February 2013 - phenixbb - phenix-online.org

how to make covelent link of BME with Cys and refine
by Rajeshwer Sankhala 14 Feb '13

14 Feb '13

Hello Sabine Yah i could specify link in the pdb and also could see it in coot but when i go for refinement then bond is broken. I given pdb mtz and cif files in refinement. The only problem i feel could be that i don't have restrains for SS bond in cif file but i don't know how to generate SS-bond restrains. Thanks RAJ

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how to make covelent link of BME with Cys and refine
by Rajeshwer Sankhala 14 Feb '13

14 Feb '13

Thanks Nigel, I am using phenix 1168 but when i type intra_chain = True command with phenix.refine it gives error message as "intra_chain = True is unknown command". The actual command i used was " phenix.refine .pdb .mtz .cif intra_chain = True". can you please explain how to resolve it. Raj

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Re: [phenixbb] how to make covelent link of BME with Cys and refine
by Ed. Pozharski 13 Feb '13

13 Feb '13

Excellent point. The difference between using bme and cme is rather ideological. I would say that incorporating cme implies that your protein was somehow synthesized with non-canonical amino acid. Usind bme seems more in line with what actually happens - betamercaptoethanol forming disulfide bond with a cysteine. In practical sense, both things work. Until IUCr comes up with a convention, one is free to ignore ideological considerations :) -------- Original message -------- From: Abhinav Kumar <abhinavk(a)slac.stanford.edu> Date: To: phenixbb(a)phenix-online.org Subject: Re: [phenixbb] how to make covelent link of BME with Cys and refine How about using residue CME which is the CYS and BME linked together. CME is included in the CCP4 monomer library, and so Phenix should accept it without a dictionary file. Thanks, Abhinav JCSG@SSRL, SLAC (650) 926-2992 On 02/13/2013 01:02 PM, Nigel Moriarty wrote: Raj In the more recent versions of PHENIX, phenix.refine can found and link atoms closer than 3 angstrom if you specify intra_chain=True. In the older versions, you can use phenix.ligand_linking to generate the needed files. Nigel PS PHENIX does not read SSBOND or LINK records but there is a script to generate the link files from the LINK records. On Tue, Feb 12, 2013 at 11:56 PM, Sabine Schneider <sabine.schneider(a)mytum.de> wrote: Hello Raj, do you have the link specified in you PDB file? Here is an example for an disulphide bond. Usually the link is the line above the CRYST1 card. SSBOND 1 CYS A 123 CYS A 123 1555 8555 2.12 Best, Sabine On 02/12/2013 11:21 PM, Rajeshwer Sankhala wrote: Hello, I can see additional density just next to Cys residues in my protein structure and it looks like BME is covalently linked to cys. I could form a disulfide bond between BME and Cys in "Refmac 5 review restrain" but when i subject it for refinement BME is thrown away (no disulfide bond). I also given Cif file in refinement but it didnot help. I have a feel that i am missing something in cif file. Can anyone suggest step by step starting from adding BME to making a link with BME (Cys-BME) and then refinement? Raj _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb -- Nigel W. Moriarty Building 64R0246B, 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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how to make covelent link of BME with Cys and refine
by Rajeshwer Sankhala 13 Feb '13

13 Feb '13

Hello, I can see additional density just next to Cys residues in my protein structure and it looks like BME is covalently linked to cys. I could form a disulfide bond between BME and Cys in "Refmac 5 review restrain" but when i subject it for refinement BME is thrown away (no disulfide bond). I also given Cif file in refinement but it didnot help. I have a feel that i am missing something in cif file. Can anyone suggest step by step starting from adding BME to making a link with BME (Cys-BME) and then refinement? Raj

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How to export difference patterson map in PHENIX
by 李翔 12 Feb '13

12 Feb '13

Hi everyone, I got a native and derivative dataset (by soaking) of my crystal and want to do MIR in phenix. I am wondering whether there is a way for me to export the difference Patterson map so I could have a better idea that whether the heavy atom is really in the crystal? Cheers, Frank

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fwd: WCPCW 21 - Abstract due...
by Nathaniel Echols 11 Feb '13

11 Feb '13

---------- Forwarded message ---------- From: "Williams, John Charles" <jwilliams(a)coh.org> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Date: Mon, 11 Feb 2013 12:47:21 -0800 Subject: WCPCW 21 - Abstract due... Dear All, March 17th is coming up soon. Looks like we have a great crowd and some really good abstracts. Those who havent submitted their abstracts are encourged to do so now. We will start to select talks shortly there after. Those who would like to still attend are encouraged to sign up - we still have space. Looking for to seeing you on St. Patty's day! Best, John

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FW: phenixbb Digest, Vol 87, Issue 3
by Phoebe A. Rice 10 Feb '13

