- phenixbb - phenix-online.org

Can geometry restraints include non-ideal target values?
by Joe Krahn 07 Dec '07

07 Dec '07

I see that phenix is using the same kind of simplistic statistical restraints as CCP4. Are there plans to improve the geometry restraints once the rest of phenix is stable? The problem with simple statistical restraints as used by CCP4 is that they completely ignore correlations due to interactions of multiple restraints. This is particularly bad for puckered rings like proline and nucleic acids. Nucleic acids get around this by using a fixed sugar pucker, which results in a lot of bad geometries for non-helical nucleic acids (many of which make it in to the PDB). However, if you consider the geometries "ideal value" and "ideal value esd" as just another way to write a harmonic restraint, then it is possible to make an improved restraint library. In this case, some individual geometry restraints will have target values that restrain towards non-ideal values in order to produce the correct result when all terms are combined. The problem is that these terms will give higher RMSD values, which would probably confuse software like REFMAC, which is designed to tweak restraint weights based on RMSDs. So, does phenix have any built-in restraint adjustments that is based on current rmsds? If so, is there a way to disable it? Joe Krahn

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Hydrogens of ligands generated in elbow explode in coot realspace refinement
by Schubert, Carsten [PRDUS] 06 Dec '07

06 Dec '07

Hi, when I refine a ligand with hydrogens in coot using realspace refinement, the hydrogens explode into the surrounding density. This only happens with ligand/cif files generated in elbow and not libcheck. Coot apparently needs and additional loop in the .cif file: _chem_comp_tree.xxxx, which is missing from the elbow output. Unfortunately the geometry generated by libcheck is pretty dismal, so I can probably get around this by running libcheck on the refined coords from elbow ... Nigel, is it possible to fix elbow for the next rc? PS I am running the latest phenix (rc6) and coot 0.33 if that helps. Cheers Carsten

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Question about adding hydrogrens with reduce -- parameters for phenix.refine
by Schubert, Carsten [PRDUS] 06 Dec '07

06 Dec '07

Hi I am trying to generate a model with all hydrogens placed using reduce. To my surprise it only applies hydrogens to a selected few residues. How do I coax reduce to add ALL hydrogens to my model, according to the Richardson Lab paper this should be possible? The help from reduce was not helpful in that regard. Or is adding all hydrogens a bad idea? Along those lines. If I would use another tool to generate the hydrogens, like CNS(X) or Maeastro, how compatible are the parameter files? Thanks for any input Carsten

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Re: [phenixbb] Forcing autobuild wizard to do a complete rebuild
by Tom Terwilliger 03 Dec '07

03 Dec '07

Hi Carsten, Yes, I see this is unclear. All commands listed at the end of the documentation for each wizard can be applied at the command line. (Not just the ones labelled command-line only). All the best, Tom T At 11:15 AM 12/3/2007, you wrote: >Thanks Tom, Peter > >As a follow-up question, which may have been addressed in the >manual, but I don't recall seeing it: Does the (wizard) command line >accept ALL keywords under the autobuild/autosol scope or ONLY the >ones listed as "command-line-only"? I assumed (wrongfully?) that the >command line only accepts the keywords explicitely listed under >"command-line-only", and the rest is reserved for scripts/input files. > >I know, I could test this out, but a general clarification by the >experts and an addition to the manual, if necessary, would be great. > >Cheers, > > Carsten > > > > > -----Original Message----- > > From: phenixbb-bounces(a)phenix-online.org > > [mailto:[email protected]]On Behalf Of Tom > > Terwilliger > > Sent: Monday, December 03, 2007 12:59 PM > > To: PHENIX user mailing list > > Subject: Re: [phenixbb] Forcing autobuild wizard to do a complete > > rebuild > > > > > > Hi Carsten, > > > > You can tell the autobuild wizard from the command line: > > > > rebuild_in_place=False > > > > You can also set this in the GUI on the 2nd input screen at the top > > of the screen. > > > > I hope that helps! > > -Tom T > > > > At 10:17 AM 12/3/2007, you wrote: > > >Content-class: urn:content-classes:message > > >Content-Type: multipart/alternative; > > > boundary="----_=_NextPart_001_01C835D0.68A40BB9" > > > > > >Hi, > > > > > >I am using the autobuild wizard in the latest phenix release to > > >rebuild a model from a MR solution. Since the MR-template I used > > >has been modified with chainsaw, its sequence identity to the target > > >sequence is fairly high. The autobuild wizard therefore uses the > > >rebuilt-in-place mode to rebuild the model. How can I force the > > >wizard to do a complete rebuild? > > > > > >Thanks > > > > > > Carsten > > >_______________________________________________ > > >phenixbb mailing list > > >phenixbb(a)phenix-online.org > > >http://www.phenix-online.org/mailman/listinfo/phenixbb > > > > > > > > > > Thomas C. Terwilliger > > Mail Stop M888 > > Los Alamos National Laboratory > > Los Alamos, NM 87545 > > > > Tel: 505-667-0072 email: terwilliger(a)LANL.gov > > Fax: 505-665-3024 SOLVE web site: >http://solve.lanl.gov >PHENIX web site: http:www.phenix-online.org >ISFI Integrated Center for Structure and Function Innovation web >site: http://techcenter.mbi.ucla.edu >TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB > > >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb > > >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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Re: [phenixbb] Forcing autobuild wizard to do a complete rebuild
by Tom Terwilliger 03 Dec '07

