Re: [ccp4bb] Automatic LINK generation
Dear Hailiang, While apparently no response came, here my 2 cents: Even if there would be an automatic utitility to generate links based on distances, I would never use it. Either the sugars have been properly refined and then the link cards are present in the pdb file, or the sugars have been fitted manually and may have been real space refined in coot or some other model-building program. In this case, the sugar positions are likely off, since sugars are very often rather disordered and have poor electron density. In this case distance-based link generators very likely will make wrong connections. I just cut and paste link cards from an other pdb file and manually edit them. I eagerly await the moment there will be a create link option in coot, where you just click on the two atoms to be linked and the link card gets generated. Best, Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Hailiang Zhang Sent: Wednesday, March 09, 2011 1:01 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Automatic LINK generation Hi there, I am trying to build the LINK information in PDB header for sugar-containing protein, and I am wondering whether there is some utility in CCP4 (or any others) can do it automatically (eg by measuring inter-sugar distances). Thanks in advance! Best Regards, Hailiang
Re: [ccp4bb] Automatic LINK generation
Dear Hailiang, as Herman Schreuder already wrote sugars are quite likely to contain errors. We are developing the PDB CArbohydrate REsidue check tool (pdb-care) in our group to help crystallographers locating problems in sugars. There will be an update soon, which includes checks for potentially missing LINK records and indicates the atoms that should be linked (and also checks, if linkages result in proper residues, i.e. if there are residues linked to a protein that are not known to occur in glycoproteins, such as NDG (a-D-GlcpNAc) in N-glycan chains). A beta version of the upcoming update is now available at http://www.glycosciences.de/tools/pdbcare2/ - it might help you to identify the atoms that are to be linked and to find potential issues before publishing the structure. Best regards, Thomas
[ccp4bb] La Caixa PhD fellowships at the Centro Nacional de Biotecnologia, Madrid
Dear prospective PhD students, Ten competitive PhD fellowship are available at the Centro Nacional de Biotecnologia in Madrid, Spain (www.cnb.csic.es). The webpage http://www.cnb.csic.es/content/about/lacaixa/index.php?l=0 explains how to apply, although the limit is NOT 13 Feb 2011 as the website states, but 24 March! (see the official call: www.boe.es/boe/dias/2011/03/04/pdfs/BOE-A-2011-4113.pdf in Spanish) Applications should be made directly to the CNB, not to individual research groups. Questions about applications can be addressed to: cnbfellowsh...@cnb.csic.es Greetings, Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3, Campus Cantoblanco E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/content/research/macromolecular/mvraaij/index.php?l=1
Re: [ccp4bb] Automatic LINK generation
Does anybody know the pdb codes with proteins with O-linked sugars on THR. I support a program to help interpret sugars in poor electron density by stabilizing links. Coot helps a bit but branching poses a problem. Rather than based on distance like coot operates at present it should be best if one could specify the type of link. I have crystals where sugars are in poor electron density. I can recognize sialic acid moieties at a crystal contact with symmetry related molecule, but fitting the weak density for the sugars leading to the crystal contact is almost impossible. There are good reasons to combine knowledge of normal human glycosylation with weak electron density to produce a reasonable model. With natural products and heterogeneous sugars, the density in never going to be fantastic except for the few sugar moieties close to the protein. Yet interpreting all existing density may be a step better than outright modeling. Enrico. On Thu, 10 Mar 2011 09:45:57 +0100, herman.schreu...@sanofi-aventis.com wrote: Dear Hailiang, While apparently no response came, here my 2 cents: Even if there would be an automatic utitility to generate links based on distances, I would never use it. Either the sugars have been properly refined and then the link cards are present in the pdb file, or the sugars have been fitted manually and may have been real space refined in coot or some other model-building program. In this case, the sugar positions are likely off, since sugars are very often rather disordered and have poor electron density. In this case distance-based link generators very likely will make wrong connections. I just cut and paste link cards from an other pdb file and manually edit them. I eagerly await the moment there will be a create link option in coot, where you just click on the two atoms to be linked and the link card gets generated. Best, Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Hailiang Zhang Sent: Wednesday, March 09, 2011 1:01 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Automatic LINK generation Hi there, I am trying to build the LINK information in PDB header for sugar-containing protein, and I am wondering whether there is some utility in CCP4 (or any others) can do it automatically (eg by measuring inter-sugar distances). Thanks in advance! Best Regards, Hailiang -- Enrico A. Stura D.Phil. (Oxon) ,Tel: 33 (0)1 69 08 4302 Office Room 19, Bat.152, Tel: 33 (0)1 69 08 9449Lab LTMB, SIMOPRO, IBiTec-S, CE Saclay, 91191 Gif-sur-Yvette, FRANCE http://www-dsv.cea.fr/en/institutes/institute-of-biology-and-technology-saclay-ibitec-s/unites-de-recherche/department-of-molecular-engineering-of-proteins-simopro/molecular-toxinology-and-biotechnology-laboratory-ltmb/crystallogenesis-e.-stura http://www.chem.gla.ac.uk/protein/mirror/stura/index2.html e-mail: est...@cea.fr Fax: 33 (0)1 69 08 90 71
Re: [ccp4bb] Automatic LINK generation
Dear Enrico, you can find information on PDB entries with carbohydrates in the GLYCOSCIENCES.de database: http://www.glycosciences.de/database/index.php To find entries with O-Glycans linked to Thr you can use the substructure search at http://www.glycosciences.de/database/start.php?action=form_structure_matrix (please make sure that you tick the checkbox with PDB entries to limit the search to carbohydrates that are found in the PDB). Just type THR into the center field of one of the upper input area. This will reveal all glycan chains in the database that feature a Thr residue and are represented in PDB structures. There might be more entries in the PDB than in our database, because we try and skip erroneous structures, e.g. those with a mismatch between PDB residue name and residue present in the coordinates (unless it is obvious that the coordinates are correct and just the residue name is wrong, but for O-glycans that's often difficult to tell). Best regards, Thomas
[ccp4bb] Reporting average B values for solvent, chain, ligand etc