10 Feb '13

Hi, Although its theoretically possible, I've never had 5-Br-dU cause a problem. My approach would be to pick the strand with more T's and get every T replaced with 5-Br-dU, unless the 3' nt is a T (you pay a lot more for 3' modifications). We have had issues where crystals wouldn't grow with a heavily 5-I-dU modified DNA, presumably because Iodine is significantly bigger than a the 5-methyl of T, and it annoys the protein. If you've got good footprinting data, you may be able to guess where the protein will "care" about the surface of the major groove, and avoid putting iodines in those regions. If not, its probably faster to just order several oligos and try them all. If you've got a lot of T's and are worried about locating all those heavy atoms, I'd go for one derivative with a couple of paired 5-I-dU's (in spots where you have two T's in a row) in hopes that that will give you a toehold on solving the Patterson, and then a 2nd where every T on one strand is brominated, which may provide more phasing power. Note that both of these pop off in the x-ray beam, so collect your anomalous data first and fast. Also note that if you're lucky, you can get an extra large delta f' by subtracting the last data set from the first ("radiation induced phasing"). Hope that helps! Phoebe ++++++++++++++++++++++++++++++++++++++++++ Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago 773 834 1723; PRice(a)uchicago.edu http://bmb.bsd.uchicago.edu/Faculty_and_Research/ http://www.rsc.org/shop/books/2008/9780854042722.asp

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CeBEM-CCP4 Macromolecular Crystallography Workshop 2013 at Montevideo: Application deadline extended
by Alejandro Buschiazzo 08 Feb '13

08 Feb '13

Dear Colleagues, Due to the application deadline originally scheduled for February 10, overlapping with Summer holiday dates in several South American countries, we have decided to extend the course application deadline UNTIL FEBRUARY 17, 2013. We invite all of you interested in this workshop, especially the ones that have contacted us, to take advantage of this opportunity and send your application forms (plus CV and letter of your supervisor): last days for applications open!! Find all details about the workshop and application form in www.pasteur.edu.uy/mx2013 <http://www.pasteur.edu.uy/mx2013>- for further inquiries and applications contact mx2013(a)pasteur.edu.uy <mailto:[email protected]>! *Second Macromolecular Crystallography School 2013 *at the Institut Pasteur de Montevideo (Uruguay). *Title:* "Macromolecular Crystallography School 2013: From data processing to structure refinement and beyond" *Dates:*April 9th-17th, 2013. *Site:*Institut Pasteur de Montevideo (Montevideo), Uruguay *The workshop content:* Conceived to provide theoretical background and hands-on abilities in the use of computational tools to exploit X ray diffraction data. Through lectures, tutorials and hands-on trouble-shooting, the students will be trained in state-of-the-art macromolecular crystallography. Particular emphasis will be given to data processing, phasing/structure determination and model refinement/validation. The workshop will feature authors and experts of many modern crystallographic software packages. This workshop represents the continuation within the series started in 2010 (http://www.pasteur.edu.uy/mxcourse) on Macromolecular Crystallography. In this opportunity it is being co-organized by the Center for Structural Biology of the Mercosur CeBEM (www.cebem.org.ar <http://www.cebem.org.ar>), jointly with the Collaborative Computational Project Number 4 (CCP4 -- UK www.ccp4.ac.uk <http://www.ccp4.ac.uk>). Support from the Institut Pasteur International Network, the International Union of Crystallography and Institut Pasteur de Montevideo is also greatly acknowledged. *Applicants:* Graduate students, postdoctoral researchers and young scientists are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets so they can be used during the workshop's hands-on sessions. There is no registration fee. Support for accommodation, per diem and local transportation will be provided to all participants from abroad. Support to cover travel expenses will be considered on a case-by-case basis. Specific requests should be well-grounded as we will only be able to select a limited number. *Application:* Application *deadline has now been extended until February 17, 2013*. Application form, the program, contact info and other details can be found at www.pasteur.edu.uy/mx2013 <http://www.pasteur.edu.uy/mx2013> Please address further inquiries to mx2013(a)pasteur.edu.uy <mailto:[email protected]> Ronan Keegan and Alejandro Buschiazzo -- Alejandro Buschiazzo, PhD Research Scientist Unit of Protein Crystallography Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 120 Fax: +598 25224185 http://www.pasteur.edu.uy/pxf

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phaser for long thin molecule
by Ursula Schulze-Gahmen 08 Feb '13

08 Feb '13

I am doing molecular replacment for a very elongated molecule in phaser. I would like to try different values for the maximum patterson cutoff but I am not sure which parameter I need to change in the phenix version of phaser. Does somebody have experience with this? Thanks Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

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How to model domain-wide disorder in Phenix.refine (turn off bump interactions) ?
by Phil Jeffrey 08 Feb '13

08 Feb '13

Hi, I've got a pernicious problem where the electron density for one domain appears to extensively interpenetrate another similar domain. I'm in the process of trying to work out things like: MR solution in the wrong space group courtesy of pseudo-centering. In the meanwhile I want to model it as interpenetrating domains, and need to turn off VdeW bumps at the domain (chain) level of structure. I can't just model it as a infinite list of alternate locations. I (think) I remember how to do this in CNS (constraints interaction), but is there a way to do this in phenix ? I could not track down a particularly promising section of either the manual or the .def/eff file(s). Thanks Phil Jeffrey Princeton

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