- phenixbb - phenix-online.org

bug?
by Patrick Loll 12 May '16

12 May '16

I just ran into something that might be a small bug (phenix 1.10.1-2155) Background: I have a problem data set for which the unit cell is too small to hold we thought we were crystallizing (which probably means we crystallized the wrong protein). In any case, I ran the data through Xtriage, supplying the sequence file for the too-large protein, even though I knew this is probably not correct. This sequence file contains 264 residues. I was surprised to see that the program returned with a perfectly reasonable estimate of the Matthews coefficient, making me briefly hopeful that I had been doing the calculation incorrectly. Alas, not so; when I dig through the log file, I find the following: ____begin excerpt_______________________________________________________________ determining composition from sequence file /xxxx/seq.dat Too many residues to fit in the ASU resetting numer of residues in monomer to 26 =================== Solvent content and Matthews coefficient ================== Crystallized molecule(s) defined as 264 protein residues ------------------------------------------------------------------- | Solvent content analysis | |-----------------------------------------------------------------| | Copies | Solvent content | Matthews coeff. | P(solvent content) | |-----------------------------------------------------------------| | 1 | 0.666 | 3.68 | 0.621 | | 2 | 0.331 | 1.84 | 0.379 | ------------------------------------------------------------------- Best guess : 1 copy in the ASU _____end excerpt_______________________________________________________________ So it seems as though the program, when confronted with a protein mass that’s too large for the AU, divides the mass by 10 and tries again. However, this is not clear from the results; in the results section, it states “Crystallized molecule(s) defined as 264 protein residues." So a user might be misled into thinking that everything is OK, when in fact it’s not… Cheers, Pat --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.loll(a)drexelmed.edu

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BCA/CCP4 Summer School 2016 - Applications now open
by Airlie McCoy 10 May '16

10 May '16

I am pleased to announce that applications are now open for the BCA/CCP4 Summer School in Protein Crystallography to be held at Diamond Light Source from Sunday 21st August to Friday 26th August 2016 Applications will close Friday 13th May. The registration fee of the school has been kept low due to the generous sponsorship of the BCA and CCP4. Note that up to 10 free places are available to BBSRC funded students. For a draft programme and application details see: http://www.diamond.ac.uk/Home/Events/2016/BCA-Summer-School.html The BCA/CCP4 Protein Crystallography Summer School is intended for students and researchers new to crystallography. Its dual aims are to provide comprehensive training in crystallography and to promote best practise within the British crystallographic community. The lectures cover the gamut of techniques required for a structure solution, from protein expression through to structure validation. Intensively supervised computer tutorials enable students to relate the theory presented in the lectures to practice. Although CCP5 programmes will primarily be used in these tutorials, the aim will be to approach crystallographic questions in a software-agnostic manner. There will also be a crystal manipulation and cooling workshop. (Note that the course is scheduled during Diamond synchrotron downtime, so there will not be active data collection at the Diamond beamlines.) We recognise that an active social programme plays a role in enabling students to make links that may be maintained throughout a research career. There will be a conference dinner, and a number of other events, including a boat trip on the Thames from Oxford. Airlie McCoy

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Research Technician Position at Structural Biology Lab at University of Southern California
by Xiao Lei 07 May '16

07 May '16

Dear All, The Lin Chen laboratory at the University of Southern California is seeking a research technician to join the lab. The Chen lab is interested in the structure and function of molecular complexes that control cell signaling and gene expression. We use a multi-disciplinary approach that combines structural biology, chemical biology, biochemistry/cell biology, and computational biology/bioinformatics to study the molecular basis of signal transduction and transcription regulation. For more detailed description of our research, please visit the lab page: http://structure.usc.edu/ Job Responsibilities Include: Assist postdoctoral fellows and graduate students in the lab on a variety of biochemical and biophysical studies, including gene cloning, protein expression, purification, and characterization of purified protein by various biochemical and biophysical techniques, and protein crystallization. The technician may also be involved in developing new techniques to study the structure and function of the genome. The technician is also expected to take a small amount of lab managing duty such as ordering and organizing lab supplies,. Commitment of 1 year is required; 2 years is preferred, the position is grant-funded and renewable Preferred Qualifications: • BS in Biochemistry, or Chemistry, or Molecular Biology, or related field • 2 years lab experience • Working knowledge of laboratory equipment and research protocols • Must be meticulous, detail-oriented, and responsible • Basic biochemistry, molecular biology and chemistry knowledge To apply for this position, Please send CV, three names of reference and a cover letter to: linchen(a)usc.edu Best Regards.

