- phenixbb - phenix-online.org

Questions about the Autosol water placing option
by Kaibo Zhang 07 Mar '18

07 Mar '18

Helllo, I was using AutoSol GUI for MR-SAD of my data and trying to turn off "place waters in refinement". However, the output pdb files still got waters in them. I did check the run log file and confirmed both the "place_waters" and the "flood_with_waters" flags were set to false. But in the later session, it still recorded "adding waters in refinement". Is there any parameters I should adjust to avoid adding waters during the Autosol run. Or is it just turned on in the end in order to calculate R_work/free, and doesn't affect your phasing solution? Look forward to your responses. Thank you in advance! Regards Kaibo *Kaibo* PULSe, Purdue University Hockmeyer Hall, Room 321 240 S. Martin Jischke Drive, West Lafayette, IN 47907 Telephone: 765-337-1955 E-mail: zhang644(a)purdue.edu

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Re: [phenixbb] Overlapping ligand-protein side chain density
by van den Bedem, Henry 01 Mar '18

01 Mar '18

If the phe is a gatekeeper, shouldn’t the ligand be refined at partial occupancy; i.e. occupancies not necessarily have to ‘add up’ as you suggest? Maybe this link is helpful too: www.biorxiv.org/content/early/2018/01/24/253419 H From: <phenixbb-bounces(a)phenix-online.org> on behalf of "Phan, Jason" <jason.phan(a)vanderbilt.edu> Date: Wednesday, February 28, 2018 at 1:30 PM To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Subject: [phenixbb] Overlapping ligand-protein side chain density All, A piece of a ligand and the side chain of a “gate-keeper” Phe occupy the same space with well-defined features observed for both (resolution is 1.7 A). It looks about 50:50. How do you refine both ligand and protein side chain in this case? A couple of phenixbb suggestions for dealing with ligand-ligand overlapping density have been considered. With the first suggestion, the two entities still clashed and moved apart off of their respective densities. The second suggestion is not applicable in this case since the other molecule is not a ligand but part of the protein but it was tested anyway. Although there was no bumping, the occupancies don’t add up, resulting in a big blob of negative density around the ligand piece. ------------------------------ Only two comments: 1. At that resolution, constrained group occupancy refinement should work reasonably well (provided you can model the 2 entities). Then you also do not have clashes between the molecules, because Occ(A)+Occ(B)=1, meaning when one (A) is there, the other one (B) is not. This works with refmac (external keyword file); if you need more sophisticated occupancy re/constraints SHELXL may offer more opportunities. 2. There is no necessity for the two NCS copies of the binding site to look exactly the same (non-equivalent). Maybe there is a good reason/story (accessibility, contacts etc) for one site to be occupied differently than the other one. Best, BR —————————————— Modeling two molecules that occupy overlapping binding sites in a structure simply involves designating them as alternate conformers, with the same chain and residue number, and an occupancy that sums to 1.0. For example, if you have an AMP and an ADP that occupy the same binding site, you would define them as AAMP B 501 BADP B 501 and initially set the occupancies for the atoms in each conformer to the ratio (50:50, 30:70, etc.) that you observe in the density. Refinement in this manner is straightforward in PHENIX. Diana ----------------------------

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Overlapping ligand-protein side chain density
by Phan, Jason 28 Feb '18

28 Feb '18

All, A piece of a ligand and the side chain of a “gate-keeper” Phe occupy the same space with well-defined features observed for both (resolution is 1.7 A). It looks about 50:50. How do you refine both ligand and protein side chain in this case? A couple of phenixbb suggestions for dealing with ligand-ligand overlapping density have been considered. With the first suggestion, the two entities still clashed and moved apart off of their respective densities. The second suggestion is not applicable in this case since the other molecule is not a ligand but part of the protein but it was tested anyway. Although there was no bumping, the occupancies don’t add up, resulting in a big blob of negative density around the ligand piece. ------------------------------ Only two comments: 1. At that resolution, constrained group occupancy refinement should work reasonably well (provided you can model the 2 entities). Then you also do not have clashes between the molecules, because Occ(A)+Occ(B)=1, meaning when one (A) is there, the other one (B) is not. This works with refmac (external keyword file); if you need more sophisticated occupancy re/constraints SHELXL may offer more opportunities. 2. There is no necessity for the two NCS copies of the binding site to look exactly the same (non-equivalent). Maybe there is a good reason/story (accessibility, contacts etc) for one site to be occupied differently than the other one. Best, BR —————————————— Modeling two molecules that occupy overlapping binding sites in a structure simply involves designating them as alternate conformers, with the same chain and residue number, and an occupancy that sums to 1.0. For example, if you have an AMP and an ADP that occupy the same binding site, you would define them as AAMP B 501 BADP B 501 and initially set the occupancies for the atoms in each conformer to the ratio (50:50, 30:70, etc.) that you observe in the density. Refinement in this manner is straightforward in PHENIX. Diana ----------------------------

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Plots of local real-space CC
by Murpholino Peligro 27 Feb '18

27 Feb '18

Dear all I want to get the values for the blue line (i.e. local real-space CC) in the Molprobity multicriterion plot. How can I do that? I want to plot those values with gnuplot. I do not want the whole graph (red and green lines). Thanks Murphy

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hi please unsubscribe me
by Zhenwei Su 27 Feb '18

27 Feb '18

-- Zhenwei Su 4417 Spruce Street, APT 3A Philadelphia, PA 19104 email: zwsuustc(a)gmail.com cell phone: (608) 698-4156

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hi please unsubscribe me
by Zhenwei Su 27 Feb '18

27 Feb '18

-- Zhenwei Su 4417 Spruce Street, APT 3A Philadelphia, PA 19104 email: zwsuustc(a)gmail.com cell phone: (608) 698-4156

