- phenixbb - phenix-online.org

How to locate and refine a ligand using anomalous scattering
by Jason 09 Feb '11

09 Feb '11

Hello everyone, I have a few crystals to be x-rayed next week. Before that I hope to get a clear idea about what I am doing (I am new to anomalous scattering). Facts: 1. The crystal is a protein co-crystallized with a ligand 2. The protein structure is known. 3. The ligand has a heavy atom bromide (absorption K-egde=13.47Kev) 4. Data resolution is ~3 angstrom Goals: 1. Locate the bromide position 2. Locate and refine the ligand Questions: 1. Do I need to carry out MAD experiment at 3 wavelengths or there is some other easier way since the protein structure is known (I am not expecting big change of the protein structure itself)? 2. Assuming I have the MAD data, what should I do next using phenix to achieve the two goals listed above? Here are some thoughts: - Using phenix.hyss to locate the anomalous scatterers - Using phenix.autobuild to build the protein model (which data set to use?) - Using coot to add ligands to the protein structure (Is the relative position between the protein and the ligand known based on phenix.hyss and phenix.autobuild?) - Using phenix.refine to refine the ligand+protein complex Thank you all for reading this. ====================== Jason Structural Biology Department University of Pittsburgh ======================

2 1

How to locate and refine a ligand using anomalous scattering
by Jason 09 Feb '11

09 Feb '11

Hello everyone, I have a few crystals to be x-rayed next week. Before that I hope to get a clear idea about what I am doing (I am new to anomalous scattering). Facts: 1. The crystal is a protein co-crystallized with a ligand 2. The protein structure is known. 3. The ligand has a heavy atom bromide (absorption K-egde=13.47Kev) 4. Data resolution is ~3 angstrom Goals: 1. Locate the bromide position 2. Locate and refine the ligand Questions: 1. Do I need to carry out MAD experiment at 3 wavelengths or there is some other easier way since the protein structure is known (I am not expecting big change of the protein structure itself)? 2. Assuming I have the MAD data, what should I do next using phenix to achieve the two goals listed above? Here are some thoughts: - Using phenix.hyss to locate the anomalous scatterers - Using phenix.autobuild to build the protein model (which data set to use?) - Using coot to add ligands to the protein structure (Is the relative position between the protein and the ligand known based on phenix.hyss and phenix.autobuild?) - Using phenix.refine to refine the ligand+protein complex Thank you all for reading this. ====================== Jason Structural Biology Department University of Pittsburgh ======================

3 2

using reference model for low resolution refinement
by crystallogrphy 07 Feb '11

07 Feb '11

Hi, I am refining a hexamer model using low resolution data (4.7A). I want to use a high resolution model (2.4A) which is a dimer as the reference model. The sequence identity is 100%. Does anyone know how to select the residue range from the reference model for my refinement? Thanks!

3 2

is new phenix.refine (1.7-650) comaptible with twinning refinement?
by fulvio saccoccia 04 Feb '11

04 Feb '11

Dear all, I have installed the new phenix version 1.7-650, but I have a doubt: is the real-space refinement within phenix.refine now compatible with twinning refinement?

2 1

ICSG 2011 Abstract Deadline Feb 28, 2011: International Conference on Structural Genomics
by Thomas C. Terwilliger 04 Feb '11

04 Feb '11

Dear Colleagues, We hope that you are planning to attend the International Conference on Structural Genomics 2011, which will be held in Toronto, Canada on May 10-14, 2011. The meeting is designed to serve as a forum to discuss the most recent developments in structural genomics, structural/chemical biology, and their impact on research in biology, medicine and disease. There are many speaking slots still open that will be chosen from submitted poster abstracts. We invite you to submit your abstract by February 28, 2011. Please visit http://www.icsg2011.org for ICSG 2011 meeting and workshop registration details and to submit your abstract. In addition to the main ICSG meeting, there will be a whole day of free concurrent satellite workshops (May 10, 2011), including: Small Molecule Screening Workshop- This hands-on workshop will allow participants to screen a protein of their choice for binding of selected compounds, using thermal shift assays. Eukaryotic Gene Expression Systems Workshop - This workshop will provide participants with a detailed understanding of the state-of-the-art for production of eukaryotic proteins destined for biochemical, biophysical, and structural analyses. iSee: Interactive 3D Documents for the Dissemination of Structural Biology This hands-on workshop will familiarize participants with the iSEE 3D graphical software which allows interactive viewing of 3 dimensional molecular structures and is currently used by journals such as Nature Structural & Molecular Biology and PLoS Biology and PLoS ONE. Workshop on NMR Methods for Structural Biology- This workshop will survey technologies for structure/function investigations of proteins, developed in (or in collaboration with) structural genomics projects, that are ready for widespread use by the wider biological community. Phenix Crystallography Software Workshop This workshop will introduce the PHENIX software for macromolecular structure determination and the core algorithms that it uses. It will provide hands-on tutorials for crystallographers of all levels. We hope to see you there! Best regards, Cheryl Arrowsmith ICSG 2011 Organizer Ted Baker Stephen Burley Dino Moras Joel Sussman Shigeyuki Yokoyama Tom Terwilliger ISGO Executive Committee

