[ccp4bb] Postdoctoral position in structural studies of integral membrane pyrophosphatases
The Goldman group in the Department of Biosciences at the University of Helsinki invites applications for: A postdoctoral researcher in structural studies on protozoan membrane-bound pyrophosphatases with effect from 1.9.2014, until 31.12.2015. Location: Biocentre 2, Viikinkaari 5, Helsinki University. The project is focused on the elucidation of the structure and function of protozoan membrane-bound pyrophosphatases (see Kellosalo et. al. 2012: Science 27, Vol 337). Analyzed proteins are putative drug targets against protozoan parasites, which cause severe infections like malaria, leishmaniasis, African trypanosomiasis and Chaga's disease. The position requires a strong background in protein purification, the capacity to work in a team and independently, the ability to look critically at the results as well as excellent interpersonal and communication skills. The project involves production, purification and functional characterization of protozoan membrane-bound pyrophosphatases, solving of the structures of these proteins with X-ray crystallography and screening of drug compounds in vitro and in vivo. The aim of the project is to discover lead molecules, which can be utilized in the design of anti-protozoan drugs. The successful candidate must hold a PhD degree in biochemistry, chemistry, biophysics or a related field. Excellent background in protein purification documented by peer-reviewed articles is required. Knowledge of screening of drug molecules and X-ray crystallography will be advantageous. Excellent English is also essential in the position. The application should include a complete CV including education, degrees obtained, a list of publications, prior work experience and the names and contact information for two referees. The applications (in English) should be sent to: Docent Taru Meri, P.O. Box 56, FIN-00014 UNIVERSITY OF HELSINKI, Finland or by email to taru.m...@helsinki.fi. The deadline for applications is 4 August 2014. For more information please contact Adrian Goldman, tel. +44 79 18951821; adrian.gold...@helsinki.fi signature.asc Description: Message signed with OpenPGP using GPGMail
Re: [ccp4bb] Proper detwinning?
hi Chris Can you send the date-stamped log file (called something like mosflm_20140712_140235.lp, I.e. with the year, month, date, etc when you ran the program) to me directly (i.e. not to the BB, since it's likely to be of little interest to all the other subscribers...) so I can have a look at the results of indexing, and the processing that led up to the MASKIT error? Harry -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing) On 12 Jul 2014, at 00:33, Chris Fage cdf...@gmail.com wrote: Nat and Misha, Thank you for the suggestions. Xtriage does indeed detect twinning in P1, reporting similar values for |L|, L^2, and twin fraction as in P212121. The unit cell dimensions for the 2.0-A structure (P1) are: 72.050 105.987 201.142 89.97 89.98 89.94 P 1 The unit cell dimensions for the 2.8-A structure (P212121) are: 75.456 115.154 202.022 90.00 90.00 90.00 P 21 21 21 I have been processing in HKL2000, which only recognizes one set of unit cell parameters for each Bravais lattice (does anyone know how to change this?). Specifically, for a primitive monoclinic unit cell it estimates: 104.53 71.82 200.99 89.86 91.80 91.16 This is the unit cell which refined to Rwork/Rfree ~ 27%/34%. Indexing in mosflm gives three options for primitive monoclinic: 105.6 71.7 200.9 90.0 90.1 90.0 71.7 105.6 201.0 90.0 89.9 90.0 71.7 200.9 105.6 90.0 90.3 90.0 Attempting to integrate in any of these space groups leads to a fatal error in subroutine MASKIT. I can also use the index multiple lattices feature to get a whole slew of potential space group; however, integrating reflections leads to the same fatal error. Finally, Zanuda tells me that P212121 is the best space group, according to R-factors. However, I do not believe P212121 is the correct assignment. Best, Chris On 7/10/14, Isupov, Michail m.isu...@exeter.ac.uk wrote: I would recommend to run ZANUDA in the default mode from ccp4i or on CCP4 web server. ZANUDA has resolved several similar cases for me. Misha From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Chris Fage [cdf...