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Issues with refinement of cadmium
by Mohammad Khan 26 Feb '18

26 Feb '18

Dear all, I am trying to fit Cd ion in a protein structure using Phenix. However, the refinement transposes CD to DC and returns me a result with DC ( 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE) in the validation report and gives me the missing atoms accordingly. When I open the same structure in Coot, it shows me the ion Cd. Also, the .pdb file contains Cd. Cd is present in my crystallization condition and fits well into the density. Other metal atoms such as Zn and Cl have refined well. HETATM 5535 CD CD F 1 156.533 -64.594 138.360 1.00 76.11 CD HETATM 5536 CD CD F 2 119.954-111.545 105.562 1.00 35.85 CD HETATM 5537 CD CD F 3 152.936 -93.077 102.747 1.00 28.68 CD HETATM 5538 CD CD F 4 121.467 -96.375 128.574 1.00 72.24 CD Can someone suggest what may be wrong? Thanks in advance!

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[Feature request] Exclude atoms outside user provided mask from refinement (in phenix.real_space_refine)
by Oliver Clarke 26 Feb '18

26 Feb '18

Hi, Often I would like to refine part of a model against a EM map generated by masked refinement. Such a map is typically better than the globally refined map in the region within the mask, and worse outside it. It would be useful to have the capacity to refine the same model first against the globally refined map, and then against the maps generated by masked refinement, but restricting refinement in the latter case to atoms/residues within the bounds of the mask. Is this something that could be maybe added in a future version of phenix.real_space_refine? This would mean allowing the user to provide a mask file, and setting an option to exclude all atoms/residues outside the mask boundaries from refinement. Cheers Oli

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refining a covalent-bound ligand
by Sebastiano Pasqualato 26 Feb '18

26 Feb '18

Hi there, I have a pretty basic question. I am refining a structure in which a drug has been covalently linked to a Cys of the protein. I have generated the .cif fie for the ligand, but I don’t know how to tell the program that carbon C04 has to be covalently linked to the SG of the Cys. Is that sufficient to insert a LINK record in the pdb file? What is the correct syntax for that? Thanks a lot for the feedback and sorry for the naive question, ciao, Sebastiano -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 web http://is.gd/IEOXtalUnit

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Information regarding Anisotropic atoms
by pooja kesari 22 Feb '18

22 Feb '18

I observed that phenix.refine tool is adding anisotropic atoms to the pdb file by default even at resolution more than 2A. Can anyone please suggest why is it doing so?

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lattice symmetry and free-set selection?
by Edward A. Berry 21 Feb '18

21 Feb '18

Where can I find description of the free-r selection parameters: refinement.input.xray_data.r_free_flags { lattice_symmetry_max_delta=5 use_lattice_symmetry=True } ?

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Industrial Biostructures America 2018 conference
by Leonard,Paul G 20 Feb '18

20 Feb '18

Dear all, The inaugural Industrial Biostructures America conference will be held on 20-22 May 2018 at the Hilton La Jolla Torrey Pines Hotel in San Diego, California. Conference registration and accommodation information is available at: https://industrialbiostructuresamerica.org/ This conference brings together structural biologists from across the pharmaceutical and biotech industry to showcase their cutting-edge research. Scientific sessions will cover the following topics: * Cryo-EM * X-ray crystallography * Lead discovery using NMR * Protein design * Membrane crystallography The Abstract submission deadline is 23rd March 2018. We look forward to seeing you there, Paul Leonard Institute Research Scientist MD Anderson Cancer Center pleonard1(a)mdanderson.org<mailto:[email protected]> 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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BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALLOGRAPHY
by Salbego, Cyndi 18 Feb '18

18 Feb '18

BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALLOGRAPHY AT THE TWO ID BEAMLINES OF NE-CAT AT APS. We currently have a number of days open in March. Below is a brief description of our beam lines, and links with more information. The 24-ID-C beamline can deliver X-rays in the range of 6 to 21 keV or ~2.1 to 0.5 Å. This covers most of the popular elemental edges for phasing. This wide energy-range also makes the beamline well suited for ultra high-resolution data collection and soft X-ray sulfur SAD phasing. The beamline is equipped with an optional kappa goniometer for optimal alignment of crystals. A Pixel Array Detector (PAD), Pilatus-6MF, installed on the 24-ID-C beamline helps measure very weak Bragg reflection intensities due to its noise-less readout technology and also provides a very fast data collection capability in shutter-less data collection mode. The 24-ID-E beamline is a fixed energy microdiffraction beamline delivering X-rays at 12.66 keV, optimized for Se-SAD experiments. It is equipped with an Eiger-16M Pixel Array Detector, offering advantages similar to those of the Pilatus-6MF. For more information on our beamlines (beamline and robot manuals): http://necat.chem.cornell.edu To ask about available time please contact Raj Rajashankar (rajashankar(a)anl.gov<mailto:[email protected]>) or Cyndi Salbego (csalbego(a)anl.gov<mailto:[email protected]>) for further information. To apply for General User Time (Rapid Access for current run cycle) please follow this link: https://beam.aps.anl.gov/pls/apsweb/gup0005.start_page Cyndi Salbego Administrator, NECAT 630.252.0689

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9th workshop on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 14 Feb '18

14 Feb '18

First announcement 9th Workshop on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. June 11 - June 15, 2018 Detailed information: https://conference.sns.gov/biologyneutrons18/ Application deadline: April 30, 2018 The workshop on Neutron Scattering Applications in Structural Biology aims at enabling structural biologists to fully exploit the latest instrumentation and software development at the SNS and HFIR facilities at Oak Ridge National Laboratory. Attendees will participate in lectures and tutorials focusing exclusively on neutron techniques applied in structural biology. The workshop is designed for graduate students, post-doctoral fellows and faculty new to or with limited experience of neutron scattering. Flora Meilleur, Ph. D Associate Professor, Molecular and Structural Biochemistry North Carolina State University Neutron Scattering Scientist, Neutron Sciences Directorate Oak Ridge National Laboratory

