- phenixbb - phenix-online.org

PDBTools and TLS
by Mark Saper 03 Sep '13

03 Sep '13

Hi, I couldn't find the answers to these questions in the documentation. 1. If I am refining TLS and individual isotropic ADPs, does phenix.refine derive iso-ADP from the ANISOU records presently in the file, or does it use the iso-ADP from the ATOM record and recombine it with the TLS values? 2. Consequently if I reset the B's for a range of residues on the ATOM cards only, will they be used rather than the ANISOU record to derive the ADP? Is it better to use PDBTools, specify the iso-ADP and also convert to ANISOU? I am doing this for only a selection of the residues. 3. Should phenix.refine input files retain the header lines containing the previously cycle TLS parameters? If so PDB Tools doesn't save them. PDB Editor does. Which is the preferred tool? 4. If one explicitly changes atom ADPs with Coot using Measures>Residue info... the output file reflects the change only in the ATOM lines, but the ANISOU line retains the previous 6 parameters. It seems as if coot should also change the ANISOU to reflect anisou (last 3 parameters=0). Comments or answers? Many thanks in advance! -Mark _______________________________________________ Mark A. Saper, Ph.D. Department of Biological Chemistry, University of Michigan Medical School 3040 Chemistry Building | saper(a)umich.edu | +1 (734) 764-3353

2 1

Error determining reference matches
by Dan McNamara 31 Aug '13

31 Aug '13

Hi all, I am encountering a strange crash when running phenix.refine through the command line with reference model restraints turned on. The references point to two different PDB files, one labeled as chain A and one labeled as chain B. This error occurs whether I have my refinement model in P1 with 192 chains or P2(1) with 96 chains. The chains are A-EZ (192) or A-BH (96). It appears to fail to align the reference models to the sequences in the refinement model. This error does not occur with other smaller target structures under 25 chains and reference models used with the same installation of phenix. I am hoping for any advice on why this might be happening or how I might get around it. ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (401472 atoms) torsion_angles = False (0 atoms) rigid_body = True (401472 atoms in 192 groups) individual_adp = False (iso = 0 aniso = 0) group_adp = True (201984 atoms in 25824 groups) tls = False (0 atoms in 0 groups) occupancies = False (0 atoms) group_anomalous = False n_use = 401472 n_use_u_iso = 401472 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 401472 *** Adding Reference Model Restraints *** determining reference matches automatically... Traceback (most recent call last): File "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/phenix/phenix/refinement/command_line.py", line 92, in run master_params=customized_master_params) File "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/phenix/phenix/refinement/driver.py", line 501, in __init__ log=self.log) File "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/cctbx_project/mmtbx/torsion_restraints/reference_model.py", line 147, in __init__ self.get_reference_dihedral_proxies() File "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/cctbx_project/mmtbx/torsion_restraints/reference_model.py", line 460, in get_reference_dihedral_proxies log=self.log) File "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/cctbx_project/mmtbx/torsion_restraints/reference_model.py", line 323, in process_reference_groups moving_chain = mod_h) File "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/cctbx_project/mmtbx/torsion_restraints/utils.py", line 426, in _ssm_align ssm_alignment = ccp4io_adaptbx.SSMAlignment.residue_groups(match=ssm) File "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/ccp4io_adaptbx/__init__.py", line 215, in residue_groups return cls( match = match, indexer = indexer ) File "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/ccp4io_adaptbx/__init__.py", line 176, in __init__ self.pairs.append( ( get( f, indexer1 ), get( s, indexer2 ) ) ) File "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/ccp4io_adaptbx/__init__.py", line 173, in get assert identifier in indexer, "Id %s missing" % str( identifier ) AssertionError: Id ('A', 1, ' ') missing Best, Dan

3 2

coot and mtz interpretation
by Heather L Condurso 30 Aug '13

30 Aug '13

I'm having an issue that when I launch coot from the phenix refine gui it loads the pdb and mtz fine, but the FoFc map colors are green and royal blue. When I open coot first and then load the pdb and mtz files, the FoFc map colors are green and red, but the blobs that were green in the phenix loaded maps are now red and what was royal blue is now green. Has anyone else had this issue? I am running a mac with OS X 10.6.8 and coot 0.6.1 and phenix 1.8.2-1309. I have an identical mac running all the same versions and everything loads green and red as expected. Is there a parameter file somewhere that tells coot how to display the phenix maps that may provide a clue as to what is going on? I appreciate any suggestions, Heather

3 4

a question on NAG-ASN cif file
by fn1＠rice.edu 29 Aug '13

29 Aug '13

Hi Nigel, I tried your nag_asn.cif file. I did not include hydrogen in the refinement, so i always get the error message that NAG-ASN could not be applied. So i remark the angle definition that contains hydrogen and the same for the plane definition, as follows, #NAG-ASN 1 C1 2 ND2 2 HD2 119.000 3.000 #NAG-ASN plane1 2 HD21 .020 by doing this, the program could run through. However, when i check the geometry output .geo file, only the added plane information is seen, no chirality of C1 in NAG is seen. Did i do something wrong? Thank you! Fengyun