03 Dec '07

Hi Carsten, You can tell the autobuild wizard from the command line: rebuild_in_place=False You can also set this in the GUI on the 2nd input screen at the top of the screen. I hope that helps! -Tom T At 10:17 AM 12/3/2007, you wrote: >Content-class: urn:content-classes:message >Content-Type: multipart/alternative; > boundary="----_=_NextPart_001_01C835D0.68A40BB9" > >Hi, > >I am using the autobuild wizard in the latest phenix release to >rebuild a model from a MR solution. Since the MR-template I used >has been modified with chainsaw, its sequence identity to the target >sequence is fairly high. The autobuild wizard therefore uses the >rebuilt-in-place mode to rebuild the model. How can I force the >wizard to do a complete rebuild? > >Thanks > > Carsten >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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Forcing autobuild wizard to do a complete rebuild
by Schubert, Carsten [PRDUS] 03 Dec '07

03 Dec '07

Hi, I am using the autobuild wizard in the latest phenix release to rebuild a model from a MR solution. Since the MR-template I used has been modified with chainsaw, its sequence identity to the target sequence is fairly high. The autobuild wizard therefore uses the rebuilt-in-place mode to rebuild the model. How can I force the wizard to do a complete rebuild? Thanks Carsten

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phenix gui startup problem
by david albesa-jove 30 Nov '07

30 Nov '07

Dear phenix users, After installation of phenix using phenix-installer-1.3b-rc6-intel-linux-2.6-x86_64.tar and setting up the environmental variables, phenix gui fails to startup giving the following error: (99, 'Cannot assign requested address'). See bellow for further details. Thanks for your help, David ************************************************************8 [root@bio-daj2 phenix2]# phenix +++++++++++++++++++++++++++++++++++ Warning +++++++++++++++++++++++++++++++++++ Hostname is bio-daj2.cmmi.ic.ac.uk but fully qualified domain is bio-daj2 +++++++++++++++++++++++++++++++++++ Warning +++++++++++++++++++++++++++++++++++ +++++++++++++++++++++++++++++++++++ Warning +++++++++++++++++++++++++++++++++++ IP nslookup is ls-saf-g34b.saf.ic.ac.uk but FQDN is bio-daj2 +++++++++++++++++++++++++++++++++++ Warning +++++++++++++++++++++++++++++++++++ Running the PHENIX GUI with /usr/local/phenix-1.3b-rc6/build/intel- linux-2.6-x86_64/base/bin/python PHENIX distribution located in /usr/local/phenix-1.3b-rc6/phenix Exception in thread Thread-1: Traceback (most recent call last): File "/usr/local/phenix-1.3b-rc6/build/intel- linux-2.6-x86_64/base/lib/python2.5/threading.py", line 460, in __bootstrap self.run() File "/usr/local/phenix-1.3b-rc6/build/intel- linux-2.6-x86_64/base/lib/python2.5/threading.py", line 440, in run self.__target(*self.__args, **self.__kwargs) File "/usr/local/phenix-1.3b-rc6/phenix/wxGUI/GUIServer.py", line 14, in __init__ PhenixServer.PhenixServer.__init__(self, port, GUIRequestHandler) File "/usr/local/phenix-1.3b-rc6/phenix/phenix/server/PhenixServer.py", line 50, in __init__ ddbs = apply(func, (server_address, handler),{}) File "/usr/local/phenix-1.3b-rc6/phenix/phenix/server/SocketServer.py", line 333, in __init__ self.server_bind() File "/usr/local/phenix-1.3b-rc6/phenix/phenix/server/PhenixServer.py", line 65, in server_bind SocketServer.ThreadingTCPServer.server_bind(self) File "/usr/local/phenix-1.3b-rc6/phenix/phenix/server/SocketServer.py", line 344, in server_bind self.socket.bind(self.server_address) File "<string>", line 1, in bind error: (99, 'Cannot assign requested address') ======================================================= David Albesa-Jove PhD Centre for Molecular Microbiology and Infection Division of Cell and Molecular Biology Flowers Building, Level 1 South Kensington Campus Imperial College London London. SW7 2AZ. Tel: 020.7594.3070 e-mail: d.albesa-jove(a)imperial.ac.uk