Dear CCP4BB I have been refining a structure in Refmac and I would like to report an average B value for the solvent, ligand and DNA chain seperatly. However, I cant this information in the Refmac log or .pdb file. Is there a program/option I can use to calculate the B factors for parts of the model? Thanks James Hall PhD Student University of Reading
Re: [ccp4bb] Reporting average B values for solvent, chain, ligand etc
Hi James, You can do this with MOLEMAN / MOLEMAN2 quite easily (see the manual here: http://xray.bmc.uu.se/usf/moleman2_man.html) Best Matthias Date: Thu, 10 Mar 2011 14:19:21 + From: james.pearce.h...@gmail.com Subject: [ccp4bb] Reporting average B values for solvent, chain, ligand etc To: CCP4BB@JISCMAIL.AC.UK Dear CCP4BB I have been refining a structure in Refmac and I would like to report an average B value for the solvent, ligand and DNA chain seperatly. However, I cant this information in the Refmac log or .pdb file. Is there a program/option I can use to calculate the B factors for parts of the model? Thanks James Hall PhD Student University of Reading
[ccp4bb] Coot Bad magic number errors
Hi all - Two of the grad students in our structural biology course are having similar problems installing Coot on their Mac computers using the stand-alone packageshttp://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot from Bill Scott's Crystallography on OS X website. I've pasted the Terminal outputs below from each of their machines below. They're both getting Python magic number errors, which from what I know result from one Python version trying to run a .pyc file created with another Python version, but I'm not sure exactly how to work around it in the context of the stand-alone package. The students aren't planning to do much in the structural realm outside the course, and I don't want to have to go through installing Xcode and Fink to compile on their own, since they probably won't need it much past this one assignment. Any suggestions would be greatly appreciated. Thanks! Jared Sampson First student (3 week-old Macbook Pro, 10.6.6, stand-alone package for Version 0.6.2-pre-1-3250) $ coot Acquiring application resources from /Library/Coot/share/coot/cootrc INFO:: splash_screen_pixmap_dir /Library/Coot/share/coot/pixmaps INFO:: Colours file: /Library/Coot/share/coot/colours.def loaded There are 118 data in /Library/Coot/share/coot/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ALA.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ASP.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ASN.cif [... and a bunch more monomers ...] There are 2 data in /Library/Coot/share/coot/lib/data/monomers/u/UR.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/h/HOH.cif There are 1 data in /Library/Coot/share/coot/lib/data/monomers/ener_lib.cif sbase monomer dir: /share/sbase sbase files not found in /share/sbase Reading coordinate file: /Library/Coot/share/coot/standard-residues.pdb PDB file /Library/Coot/share/coot/standard-residues.pdb has been read. Spacegroup: P 1 Cell: 40.631 109.18 93.243 90 90 90 initalize graphics molecules...done. (filter-fileselection-filenames-state) (get-active-map-drag-flag) ImportError: Bad magic number in /System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site.pyc second student (Macbook, 10.6.5, also Version 0.6.2-pre-1-3250) $ /usr/local/bin/coot Acquiring application resources from /Library/Coot/share/coot/cootrc INFO:: splash_screen_pixmap_dir /Library/Coot/share/coot/pixmaps INFO:: Colours file: /Library/Coot/share/coot/colours.def loaded There are 118 data in /Library/Coot/share/coot/lib/data/monomers/list/mon_lib_list.cif/ There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ALA.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ASP.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ASN.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/c/CYS.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/g/GLN.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/g/GLY.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/g/GLU.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/p/PHE.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/h/HIS.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/i/ILE.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/l/LYS.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/l/LEU.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/m/MET.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/e/ETH.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/c/CIT.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/AR.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/AD.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/c/CR.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/c/CD.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/g/GR.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/g/GD.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/t/TD.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/u/UR.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/h/HOH.cif There are 1 data in /Library/Coot/share/coot/lib/data/monomers/ener_lib.cif sbase monomer dir: /share/sbase sbase files not found in /share/sbase Reading coordinate file: /Library/Coot/share/coot/standard-residues.pdb PDB file /Library/Coot/share/coot/standard-residues.pdb has been read. Spacegroup: P 1 Cell: 40.631 109.18 93.243 90 90 90 initalize graphics molecules...done. (filter-fileselection-filenames-state) (get-active-map-drag-flag) ImportError: Bad magic number in
Re: [ccp4bb] Coot Bad magic number errors
Hello Jared, Two of the grad students in our structural biology course are having similar problems installing Coot on their Mac computers using the stand-alone packages from Bill Scott's Crystallography on OS X website. I did the same thing about 2 months ago. I tried out the package on about 20 student laptops for a single day class we held. About half of the installations didn't work with either the magic number error or a second error that I can't recall. $ coot My recollection is that this is a shell script wrapper that calls the actual coot-real binary, and in that wrapper there is a PYTHONPATH setting. If it hasn't changed since I last tried to use Bill's package, that PYTHONPATH contains the system python 2.5 and 2.6 modules directories, but the python that is compiled into Coot via Fink is python 2.7. Removing the non-2.7 directories from the PYTHONPATH got about 5 more of the installations working. The remaining machines wouldn't run the package no matter what I tried. Good luck! -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |
Re: [ccp4bb] Coot Bad magic number errors
They're both getting Python magic number errors, which from what I know
result from one Python version trying to run a .pyc file created with another Python
version, but I'm not sure exactly how to work around it in the context of the stand-alone
package. The students aren't planning to do much in the structural realm outside the
course, and I don't want to have to go through installing Xcode and Fink to compile on
their own, since they probably won't need it much past this one assignment.
