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Question related to Phenix refinement
by Smith Lee 01 Feb '15

01 Feb '15

Dear All, Which strategy or parameter input can be used to reduce the rotamer outliers? Which strategy or parameter input can be used to reduce the bond outliers? For all the Phenix refine strategies, can you sequence it from rough refinement to fine refinement in order? I am looking forward to getting your reply. Smith

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Rwork and Rfree
by Dialing Pretty 31 Jan '15

31 Jan '15

Dear All, After a Phenix refinement (for crystal 2.5A), my Rwork is about 0.19, and my Rfree is about 0.26. Is the gap between Rwork and Rfree too karge? If too large, why it is too large and how to avoid it? I am looking forward to getting your reply. Dialing

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Re: [phenixbb] making coarse maps
by Terwilliger, Thomas Charles 30 Jan '15

30 Jan '15

Hi Scott, You can use the reflection file converter in the GUI to write out map coefficients with any resolution cutoff that you like. That may be the easiest. Alternatively you can take your refined model and use phenix.maps to calculate a map at any resolution that you like without further refinement. You might also consider just adjusting the sharpening on your map which will have something of the same effect as cutting the resolution. All the best, Tom T ________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Scott Horowitz [horowsah(a)umich.edu] Sent: Friday, January 30, 2015 6:09 AM To: PHENIX user mailing list Subject: [phenixbb] making course maps Hi all, Although I realize this sounds counterproductive, I'd really like to be able to make a map with grid spacing that is around 3 A, even though I have a ~2 A structure, and I don't want to have to cut data before refinement. However, it seems like the max number I can give to the grid resolution factor is 0.5. Is there a way to break this limit without it crashing? Thanks, Scott -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226

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making course maps
by Scott Horowitz 30 Jan '15

30 Jan '15

Hi all, Although I realize this sounds counterproductive, I'd really like to be able to make a map with grid spacing that is around 3 A, even though I have a ~2 A structure, and I don't want to have to cut data before refinement. However, it seems like the max number I can give to the grid resolution factor is 0.5. Is there a way to break this limit without it crashing? Thanks, Scott -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226

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calculating map from pdb
by Scott Horowitz 29 Jan '15

29 Jan '15

Hi all, I was wondering how to quickly back-compute an electron density map from a PDB using phenix from the command line. I'm assuming it's not hard, but I can't find documentation that would lead me to it. Thanks, Scott -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226

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question about mmtbx.prepare_pdb_deposition
by Gerwald Jogl 28 Jan '15

28 Jan '15

Hi, How does the sequence file for this tool have to be formatted when there are more than one proteins/sequences in the asu? Does the program match this automatically? Thanks, Gerwald

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Old Phenix jobs
by Mark A Saper 27 Jan '15

27 Jan '15

I was looking at some old Phenix GUI jobs run in Sept 2010 with Phenix version 1.6.4. Can these jobs be opened with the current (dev-1932) GUI ? When I try to restore a refinement job opens, a window opens with the parameters used for the job, but no tab with the results. When I try to restore other jobs, I receive an error when trying to open them: “UnicodeDecodeError : ‘utf8’ codec can’t decode byte 0x81 in position 35: invalid start byte”. Another thing I noticed about some of these jobs was that there are *.libtbx_info files in the phenix/tmp subdirectorty that are >100 Mbytes, even one that is 1.2 Gbytes! Can these files be deleted. I only see such large files for one particular structure. Any info about this would be helpful. Mark _______________________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, U-M Medical School 3040 Chemistry Building | saper(a)umich.edu | +1 (734) 764-3353

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R/ R free (overall) and R/Rfree (for highest resolution shell)
by George Devaniranjan 26 Jan '15

26 Jan '15

Hi, I calculated/validated several PDB structures in Phenix.Validation (GUI) The R/R-free (overall) is 0.1271/0.1348 Further down I looked at the R/R-free for the highest resolution shell. Its 0.2538/0.2446 I am curious why the R-free for the *highest resolution shell* seems to be LOWER than R (work). Am I reading the information wrong? PDB: 3QL9 Thank you, George

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Re: [phenixbb] phenixbb Digest, Vol 110, Issue 12
by Kay Diederichs 25 Jan '15

25 Jan '15

Patrick, see my posting at https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;f6735c0c.1501 . The "Advanced Search" interface of the RCSB also lets you search for resolution range and many other criteria. "Text search" won't help you much if you are searching specific numeric values, I guess. best, Kay Am 25.01.15 um 09:21 schrieb phenixbb-request(a)phenix-online.org: > Date: Sat, 24 Jan 2015 09:41:36 -0800 > From: Patrick <patrick.cossins(a)inbox.com> > To: PHENIX list <phenixbb(a)phenix-online.org>, ccp4bb(a)jiscmail.ac.uk > Subject: [phenixbb] extracting PHENIX structures > Message-ID: <5D1147D5283.0000050Apatrick.cossins(a)inbox.com> > Content-Type: text/plain; charset=US-ASCII > > Hi, > > not directly related but I wanted to know how to extract from the PDB all the PHENIX/CCP4 refined structures currently deposited. > > Do I use the "text" search in quarry to get the result or do I use the software? > > I tried it for both but seems to give different results (no's). > > I tried for another refinement package (shelx) and same, different no's > > Using software, and looking for contains 320 > > using text search 130 > > Is there another way to get structure of a certain resolution ? > > Patrick

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extracting PHENIX structures
by Patrick 24 Jan '15

24 Jan '15

Hi, not directly related but I wanted to know how to extract from the PDB all the PHENIX/CCP4 refined structures currently deposited. Do I use the "text" search in quarry to get the result or do I use the software? I tried it for both but seems to give different results (no's). I tried for another refinement package (shelx) and same, different no's Using software, and looking for contains 320 using text search 130 Is there another way to get structure of a certain resolution ? Patrick ____________________________________________________________ Can't remember your password? Do you need a strong and secure password? Use Password manager! It stores your passwords & protects your account. Check it out at http://mysecurelogon.com/password-manager

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