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HHMI X-ray lab manager/Research Scientist Job
by Marcelo Carlos Sousa 28 Nov '07

28 Nov '07

To all interested parties: A Research Scientist / X-ray lab manager position in the lab of Tom Cech in Boulder, Colorado is open. Job Description: The Howard Hughes Medical Institute, a leading biomedical research organization, is seeking an experienced scientist to manage our X-ray crystallography facility at the Cech research laboratory at the University of Colorado campus in Boulder. The facility is equipped with two Rigaku generators and R-Axis IV++ detectors for data collection, a linux cluster, and Macintosh computers for calculations and graphics, and a Fluidigm microfluidics crystallizer. The successful candidate will (1) Carry out routine maintenance on these instruments and coordinate service under service contracts; (2) perform routine Unix system administration and crystallographic software management; (3) provide basic training in the use of x-ray crystallographic equipment and software to users; and (4) engage in independent or collaborative research. Preferred qualifications include a Ph.D. degree in an appropriate field of science or technology, and three years of experience in a Research Specialist level position. Previous experience in Unix/Linux system administration and routine maintenance of crystallography hardware is essential. HHMI offers an excellent salary and comprehensive benefits package. Interested candidates please forward a statement of interest, CV, publications and references by December 30, 2007 to Ms. Robbie Haywood Oglesby, Administrative Assistant, 1200 Moursund Ave S101, Houston, Texas 77030 or e-mail regiondjobs(a)hhmi.org (Include Research Specialist - Cech Laboratory in the subject line of your e-mail). ____________________________________________ Marcelo C. Sousa, Ph.D. Department of Chemistry and Biochemistry Cristol Chemistry Building. Room 100 215 UCB University of Colorado at Boulder Boulder, CO 80309 Phone: (303) 735 4341 Fax: (303) 492 5894

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ICSG 2008 Oxford: First announcement
by Tom Terwilliger 27 Nov '07

27 Nov '07

Dear PHENIX users, You may be interested in this announcement for the International Conference on Structural Genomics to be held in Oxford, UK Sept. 20-24, 2008. All the best, Tom T Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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hydrogens in low resolution structure refinement
by Stefanie Krieg 16 Nov '07

16 Nov '07

Dear all! I am refining two structures at 3.0 and 2.7 A. In some older threads on this board I found that you recommended adding hydrogens to the pdb file even at this resolution. I tried that (adding hydrogens with reduce and refine with riding hydrogens) but inspite of what I read in your postings, my R-Factors went up by 1% (not down as was predicted). Are there any other keywords which could be changed or do you have any other ideas why this could be? Thanks in advance! Stefanie

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Re: [phenixbb] use of wavelength_list=
by Tom Terwilliger 12 Nov '07

12 Nov '07

Hi Bryan, phenix.autosol uses the values in wavelength_list to guess scattering factors if you do not supply values for scattering factors. All the best, -Tom T At 03:21 PM 11/10/2007, you wrote: >does phenix use the 'wavelength_list=' command line flag in calculations? >or is it used for no more than data set labeling e.g. derivatives, as >solve works? > >-bryan >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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use of wavelength_list=
by Bryan W. Lepore 10 Nov '07