Usually python will regenerate pyc files as needed (assuming the source
files are available). So find $COOTDIR -name *.pyc -exec rm {} \;
might be worth a try.
Pete
Any suggestions would be greatly appreciated. Thanks!
Jared Sampson
First student (3 week-old Macbook Pro, 10.6.6, stand-alone package for Version
0.6.2-pre-1-3250)
$ coot
Acquiring application resources from /Library/Coot/share/coot/cootrc
INFO:: splash_screen_pixmap_dir /Library/Coot/share/coot/pixmaps
INFO:: Colours file: /Library/Coot/share/coot/colours.def loaded
There are 118 data in
/Library/Coot/share/coot/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ALA.cif
There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ASP.cif
There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ASN.cif
[... and a bunch more monomers ...]
There are 2 data in /Library/Coot/share/coot/lib/data/monomers/u/UR.cif
There are 2 data in /Library/Coot/share/coot/lib/data/monomers/h/HOH.cif
There are 1 data in /Library/Coot/share/coot/lib/data/monomers/ener_lib.cif
sbase monomer dir: /share/sbase
sbase files not found in /share/sbase
Reading coordinate file: /Library/Coot/share/coot/standard-residues.pdb
PDB file /Library/Coot/share/coot/standard-residues.pdb has been read.
Spacegroup: P 1
Cell: 40.631 109.18 93.243 90 90 90
initalize graphics molecules...done.
(filter-fileselection-filenames-state)
(get-active-map-drag-flag)
ImportError: Bad magic number in
/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site.pyc
second student (Macbook, 10.6.5, also Version 0.6.2-pre-1-3250)
$ /usr/local/bin/coot
Acquiring application resources from /Library/Coot/share/coot/cootrc
INFO:: splash_screen_pixmap_dir /Library/Coot/share/coot/pixmaps
INFO:: Colours file: /Library/Coot/share/coot/colours.def loaded
There are 118 data in
/Library/Coot/share/coot/lib/data/monomers/list/mon_lib_list.cif/
There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ALA.cif
There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ASP.cif
There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ASN.cif
There are 2 data in /Library/Coot/share/coot/lib/data/monomers/c/CYS.cif
There are 2 data in /Library/Coot/share/coot/lib/data/monomers/g/GLN.cif
There are 2 data in /Library/Coot/share/coot/lib/data/monomers/g/GLY.cif
There are 2 data in /Library/Coot/share/coot/lib/data/monomers/g/GLU.cif
There are 2 data in /Library/Coot/share/coot/lib/data/monomers/p/PHE.cif
There are 2 data in /Library/Coot/share/coot/lib/data/monomers/h/HIS.cif
There are 2 data in /Library/Coot/share/coot/lib/data/monomers/i/ILE.cif
There are 2 data in /Library/Coot/share/coot/lib/data/monomers/l/LYS.cif
There are 2 data in /Library/Coot/share/coot/lib/data/monomers/l/LEU.cif
There are 2 data in /Library/Coot/share/coot/lib/data/monomers/m/MET.cif
There are 2 data in /Library/Coot/share/coot/lib/data/monomers/e/ETH.cif
There are 2 data in /Library/Coot/share/coot/lib/data/monomers/c/CIT.cif
There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/AR.cif
There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/AD.cif
There are 2 data in /Library/Coot/share/coot/lib/data/monomers/c/CR.cif
There are 2 data in /Library/Coot/share/coot/lib/data/monomers/c/CD.cif
There are 2 data in /Library/Coot/share/coot/lib/data/monomers/g/GR.cif
There are 2 data in /Library/Coot/share/coot/lib/data/monomers/g/GD.cif
There are 2 data in /Library/Coot/share/coot/lib/data/monomers/t/TD.cif
There are 2 data in /Library/Coot/share/coot/lib/data/monomers/u/UR.cif
There are 2 data in /Library/Coot/share/coot/lib/data/monomers/h/HOH.cif
There are 1 data in /Library/Coot/share/coot/lib/data/monomers/ener_lib.cif
sbase monomer dir: /share/sbase
sbase files not found in /share/sbase
Reading coordinate file: /Library/Coot/share/coot/standard-residues.pdb
PDB file /Library/Coot/share/coot/standard-residues.pdb has been read.
