May 2016 - phenixbb - phenix-online.org

Scale and merge multiple data sets
by Sam Tang 06 Feb '17

06 Feb '17

Dear colleagues Hello again. I would like to scale and merge two different native datasets for a same protein complex (which semed to die off gradually in the beam) using the scale_and_merge tool. The error message was received "Multiple intensity arrays - please specify one: data_labels=I,SIGI data_labels=IPR,SIGPR" However I looked into the log file and I have actually included "data_labels = "IPR,SIGIPR,merged" . Perhaps I have missed something else in the setting? Regards Sam Sam Tang Biochemistry Programme, School of Life Sciences, CUHK

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Refine pixel size of map (for EM data)?
by Oliver Clarke 26 Jul '16

26 Jul '16

Hello, I wonder whether it would be possible to add an option for phenix.real_space_refine to allow refinement of the pixel size of the map (or the unit cell dimensions - just an overall size scale factor), and write out the altered map at the end of refinement. Although we try to calibrate this as best as we are able at the time of data collection, it is never perfect - for example, in one case I have dealt with, our nominal pixel size out of the scope is 1.19 Å, but the pixel size calibrated based on a crystal structure of a fragment of the protein is 1.25 Å. This is not a huge difference, but it is sufficient I think to have a substantial impact on refinement, particularly as regards clash assessment and H-bond/sec struc restraints. In cases where one does not have a solved crystal structure to use for calibration, perhaps refining the pixel size in conjunction with the geometry might be of some use? Cheers, Oli

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GPU acceleration of phenix.real_space_refine?
by Oliver Clarke 03 Jun '16

03 Jun '16

Hi all, phenix.real_space_refine takes a very long time to run on large systems when using any of the more computationally expensive options (e.g. morphing). I was wondering if there has been any consideration towards optimizing this code (and maybe that of phenix.map_to_model) for GPU acceleration? There is somewhat of a shift occuring in the EM community towards using GPU workstations for data processing - if we could use already purchased capabilities to accelerate model refinement as well that would be a huge bonus. I saw a discussion on the bb from a while back concerning the same question applied to phenix.refine, and the conclusion was that in that case the benefits would be minimal, but I'm not sure whether the same applies to real space operations. Cheers, Oli. PS has there been any consideration of including an option to allow users to supply two half maps at run time, one "work" and one "test" map for cross validation purposes? It is possible to do this with two separate runs right now but having the option integrated would be wonderful.

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rosetta_refine connecting non-consecutive residues around break in chain
by wtempel 28 May '16

28 May '16

Hello, can one prevent rosetta_refine from connecting two residues that surround a gap? For example, how do I keep near-by residues 108 and 115 apart when 109 through 114 are missing? Thank you. Wolfram Tempel

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Fwd: Re: Scultor model with gaps included
by Gabor Bunkoczi 26 May '16

26 May '16

Apologies, this should have been directed to the mailing list. Gabor -------- Original Message -------- Subject: Re: [phenixbb] Scultor model with gaps included Date: 2016-05-25 14:33 From: Gabor Bunkoczi <gb360(a)cam.ac.uk> To: Joseph Brock <joseph.brock(a)ki.se> Dear Joseph, apologies for the late response, and sorry for the trouble. Please find some answers inlined. On 2016-05-24 15:10, Joseph Brock wrote: > Dear Phenix community, > > I was hoping if someone could help me with using Phaser correctly, > since I can't seem to produce the desired search model. > > The first thing that I was wondering about is that the CLUSTAL > alignment from the log file is quite different to the .aln alignment I > made with phenix --> other tools --> multiple sequence alignment. Why > is a sequence alignment required as input if sculptor performs it's > own internally? Sculptor can perform sequence alignment, but the algorithm is relatively basic, and you can get much better results with an external method (such as HHPRED), and hence alignment input is preferred over the target sequence. The alignment selected is printed into the logfile for reference. On the other hand, Sculptor does align the structure of your model chain to the sequence of your model (this is a surprisingly non-trivial task). However, this alignment should be close to 100% identical, unless a mistake has been made (such as using the wrong alignment file). You should get a warning if the sequence identity is too low. It is normally OK to have a couple of mismatches (such as having SeMet in the model structure with translates to "X" and not as "C"). > > My model sequence aligned to my target sequence in the log file has > several gaps in the alignment . For e.g., > > MASTER ......AASFIMV...... > CHAIN_A ......AKM--MF....... > > I would like to great a search model in which the residues aligned to > gaps in the MASTER chain are included, however the resulting sculptor > .pdb file has these residues removed. Shouldn't they be inserted so > that the rest of the chain is in the correct register? You need to do homology modelling to achieve this, as an insertion can affect the whole structure. Sculptor is designed for quick model improvement, and just renumbers/renames residues. However, the new residues numbers should reflect your sequence, i.e. in your example alignment the two methionines on both sides of the gap will get a non-consecutive number and are displayed as non-bonded in e.g. Coot. > > If anyone can let me know the parameters to allow this, I would > greatly appreciate it. I tried unselecting 'gap' in main-chain > deletion scope and some other variations, but this didn't seem to > help. > > I seem to get the same result even if I change the target index from 1 > to 2 in the associated .aln alignment. Does anyone know why this is? Hmm, this does not sound right. Can you send me the logfile so that I can have a look (please use my direct email address)? Best wishes, Gabor > > Apologies if this is quite obvious, I have been reading the > documentation but can't seem to figure it out. > > All the best, > > Joseph. > > Joseph Brock | PhD > Division of Physiological Chemistry II > Department of Medical Biochemistry and Biophysics > Karolinska Institutet > Scheeles väg 2 > SE-171 77 Stockholm, Sweden > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org -- ################################################## Dr Gabor Bunkoczi Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital Hills Road Cambridge CB2 0XY ##################################################