1 0

Phenix version 1.7-650 and Pymol
by Leonid Flaks 04 Feb '11

04 Feb '11

>On Tue, Feb 1, 2011 at 5:49 AM, Leonid Flaks<flaks at bnl.gov <http://phenix-online.org/mailman/listinfo/phenixbb>> wrote: >>/ Nat, As I reported minutes ago coot issue is solved. Now I clicked on pymol />>/ button - got an error: />>/ />/> /usr/local/crys/64/phenix-1.7-650/pymol/pymol.exe: error while loading />/> shared libraries: libXmu.so.6: cannot open shared object file: No such file />>/ or directory /> >That's a system library, and not something we distribute or otherwise >interfere with. Does PyMOL even work on the command line? > >thanks, >Nat Nat, pymol is installed as rpm binary and works fine from command line. The library in question is also installed from rpm: dunkin:/home/pxuser 104: rpm -qf /usr/lib64/libXmu.so.6 libXmu-1.0.5-2.fc13.x86_64 dunkin:/home/pxuser 105: rpm -q pymol pymol-1.3-3.20100705svn3911.fc14.x86_64 Could it be something like LD_LIBRARY_PATH or similar? To tell the truth my users are happy to have coot working but don't care too much about the pymol at the moment, so I would not put very high priority on this problem. By the way, I never received you reply - had to cut-and-paste from the web interface. I am subscribed to digest, which has not showed up yet. Thanks, Leon -- Leonid Flaks Phone: (631) 344-2682 Fax : (631) 344-2741

5 8

Phenix version 1.7-650 and Pymol
by Leonid Flaks 01 Feb '11

01 Feb '11

On 02/01/2011 04:20 AM, phenixbb-request(a)phenix-online.org wrote: > Message: 11 > Date: Mon, 31 Jan 2011 16:37:14 -0800 > From: Nathaniel Echols<nechols(a)lbl.gov> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] Phenix version 1.7-650 and coot > Message-ID: > <AANLkTim6ux3V6FcfhXr_0vhNf2P9GWXfBh3aexbZcZ41(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Fri, Jan 28, 2011 at 8:00 AM, Leonid Flaks<flaks(a)bnl.gov> wrote: >> > Hi! >> > I just installed phenix version 1.7-650 on fedora 14 64-bit and noticed that >> > if I start coot from within phenix interface, most of the icons on the right >> > hand side of the coot window are not displayed. >> > There is a lot of messages like this: >> > >> > Error loading icon: Couldn't recognize the image file format for file >> > '/usr/share/coot/pixmaps/residue-info.png' > Okay, apparently we missed an important environment variable in the > script that launches Coot from Phenix - several library paths need to > be cleansed to prevent conflicting with the libraries we distribute. > The one we didn't know about (because it never caused problems before) > appears to be XDG_DATA_DIRS. The crude fix for this is to edit > $PHENIX/phenix/phenix/command_line/start_coot.sh and add this line at > the end of a list of "unset" commands: > > unset XDG_DATA_DIRS > > It'll be fixed in the next build too. If this doesn't totally solve > the problem, let me know - I'm going to unset several other paths too, > but those didn't appear to have any effect on our Fedora 14 machine. > > -Nat Nat, As I reported minutes ago coot issue is solved. Now I clicked on pymol button - got an error: /usr/local/crys/64/phenix-1.7-650/pymol/pymol.exe: error while loading shared libraries: libXmu.so.6: cannot open shared object file: No such file or directory So, looks like we need to unset more variables indeed ;-) Meanwhile I'll just keep clicking on buttons... All the best, Leon -- Leonid Flaks Phone: (631) 344-2682 Fax : (631) 344-2741