2 1

a question on NAG-ASN cif file
by fn1＠rice.edu 28 Aug '13

28 Aug '13

Hi everyone, I am refining a glycoprotein model, and I have applied NAG-ASN link to the ASN. But the beta-conformation of NAG could not be retained after refinement for some sites. I read the cif file and find that there are only angle definitions for NAG-ASN. The dihedral and charility information are missing. Is there a way that I could retain the charility of C1 of NAG? Thank you! Fengyun

3 3

ALS Call for General User Proposals - DEADLINE SEPTEMBER 4 , 2013
by Banumathi Sankaran 28 Aug '13

28 Aug '13

> > The deadline for Jan/July 2014 Collaborative > Crystallography proposals will be *Sep 4, 2013. * > > ---------------------------------------------------------------------------------------- > Through the Collaborative Crystallography Program (CC) at the > Advanced Light Source (ALS), scientists can send protein crystals > to Berkeley Center for Structural Biology (BCSB) staff researchers > for data collection and analysis. The CC Program can provide a > number of benefits to researchers: > > * Obtain high quality data and analysis through collaborating with > expert beamline > researchers; > * Rapid turn around on projects; and > * Reduced travel costs. > > To apply, please submit a proposal through the ALS General User > proposal review process for beamtime allocation. Proposals are > reviewed and ranked by the Proposal Study Panel, and beamtime is > allocated accordingly. BCSB staff schedule the CC projects on > Beamlines 5.0.1 and 5.0.2 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: > > Please follow the instructions for proposal submission at: > http://www-als.lbl.gov/index.php/user-information/user-guide/58.html > Scroll down to "*Structural Biology beamlines (includes protein SAXS)*" > and click on "New Proposal." Enter your proposal information. > > > > Regards, > Banumathi Sankaran >

1 0

processor usage controlin DEN
by miyatake 24 Aug '13

24 Aug '13

Dear phenixbb, Hello, I run DEN refinements using GUI (dev-1439). I wonder whether I can control the number of the processor used during the DEN refinement. I know that we can use nproc in command line, but I'd like use it in GUI. Best regards, H. Miyatake

2 4

phenix.real_space_refine
by Heather L Condurso 23 Aug '13

23 Aug '13

I tried to run the phenix.real_space_refine that was discussed in the CCN but I get the following error. import mmtbx.refinement.real_space.driver ImportError: No module named driver I downloaded the latest nightly build dev-1463. Even when asking for the help I get the same error. I did however successfully create some FEMs which look lovely. Heather Condurso UF-Department of Chemistry condurso(a)ufl.edu

3 3

Post-doc position for SAXS at the MAX IV Laboratory
by Marjolein Thunnissen 23 Aug '13

23 Aug '13

The MAX IV laboratory in Lund has opened a position for a Postdoctoral fellow to strengthen the biological SAXS environment at the current SAXS beam line at the MAX-II ring. The position will be for two years and is embedded in the BIOSTRUCT-X EU program. Full information of the position is available at: http://admin.lu.se/o.o.i.s?id=22598&Dnr=554436&Type=E. More information can be obtained from Tomás Plivelic (tomas.plivelic(a)maxlab.lu.se<mailto:[email protected]>). Information about the MAX IV laboratory can be obtained at the homepage www.maxlab.lu.se<http://www.maxlab.lu.se> . best regards Marjolein Thunnissen ________________________________________________________________________ Marjolein Thunnissen Phone +46-(0)76-632 0417 Associate Professor Fax +46-(0)46-22 24692 Dept of Biochemistry and Structural Biology, Lund University http://www.mps.lu.se<http://www.mps.lu.se/> PO-Box 124 S-221 00 Lund, Sweden Scientific coordinator MX (The MAX IV Laboratory): I911 and BioMAX ________________________________________________________________________

1 0

Find peaks and holes documentation
by Morten Grøftehauge 22 Aug '13

22 Aug '13

Hi, I wanted to try phenix.find_peaks_holes with anomalous structure factors from XPREP but I ran into a few problems. And then I tried to fix them by reading the manual and that was really hard too. So first the missing manual. If I google it I get this page http://www.phenix-online.org/documentation/find_peaks_holes.htm which is for the GUI. When I go back to the documentation http://www.phenix-online.org/documentation/phenix_documentation.html I can't find the link for it (which is also why I was using Google to find it in the first place). I also checked the source to see if the link was somehow misnamed. Anyway, running it from the command line with default settings is not hard. phenix.find_peaks_holes model.pdb reflections.hkl but I run into this error message Sorry: Unresolved amplitude/intensity ambiguity: /path/path/path/reflections.hkl SHELX reflection files may contain amplitudes or intensities. Please append =amplitudes or =hklf3 or =intensities or =hklf4 to the file name argument or parameter to resolve the ambiguity. and I don't how to do that. If I add .hklf3 at the end of the file name I get the same error. If I go reflections.hkl=hklf3 I just get a message that I need to supply a reflection file. What is the syntax? Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

2 4