[ccp4bb] Is there an easy way to down-weight figures of merit?
Hi Citizens: I realize this is one of those warranty-violating questions, but is there a simple way to down-weight figures of merit, or the equivalent in terms of Hendrickson-Lattman coefficients? I'm trying to generalize and automate a procedure for solving RNA structures without heavy-atom phases by feeding phaser random-sequence model A-form RNA helices. It pretty much works, but there comes a point where I want to use the phase probability distribution from the partial/inaccurate model in solvent-flattening while discarding the model, with the hope of minimizing model bias. The problem is that if the refinement of the partial/inaccurate model goes reasonably well, the FOM become inflated to the point where solvent-flattening becomes less effective for improving and correcting phases. Thanks. Bill Scott
[ccp4bb] Postdoctoral position at The Scripps Research Institute
A postdoctoral position focusing on structural and functional basis of autophagy is available immediately in the laboratory of Takanori Otomo in the Department of Molecular Biology at The Scripps Research Institute (California). This is a new laboratory and the research field is young. Thus your contribution to the lab and the field will be enormous. Highly motivated recent PhD graduates who have training in structural biology (X-ray crystallography and/or other methods) and biochemistry are encouraged to apply. Interested candidates should send a CV, brief summary of research accomplishments and interests, and three professional references to [EMAIL PROTECTED] For more information, please visit http://www.scripps.edu/mb/otomo. -- Takanori Otomo Assistant Professor Departments of Molecular Biology and Cell Biology The Scripps Research Institute 858-784-2898 (office) 858-784-1000 ext.43335 (lab) email: [EMAIL PROTECTED] Mailing address: The Scripps Research Institute CB-207 10550 North Torrey Pines Road La Jolla, CA 92037
Re: [ccp4bb] ArpWarp error
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Mark; Could you give us a bit more information, in particular what is the last step that runs before this one? Could you send me (or post here) the last 10/20 lines of summary logfile (the one where the lines you reported are) ? Hopefully with this information we might be able to have a better idea of what was the problem? Serge. PS : most likely this is due to a refinement problem (error happens when parsing the refmac log file), likely the model provided to refmac has a chemistry issue... Le 11 juil. 08 à 05:20, Mark Del Campo a écrit : I'm running flexWarp on a MacBook Pro and on a Linux box. The program goes through several cycles and then gives the following errors when trying to improve an MR solution: If I start from the PDB file as is ERROR Exception class : 'IndexError' Message : '' BackTrace (limited to level 20) : => File "flex-wARP-src-261/CArc.py", line 79, in checkAndProcess => File "flex-wARP-src-261/CDecision.py", line 419, in checkAndProcess If I reset the identity of the atoms (DUM) ERROR Exception class : 'ValueError' Message : '' BackTrace (limited to level 20) : => File "flex-wARP-src-261/CArc.py", line 79, in checkAndProcess => File "flex-wARP-src-261/CRefmacController.py", line 43, in checkAndProcess => File "flex-wARP-src-261/CRefmacController.py", line 107, in _parse Can anybody give me a tip? -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.8 (Darwin) iEYEARECAAYFAkh31XcACgkQlz6UVQtc2uwqzwCfZNTK/fBmRyCTq4J/AaI2m8t9 RdgAoOr4/eWvKjlZ3G5rA9NQY/+CPtp1 =lnZr -END PGP SIGNATURE-
[ccp4bb] progrant to calculate error in derived parameters
Dear colleagues, Is there a program to calculate error in bond ables or other angles between coordinates from Luzzati error? Thanks. Mike
[ccp4bb] Version 1.21 of the Crystallography and NMR System (CNS)
CNS 1.21 is now available. A particular highlight is automatic
dimensioning
of torsion angle dynamics arrays (e.g., MAXTREE), so no user
intervention
is needed anymore. There are many bug fixes in source code, modules,
and input files.
I would like to thank Joe Krahn, Ben Eisenbraun, and many others for
helpful
comments, bug reports, and extensive testing of the new version.
==
Announcing version 1.21 (general release) of the software:
Crystallography & NMR System (CNS)
(copyright 1997-2008, Yale University)
==
Information about the software and instructions for downloading
the most recent version are available at:
**
http://cns-online.org
**
The software is available for download, free-of-charge, by all
academic (non-profit) users.
--
Installation instructions and documentation can be found in:
$CNS_SOLVE/doc/html/cns_solve.html
once you have downloaded and installed the software.
--
Please cite the following references for CNS in
publications:
1. Brunger, A.T., Adams, P.D., Clore, G.M., Delano, W.L., Gros, P.,
Grosse-Kunstleve, R.W., Jiang, J.-S., Kuszewski, J., Nilges, M.,
Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T., Warren, G.L.
Crystallography & NMR system: A new software system for
macromolecular structure determination,
Acta Cryst. D54, 905-921 (1998).
2. Brunger, A.T. Version 1.2 of the Crystallography and NMR System.
Nature Protocols 2, 2728-2733 (2007).
Please cite additional original papers when using specific
methods.
--
Do not distribute CNS to third parties without approval. By
downloading the software you agree to the License in the FTP
directory.
--
While this new version is compatible with version 1.2 input files it
is highly recommended that you use the new input files and
modules in conjunction this new version of CNS. The http://cns-online.org
website is now pointing to the new 1.21 version by default.