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Postdoctoral position in membrane protein structure and function at the NIH
by Anirban Banerjee 12 Feb '18

12 Feb '18

There is an open postdoctoral position for a membrane protein structure-function project in my lab at the NIH. We are currently focusing on integral membrane enzymes (Science. 2018, doi: 10.1126/science.aao6326) and transporters of transition metal ions (J Biol Chem. 2018, doi: 10.1074/jbc.M117.817478). Here is the formal announcement - EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT, BETHESDA, MD AND SURROUNDING AREA Position Description: The research group of Dr. Anirban Banerjee at the National Institutes of Health (NIH) is seeking candidates for postdoctoral fellows . The broad interests of the lab are in membrane protein structure and function. We combine structural techniques such as macromolecular crystallography with biophysical and biochemical methods such as reconstitution based assays, high resolution microscopy and small molecule screening to investigate the structural bases of the mechanisms of a number of membrane proteins. The lab has state-of-the-art equipment and facilities. We have dedicated periodic access to the 22-ID beamline at the APS, for crystallographers at the NIH, as well as access to 23-ID and 24-ID beam lines at the APS. Our laboratory is part of the Cell Biology and Neurobiology Branch in the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD). We also have an affiliation to the National Institute of Neurological Disorders and Stroke (NINDS). Qualifications: The candidates should hold a Ph. D. degree, be author of at least one first author publication and have a strong background in biochemistry or structural biology. Experience with basic molecular biology, protein expression, purification and biochemical characterization are required. Prior experience in membrane protein biochemistry or mammalian expression system for protein purification will be added advantages. It is absolutely essential the candidate is motivated and prepared to put in the best efforts for fruition of the project goals. We are a small, friendly lab and ability to work as part of a cohesive group is important. To Apply: Interested candidates can send an e-mail to anirban.banerjee(a)nih.gov with a CV and a summary of previous research experience and future interests. The NIH is dedicated to building a diverse community in its training and employment programs.

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how to inhibit selectively undue H....O repulsion during refinement with phenix.refine ?
by Maxime Cuypers 10 Feb '18

10 Feb '18

Hello, i am refining neutron data with hydrogens on water molecules complexes that systematically bounce the whole molecule away from the hydroxyls or carboxylic groups or other waters. the Fo-Fc map is crystal clear about where the H atoms should go... any commands i can enter in i.e. a .param file to inhibit repulsion and promote closer h bonds? thanks for your help, cheers, Dr. Maxime Cuypers Post-Doctoral Research Associate, Structural Biology St Jude Children s Research Hospital, 262 Danny Thomas Place Memphis, TN 38105-3678, USA

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query re local grid search in phenix.real_space_refine
by Oliver Clarke 10 Feb '18

10 Feb '18

Hi all, Related to the last message - when using local_grid_search, does phenix attempt to torsion-angle search every residue, or just outliers? It would seem like maybe using EMRinger or similar to identify residues where there is strong sidechain density, but in a non-rotameric position or with an incorrectly fit rotamer might be one way to make it more efficient if it is the former. I don’t want phenix trying to do a local grid search on residues with no sidechain density - these may be in an area of the map with poor local resolution, perhaps where I have docked a crystal structure, or carefully manually adjusted rotamers - local grid search in these regions is likely to make things worse if it is not focused on residues with clear sidechain density. Cheers Oli

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parallelization of local_grid_search in phenix.real_space_refine?
by Oliver Clarke 10 Feb '18

10 Feb '18

Hi all, phenix.real_space_refine runs pretty decently with run=minimization_global+adp, and the adp part is already parallelized. Using local_grid_search though, it slows down enormously, particularly for large structures, and I’d really like to try using it to correct poorly fit rotamers. Is there any prospect for parallelizing this function? Naively it seems like something that might be amenable to parallelization - so long as adjacent local grids aren’t searched at the same time, it would seem like one might be able to split up the job to run on multiple threads? These days a lot of folks have GPU workstations for cryoEM, which often (in addition to GPUs) have Xeon or Threadripper CPUs with many cores - I’d love to be able to use that computational horsepower effectively for refining my structures. Cheers Oli

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Phenix.molprobity PDB pre-test
by Rune Thomas Kidmose 09 Feb '18

09 Feb '18

Hi, After using Phenix.molprobity I noticed it does a test of the input PDB file in the beginning, where it, among other things, identifies duplicate atom labels and then proceeds to list some of them (and hides the rest some where I guess). It also identifies mismatches between the atom label and the atom type, e.g. if a CB is by mistake listed as an O instead of a C, in the last column in the PDB file. I would like to know if it is possible to somehow call this PDB pre-test function used within phenix.molprobity? or maybe something similar in the phenix package? I would like to use the feature in a small MD pipeline I am developing where the input PDB files are checked for duplicate atoms and mismatches between atom label and type. I believe something like the mentioned pre-test feature would work much better, than my current bash script solutions using combinations of awk, grep, sort, uniq etc. Cheers Ruki

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clashscore
by 潘晓伟 09 Feb '18

09 Feb '18

Hello everyone I refine a cryo EM data with 3.1 angstrom, the model fit well with the map, but the clashscore is high, abot 23. How can I decrease the value of clashscore with realspace.refinement in Phenix GUI. Thanks! Pan ________________________________ xiaowp82(a)hotmail.com

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Computational Crystallography Newsletter, Volume 9, Number 1
by Nigel Moriarty 08 Feb '18

