795 195.666 302.490 254.898 1.00 91.20 O ATOM 6442 CB ASN I 795 195.497 300.970 251.599 1.00 91.20 C ATOM 6443 CG ASN I 795 196.000 301.190 250.183 1.00 91.20 C ATOM 6444 ND2 ASN I 795 195.297 302.023 249.427 1.00 91.20 N ATOM 6445 OD1 ASN I 795 197.011 300.617 249.776 1.00 91.20 O ATOM 6446 OXT ASN I 795 195.241 300.505 254.300 1.00 91.20 O END -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 31 84031 - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] COOT download site
Hi Eleanor, thanks for the tips. However, I am still unsure whether I really got the latest pre-release version Google sends me to: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/devel/build-info.html which is lacking the 0.9.x pre-release version. With ccp4 I got packaged the 0.9 "Arteixo" pre-release but the menues look somehow different from that what I can see in the latest presentations on Youtube ... Clemens Zitat von Eleanor Dodson : Certainly it has moved. Now latest from Emsleu Marc Cambridge. Search coot in google for full address. Or it comes with ccp4 On Thu, 4 Jun 2020 at 15:41, Clemens Grimm < clemens.gr...@biozentrum.uni-wuerzburg.de> wrote: Dear All, accessing the COOT download pages at http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/ gives me an "The requested URL /~emsley/software/binaries/nightlies/pre-release/ was not found on this server." error since a few days. Is the site down or has it moved? Thanks, Clemens ------ Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 31 84031 - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ ------ Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 31 84031 - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] COOT download site
Dear All, accessing the COOT download pages at http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/ gives me an "The requested URL /~emsley/software/binaries/nightlies/pre-release/ was not found on this server." error since a few days. Is the site down or has it moved? Thanks, Clemens -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 31 84031 - To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] [ccpem] Topaz picking in Relion
I figured out that setting 'Particle diameter' from default=-1 to a positive value results in single picks. Zitat von Clemens Grimm : Dear Developers and Users, after picking with a model trained with a pre-classified particle set, I get the following situation (see attached picture): All particles are picked with high accuracy. However, every single particle is picked several times - up to more than 100fold. It seems the higher the confidence, the more often the particle is picked. Is this the intended behavior? How is this handled during extraction? Best, Clemens -- Dr. Clemens Grimm Institut für Biochemie Biozentrum der Universität Würzburg Am Hubland D-97074 Würzburg Germany e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de phone : +49 0931 31 84031 - To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM=1 This message was issued to members of www.jiscmail.ac.uk/CCPEM, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] A postdoctoral and a PhD position funded by the Volkswagen Foundation in Wuerzburg
The biochemistry department at the Biocenter of the University of Wuerzburg seeks to fill: A postdoctoral and a PhD position funded by the Volkswagen Foundation. The successful candidates will work on the structural elucidiation of poxviral transcription complexes and the rational design of inhibitors targeting the poxviral cytosolic transcription machinery. Ideal PhD candidates should hold an excellent diploma or master degree in physics, biology, biochemistry, biophysics, or a related field of science. Ideal PostDoc candidates should hold an excellent PhD in structural biology, biophysics, physics or in an equivalent area with previous experience in structural biology or protein biochemistry. The positions offer the opportunity to be involved I a wide spectrum of current methods from recombinant DNA technology over protein biochemistry (protein purification and analytics of large viral complexes), in silico drug design, high throughput screening to single particle cryo EM. The latter method is a major focus of the group which has regular access to the 300 keV Titan Krios-TEM of the university. The PhD position furthermore offers a structured educational program within the framework of the Graduate School of Life Sciences (GSLS). Both positions include the possibility to transition through an industrial setting at Intana Bioscience GmbH (Martinsried), which is our cooperation partner for high throughput screening. Interested candidates should contact directly: Utz Fischer (utz.fisc...@uni-wuerzburg.de) or Clemens Grimm (clemens.gr...@uni-wuerzburg.de) To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Open positions for one Postdoc and one PhD student
Dear All, Two research positions funded by the VolkswagenStiftung are available in the group of Prof. Utz Fischer at the Theodor-Boveri Institute of the Julius-Maximilians-Universität Würzburg. The successful candidates will participate in a structure-based drug design approach to combat the zoonotic risk imposed by poxviral reservoirs and human pathogenic poxvirus strains. To this end, we target the unique poxviral transcription machinery, which relies exclusively on virus-encoded proteins. As a basis, we recently reported the isolation and comprehensive structural investigation of this machinery in different phases of action. This now enables the identification and design of small molecules that interfere with poxviral gene expression and their subsequent translation into antiviral pharmaceuticals. Last but not least, the unexpected severity of the ongoing monkeypox outbreak underlines the timeliness of this project. See our recent publications on the topic: Grimm et al., Cell 179 (7): 1537-1550 (2019) Hillen et al., Cell 179 (7): 1525-1536 (2019) Grimm et al., Nat. Struct. Mol. Biol. 28 (10), 779-788 (2021) Grimm et al., TIBS (2022) or for a quick overview our website: https://www.biozentrum.uni-wuerzburg.de/biochem/research-groups/grimm-group-structural-biology/projects/ We offer: A stimulating international research environment in a well-equipped and modern department at the Biocenter of the University, which provides diverse opportunities for collaborations. The GSLS provides the framework for a structured PhD education program. Remuneration will be according to public service positions in Germany, 100% TV-L E13 (Postdoc) or 65% TV-L E13 (PhD student). Disabled applicants will be preferentially considered in case of equivalent qualifications. Requirements: The candidates should possess a solid background in biochemistry or virology. The Postdoc position requires a PhD in the life sciences. The PhD Student position requires an M.Sc. in the life sciences or equivalent for enrolment at the Würzburg Graduate School of Life Sciences (GSLS). Experience in protein bioinformatics, biophysics or structural biology is beneficial. Application/ Contact: Please send your application, which should include a statement of motivation, a detailed CV and the contact details of two referees as a single file by e-mail to the Department of Biochemistry. For further information, please contact Utz Fischer utz.fisc...@uni-wuerzburg.de Tel.: +49 931-3184029 or Clemens Grimm clemens.gr...@uni-wuerzburg.de Tel.: +49 931-3184031 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