10 Nov '07

does phenix use the 'wavelength_list=' command line flag in calculations? or is it used for no more than data set labeling e.g. derivatives, as solve works? -bryan

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Collaborative Crystallography Program - Advanced Light Source
by Paul Adams 09 Nov '07

09 Nov '07

The Berkeley Center for Structural Biology (BCSB) is pleased to announce the launch of a Collaborative Crystallography Pilot Program (CC) at the Advanced Light Source in Berkeley. Through this program, scientists will be able to send protein crystals to BCSB staff researchers for data collection and analysis. The CC Pilot Program can provide an number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; * Reduced travel costs. Thumbnail Description: ====================== The Collaborative Crystallography program will be piloted on beamlines 5.0.1 and 5.0.2 for one year; if successful it will be implemented on a permanent basis. CC proposals will go through the regular ALS General User proposal review process for beamtime allocation. Proposals will be reviewed and ranked by the Proposal Study Panel, and beamtime will be allocated accordingly. BCSB staff will schedule the projects to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography. How To Apply: ============= To submit a proposal, go to: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/ Initialize. For question 3 select "Collaborative PX 501/502." For question 9, please describe a specific research project with a clear end point. In order to request CC time for January/February, 2008, proposals must be submitted by November 15, 2007. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --

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Re: [phenixbb] phenix.autobuild opinion on sequence file
by Tom Terwilliger 08 Nov '07

08 Nov '07

Hi Bryan, I haven't tried your approach, but my guess would be that the correct sequence file will be the better way to go... The side chains are fitted after building main-chain so the sequence is not going to affect the main-chain build in any direct way (though the sequence will help the wizard in identifying and correcting places where loops are built with the wrong number of residues). -Tom T At 01:32 PM 11/8/2007, you wrote: >i was thinking about giving phenix.autobuild a poly-Ser/Gly,Ala-intact (or >other incomplete variant) _sequence_file_, so it doesn't inter alia put >arginine into strands... though the solvent content will be imprecise.. > >has anyone noticed if such a trick was more/less favorable to the (proper) >complete sequence approach? any pertinent detail or criticisms >appreciated. > >-bryan >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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phenix.autobuild opinion on sequence file
by Bryan W. Lepore 08 Nov '07

08 Nov '07

i was thinking about giving phenix.autobuild a poly-Ser/Gly,Ala-intact (or other incomplete variant) _sequence_file_, so it doesn't inter alia put arginine into strands... though the solvent content will be imprecise.. has anyone noticed if such a trick was more/less favorable to the (proper) complete sequence approach? any pertinent detail or criticisms appreciated. -bryan

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problem finding large no of sites in high symmetry
by Banumathi Sankaran 08 Nov '07

08 Nov '07

Hi, I am working with a data set collected in P23 space group. I am expecting 23 Se sites. Hyss gives me warning:run time error for finding large no of site. I did not interupt the run. I waited for 1hr and still it could not find sites. Shelx gave me out of 100 solutions only one had good CC and found 15 sites. IS there a way that this problem can be solved in hyss ? Thanks Banu

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Re: [phenixbb] Advice about phasing procedure and phase extension in AutoSol-AutoBuild
by Tom Terwilliger 08 Nov '07

08 Nov '07

Hi Carsten, >1. can I input known HA-positions into the AutoSol wizard to help >Hyss find other positions? Does Hyss actually eliminate bogus sites? >Solve seems to refine bogus sites to occupancies ~0.1-0.5 but with a >B-factor of one, but does not toss them. How does Hyss handle this situation? As far as I know, you cannot seed hyss with sites. If you have SAD data, try the autosol wizard which uses Phaser. Phaser has a good LLG map algorithm for finding addtional sites. >2. What is the best way to handle phase extension in the Wizards, >how would one go about this? I would like to fine-tune the >resolution steps myself as not to jump to far out to higher resolution. The wizards use the defaults for phase extension in resolve. If you want to fine-tune the resolution steps you can say, resolve_command_list=" 's_step 0.05 ' " Note the 2 sets of quotation marks.... This will use steps of 0.05 A for phase extension (type phenix.autobuild --help resolve_command_list for documentation of this command) >3. What quality indicators should I look at? A couple of FOMs in the >resolve runs were in the region of 0.7, but the maps were not >interpretable and resolve failed to build anything. Anything else I >should look at? Best is the R-factor at the end of density modification. If it's around 0.30 you are doing well. 0.4 is bad, 0.25 is great. All the best, Tom T Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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Advice about phasing procedure and phase extension in AutoSol-AutoBuild
by Schubert, Carsten [PRDUS] 08 Nov '07