08 Feb '18

I am pleased to announce the publication of the latest issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of interest to all crystallographers. Please send any articles to me at NWMoriarty(a)lbl.gov noting that there is a Word Template on the website to streamline production. January 2018 <http://phenix-online.org/newsletter/CCN_2018_01.pdf> Articles - Cβ deviations and other aspects in Amber versus CDL refinements <http://phenix-online.org/newsletter/CCN_2018_01.pdf#page=21> - A few benchmark tests of various compilers on Linux and Windows <http://phenix-online.org/newsletter/CCN_2018_01.pdf#page=25> Short Communications - Tools for model-building with cryo-EM maps <http://phenix-online.org/newsletter/CCN_2018_01.pdf#page=7> - Gemmi – a new MX library <http://phenix-online.org/newsletter/CCN_2018_01.pdf#page=13> - Overfitting to Ramachandran and geometry criteria in the cryoEM Model Challenge <http://phenix-online.org/newsletter/CCN_2018_01.pdf#page=16> Fitting tips #15 – New help to make your 2.5–4Å cryoEM structure even better <http://phenix-online.org/newsletter/CCN_2018_01.pdf#page=2> FAQ - What happens when the Phenix GUI prompts me to send an error report? <http://phenix-online.org/newsletter/CCN_2018_01.pdf#page=6> Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging 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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Residual B values after refinement
by ANAN YUENYAO 07 Feb '18

07 Feb '18

Dear All, I have encountered some error during the PDB validation process after refinement with PHENIX (1.13). After uploading the coordinates and structure factor file, in the header 'Basic coordinate validity', it says that the data contains residual B values. Could anyone please explain the reason behind this error message. Is it going to be problematic for the future PDB deposition? P.S. I have already performed TLS and group B-factor refinement. Thank you in advance! Anan

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FASTA format for sequence file
by egoers＠uoregon.edu 06 Feb '18

06 Feb '18

Hello, I'm trying to run Phase-MR on Phenix (older version) and having trouble formatting my sequence properly. I keep getting error "Protein Sequence not recognized in Composition". I have a good idea of what FASTA should look like (carrot with a name, no spaces or weird characters, followed by the sequence in all capital letter on the next line). I have tried many things, mainly using gedit and plain text files (.txt). I've made sure the file name doesn't have any strange characters as well. If I cut and paste a FASTA file from the PDB into gedit, save that at a .txt, Phaser accepts it. If I cut and paste my protein sequence into the same file, it rejects it. Suggestions?

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how to bypass/deactivate dictionnary check for restraints in phenix.refine
by Maxime Cuypers 02 Feb '18

02 Feb '18

Hello All, I am refining an unusual complex moiety in a protein xl with neutron data. Does anyone know if it is possible to bypass/deactivate dictionnary .cif check i got the blocking error message "it looks like angle and bond restraints are conflicting." and Phenix.refine stops. but really it s not conflicting: my .cif file works great in coot to model the complex. it is hydrogen based, so i really need restraints to get it optimal. any clues welcome, many thanks in advance. Dr. Maxime Cuypers Post-Doctoral Research Associate, Structural Biology St Jude Children s Research Hospital, 262 Danny Thomas Place Memphis, TN 38105-3678, USA

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side-chain on special position.
by Aaron Oakley 01 Feb '18

01 Feb '18

Hello fellow Phenix-ers, I have a structure I am trying to finish in Phenix.refine The is one problem: a glutamate residue sitting on a crystallography 2-fold axis with partial occupancy (picture attached). This residue and its symmetry mate appear to take turns sitting at this position: filling the density leads to severe collision with its symmetry mate. Building the side-chain with occupancy 0.5 doesn’t seem to help, as the residue is pushed out of density during refinement. Any work-arounds? Thanks all, Aaron [cid:[email protected]]

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phenix auto sharpen local sharpening masking artifacts?
by Oliver Clarke 01 Feb '18

01 Feb '18

Hi, I’m trying to run phenix.auto_sharpen with local sharpening, because I have an EM map that has a reasonably substantial variation in local resolution. This is the command I used: phenix.auto_sharpen cryosparc_exp001049_008.mrc resolution=3.26 local_sharpening=true local_aniso_in_local_sharpening=true model.pdb nproc=4 seq_file=seq.fasta >& log & The resulting map looks beautiful (maybe a little too beautiful??) around the model, but shows some funky looking masking artifacts in the density further away from the model (in the micelle region) - see screenshot. Am I doing something wrong? And can I trust that the density is completely free of model bias? Cheers Oli

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Unwanted LINK Records
by Whitley, Matthew J 26 Jan '18

26 Jan '18

Hello all, I am currently refining a structure using Phenix 1.13-2998. Present in this structure is a diphosphate-containing ligand. In the protein chain surrounding the binding site, there is an arginine side chain that points generally toward the diphosphate group, but I cannot define the specific location of the side chain because the side chain density is very poor. The density for the ligand is unambiguous. Upon refinement, Phenix places the Arg side chain so close to the ligand that it draws a covalent bond between the two, and the post-refinement PDB file contains a LINK record for this bond. In reality, the two are not covalently connected, and ideally Phenix would find a conformation for this side chain that is outside of covalent bonding distance. I have tried refining after manually moving the side-chain to a non-clashing position multiple times, but in every case the output PDB contains a LINK for a covalent bond between ligand and side chain. My question: How can I tell Phenix NOT to allow these atoms to come with covalent bonding distance? Is there some kind of "anti-LINK" information I can feed it that will force phenix.refine to select some other conformation for the side chain? Thanks for your advice. Sincerely, Matthew Whitley --- Matthew J. Whitley, Ph.D. Research Instructor Department of Pharmacology & Chemical Biology University of Pittsburgh School of Medicine

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Open Research Positions: Structural Biophysics of Protein Allostery, in New York City
by Daniel Keedy 26 Jan '18