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Appropriate model_vs_data usage over part of a structure
by Andy Watkins 26 May '16

26 May '16

Perhaps necessary preface: I am largely learning as I go, and large parts of Phenix (and the details of refinement data file formats) are still black boxes for me. Suppose I have a model of one chain of a complex and an .mtz describing the entire complex. I have performed some refinement procedure altering the model of that single chain. My aim is to determine how this refinement procedure has affected the fit to the experimental data--or, really, the subset of the experimental data expected to be relevant for my model. For obvious reasons, phenix.model_vs_data chain_A.pdb whole_complex.mtz phenix.model_vs_data chain_A_refined.pdb whole_complex.mtz are undesirable: they evaluate the model of a single chain against the whole complex's data, and there's obviously a lot of unsatisfied electron density. So, while this command *works*, it reports an unrepresentative fit. (In theory, one solution to my problem would be to re-combine each chain's refined version, then run model_vs_data on the recombined, refined complex. I'm interested nonetheless in how it would work on the chains separately. Now, during the refinement procedure, we of course generate .ccp4 density maps for the individual chain models: phenix.maps chain_A.pdb whole_complex.mtz which produces the ccp4 file as well as, crucially, chain_A_map_coeffs.mtz. Attempting to employ that resulting .mtz file, i.e. phenix.model_vs_data chain_A.pdb whole_complex.mtz phenix.model_vs_data chain_A_refined.pdb whole_complex.mtz leads to an evocative error: Sorry_No_array_of_the_required_type: No reflection arrays available. My highest suspicion is that I need to alter maps.params in a particular way so that reflection arrays are also output to model_map_coeffs.mtz. I could also imagine that I need to be using another program entirely! Thanks in advance for whatever help you can provide; unfortunately, I can't provide any input files.

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July ACA meeting in Denver early registration still open!
by Terwilliger, Thomas Charles 25 May '16

25 May '16

?Hi Phenix colleagues! Heading to Denver for ACA's Annual Meeting in July? Early registration ends May 31 (abstracts still being accepted too!) See: http://www.amercrystalassn.org/2016-meeting-homepage ?All the best, Tom T Tom Terwilliger (2016 ACA President)

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Scultor model with gaps included
by Joseph Brock 24 May '16

24 May '16

Dear Phenix community, I was hoping if someone could help me with using Phaser correctly, since I can't seem to produce the desired search model. The first thing that I was wondering about is that the CLUSTAL alignment from the log file is quite different to the .aln alignment I made with phenix --> other tools --> multiple sequence alignment. Why is a sequence alignment required as input if sculptor performs it's own internally? My model sequence aligned to my target sequence in the log file has several gaps in the alignment . For e.g., MASTER ......AASFIMV...... CHAIN_A ......AKM--MF....... I would like to great a search model in which the residues aligned to gaps in the MASTER chain are included, however the resulting sculptor .pdb file has these residues removed. Shouldn't they be inserted so that the rest of the chain is in the correct register? If anyone can let me know the parameters to allow this, I would greatly appreciate it. I tried unselecting 'gap' in main-chain deletion scope and some other variations, but this didn't seem to help. I seem to get the same result even if I change the target index from 1 to 2 in the associated .aln alignment. Does anyone know why this is? Apologies if this is quite obvious, I have been reading the documentation but can't seem to figure it out. All the best, Joseph. Joseph Brock | PhD Division of Physiological Chemistry II Department of Medical Biochemistry and Biophysics Karolinska Institutet Scheeles väg 2 SE-171 77 Stockholm, Sweden

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Senior Research Assistant position - MD Anderson Cancer Center
by Leonard,Paul 24 May '16

24 May '16

Dear all, This post is to bring your attention to a job opportunity for a Senior Research Assistant position at the University of Texas, MD Anderson Cancer Center (in Houston, Texas, USA). MD Anderson Cancer Center is the number one cancer center in the United States and a center of excellence for both oncology treatment and research. This is an opportunity to join a dedicated team of researchers that are working together to develop new cancer therapeutics to positively impact the lives of our patients. We are looking for a highly motivated individual with experience in molecular biology and protein production to work within our structural biology team to support research projects across the MD Anderson research community and the drug discovery pipeline of the Institute for Applied Cancer Science. The research that stems from the proteins produced has a direct impact on the lives of our patients. Salaries are competitive and based on the level of experience of the applicant. We are looking for applicants with a Bachelors or Masters degree in Biochemistry, Biotechnology, Pharmacology or a related subject. Previous experience working in a research lab environment is desired. The ideal candidate will have previous molecular biology or protein purification experience. For more information and to submit a job application please refer to the job posting… https://mdanderson.referrals.selectminds.com/jobs/sr-research-asst-genomic-… We look forward to reviewing your application. Please use the above link to submit your application, CV and cover letter. Best wishes, Paul Leonard The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

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ncs average map
by Jarrod Mousa 22 May '16

22 May '16

Hi all I am trying to use phenix refine to NCS average my density map during refinement. If I check refinement, I get an error saying 'Missing a map type defiinition for one or more CCP4 or XPLOR maps." If I try to upload a 2Fo-Fc map generated from FFT map coefficients, I get an error saying that phenix does not recognize the file. Any tips or other methods to calculate such a map? thanks, Jarrod Mousa

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