08 Nov '07

Hi, I am trying to bootstrap my way into a couple of weak derivatives using a combination of Solve and the AutoSol and AutoBuild wizards. I have probably one or two fairly weak diffracting derivatives (~3A) with low FOMs (~0.3) from Solve, the native extend to ~2.A. I have a couple of questions about how to best proceed with the phasing procedure using either the wizards or a Solve/Resolve combination. 1. can I input known HA-positions into the AutoSol wizard to help Hyss find other positions? Does Hyss actually eliminate bogus sites? Solve seems to refine bogus sites to occupancies ~0.1-0.5 but with a B-factor of one, but does not toss them. How does Hyss handle this situation? 2. What is the best way to handle phase extension in the Wizards, how would one go about this? I would like to fine-tune the resolution steps myself as not to jump to far out to higher resolution. 3. What quality indicators should I look at? A couple of FOMs in the resolve runs were in the region of 0.7, but the maps were not interpretable and resolve failed to build anything. Anything else I should look at? Thanks Carsten

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Re: [phenixbb] autobuild 'hires_file'->now FreeR flags, merging, ...
by Tom Terwilliger 07 Nov '07

07 Nov '07

Hi Bryan, >On Tue, 6 Nov 2007, Thomas C. Terwilliger wrote: > > The problem is in that version of phenix. I'm sorry about that! Can you > >that solved it, thanks. Oh good. > >> [1 A] in phenix.autobuild, e.g. a SAD dataset, does the flag > >> 'hires_file=w1.sca' (help says "Merge in hires data"), mean that phases > >> will be extended to a high resolution limit as found in w1.sca? (vide > >> infra) > > > > Yes, that is correct. > >ok, then i have to ask - is phenix merging each reflection? i.e, i >wouldn't want to do this w/ a derivative and hi-res native, right? Yes, it is merging in each reflection, if I understand the question. Yes, you might do it with phases from a native+derivative and a hi-res native. (We're only talking about doing this in autobuild, after you have "experimental" phases from something.) -Tom T Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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error message running example
by Kairies, Norman 07 Nov '07

07 Nov '07

Hi - I tried to run the example: phenix.run_example gene-5-mad However, it stopped, with following error messages: Done with gene-5-mad ...Your results are in the directory: gene-5-mad/AutoSol_run_1_ Missing the summary file: gene-5-mad/AutoSol_run_1_/ Something did not work properly...not all output files produced and the LAST.LOG reports: ************************************************************************ *** 6769 SOLVE STATUS 07-nov-07 12:47:15 6770 6771 DATASET TITLE: SOLVE 07-Nov-07 STATUS 6772 STATUS: UNABLE TO FIND UNIQUE NAME FOR SCRATCH 6773 ------------------------------------------------------------------------ --- 6774 Sorry -- ERROR ENDING. SEE the end of your log file or output STATUS 6775 and solve.log 6776 for more information STATUS Any idea what is going wrong? (phenix version 1.3 beta rc4, 64bit computer, 2 dual core proc.) Many thanks, Norman

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autobuild 'hires_file'
by Bryan W. Lepore 06 Nov '07

06 Nov '07

i have phenix 2007_08_18_1856, (and i think latest cci apps). i have a jumble of questions, i'll try step by step: [1 A] in phenix.autobuild, e.g. a SAD dataset, does the flag 'hires_file=w1.sca' (help says "Merge in hires data"), mean that phases will be extended to a high resolution limit as found in w1.sca? (vide infra) [1 B] can the labels be the same as the 'other' data (the documentation suggests this)? i have tried a few things like : phenix.autobuild data=resolve.mtz hires_file=high_resolution.mtz input_hires_labels='FPnat SIGFPnat' seq_file=seq.txt ... and i see Cell: [99.810997009277344, 99.810997009277344, 140.37300109863281, 90.0, 90.0, 90.0] New resolution: 2.20520367253 High-res file input labels: ['FPnat', 'SIGFPnat'] ... which is good, but the job promptly fails with this cryptic (to me) error message: ************************************************************ Failed to carry out AutoBuild_datafile_info_inputs: 'all_input_hires_labels' ************************************************************ ... (google:all_input_hires_labels and looking through docs quick didn't find it) -bryan