26 Jan '18

The Daniel Keedy Lab at the ADVANCED SCIENCE RESEARCH CENTER (ASRC) AT CUNY in New York City has available positions for a POSTDOCTORAL SCHOLAR and a LABORATORY TECHNICIAN starting in 2018. The lab’s goal is to elucidate the role of protein flexibility in allosteric regulation — and to use that knowledge to control the function of dynamic, biomedically important enzymes such as tyrosine phosphatases. To do so, we combine cutting-edge experimental and computational techniques in structural biology, including multitemperature X-ray crystallography, high-throughput protein:ligand structure determination, and new algorithms for modeling alternative protein conformations based on electron density maps. REQUIREMENTS FOR THE POSTDOCTORAL SCHOLAR POSITION: a PhD in structural biology, biophysics, computational biology, or a related field; multiple years of experience studying proteins or other macromolecules; and excitement to try new techniques at both the bench and the keyboard. Familiarity with X-ray crystallography, a programming language, and the command line are preferred. REQUIREMENTS FOR THE LABORATORY TECHNICIAN POSITION: an MS, BS, or similar degree in biochemistry, molecular biology, or a related field; experience conducting research in a laboratory setting; and excellent organizational and communication skills. Experience with cloning, protein purification, and/or X-ray crystallography are preferred. OFFICIAL APPLICATIONS: For the postdoctoral scholar position, please apply here: https://cuny.jobs/new-york-ny/research-associate-structural-biology-advance… For the laboratory technician position, please apply here: https://cuny.jobs/new-york-ny/research-assistant-laboratory-technician-stru… ABOUT THE ASRC: The ADVANCED SCIENCE RESEARCH CENTER (ASRC) at the Graduate Center of the City University of New York (CUNY) elevates scientific research and education at CUNY through initiatives in five distinctive, but increasingly interconnected disciplines: STRUCTURAL BIOLOGY, NANOSCIENCE, PHOTONICS, NEUROSCIENCE, and ENVIRONMENTAL SCIENCES. The ASRC promotes a collaborative, interdisciplinary research culture with researchers from each of the initiatives working side-by-side in the ASRC’s core facilities, sharing equipment that is among the most advanced available. The ASRC is next-door to the cutting-edge inter-institutional NEW YORK STRUCTURAL BIOLOGY CENTER (NYSBC), and is also just 70 miles from the newly-constructed NATIONAL SYNCHROTRON LIGHT SOURCE II (NSLS-II), now the brightest synchrotron light source in the US. — Daniel A. Keedy, Ph.D. Assistant Professor Structural Biology Initiative, CUNY Advanced Science Research Center Department of Chemistry and Biochemistry, City College of New York Biochemistry and Chemistry Ph.D. Programs, CUNY Graduate Center http://www.keedylab.com // daniel.keedy(a)asrc.cuny.edu<mailto:[email protected]> // 212-413-3246

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Amber force field for phenix.real_space_refinement?
by Sebastian Eustermann 24 Jan '18

24 Jan '18

Dear All, I just wondered whether/how one can use the Amber force field also for phenix.real_space_refinement? I tried “use_amber=True” as it is implemented for phenix.refine but that option does exists for phenix.real_space_refinement … Thanks for your help BW Sebastian -------------------------------------- Sebastian Eustermann, PhD Gene Center LMU Munich, Germany

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phenix.auto_sharpen expected filtration of input map
by Ricardo Righetto 24 Jan '18

24 Jan '18

Hi, So far I have liked very much the results of phenix.auto_sharpen, but one thing is not yet clear to me: how does it expect the input map to be filtered? Would be something like: a) Unsharpened, unfiltered map (e.g. the simple average of the half-maps) b) Unsharpened, SSNR-weighted (Cref) (Rosenthal & Henderson, JMB 2003) c) Doesn't matter / other? Thanks in advance! Best wishes, -- Ricardo Diogo Righetto

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Error with Phenix refine after adding ligand
by Mian-Chee Gor 23 Jan '18

23 Jan '18

Hello all, I run into this problem when I tried to refine my protein structure after adding ligand. The ligand that I am adding is a malonate, and the 3-letter chemical code is MLI. I add the ligand using Coot and it fit perfectly into the electron density map. I then tried to run phenix.refine by giving the protein structure pdb file, the original mtz file and the protein sequence fasta file. However, there was an error message saying missing restraints for the ligand. So I generate the CIF file for the ligand using the Ready Set icon in the toolbar. The ligand CIF file and a updated protein structure pdb file was generated and automatically added to the refinement windows. However, when I run the refinement, I saw this error message: Number of nonbonded interaction distances <0.001:2. Please inspect the output above (or in the log window) and correct the input model file. When I inspect the log window, the error is due to the oxygen atoms in the ligand being too close to each other. Why is there an error if the ligand was generated automatically in Phenix? Has anyone encounter this problem before? How do you solve that? Many thanks in advance! -- Dr Mian-Chee Gor Research Fellow Griffith Institute for Drug Discovery (GRIDD) Don Young Road, Nathan, QLD 4111 Mobile: +61 4 2084 7785 Email: m.gor(a)griffith.edu.au

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Neutron diffraction protein refinement with Phenix
by Rex Palmer 22 Jan '18

22 Jan '18

I would like to contact someone based in or near London whois familiar with Phenix refinement of neutron diffraction protein structures and interpretation of the results. Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://www.springer.com/978-1-4641-3954-7

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secondary structure presentation in VMD
by CPMAS Chen 22 Jan '18