Spacegroup: P 1
Cell: 40.631 109.18 93.243 90 90 90
initalize graphics molecules...done.
(filter-fileselection-filenames-state)
(get-active-map-drag-flag)
ImportError: Bad magic number in
/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site.pyc
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
New York, NY 10016
212-263-7898
Re: [ccp4bb] Coot Bad magic number errors
Hi Pete,
Usually python will regenerate pyc files as needed (assuming the source
files are available). So find $COOTDIR -name *.pyc -exec rm {} \;
might be worth a try.
This is true, but the import error is being generated by Coot trying to
read the _system_ .pyc files:
ImportError: Bad magic number in
/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site.pyc
ImportError: Bad magic number in
/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site.pyc
And I would be hesitant to delete those. That said, in theory it really
shouldn't matter.
-ben
--
| Ben Eisenbraun
| SBGrid Consortium | http://sbgrid.org |
| Harvard Medical School | http://hms.harvard.edu |
[ccp4bb] PDBportfolio - slideshows of salient images for all your favourite PDB entries
Hi all, As part of its recent winter update, the Protein Data Bank in Europe (PDBe; http://pdbe.org) released a new widget, called PDBportfolio, that we hope will find widespread use. It displays a slideshow of images that convey important information about the entry (or entries). Every image comes with a legend that explains what is shown and one or more links that provide further information. If you have ever wanted to show off your favourite or own structure(s) on your website, PDBportfolio provides an easy-to-use alternative to a static image. Examples of uses include: - the PDBe summary pages for all PDB entries, for instance: http://pdbe.org/1cbs - the summary pages of the Uppsala Electron Density Server, for example: http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode=1fcc - on your own webpages, for example: http://xray.bmc.uu.se/gerard/structures_pdbportfolio.html The images/legends cover a number of categories of information, including: - Quaternary structure - the largest assembly identified by the authors or PISA is shown - Deposited model - a cartoon and a surface representation are shown (separately). The cartoon is coloured by chain and shown with non-polymeric entities as space-filling (CPK) models. The surface is coloured by atom properties using some simple rules (a la PyMol). For protein-DNA/RNA complexes, only the protein surface is shown - Domains - domains as defined by SCOP, CATH and Pfam are highlighted on the structure in separate images. A unique colour is used for each type of domain and each domain is rendered as a cartoon of that colour; the domain boundaries are further indicated by a semi-transparent surface of the same colour around the domain. Different surface styles are used to help in distinguishing multiple occurrences of the same domain - Compounds - small molecules are shown with their binding environment. Compounds that are most likely experimental additives (such as glycerol) are ignored. Of the remaining ligands, at most three different ones are shown - Experiment - for X-ray entries, a B-factor putty is shown and red surface patches indicate where crystal contacts occur. For NMR entries, the entire ensemble of models is shown. For EM entries, the map is shown (and sometimes a fitted model) PDBportfolio can be used to display information about a single or multiple PDB entries. PDBprints can also be shown to provide additional information about the entry or entries (see http://pdbe.org/pdbprints for more information). The PDBportfolio user-interface contains a number of elements, including: - buttons that control the speed and allow you to start/stop the slideshow or go to the next or previous image - an entry/image-selection pull-down (if you select an entry or a category of images, only the images belonging to it will be shown) - action icons (below the images) - these allow you to get more information about the information category of the current image, download an archive with all the images plus the PyMol scripts used to generate them, and see a page with all the images and legends in one table - the legend for most images contains links to pages with further information The information used to generate the images (e.g., mapping of Pfam or CATH domains) is taken from the PDBe search database and will thus be kept up-to-date automatically (as far as you as a user are concerned - see http://pdbe.org/sifts for more information about what goes on under the hood). To the right of the control buttons you will find a help icon - this will take you to the following page: http://pdbe.org/pdbportfolio This page also contains details on how to incorporate the widget in your own webpages. It's so simple that even yours truly can do it... We welcome your comments, bug reports and feature requests on this widget. Please use the feedback button at the top of any PDBe web page. --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
Re: [ccp4bb] Coot Bad magic number errors
Ben Eisenbraun wrote:
Hi Pete,
Usually python will regenerate pyc files as needed (assuming the source
files are available). So find $COOTDIR -name *.pyc -exec rm {} \;
might be worth a try.
This is true, but the import error is being generated by Coot trying to
read the _system_ .pyc files:
Whoops - missed that.
ImportError: Bad magic number in
/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site.pyc
ImportError: Bad magic number in
/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site.pyc
And I would be hesitant to delete those. That said, in theory it really
shouldn't matter.
-ben
--
| Ben Eisenbraun
| SBGrid Consortium | http://sbgrid.org |
| Harvard Medical School | http://hms.harvard.edu |
[ccp4bb] Can procheck or other tools report bad geometry for ligand?