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autoBuild error, OSError: [Errno 12] Cannot allocate memory
by luzuok 07 May '16

07 May '16

Hello, The autobuild had been running for almost 2 hours in my Desktop, but it suddenly stopped and posed an error message as indicated below. Is this caused by my insufficient memory? Best wishes! Luzuokun Splitting work into 4 jobs and running with 2 processors using sh background=True in /home/lu/Documents/StructurePro/why/P43212/AutoBuild_run_2_/TEMP0 Starting job 1...Log will be: /home/lu/Documents/StructurePro/why/P43212/AutoBuild_run_2_/TEMP0/RUN_FILE_4.log Starting job 2...Log will be: /home/lu/Documents/StructurePro/why/P43212/AutoBuild_run_2_/TEMP0/RUN_FILE_5.log Starting job 3...Log will be: /home/lu/Documents/StructurePro/why/P43212/AutoBuild_run_2_/TEMP0/RUN_FILE_6.log Starting job 4...Log will be: /home/lu/Documents/StructurePro/why/P43212/AutoBuild_run_2_/TEMP0/RUN_FILE_7.log Traceback (most recent call last): File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/autosol/AutoBaseExtend.py", line 987, in DoNextMethod self.CarryOutBest() # to be obtained after it is finished File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/autosol/AutoBaseExtend.py", line 2147, in CarryOutBest getattr(self,str(self.application_method))() # call this fn File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/wizards/AutoBuild.py", line 2372, in AutoBuild_build_cycle self.AutoBuild_rebuild_cycle_run() File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/wizards/AutoBuild.py", line 4714, in AutoBuild_rebuild_cycle_run always_reuse_model=always_reuse_model) File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/wizards/AutoBuild.py", line 7589, in AutoBuild_build_refine mtz_file=mtz_file,mtz_ref_file=mtz_ref_file) File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/wizards/AutoBuild.py", line 7833, in run_standard_build_in_parallel r.run(out=sys.stdout) File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/autosol/run_group_of_wizards.py", line 294, in run self.start_run(run_file,last=is_last) File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/autosol/run_group_of_wizards.py", line 604, in start_run cmd+" "+self.add_double_quote(run_file,escape_space=False)) File "/usr/local/phenix-1.10.1-2155/modules/cctbx_project/libtbx/easy_run.py", line 160, in __init__ close_fds=not subprocess.mswindows) File "/usr/local/phenix-1.10.1-2155/base/lib/python2.7/subprocess.py", line 710, in __init__ errread, errwrite) File "/usr/local/phenix-1.10.1-2155/base/lib/python2.7/subprocess.py", line 1223, in _execute_child self.pid = os.fork() OSError: [Errno 12] Cannot allocate memory -- 卢作焜南开大学新生物站A202 Lu Zuokun, Ph.D. Candidate College of Life Science, Nankai University

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Re: [phenixbb] Self Rotation Function
by Sharan Karade 04 May '16

04 May '16

Thank you for your valuable Edward, Patrick, Francis. I will try with your suggestions. And let you know the results. On 4 May 2016 20:03, "Edward A. Berry" <BerryE(a)upstate.edu> wrote: On 05/04/2016 10:17 AM, Patrick Loll wrote: > You won’t see peaks in the self-rotation function unless the AU contains > non-crystallographic rotational symmetry, which frequently is not the case > (just because you have multiple copies of your protein in the AU does not > imply that they are arranged in any specific, symmetric manner). And even > if there is rotational NCS, if the axis of rotation is parallel to a > crystal symmetry operator, the effect of the NCS will be masked. So > everything may be working as it should. > > If you’re not certain if you have the program working correctly, then I > suggest that you find a structure in the PDB that contains rotational NCS, > download the structure factors, and calculate the self-rotation map, as a > positive control. > > Try bacterioferritin (in a low-symmetry space group) or GroEL ! > On 4 May 2016, at 12:10 AM, Sharan Karade <sharankarade(a)gmail.com> wrote: >> >> Hello everyone, >> >> i am working on data set which has resolution of 2.8 A >> space group C2, the protein have 394 a a . when i estimate Mathews >> coefficient it shows four to five molecules in asymmetric unit. when i try >> to get self rotation function Map by default parameter (10A-3A and 25 >> radius of integration) i was not getting any peak at all 180, 90, 120, 60. >> Or radius of integration affect the results. >> >> Can anybody please help me to sort out with this problem, welcome for >> suggestions, thanks in advance. >> >> -- >> Sharan >> C/O Dr. J V Pratap >> Senior Research Fellow, >> CSIR-Central Drug Research Institute, >> Lucknow >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org >> > > > > > --------------------------------------------------------------------------------------- > Patrick J. Loll, Ph. D. > Professor of Biochemistry & Molecular Biology > Director, Biochemistry Graduate Program > Drexel University College of Medicine > Room 10-102 New College Building > 245 N. 15th St., Mailstop 497 > Philadelphia, PA 19102-1192 USA > > (215) 762-7706 > pat.loll(a)drexelmed.edu > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org > >

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Self Rotation Function
by Sharan Karade 04 May '16

04 May '16

Hello everyone, i am working on data set which has resolution of 2.8 A space group C2, the protein have 394 a a . when i estimate Mathews coefficient it shows four to five molecules in asymmetric unit. when i try to get self rotation function Map by default parameter (10A-3A and 25 radius of integration) i was not getting any peak at all 180, 90, 120, 60. Or radius of integration affect the results. Can anybody please help me to sort out with this problem, welcome for suggestions, thanks in advance. -- Sharan C/O Dr. J V Pratap Senior Research Fellow, CSIR-Central Drug Research Institute, Lucknow