22 Jan '18

Hi, Phenix users, This may be a little off-topic. I have posted this in VMD users mail list. I want to try here too to see if anyone experienced similar issue. VMD and pymol gave different presentation on the secondary structure of a protein. During phenix.refinement, I added secondary structure restraints and correctly labelled all helices and sheets. However, VMD does not correctly present the secondary structure in cartoon/new-cartoon presentation. A little more detail. In VMD-1.9.4a12, after I loaded the pdb, I chose new cartoon to present the secondary structure. All chains are presented as random coil, the same as tube representation. However, pymol correctly shows the secondary structure of the same pdb file in cartoon representation. Has anyone encountered similar situation? what would be the fix? Thanks! Best Regards, Charles -- *************************************************** Charles Chen Research Instructor University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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Refining a neutron structure
by Rex Palmer 19 Jan '18

19 Jan '18

When refining a neutron structure with Phenix why would the program appear to think it was an X-ray structure? Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://www.springer.com/978-1-4641-3954-7

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XChem compound design: recruiting programmer / software engineer
by Frank von Delft 19 Jan '18

19 Jan '18

Dear MXers We are recruiting a software engineer (or scientific programmer, or geek-minded scientist, or scientifically-minded geek) to help us get a lot better at designing compounds from hits from crystallographic fragment screening. The post is linked to the XChem facility <http://www.diamond.ac.uk/Beamlines/Mx/Fragment-Screening.html> at Diamond's beamline I04-1, set up in partnership with the SGC-Oxford, which is now routinely hosting users every week, allowing them to find convincing fragment hits with a few days' worth of experiments. In 2017, over 30 users measured over 35,000 crystals in academic and industrial XChem experiments. To confront the next bottleneck, namely converting low potency fragments into high-potency compounds, we are setting up a suite of easily accessible computational tools that streamline the obvious yet surprisingly fiddly analyses by which to identify the most sensible follow-up compounds that are easy to make or procure. The (initially) two-year post will, in a team of three and depending on interests, build infrastructure, harden existing algorithms or help evolve new ones, do web interface design, or any combination of the above. The project is seeding a nascent effort, for now aspirationally code-named CCP-CMC (/CompMedChem/, http://www.ccp-cmc.org/), to bring the awesome collaborative ethos of CCP4 and other MX tools to computational medicinal chemistry. Recruitment details are here <https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.disp…>. Deadline is Monday 29 Jan (it's wrong in the link). -- Prof Frank von Delft Principal Beamline Scientist: I04-1 Diamond Light Source +44 1235 778997 (office: M,T,T) +44 7471 026103 (mobile) Principal Investigator: Protein Crystallography Structural Genomics Consortium Oxford University +44 1865 617583 (office: W,F)

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Calculate F/sigma(F)
by Cygler, Miroslaw 19 Jan '18

19 Jan '18

Hi, I would like to calculate distribution of F/sigma(F) as a function of resolution for reflections in an mtz file. Is it possible to do it Phenix? Thanks, Mirek

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Re: [phenixbb] Fourier_shell_correlation_(FSC)_in_cryo-EM_refinement
by Takanori Nakane 18 Jan '18

18 Jan '18

Hi Oleg, Do you mean FSC between a model and a map? You can calculate it with phenix.model_vs_map. Best regards, Takanori Nakane > I started to do some refinements of cryo-EM structures. But I could not > find FSC (e.g. FSC average) quality metrics in the refinement log. Is it > because of the real space refinement methodology or some features need to > be activated? Please advise > Thanks > Oleg ? > _______________________________________________ > 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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Local sharpening error
by Ricardo Righetto 18 Jan '18

18 Jan '18

Hi, I am trying to do local sharpening with phenix.auto_sharpen, with the following command: phenix.auto_sharpen map.mrc resolution=4.0 local_sharpening=True Then it runs the global sharpening first as expected, but when it gets to the local sharpening it crashes with the following error: Sorry: Please specify a sequence file with seq_file=myseq.seq Nowhere it says that I would need a .seq file in order to do local sharpening (global sharpening works fine). Any ideas? Thanks, -- Ricardo Diogo Righetto

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Autobuild in to "extra density"
by Tom Terwilliger 18 Jan '18

18 Jan '18

Hi Ben, I think you've done the hard part already by building a poly-ala model into your extra density! If you want to try and sequence it using the density, you can use phenix.replace_side_chains with the keyword "sequence_from_density=True" to do this. See: https://www.phenix-online.org/documentation/ reference/replace_side_chains.html To use autobuild with this, add an extra line to your sequence file with the sequence of the extra piece (separate it from the previous sequence with a blank line or a ">".) I would try rebuild_in_place=True to try and optimize the position of your extra chain. You can specify what residues to work on with something like: rebuild_chain_list=A rebuild_res_start_list=27 rebuild_res_end_list=35 This will rebuild chain A27 through A35. For density modification you might want to use a mask based on your model. For this you would say: mask_from_pdb=my_existing_pdb_file.pdb Let me know if that doesn't do it! All the best, Tom T Date: Tue, 9 Jan 2018 20:50:41 +0000 From: "Flath, Ben" <bef206(a)mail.usask.ca> To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Subject: [phenixbb] Autobuild in to "extra density" Message-ID: <52cba352941e48869fc9d5223a97ccaf(a)Mail06.usask.ca> Content-Type: text/plain; charset="us-ascii" Hi All I have a structure I am building/refining at 2.6 A resolution, there are three NSC molecules in P321 unit cell. Each monomer contains 150 aa and are at least 95% built. Here is where I need some help. There is extra density. Gel and Mass Spec data suggests that there is a smaller MW weight protein/band contained in the crystals which is most likely a fragment of my target protein. Basically I have 3 NCS copies plus a half a molecule that does not appear to have the same tertiary structure (LSQ & SSM do not align well) as the other 3 molecules. I have been able to build several poly-A helices in to this density and R/Rfree are now 0.25/0.31. My Question is, how do I set up a phenix run (presumably autobuild) So that I can begin to dock my sequence in to these chains and have them extended? Does my sequence input file need to include more than one sequence string? Asking autobuild to find and build 4 NCS groups does not seem to build anything in to this extra density (Also the sigma level for the extra density chains seems to be somewhat less than the well-defined part) I am guessing this is a rebuild_in_place=false job? Can I specify only a certain chain only to be rebuilt? Also are there some special considerations with regard to density modification I should be aware of? Any help would be much appreciated. Regards Benjamin Flath, M.Sc. Research Assistant, Cygler Lab University of Saskatchewan Department of Biochemistry Room 3D40 HSCI Box 27, 107 Wiggins Road Saskatoon, SK S7N 5E5 Phone: 306 220-7355 email: benjamin.f(a)usask.ca<mailto:[email protected]> -- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: tterwilliger(a)newmexicoconsortium.org Tel: 505-431-0033