Hi there, I want to found some bad geometry for my ligand (sugar rings). The procheck .out file seems only shows the bad bond length or angles for protein. Is there any way we can get these information for sugar rings? Thanks in advance! Hailiang
Re: [ccp4bb] Reporting average B values for solvent, chain, ligand etc
Hi James, (...) Is there a program/option I can use to calculate the B factors for parts of the model? phenix.model_vs_data model.pdb data.mtz will do this: report B-factor statistics for macromolecule, water and ligands. Pavel.
Re: [ccp4bb] Coot Bad magic number errors
Hi Ben and Pete - I did think about deleting (or moving) the .pyc files, but in
the newer of the two students' computers (3 weeks out of the box), there wasn't
a site.py file in that directory, only .pyc and .pyo, so I figured I'd better
not mess with it.
Thanks for the suggestions so far. I'll see if I can get the students back
here again and try editing the wrapper script.
Cheers,
Jared
On Mar 10, 2011, at 12:05 PM, Pete Meyer wrote:
Ben Eisenbraun wrote:
Hi Pete,
Usually python will regenerate pyc files as needed (assuming the source
files are available). So find $COOTDIR -name *.pyc -exec rm {} \;
might be worth a try.
This is true, but the import error is being generated by Coot trying to
read the _system_ .pyc files:
Whoops - missed that.
ImportError: Bad magic number in
/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site.pyc
ImportError: Bad magic number in
/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site.pyc
And I would be hesitant to delete those. That said, in theory it really
shouldn't matter.
-ben
--
| Ben Eisenbraun
| SBGrid Consortium | http://sbgrid.org |
| Harvard Medical School | http://hms.harvard.edu |
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=
Re: [ccp4bb] Can procheck or other tools report bad geometry for ligand?
Hi Halliang, If the ligands are in the pdb het dictionary I think MolProbity will look at bonds and angles...maybe even dihedrals. Cheers, -bob On Thu, Mar 10, 2011 at 12:23 PM, Hailiang Zhang zhan...@umbc.edu wrote: Hi there, I want to found some bad geometry for my ligand (sugar rings). The procheck .out file seems only shows the bad bond length or angles for protein. Is there any way we can get these information for sugar rings? Thanks in advance! Hailiang
Re: [ccp4bb] Can procheck or other tools report bad geometry for ligand?
Hi, Swiss-pdb viewer works well for small peptides, you can check if it serves your objective too... Even WHAT IF provides clues to bond angles, bond length and torsion angles. Gauri On Thu, Mar 10, 2011 at 3:56 PM, Robert Immormino immorm...@gmail.comwrote: Hi Halliang, If the ligands are in the pdb het dictionary I think MolProbity will look at bonds and angles...maybe even dihedrals. Cheers, -bob On Thu, Mar 10, 2011 at 12:23 PM, Hailiang Zhang zhan...@umbc.edu wrote: Hi there, I want to found some bad geometry for my ligand (sugar rings). The procheck .out file seems only shows the bad bond length or angles for protein. Is there any way we can get these information for sugar rings? Thanks in advance! Hailiang
[ccp4bb] glycerol
Hi all, I was intrigued by the recent question of whether glycerol had any adverse effects on the final purity of protein isolated by chromatography. Glycerol certainly helps to solubilize some proteins. Does anyone know of any negative effects of glycerol in protein purification, on protein crystal quality or use in cryocrystallography and on X-ray diffraction results? Cheers. Ray Brown
Re: [ccp4bb] glycerol
Hi Ray I have seen glycerol at less than 5% in the protein buffer prevent crystal growth completely and when removed from the buffer has resulted in very nice crystal growth of the glycerol free protein. Best Gina From: CCP4 bulletin board on behalf of Ray Brown Sent: Thu 10/03/2011 17:04 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] glycerol Hi all, I was intrigued by the recent question of whether glycerol had any adverse effects on the final purity of protein isolated by chromatography. Glycerol certainly helps to solubilize some proteins. Does anyone know of any negative effects of glycerol in protein purification, on protein crystal quality or use in cryocrystallography and on X-ray diffraction results? Cheers. Ray Brown Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
Re: [ccp4bb] glycerol
Glycerol is just another additive to crystallizations and a reasonably good cryoprotectant. Sometimes it helps to grow crystals, sometimes it has no effect, and sometimes it interferes with crystal growth. Have I covered all the possiblities? One thing is the glycerol often makes a protein more soluble, so one will often need a higher protein concentration or higher precipitant concentration in order to get crystals. If someone tells me that glycerol prevented crystal growth, I always ask them if they increased the protein concentration or precipitant concentration or if they just used their old recipe. That is a revealing question. Also note that ethylene glycol has a similar effect, yet is sometimes very different. Furthermore, these compounds can bind in active sites and elsewhere on proteins and interfere with assays and other stuff. Nevertheless, they are always one of the first additives to try. _ From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ray Brown Sent: Thursday, March 10, 2011 4:05 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] glycerol Hi all, I was intrigued by the recent question of whether glycerol had any adverse effects on the final purity of protein isolated by chromatography. Glycerol certainly helps to solubilize some proteins. Does anyone know of any negative effects of glycerol in protein purification, on protein crystal quality or use in cryocrystallography and on X-ray diffraction results? Cheers. Ray Brown
Re: [ccp4bb] glycerol