@gmail.com] Sent: 10 July 2014 01:14 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Proper detwinning? Hi Everyone, Despite modelling completely into great electron density, Rwork/Rfree stalled at ~38%/44% during refinement of my 2.0-angstrom structure (P212121, 4 monomers per asymmetric unit). Xtriage suggested twinning, with |L| = 0.419, L^2 = 0.245, and twin fraction = 0.415-0.447. However, there are no twin laws in this space group. I reprocessed the dataset in P21 (8 monomers/AU), which did not alter Rwork/Rfree, and in P1 (16 monomers/AU), which dropped Rwork/Rfree to ~27%/32%. Xtriage reported the pseudo-merohedral twin laws below. P21: h, -k, -l P1: h, -k, -l; -h, k, -l; -h, -k, l Performing intensity-based twin refinement in Refmac5 dropped Rwork/Rfree to ~27%/34% (P21) and ~18%/22% (P1). Would it be appropriate to continue with twin refinement in space group P1? How do I know I'm taking the right approach? Interestingly, I solved the structure of the same protein in P212121 at 2.8 angstroms from a different crystal. Rwork/Rfree bottomed out at ~21%/26%. One unit cell dimension is 9 angstroms greater in the twinned dataset than in the untwinned. Thank you for any suggestions! Regards, Chris
[ccp4bb] AMPLE failure
Hi, I'm trying to run AMPLE from ccp4-6.4.0 on Linux Ubuntu. It looks like it found all the program dependencies that it needs and Rosetta looks like it ran okay and I think MRBUMP looks alright, but then the program stopped with the following error message: MR and shelx DONE ALL DONE (in 1.64101706141 hours) Saved results as file: /home/rob/Crystal/108_B7U_3/ccp4/ROSETTA_MR_1/resultsd.pkl *** * Information from CCP4Interface script *** The program run with command: /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ccp4-python -u /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ample -mtz /home/rob/Crystal/108_B7U_3/ccp4/XDS_ASCII_scaled2.mtz -fasta /home/rob/Crystal/108_B7U_3/phenix/RNK149.fasta -nmodels 1000 -name MVD0 -run_dir /home/rob/Crystal/108_B7U_3/ccp4 -nproc 8 -make_models True -rosetta_dir /home/rob/Xstal_Programs/Rosetta/rosetta-3.5 -frags_3mers /home/rob/Crystal/108_B7U_3/ccp4/aat000_03_05.200_v1_3 -frags_9mers /home/rob/Crystal/108_B7U_3/ccp4/aat000_09_05.200_v1_3 -make_frags False -F F_XDSdataset -SIGF SIGF_XDSdataset -FREE FreeR_flag -early_terminate True -use_shelxe True -use_arpwarp False has failed with error message Traceback (most recent call last): File /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ample, line 838, in summary = amopt.final_summary() File /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/share/ample/python/ample_options.py, line 197, in final_summary result_summary.append( getattr( result, title2attr[ h ] ) ) KeyError: 'SHELXE_ACL' Any thoughts on how I might troubleshoot this? Thanks and Best wishes, Rob
Re: [ccp4bb] AMPLE failure
Dear Rob, Sorry to hear that this issue has affected you - it's a known bug which will be fixed in the next ccp4 update. AMPLE has run to completion but crashed printing out the results. To see the results, you can run the following command at the terminal (command-line): /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ccp4-python /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/share/ample/python/mrbump_results.py /home/rob/Crystal/108_B7U_3/ccp4/ROSETTA_MR_1/MRBUMP/cluster_1 If that doesn't work or you need any additional help, please contact me off-list. Best wishes, Jens From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Robert Kirchdoerfer [rkirc...@scripps.edu] Sent: 12 July 2014 18:58 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] AMPLE failure Hi, I'm trying to run AMPLE from ccp4-6.4.0 on Linux Ubuntu. It looks like it found all the program dependencies that it needs and Rosetta looks like it ran okay and I think MRBUMP looks alright, but then the program stopped with the following error message: MR and shelx DONE ALL DONE (in 1.64101706141 hours) Saved results as file: /home/rob/Crystal/108_B7U_3/ccp4/ROSETTA_MR_1/resultsd.pkl *** * Information from CCP4Interface script *** The program run with command: /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ccp4-python -u /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ample -mtz /home/rob/Crystal/108_B7U_3/ccp4/XDS_ASCII_scaled2.mtz -fasta /home/rob/Crystal/108_B7U_3/phenix/RNK149.fasta -nmodels 1000 -name MVD0 -run_dir /home/rob/Crystal/108_B7U_3/ccp4 -nproc 8 -make_models True -rosetta_dir /home/rob/Xstal_Programs/Rosetta/rosetta-3.5 -frags_3mers /home/rob/Crystal/108_B7U_3/ccp4/aat000_03_05.200_v1_3 -frags_9mers /home/rob/Crystal/108_B7U_3/ccp4/aat000_09_05.200_v1_3 -make_frags False -F F_XDSdataset -SIGF SIGF_XDSdataset -FREE FreeR_flag -early_terminate True -use_shelxe True -use_arpwarp False has failed with error message Traceback (most recent call last): File /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ample, line 838, in summary = amopt.final_summary() File /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/share/ample/python/ample_options.py, line 197, in final_summary result_summary.append( getattr( result, title2attr[ h ] ) ) KeyError: 'SHELXE_ACL' Any thoughts on how I might troubleshoot this? Thanks and Best wishes, Rob