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Phenix.multi_crystal_average
by Sam Tang 04 May '16

04 May '16

Hello colleagues May I enquire if the captioned programme is still supported in the latest version of Phenix and, if not, which programme is now in place for this? Thanks in advance. Cheers Sam Tang Biochemistry Programme, School of Life Sciences, CUHK

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CCN submissions
by Nigel Moriarty 02 May '16

02 May '16

Folks Calling for articles and short communications of interest to structural biologists. The initial deadline for submission in the July 2016 issue is 1 June 2016. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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Refmac error using PDB coordinates generated by Phenix PDB File Editor
by Xiao Lei 30 Apr '16

30 Apr '16

Hi Phenixbb members, I'm using Phenix PDB File Editor under Phenix GUI "Model Tool" to change occupancy of two short 7 polyalanine alpha helix peptide chain (chain I and K, placed in reverse orientation of each other in one region (or density blob) of my model, each chain half occupancy) , I can change the occupancy very easily with the tool, but I have two types of errors using the coordinates generated by the tool in Refmac. 1. If I set chain ID of chain K to chain I with the same residue number with half occupancy but in reverse order (Chain I, Ala7th--13th 0.5 occupancy and Chain I, Ala7th--13th 0.5 occupancy) , Refmac could not refine the model with an error message below: I am reading library. Please wait. mon_lib.cif ERROR : ALA : duplicated atom_name : "N ". chain: II residue: 7 ERROR : ALA : duplicated atom_name : "CA ". chain: II residue: 7 ERROR : ALA : duplicated atom_name : "CB ". chain: II residue: 7 ERROR : ALA : duplicated atom_name : "C ". chain: II residue: 7 ERROR : ALA : duplicated atom_name : "O ". chain: II residue: 7 IERR = 1 There is an error. See above ===> Error: Fatal error. Cannot continue. I understand Refmac can not allow two peptide chain with the same ID and residue number if both peptides are full occupancy (1), but why in this case even half occupancy of the same chain ID and residue number is not tolerated? 2. If I set chain ID of chain K and chain I half occupancy (Chain K, Ala7th--13th 0.5 occupancy and chain I, Ala7th--13th 0.5 occupancy) , put chain K and chain I in the same density blob with reverse direction, and run Refmac, this time Refmac can finish but gave me error message in log file as below: I am reading library. Please wait. mon_lib.cif INFO: link is found (not be used) dist= 1.486 ideal_dist= 1.240 ch:II res: 7 ALA at:N .->ch:KK res: 11 ALA at:O . INFO: link is found (not be used) dist= 1.625 ideal_dist= 1.080 ch:II res: 8 ALA at:O .->ch:KK res: 9 ALA at:O . INFO: link is found (not be used) dist= 1.584 ideal_dist= 1.400 ch:II res: 10 ALA at:N .->ch:KK res: 11 ALA at:N . INFO: link is found (not be used) dist= 1.397 ideal_dist= 1.530 ch:II res: 10 ALA at:CB .->ch:KK res: 11 ALA at:CB . INFO: link is found (not be used) dist= 1.153 ideal_dist= 1.400 ch:II res: 11 ALA at:N .->ch:KK res: 10 ALA at:N . INFO: link is found (not be used) dist= 1.820 ideal_dist= 1.524 ch:II res: 11 ALA at:CA .->ch:KK res: 10 ALA at:CB . INFO: link is found (not be used) dist= 0.888 ideal_dist= 1.530 ch:II res: 11 ALA at:CB .->ch:KK res: 10 ALA at:CB . INFO: link is found (not be used) dist= 1.808 ideal_dist= 1.530 ch:II res: 12 ALA at:CB .->ch:KK res: 9 ALA at:CB . INFO: link is found (not be used) dist= 1.764 ideal_dist= 1.400 ch:II res: 13 ALA at:N .->ch:KK res: 7 ALA at:N . -------------------------------- I do not know why Refmac gave me this message, is it because the two helix chain (I and K) are placed in the same region, even though both with 0.5 occupancy of both chain, Refmac still automatically tries to connect the main chain atom between two different chains (I and K) because main chain atoms are placed too close to each other (Refmac think there is a link between them?) ? 3. In summary, should I use Phenix Refine instead of Refmac to handle the pdb coordinates generated by Phenix PDB file editor because Phenix Refine may have better compatibility? Thanks in advance.

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build two helix run in opposite direction and set half occupancy or each in Coot
by Xiao Lei 30 Apr '16

30 Apr '16

Hi Phenixbb members, Is there a way in the Coot GUI that I can build two helix of the same sequence (or just short 5aa or 6aa peptide chains of the same sequence) that run in the opposite direction (180 degree opposite direction) of each other and set half occupancy of each peptide chain? I tried to use Calculate---> Model/fit/refine/----> add alternative conformation, but it seems I only have two options: "split single residue at C-alpha" or "split all of a single residue", which are applying to single residue only, not a short peptide chain. Thanks.

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