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PDB deposition of tls refined structure
by Rene Jorgensen 01 Nov '07

01 Nov '07

Dear phenix users, I am about to deposit a 2.5A structure at the PDB. The structure has been refined using phenix.refine with strategy=tls+individual_sites +individual_adp, which actually works very well but (because of the tls refinement) also results in the output of ANISOU records for the atoms in the PDB file. When using PDB_extract during the PDB submission process the ANISOU record is picked up as regular anisotropic refinement although the resolution is too low for that. Should I just accept it and leave it as it is or should I correct the info in the Auto Dep Input Tool (ADIT) to isotropic with just the regular b-factor values? Thanks in advance, Rene Jorgensen

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Pango
by Frank von Delft 01 Nov '07

01 Nov '07

Hi, I just installed the latest phenix version (long overdue), and it burps with the following when I try to run the GUI. Looks like an absolute path was left lying around, no? Cheers phx ---------------------------------------------------- Running the PHENIX GUI with /usr/local/phenix/1.3b/phenix-1.3b/build/intel-linux-2.4/base/bin/python PHENIX distribution located in /usr/local/phenix/1.3b/phenix-1.3b/phenix Shell variable SSH_PATH not set Variable PYMOL_PATH set to /usr/local/phenix/1.3b/phenix-1.3b/pymol Shell variable RSH_PATH not set (python:31886): Pango-WARNING **: No builtin or dynamically loaded modules were found. Pango will not work correctly. This probably means there was an error in the creation of: '/net/ribbon/scratch1/phenix/phenix-1.3b/build/intel-linux-2.4/base/etc/pango/pango.modules' You should create this file by running pango-querymodules. (python:31886): Pango-WARNING **: pango_shape called with bad font, expect ugly output (python:31886): Pango-WARNING **: pango_font_get_glyph_extents called with null font argument, expect ugly output (python:31886): Pango-WARNING **: pango_font_get_metrics called with null font argument, expect ugly output (python:31886): Pango-WARNING **: _pango_cairo_font_install called with bad font, expect ugly output ----------------------------------------------------

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Re: [phenixbb] lower limits on grid spacing/binning
by Ralf W. Grosse-Kunstleve 31 Oct '07

31 Oct '07

Probably, the original poster already got more than he bargained for, but for the records, a few more comments: > All FFT based structure factor programs require that the sampling > rates along each axis be even. I don't think this is true, unless I'm misunderstanding what "sampling rate" means. The FFT in phenix is based on FFTPACK (written in the 80s) which works for any number of grid points. FFTw also supports arbitrary gridding. > They may have other required factors > depending on the space group, but they will be happy to inform you > if you make a choice it doesn't like. They are also more efficient > when the prime factors of the sampling rates are small numbers. Try > to stick with multiples of 2,3, and 5 if possible. That's good advice. FFTPACK is fastest for transform sizes that are multiples of 2,3,4 and 5. The map calculation algorithms in phenix automatically take this into account. > All FFT programs will fail if you > sample your map courser than twice that frequency, as SFALL did for > you. This may be true for SFALL, but not for the FFT algorithms in the phenix libraries ($PHENIX/cctbx/include/cctbx/maptbx/structure_factors.h). The critical reference is: David A. Langs (2002), J. Appl. Cryst. 35, 505. As short as it is, this was an incredibly important paper. In retrospect, it is amazing that it took so long for someone to discover the trick. Ralf

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lower limits on grid spacing/binning
by Terry Lang 30 Oct '07

30 Oct '07

Hey Everyone, I have been told by several crystallographers that the general rule of thumb for grid spacing when generating a map is one third the resolution (eg If your crystal structure has a resolution of 1.2 A, your grid spacing should be 0.4). Is there a mathematical reason why this ratio should be maintained or is this simply a holdover from slower computers with lower memory? More importantly for my application, is there a lower limit on how fine the grid spacing can be? In other words, is there a lower limit at which one is oversampling the data for a particular resolution? Any information and/or references would be greatly appreciated. Sincerely, Terry -- P. Therese Lang Post Doc Alber Lab, UC Berkeley

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