Hi Ray; In case of my protein 5%-10% of glycerol help to increase the solubility both of the soluble domain as well as the trans-membrane domain,improve crystal quality dramatically and even prevent radiation damage to some extent. Best of luck Bashir On Thu, March 10, 2011 23:04, Ray Brown wrote: Hi all, I was intrigued by the recent question of whether glycerol had any adverse effects on the final purity of protein isolated by chromatography. Glycerol certainly helps to solubilize some proteins. Does anyone know of any negative effects of glycerol in protein purification, on protein crystal quality or use in cryocrystallography and on X-ray diffraction results? Cheers. Ray Brown -- Muhammad Bashir Khan ** Department for Structural and Computational Biology Max F. Perutz Laboratories University of Vienna Campus Vienna Biocenter 5 A-1030 Vienna Austria Austria Phone: +43(1)427752224 Fax: +43(1)42779522
Re: [ccp4bb] glycerol
I think adding 5% glyecrol has a big effect on the solubility, so conditions would have to be re-optimized if glycerol is included. In the case i am aware of also solubility was increased, but that could be compensated by higher PEG and/or lower salt concentration (in the salting-in region). There are really two questions here: If crystallization conditions have already been optimized, will adding glycerol interfere with crystallization? probably yes. If I am starting work on crystallizing a new protein and I know it is stabilized by glycerol, should I avoid glycerol? No. eab Clayton, Gina Martyn wrote: Hi Ray I have seen glycerol at less than 5% in the protein buffer prevent crystal growth completely and when removed from the buffer has resulted in very nice crystal growth of the glycerol free protein. Best Gina *From:* CCP4 bulletin board on behalf of Ray Brown *Sent:* Thu 10/03/2011 17:04 *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] glycerol Hi all, I was intrigued by the recent question of whether glycerol had any adverse effects on the final purity of protein isolated by chromatography. Glycerol certainly helps to solubilize some proteins. Does anyone know of any negative effects of glycerol in protein purification, on protein crystal quality or use in cryocrystallography and on X-ray diffraction results? Cheers. Ray Brown Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
[ccp4bb] Protease inhibitor cocktails and protein crystallization.
Dear All, I apologize if the questions has already been asked on this forum. We are purifying a membrane that seems prone to proteolysis. Although we use Protease Inhibitor cocktails during lysis and the first step of purification we get rid of them after and only keep PMSF and EDTA as general anti-protease control agents. I am considering reincluding the cocktail of inhibitors at the last purification step (a size exclusion in our case) and was wondering if having this infamous mixture of peptidic inhibitors (for the most part) around during crystallization would be a problem: specifically getting crystals of these inhibitors. Does anyone have extended experience in this matter. Many thanks in advance. -- Pascal F. Egea, PhD Assistant Professor UCLA, David Geffen School of Medicine Department of Biological Chemistry 314 Biomedical Sciences Research Building office (310)-983-3515 lab (310)-983-3516 email pe...@mednet.ucla.edu
Re: [ccp4bb] Coot Bad magic number errors
Sorry about this. Issue the command sudo perl -pi -e 's|/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6\:/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5\:||g' /Library/Coot/bin/coot and that will fix it. I'll make a new one. Bill On Mar 10, 2011, at 7:55 AM, Sampson, Jared wrote: Hi all - Two of the grad students in our structural biology course are having similar problems installing Coot on their Mac computers using the stand-alone packageshttp://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot from Bill Scott's Crystallography on OS X website. I've pasted the Terminal outputs below from each of their machines below. They're both getting Python magic number errors, which from what I know result from one Python version trying to run a .pyc file created with another Python version, but I'm not sure exactly how to work around it in the context of the stand-alone package. The students aren't planning to do much in the structural realm outside the course, and I don't want to have to go through installing Xcode and Fink to compile on their own, since they probably won't need it much past this one assignment. Any suggestions would be greatly appreciated. Thanks! Jared Sampson First student (3 week-old Macbook Pro, 10.6.6, stand-alone package for Version 0.6.2-pre-1-3250) $ coot Acquiring application resources from /Library/Coot/share/coot/cootrc INFO:: splash_screen_pixmap_dir /Library/Coot/share/coot/pixmaps INFO:: Colours file: /Library/Coot/share/coot/colours.def loaded There are 118 data in /Library/Coot/share/coot/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ALA.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ASP.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ASN.cif [... and a bunch more monomers ...] There are 2 data in /Library/Coot/share/coot/lib/data/monomers/u/UR.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/h/HOH.cif There are 1 data in /Library/Coot/share/coot/lib/data/monomers/ener_lib.cif sbase monomer dir: /share/sbase sbase files not found in /share/sbase Reading coordinate file: /Library/Coot/share/coot/standard-residues.pdb PDB file /Library/Coot/share/coot/standard-residues.pdb has been read. Spacegroup: P 1 Cell: 40.631 109.18 93.243 90 90 90 initalize graphics molecules...done. (filter-fileselection-filenames-state) (get-active-map-drag-flag) ImportError: Bad magic number in /System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site.pyc second student (Macbook, 10.6.5, also Version 0.6.2-pre-1-3250) $ /usr/local/bin/coot Acquiring application resources from /Library/Coot/share/coot/cootrc INFO:: splash_screen_pixmap_dir /Library/Coot/share/coot/pixmaps INFO:: Colours file: /Library/Coot/share/coot/colours.def loaded There are 118 data in /Library/Coot/share/coot/lib/data/monomers/list/mon_lib_list.cif/ There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ALA.