2 1

AutoBuild fails using NFS on Snow Leopard
by Chris Richardson 01 Feb '11

01 Feb '11

I've been having a problem running AutoBuild jobs in NFS-mounted project directories on Snow Leopard. The jobs start ok, but typically fail in a build cycle with the error "File exists". The problem is reproducible, but the exact details of the failure are not - the point at which the error occurs changes from run to run. Identical jobs run to completion if the project directory is on a local disk or an AFP-mounted volume. My guess is that it's a file locking issue, or maybe some sort of race condition in file creation. Has anybody else experienced this and if so, is there a solution? The details are: OS X 10.6.6, mounting volumes by NFS from a variety of machines (Ubuntu 10.0.4, OS X 10.6.6 & 10.4), Phenix 1.7-650. Regards, Chris -----%<----{ Log Extract }----- Sorry, a subprocess has failed... END OF LOG FILE /work/nedu/foop/phenix_nedu_nfs/AutoBuild_run_3_/TEMP0/RUN_FILE_3.log : rd desired_run_number=self.desired_run_number) File "/common/app/phenix-1.7-650/phenix/phenix/autosol/wizard_command_line.py", line 132, in __init__ overwrite_defaults=False,desired_run_number=desired_run_number) File "/common/app/phenix-1.7-650/phenix/phenix/wizards/AutoBuild.py", line 83, in __init__ init_OutputDir=init_OutputDir,init_RunInstance=init_RunInstance) File "/common/app/phenix-1.7-650/phenix/phenix/autosol/AutoBaseExtend.py", line 613, in local_init quiet=self.quiet,OutputDir=self.OutputDir) #032107 OutputDir File "/common/app/phenix-1.7-650/phenix/phenix/autosol/RunWizardPDS.py", line 65, in __init__ self.ScriptPDS=ScriptPDS(workspace=workspace) File "/common/app/phenix-1.7-650/phenix/phenix/pds/ScriptPDS.py", line 29, in __init__ PhenixDataStorage.__init__(self, dirname) File "/common/app/phenix-1.7-650/phenix/phenix/pds/PDS.py", line 233, in __init__ os.mkdir(self.dirname) OSError: [Errno 17] File exists: 'PDS/AutoBuild_run_1_' Possibly this subprocess is run on a machine with different architecture than the main process? -- Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

3 4

Re: [phenixbb] Phenix version 1.7-650 and coot - SOLVED!
by Leonid Flaks 01 Feb '11

01 Feb '11

On 02/01/2011 04:20 AM, phenixbb-request(a)phenix-online.org wrote: > Message: 11 > Date: Mon, 31 Jan 2011 16:37:14 -0800 > From: Nathaniel Echols<nechols(a)lbl.gov> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] Phenix version 1.7-650 and coot > Message-ID: > <AANLkTim6ux3V6FcfhXr_0vhNf2P9GWXfBh3aexbZcZ41(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Fri, Jan 28, 2011 at 8:00 AM, Leonid Flaks<flaks(a)bnl.gov> wrote: >> > Hi! >> > I just installed phenix version 1.7-650 on fedora 14 64-bit and noticed that >> > if I start coot from within phenix interface, most of the icons on the right >> > hand side of the coot window are not displayed. >> > There is a lot of messages like this: >> > >> > Error loading icon: Couldn't recognize the image file format for file >> > '/usr/share/coot/pixmaps/residue-info.png' > Okay, apparently we missed an important environment variable in the > script that launches Coot from Phenix - several library paths need to > be cleansed to prevent conflicting with the libraries we distribute. > The one we didn't know about (because it never caused problems before) > appears to be XDG_DATA_DIRS. The crude fix for this is to edit > $PHENIX/phenix/phenix/command_line/start_coot.sh and add this line at > the end of a list of "unset" commands: > > unset XDG_DATA_DIRS > > It'll be fixed in the next build too. If this doesn't totally solve > the problem, let me know - I'm going to unset several other paths too, > but those didn't appear to have any effect on our Fedora 14 machine. > > -Nat Nat, Just to confirm - your fix worked! Thank you very much, Leon -- Leonid Flaks Phone: (631) 344-2682 Fax : (631) 344-2741

1 0

(no subject)
by Shuchi 01 Feb '11

01 Feb '11

hello, i have solved one structure and after solving the average B factor of the model is 107 and average B factor from wilson plot of DATA is 85.5 . is this fine or i did some wrong while fitting and refinement. resolution is 3.0 Angstroms . -- vandana kukshal CSIR-senior research fellow X ray lab ,MSB division central drug research institute lucknow

2 1