- phenixbb - phenix-online.org

Fwd: FINAL REMINDER: ALS Call for General User Proposals - DEADLINE March 6 2013
by Banumathi Sankaran 05 Mar '13

05 Mar '13

Dear Users, I am forwarding the reminder mail from ALS to submit your proposal for the CC time and general user time at ALS. Please submit your proposals before time. Thanks Banu FINAL REMINDER: CALL FOR GENERAL USER PROPOSALS AT THE ALS The User Services Office is accepting General User Proposals from scientists who wish to conduct research at the ALS in the next cycle. PROPOSAL SUBMISSION DEADLINE cycle: 2013-2 August-December Deadline: March 6, 2013 NEW PROPOSALS Please follow the instructions for proposal submission at: http://www-als.lbl.gov/index.php/user-information/user-guide/58.html BEAM TIME REQUEST for an ACTIVE PROPOSAL Proposals remain active for two years (up to four cycles), but beam time is only allocated if a beamtime request is made each cycle. After two years the proposal expires and a new proposal must be submitted. If you have an eligible active proposal you will already have received an email from us which includes your login number and password. PUBLICATION REMINDER The proposal form now includes a section on publications from previous ALS work. Please make sure your publications are entered into our database: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PublicationSearch.shtml/Initialize If you have questions, please feel free to contact me. Cheers, Clyde Lewis Proposal Coordinator ALS

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Memory and CPU usage
by Jon Agirre 05 Mar '13

05 Mar '13

Dear community, I'm planning on buying a new macbook for my first abroad postdoc venture, and I'm currently trying decide what amount of RAM & CPU to choose. My question is a little bit intricate: is there any rule of thumb to estimate the needed RAM versus the number of input atoms for any particular refinement type? I'm planning on tackling some big (18,000 residues/asu) refinements but I don't have any estimation as to how many GBs of RAM they might require. The maximum amount of RAM I can install is 16GB, but it is a non-standard configuration that might void Apple's warranty. About the CPU: how scalable are typical phenix processes? Would it be sensible to invest in a quad-core machine with HT? In this particular case, and since HT would present 8 logical cores, would I get any speed up from launching phenix tasks configured for 8 processors instead of 4? Thanks in advance! Jon

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Unusually low B factors with phenix 1.8, but not with phenix 1.7 (data set has ice rings)
by Oliv Eidam 04 Mar '13

04 Mar '13

Hi, I would like to continue the B-factor discussion started by Demetres D. Leonidas on Nov 2, 2012 on CCP4BB: http://www.mail-archive.com/[email protected]/msg29012.html I make the same observations like Demetres and Mingzhu Wang: unusually low B-factors when refining with Phenix 1.8-1069 and 1.8.1-1168, but not with Phenix 1.7.1-743. In numbers: the average B-factor is 10 A2 but it should be 20 A2 (based on Wilson B and similar structures). A few atoms (~20) have Bf = 0.00. The following is important: I refined dozens of similar structures without that problem and I observe this phenomenon only for a single data set. That specific data set is different because 1) I excluded regions with ice rings in XDS and 2) I limited the resolution to 2.28 Angstroem, although the crystal diffracted to ~1.8 Angstroem. While the preparation of the data set might be questionable in itself, I would prefer that this would not be the topic of this thread. My questions are: What can I do to refine my structure with Phenix 1.8.X using this truncated data set? What causes the difference in average B-factor values between Phenix 1.7 and 1.8 for this data set? Your advice is much appreciated. Oliv On 11/04/12 19:21, mingzhu wang wrote: > Pavel, > > 1.8.1-1168 also has this problem. > > I found this problem existed with some dataset, but not all dataset. > > 1.8.1 give better map, so I built model with 1.8.1 map and go back to > 1.7.3 before I deposit the structure to PDB. > > When I compared the B factor from 1.8.x and 1.7.3, I found > B(1.7.3)=B(1.8.x)+Boverall(1.8.x). Perhaps this is the problem. > > > > 2012/11/3, Pavel Afonine<pafonine(a)gmail.com>: >> Joao, >> >> I am using the latest version of phenix 1.8.1-1168 >> >> >> 1.8.1-1168 should not have that "problem". >> >> If you suspect there is still a problem, you can send me the data and model >> files off list, explain what exactly the problem is, and I will have a look >> right away. >> >> FYI: there is Phenix mailing list for Phenix-specific questions, where I >> can also explain in great details the behavior with the B-factors you >> observe. >> >> All the best, >> Pavel >> -- Oliv Eidam, Ph.D. Postdoctoral fellow University of California, San Francisco Dept. of Pharmaceutical Chemistry 1700 4th Street, Byers Hall North, Room 501 San Francisco, CA 94158 - Box 2550 Phone: 415-514-4253 Fax : 415-514-4260 Email:[email protected]

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fwd: Reminder: CCP4 summer school at APS, USA
by Nathaniel Echols 04 Mar '13