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Fourier shell correlation (FSC) in cryo-EM refinement
by oleg＠quantumbioinc.com 18 Jan '18

18 Jan '18

I started to do some refinements of cryo-EM structures. But I could not find FSC (e.g. FSC average) quality metrics in the refinement log. Is it because of the real space refinement methodology or some features need to be activated? Please advise Thanks Oleg

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model statistics
by wtempel 17 Jan '18

17 Jan '18

Pre-1.13, the `model_statistics=True` option of PDBTOOLS produced a listing of average B-Factors, atom counts, etc. Is this functionality provided by another command in the current version of PHENIX? Many thanks. Wolfram Tempel

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keeping ligand rigid in phenix refine
by Vikram Dalal 12 Jan '18

12 Jan '18

Hi all, I want to keep my ligand positions rigids during phenix refine, so that its position wont affected after phenix refine. Thanks & Regards, VIKRAM DALAL Research Scholar

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"standard" monomer restraints
by wtempel 10 Jan '18

10 Jan '18

Hello, how/where (in the PHENIX installation tree?) can one look up target values (effective during restrained refinement in PHENIX) for specific bond lengths and angles of monomers like amino acids or nucleosides? Thanks. Wolfram Tempel

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Autobuild in to "extra density"
by Flath, Ben 09 Jan '18

09 Jan '18

Hi All I have a structure I am building/refining at 2.6 A resolution, there are three NSC molecules in P321 unit cell. Each monomer contains 150 aa and are at least 95% built. Here is where I need some help. There is extra density. Gel and Mass Spec data suggests that there is a smaller MW weight protein/band contained in the crystals which is most likely a fragment of my target protein. Basically I have 3 NCS copies plus a half a molecule that does not appear to have the same tertiary structure (LSQ & SSM do not align well) as the other 3 molecules. I have been able to build several poly-A helices in to this density and R/Rfree are now 0.25/0.31. My Question is, how do I set up a phenix run (presumably autobuild) So that I can begin to dock my sequence in to these chains and have them extended? Does my sequence input file need to include more than one sequence string? Asking autobuild to find and build 4 NCS groups does not seem to build anything in to this extra density (Also the sigma level for the extra density chains seems to be somewhat less than the well-defined part) I am guessing this is a rebuild_in_place=false job? Can I specify only a certain chain only to be rebuilt? Also are there some special considerations with regard to density modification I should be aware of? Any help would be much appreciated. Regards Benjamin Flath, M.Sc. Research Assistant, Cygler Lab University of Saskatchewan Department of Biochemistry Room 3D40 HSCI Box 27, 107 Wiggins Road Saskatoon, SK S7N 5E5 Phone: 306 220-7355 email: benjamin.f(a)usask.ca<mailto:[email protected]>

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Phenix version 1.13 released
by Paul Adams 09 Jan '18

09 Jan '18

The Phenix developers are pleased to announce that version 1.13 of Phenix is now available (build 1.13-2998). Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site: http://phenix-online.org/download/ Highlights for this version: - phenix.map_to_model - better symmetry support and improved runtime efficiency - phenix.structure_search - structural library and internal support for mmCIF - phenix.ligand_identification - limit ligand size for search - Phaser 2.8.1 - various bug fixes - Structure Comparison - more/improved validation information (ligands, waters, cis/trans peptides, HIS protonation) - GUI - automatic validation after phenix.real_space_refine; visual improvements in validation - Improved handling of model mmCIF input/output - New Phenix video tutorials - Internal bug fixes and performance improvements - NEW FEATURES - Phenix.map_to_model: - Allows cases where symmetry that is neither point-group nor helical is present - Allows splitting runs into many small independent steps - Set defaults for quick=True to run somewhat more quickly - GUI - Validation information added to phenix.real_space_refine results - phenix.real_space_refine GUI accepts input for reference models - Polygon stand-alone GUI deprecated; rolled into Comprehensive Validation GUI - Old Polygon jobs cannot be restored - Validation GUI - Stoplight colors (green/orange/red) added to validation summary - In rotamer outlier table, uncalculated chi angles now display blank instead of None - Validation table columns adjusted to reduce whitespace - Updated dependencies - Python 2.7.13 -> 2.7.14 - Boost 1.56 -> Boost 1.63 - Numpy 1.8.1 -> 1.8.2 - phenix.structure_search: - Updated to November 2017 RCSB non-redundant library (representatives of 100% sequence-identity clusters.) - Changed to mmcif-based coordinate handling internally. - phenix.ligand_identification: - Added search limit on ligand sizes (Non-H atoms) - Run LigandFit algorithm internally as default. - Phaser-2.8.1 - bugfixes - anisotropy correction of map coefficients after MR - detection of duplicate solutions - correct cell for PDB after refinement of cell for input data - packing places molecules near origin in compact arrangement - Structure Comparison - Updated to include favoured, allowed and outliers for validations tabs such as rotamers - Add featurs such as ligands information & locations; water locations; cis/trans peptides; and histidine protonation - General increase of robustness and flexibility - Greater flexibility for model/data input including directory tree travesal and user defined scripts - Restraints - Added better SF4 restraints - Added mechanism to improve SF4 linking - Various performance enhancements - Better handling of model mmCIF input/output - New Phenix video tutorials: - Cryo-EM tools in Phenix - overview - How to run MolProbity - step by step (web interface and Phenix GUI) - MolProbity: All atom contacts tutorial For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 33, Room 347 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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How to change the FOBS/SIGMA_FOBS value in phenix.refine
by 齐建勋 08 Jan '18