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ASP.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ASN.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/c/CYS.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/g/GLN.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/g/GLY.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/g/GLU.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/p/PHE.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/h/HIS.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/i/ILE.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/l/LYS.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/l/LEU.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/m/MET.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/e/ETH.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/c/CIT.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/AR.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/AD.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/c/CR.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/c/CD.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/g/GR.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/g/GD.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/t/TD.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/u/UR.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/h/HOH.cif There are 1 data in /Library/Coot/share/coot/lib/data/monomers/ener_lib.cif sbase monomer dir:
[ccp4bb] Getting the triangulated solvent excluded surface of a protein (PDB) as a .obj file
Hello, What are the good software to do this? I already know of Pymol and Jmol. Both can export the result to a .obj file, which is interesting for later processing. However, Pymol's algorithm is not exactly what Connolly described, cf. http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg00179.html Also, Pymol will save the surface with some translation and rotation which are not present in the PDB read in, which is a real pain. For Jmol, sometimes the surface is not a closed polyhedra, so it is kind of useless for my purpose. I know of MSMS, but I don't think it is that robust (I read some source code where someone was using MSMS, the source code had many dirty things in order to try handling the apparently many cases where MSMS was crashing). Is there something freely usable for research, using beta shapes internally, for example? That should be a robust approach. A robust software would be much appreciated (not crashing, whatever the PDB we give it as input). Open source and not in Fortran would be heaven. ;) Thanks a lot for suggestions, F.
Re: [ccp4bb] glycerol
Hi Ray, Beyond what has already been mentioned and anecdotal evidence, at least one structural genomics consortium solves a substantial number, if not most, of its proteins from crystals grown in the presence of 5-10% glycerol. You can search crystallization conditions as well as protein preparations for the structures (Materials and Methods) here: http://www.thesgc.org/structures/ Just my 2-cents. Florian On Thu, 10 Mar 2011 17:57:02 -0500, Edward A. Berry ber...@upstate.edu wrote: I think adding 5% glyecrol has a big effect on the solubility, so conditions would have to be re-optimized if glycerol is included. In the case i am aware of also solubility was increased, but that could be compensated by higher PEG and/or lower salt concentration (in the salting-in region). There are really two questions here: If crystallization conditions have already been optimized, will adding glycerol interfere with crystallization? probably yes. If I am starting work on crystallizing a new protein and I know it is stabilized by glycerol, should I avoid glycerol? No. eab Clayton, Gina Martyn wrote: Hi Ray I have seen glycerol at less than 5% in the protein buffer prevent crystal growth completely and when removed from the buffer has resulted in very nice crystal growth of the glycerol free protein. Best Gina *From:* CCP4 bulletin board on behalf of Ray Brown *Sent:* Thu 10/03/2011 17:04 *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] glycerol Hi all, I was intrigued by the recent question of whether glycerol had any adverse effects on the final purity of protein isolated by chromatography. Glycerol certainly helps to solubilize some proteins. Does anyone know of any negative effects of glycerol in protein purification, on protein crystal quality or use in cryocrystallography and on X-ray diffraction results? Cheers. Ray Brown Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
Re: [ccp4bb] Getting the triangulated solvent excluded surface of a protein (PDB) as a .obj file
Sorry, I forgot to mention about what is the .obj file I need. It is a pure ASCII geometric description of a polyhedra. Cf. http://en.wikipedia.org/wiki/Wavefront_.obj_file It looks rather easy to parse compared to some VRML file, for example. Thanks, F. Francois Berenger wrote: Hello, What are the good software to do this? I already know of Pymol and Jmol. Both can export the result to a .obj file, which is interesting for later processing. However, Pymol's algorithm is not exactly what Connolly described, cf. http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg00179.html Also, Pymol will save the surface with some translation and rotation which are not present in the PDB read in, which is a real pain. For Jmol, sometimes the surface is not a closed polyhedra, so it is kind of useless for my purpose. I know of MSMS, but I don't think it is that robust (I read some source code where someone was using MSMS, the source code had many dirty things in order to try handling the apparently many cases where MSMS was crashing). Is there something freely usable for research, using beta shapes internally, for example? That should be a robust approach. A robust software would be much appreciated (not crashing, whatever the PDB we give it as input). Open source and not in Fortran would be heaven. ;) Thanks a lot for suggestions, F.