04 Mar '13

---------- Forwarded message ---------- From: "Ruslan Sanishvili (Nukri)" <nukri(a)aps.anl.gov> To: phenixbb(a)phenix-online.org Date: Mon, 4 Mar 2013 16:14:43 -0600 (CST) Subject: Reminder: CCP4 summer school at APS, USA Dear Colleagues, This is a reminder that the deadline for applications for the 6th annual CCP4 Summer School “From data collection to structure refinement and beyond” is April 5, 2013. The school will take place from June 18 through June 26, 2013 at the Advanced Photon Source (APS) near Chicago. There is no registration fee for the school. The students will be responsible for their own travel and lodging expenses. These and other details (the program, the list of speakers, the application process, accommodations, site access, contacts etc) can be found at the workshop website at http://www.ccp4.ac.uk/schools/APS-2013/index.php The school will include data collection, processing, structure solution, model building, refinement, validation, automation of many steps etc. Participants are encouraged to bring their own crystals, raw data or processed data for hands-on problem solving under the guidance of software developers and other experts. We hope to see you in June Garib, Ronan and Nukri Ruslan Sanishvili (Nukri) Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov

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Bay Area and Beyond Phenix User Meeting (March 14th)
by Paul Adams 04 Mar '13

04 Mar '13

Dear Colleagues, On Thursday March 14th, a Bay Area and Beyond Phenix User Meeting will be held at Lawrence Berkeley Lab. During the workshop, the Phenix developers will give lectures on the latest developments and Phenix usage. Half of the user meeting will be in the form of informal hands on sessions, allowing participants to work with the developers. Participants are encouraged to bring their own (reduced) data to be used during hands on sessions, but tutorial data will also be available. We also recommend bringing a relatively recent laptop computer (any OS). Due to the highly interactive format of the meeting there will be space for approximately 20 participants. If I have missed any of your colleagues on this invitation please feel free to pass on the message. To apply, researchers should send a short summary email describing their level of expertise and motivation for attending the workshop to NEchols(a)lbl.gov and PDAdams(a)lbl.gov by Friday March 8th. Cheers, Paul -- Paul Adams Deputy Division Director, Physical Biosciences Division, 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 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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phenix.refine multiple twin laws?
by Kip Guja 03 Mar '13

03 Mar '13

Hi All, Is the newest version of Phenix capable of refinement with multiple twin laws (eg, tetartohedral twinning)? If so, any advice on input parameters, etc. would be greatly appreciated. Best wishes, Kip

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Re: [phenixbb] Magnesium or calcium
by Daniel Slade 02 Mar '13

02 Mar '13

So the resolution is 1.6 and I remember the B factor for mg at 16. I haven't checked the coordinating residues. It coordinates acidic residues, a backbone carbonyl and one water. I'm now leaning towards calcium as the other calciums have bonds distances similar to this one, but not nearly as high an affinity. Thanks

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Magnesium or calcium
by Daniel Slade 02 Mar '13

02 Mar '13

I have several structures that has multiple known calcium binding sites, and I found a new site that seems to accept calcium or magnesium. I say this because if a magnesium is put in the structure, the bond lengths are ~ 2.1. But if you put a calcium in it, they go to ~2.6. All of these refinements were done without ReadySet, which I recently used with metal restraints and it seemed to change the bond length of calcium to ~2.4. I'm a bit confused as to what to do here as either metal seems to be right. Worth noting, this is a very strong metal binding site that can't be removed with 10 mM EDTA. Any help here on how to figure this out which ion this is would be great. Thanks in advance Dan

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Re: [phenixbb] Magnesium or calcium
by Ed. Pozharski 02 Mar '13

02 Mar '13

Magnesium has fewer electrons. So if you place it and it's actually calcium you should see extra density and the B-factor will be unreasonably lower than surrounding atoms. Distances are less reliable at intermediate resolutions as they are largely controlled by restraints. Maybe. Assuming that you have 100% occupancy. -------- Original message -------- From: Daniel Slade <DSlade(a)scripps.edu> Date: To: phenixbb(a)phenix-online.org Subject: [phenixbb] Magnesium or calcium I have several structures that has multiple known calcium binding sites, and I found a new site that seems to accept calcium or magnesium. I say this because if a magnesium is put in the structure, the bond lengths are ~ 2.1. But if you put a calcium in it, they go to ~2.6. All of these refinements were done without ReadySet, which I recently used with metal restraints and it seemed to change the bond length of calcium to ~2.4. I'm a bit confused as to what to do here as either metal seems to be right. Worth noting, this is a very strong metal binding site that can't be removed with 10 mM EDTA. Any help here on how to figure this out which ion this is would be great. Thanks in advance Dan _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

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question about reflection file tools behavior
by Michael Thompson 01 Mar '13

01 Mar '13

Hello All, I have a question about the behavior of the reflection file tools within the PHENIX GUI: I am trying to simply copy a set of FreeRFlags from a higher resolution dataset to a lower resolution dataset. The low-res dataset contains 35264 reflections in the original input mtz. The high-res set contains 43731 reflections. When I use the GUI to write a new mtz using the low-res amplitudes and the high-res FreeRFlags, the result is an mtz with 46323 reflections. I am confused about why the output has so many reflections, even more than the high res dataset? Also, I noticed that while both input mtz files have a low-res cutoff of 20A, the output mtz has a low-res cutoff around 75A. Can anyone please explain what is going on here? I would like my output file to have the same reflections as the input, and no more. I have noticed that the CCP4 program FreeRFlag seems to behave in a similar way, so my guess is that what is happening is a common procedure, but I'm at a loss for an explanation of why this is the case. Also, if there's a better way to implement what I am trying to do I'd be grateful to hear it (perhaps generate entirely new flags for both datasets using the same random seed?). Thanks for the help!! Mike -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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