08 Jan '18

Dear PhenixBB, Is there place to set the I/SIGMA_I or FOBS/SIGMA_FOBS values in phenix.refine? I found the default FOBS/SIGMA_FOBS threshold in phenix.refine is 1.35, which means any reflection lower than 1.35 will be excluded in the refinement process. This will generally result in a lower completeness range especially for the relatively weak datasets. When I uses the xray_data.remove_outliers=False, I got the error message "Sorry: Unknown command line parameter definition: remove_outliers = False", and my PHENIX version is phenix-1.12-2829, thanks. Regards Jianxun ******************************************************************* Dr. Jianxun Qi A321, Institute of Microbiology, Chinese Academy of Sciences No.1 West Beichen Road, Chaoyang District Beijing 100101, China Email: jxqi(a)im.ac.cn Tel : 86-10-64806182 *******************************************************************

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Install Problem Linux CentOs 5
by Whitley, Matthew J 03 Jan '18

03 Jan '18

Hello all, We are trying to install the new 1.13-2998 release of Phenix on 64 bit Linux CentOs 5 and have run into some problems. We are logged in as root, and we were able to unzip and untar the archive with no problem. However, when we run the install script, we immediately get the following errors: root@linux7 phenix-installer-1.13-2998-intel-linux-2.6-x86_64-centos5]# ./install Traceback (most recent call last): File "./bin/install.py", line 20, in ? from libtbx.auto_build import install_distribution File "/usr/local/phenix-installer-1.13-2998-intel-linux-2.6-x86_64-centos5/lib/libtbx/auto_build/install_distribution.py", line 75, in ? from libtbx.auto_build import install_base_packages File "/usr/local/phenix-installer-1.13-2998-intel-linux-2.6-x86_64-centos5/lib/libtbx/auto_build/install_base_packages.py", line 864 os.chmod(filename, 0o755) # set permissions to -rwxr-xr-x ^ SyntaxError: invalid syntax [root@linux7 phenix-installer-1.13-2998-intel-linux-2.6-x86_64-centos5]# Any idea as to what the source of the problem is and how to get around it? Thanks for your help. Matthew Whitley --- Matthew J. Whitley, Ph.D. Research Instructor Department of Pharmacology & Chemical Biology University of Pittsburgh School of Medicine

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target bond/angle RMS deviations from ideal
by wtempel 13 Dec '17

13 Dec '17

Hello all, the documentation <https://www.phenix-online.org/documentation/faqs/refine.html> states that This is somewhat controversial, but absolute upper limits for a well-refined protein structure at high resolution are typically 0.02 for RMS(bonds) and 2.0 for RMS(angles); usually they will be significantly lower. I understand that exceedingly high RMSDs from ideal could indicate overfitting. On the other hand, local deviations from ideal geometry may point to correctable modeling errors, and I am concerned that overly tight restraints may cause that diagnostic tool to become less sensitive, or local errors to be spread in to the model. For what bond and angle rms deviations from ideal do my colleagues on the BB aim and how have they arrived at those targets? Did my web search miss a relevant paper? Thank you in advance. Wolfram Tempel

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Announcing the release of the Detergent Belt Server
by vincent Chaptal 13 Dec '17

13 Dec '17

This message is especially directed towards the membrane proteins community. Dear everyone, we are very pleased to announce the release of the Detergent Belt Server -> http://detbelt.ibcp.fr Following our discovery of a method to quantify detergents around membrane proteins, we have build the detbelt server to allow for a simple _representation of the detergent belt around your protein of interest_. This representation is a simple approximation and grants a rapid estimation of the detergent belt, especially fitted to _biochemists_ to better understand what is going on in your test tube. (Details on the server and the publication of the detergent quantification method are available on the tutorial page). The server allows you to play with different detergents interactively by recomputing the belt in your web browser, which allows you to refine your biochemical hypothesis. The server allows you to add several detergents, each with different values, and will compute the volume associated with these detergents mixtures. It outputs different metrics making it easier to compare detergent-occupied volumes, and a PyMOL script to generate a publication quality image. For the moment, membrane protein pdb file should be pre-oriented using the PPM server procedure as it runs slow on the server; please visit the tutorial web page for more details (see "1"). We are working towards speeding up this process and making it all integrated in the near future. For testing purposes, I attach a pre-oriented pdb so that you can have an idea of the information you can obtain. Finally, we welcome any feedback to this alpha release; we welcome bug reports as well as creative feedback: if you think this tool has some potential for your research, please contact us and we will see what can be done. Wishing you good visualization All the best The DetBelt team -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug Resistance and Membrane Proteins Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.ibcp.fr

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reference_xray_structure
by yamei yu 06 Dec '17

06 Dec '17

Dear all, I want to use “reference model” in a low resolution structure refinement. Do I need to set this parameter “reference_xray_structure”? What does “reference_xray_structure” stand for? Many thanks and best wishes ************************************************ Yamei Yu Associate Professor State Key Laboratory of Biotherapy／Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University,Chengdu,610041, P.R.China Tel: 15882013485 Email: ymyuxtal(a)gmail.com ymyuxtal(a)163.com yamei_yu(a)scu.edu.cn

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