Re: [ccp4bb] Protease inhibitor cocktails and protein crystallization
Regarding adding inhibitors. I'm not sure the effect on crystallization but if you use too much you will get covalent modification of your protein from one of them (I can check my notes as to which one). We searched many MS databases of protein modifications to realize why our protein was the wrong Mr. Then my student happened to mention that he had added 10 times top much. Well at least we now know what not to do. Mark Saper sa...@umich.edu
[ccp4bb] map format conversion
Dear all We are trying to combine a protein crystallography with computational chemistry for a metalloprotein. Does anyone know whether it would be possible to convert a ccp4 electron density map to an electron density plot in a format of a 'cube' file as in http://www.gaussian.com/g_tech/g_ur/u_cubegen.htm that we could easily convert to a constrain definition for the optimization? Alternatively, providing a method to make a long list of x,y,z coordinates around the protein structure and themagnitude of the electron density at the given point would be very valuable. Please let me know if this is possible. It would help our calculations enormously. Best regards ~ Masaki UNNO, Ph.D. Frotier Research Center for Applied Atomic Sciences, Ibaraki University Ibaraki Quantum Beam Research Center 162-1 Tokai, Shirakata, Naka, Ibaraki 319-1106, Japan Tel: 029-352-3239, Fax: 029-287-7872 E-mail: unn...@mx.ibaraki.ac.jp ~
Re: [ccp4bb] glycerol
Dear Ray, The solubility and stability effect of glycerol is protein dependent and highly concentration dependent. When used at the wrong concetration or molar ratio to protein, preferential interaction could result in adverse effects. Likewise at concentrations higher than 15% in drops for crystal growth, the protein could remain under the solubility curve of the phase diagram for a long period. This is particularly the case when preciptant concetration is not balanced with glycerol concentration used. Generally, sugar alcohols, which glcerol is one, are well documented as excellent protein stabilizers (protect protein against proteases in solution, against thermal denaturation, to some extent reduce conformational flexibility and increased molecular contacts in solution based on its viscosity and experimetally determined effect on chemical potential/hydration on protein surfaces; see Biochemistry 1982, 21, 6536-6544 and others). However, the right concentration or molar ratio to have the desired effect on protein needs to be determined a priori, especially when used as an additive in drops for protein crystal growth. 10% glycerol is approx 1M and help solubiize as well as stabilize most protein sufficiently during preparation and storage. From my little experience and literature knowledge, when used as additive in crystallization, concentration series need to be screened together with the preciptant of choice, and I would recommend 0.1M a safe starting point. all the best. Ade On Thu, March 10, 2011 23:04, Ray Brown wrote: Hi all, I was intrigued by the recent question of whether glycerol had any adverse effects on the final purity of protein isolated by chromatography. Glycerol certainly helps to solubilize some proteins. Does anyone know of any negative effects of glycerol in protein purification, on protein crystal quality or use in cryocrystallography and on X-ray diffraction results? Cheers. Ray Brown -- Adekunle Onipe, PhD Student Djinovic-Carugo Group Dept of Structural and Computational Biology University of Vienna | Max F. Perutz Laboratories Dr Bohrgasse 9 | A-1030, Vienna, Austria.
Re: [ccp4bb] map format conversion
Hi, MAPMAN can read and write a number of formats - see: http://xray.bmc.uu.se/usf/mapman_man.html#H8 While it doesn't write cube format, it can produce maps in various ASCII formats (e.g., NEWEZD, CNS, X-PLOR) that you should be able to convert into something that suits your needs. --dvd
Re: [ccp4bb] Can procheck or other tools report bad geometry for ligand?
Hello, One can use PARST to check the geometry of the molecules. The idea is to compare geometries with a standard molecule. -Divya On 3/11/11, gauri misra kamga...@gmail.com wrote: Hi, Swiss-pdb viewer works well for small peptides, you can check if it serves your objective too... Even WHAT IF provides clues to bond angles, bond length and torsion angles. Gauri On Thu, Mar 10, 2011 at 3:56 PM, Robert Immormino immorm...@gmail.comwrote: Hi Halliang, If the ligands are in the pdb het dictionary I think MolProbity will look at bonds and angles...maybe even dihedrals. Cheers, -bob On Thu, Mar 10, 2011 at 12:23 PM, Hailiang Zhang zhan...@umbc.edu wrote: Hi there, I want to found some bad geometry for my ligand (sugar rings). The procheck .out file seems only shows the bad bond length or angles for protein. Is there any way we can get these information for sugar rings? Thanks in advance! Hailiang
[ccp4bb] postdoctoral fellow position in Duke-NUS Graduate Medical School
A postdoctoral position is available at the Laboratory of Virus Structure and Function in the Duke-NUS Graduate Medical School, Singapore. The Laboratory of Shee-Mei Lok (http://www.duke-nus.edu.sg/web/research_faculty_sheemei.htm) is looking for a post-doctoral fellow to work on the structural studies of dengue viruses and its complexes. Her laboratory uses a combination of techniques such as x-ray crystallography and cryo-electron microscopy (CryoEM) including single particle analysis and cryotomography. Facilities such as in-house x-ray machines and cryoelectron microscope (Titan Krios, FEI) are available in the National University of Singapore. The post-doctoral fellow will mainly participate in the computational side of structure solving and thus should have prior experience in solving either cryoEM or x-ray structures. Training in crystallography or cryoEM data collection and image processing however, will also be available if necessary. Interested individuals are invited to send cover letter, cv and a list of referees to Dr Shee-Mei Lok by email (sheemei@duke-nus.edu.sg).