--
Attached release notes for CNS version 1.21:
===
=
= Crystallography & NMR System
=
= A.T.Brunger, P.D.Adams, G.M.Clore, W.L.Delano, P.Gros,
= R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges,
= N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warren
=
= Copyright (c) 1997-2008 Yale University
=
===
Program: CNS
Version: 1.21
Patch level: 1
Status: general release
Changes for version 1.21
Program:
- multiple changes to source/ dtorsion_top.f
1 removed disfunctional GROUp option
2 automatic dimensioning for MAXTREE, MAXLEN, MAXCHN
3 automatic dimensioning for MAXBND
4 automatic dimensioning for MAXJNT
5 automatic dimensioning for MAXDIHE
6 removed dysfunctional GROUp option
7 updated helplib/cns-dynamics-torsion-topology
8 old line 2135 -- No close quote at the end:
changed to:
WRITE(6,'(17A)')
@ '%atoms "', SEGID(OUTATM),'-',RESID(OUTATM),'-',
@ RES(OUTATM),'-',TYPE(OUTATM),'" and "',
@ SEGID(JB(JBONDS(CONGRP(THISONE,3-I),J))),'-',
@ RESID(JB(JBONDS(CONGRP(THISONE,3-I),J))),'-',
@ RES(JB(JBONDS(CONGRP(THISONE,3-I),J))),'-',
@ TYPE(JB(JBONDS(CONGRP(THISONE,3-I),J))),'"'
also following statement.
9 old line 3081:redefined IND(3) to INTEGER
10 fixed bug in routine TORMD when the majority of the molecule is
fixed, changed to:
HPIBXCL=ALLHP(INTEG4(2*NBOND))
HPJBXCL=ALLHP(INTEG4(2*NBOND))
...
CALL FREHP(HPJBXCL,INTEG4(2*NBOND))
CALL FREHP(HPIBXCL,INTEG4(2*NBOND))
- source/noe.f and noe.inc: included DEN function (ongoing development)
- modifications in instlib/machine/unsupported/mac-intel-darwin/
machine_f.f:
1 replaced call to INDEX(FILE,' ') with call to TRIMM(FILE,,,).
2 fixed last argument in call to LINSUB in subroutine SYTASK
3 removed leading UNIX pathname in file INQUIRE
- modifications in instlib/machine/unsupported/mac-intel-darwin/
machine_c.c: removed rename_() function.
- copied these machine_f.f and machine_c.c files to
instlib/machine/supported/linux/
instlib/machine/unsupported/intel-x86_64bit-linux/.
instlib/machine/unsupported/intel-itanium-linux
instlib/machine/unsupported/g77-linux
instlib/machine/unsupported/mac-ppc-linux
instlib/machine/unsupported/mac-ppc-darwin
Re: [ccp4bb] From the CNS1.2 trnaslation error
Hi again,
Thank you for your replies. I am jast running CNS translation function to learn
it. Phaser has successfully solved that but I also want to learn how CNS do the
MR.
My protein is a tetramer. I will be highly benifitted if kindly one help me
instructing how to fit the multimers while using CNS MR module.
Thank you all of you
Sincerely Yours
Debajyoti Dutta
On Fri, 11 Jul 2008 Ed Pozharski wrote :
>There is only one map format in CNS, and mapman should open it. Then
>you can convert it to all other formats. Does mapman report some error?
>
>You can rotate/translate molecules with CNS using
>realspace_transform.inp (when you have a question like that it always
>helps to read the list of available scripts). However, what you have in
>mind will not work (if I understand correctly what you have in mind).
>Let's say there is strong peak in self-rotation function and that
>indicates that you have more than one copy in asu and gives you the
>correct rotation to obtain mutual orientation of copies. But you can't
>create a useful model from this because you don't know the translation
>for the copies.
>
>There is, however, the so-called locked rotation function, which takes
>the self-rotation peaks into account. This is not, to my knowledge,
>available in CNS, but you can try AmoRe or glrf. Why do you want to do
>this anyway - is your MR not working? Then try phaser first.
>
>Good luck.
>
>On Fri, 2008-07-11 at 06:31 +, Debajyoti Dutta wrote:
> >
> > Hallow,
> >
> > Thank you for your kind attention. I am using CNS 1.2 to solve my
> > structure with molecular replacement. As a novice CNS user, I was
> > trying to follow the tutorial given at the CNS website. I have a
> > tetramer. I have two queries.
> >
> > 1. There are two maps prepared from the self_rotaion.inp. Those are
> > patterson maps, namely
> > self_rotation_ p1.map and
> > self_rotation_ p2.map
> >
> > I was trying to open those with mapman but probably mapman is more
> > inclined to electron density maps,(may be wrong as I am very new user
> > of these softwares). While trying to convert it into ps file with o2d,
> > pltdev etc I was not successful. I am just inquiring if there is any
> > tool to convert those map files to *.ps file, or can see those map
> > files.
> >
> > 2. Another thing I want to learn if there is any direct way in CNS
> > (such as feeding the self_rotation_list or self_rotation_ matrix to)
> > to automatically find out all the different chains present in an
> > asymmetric unit and prepare the model (with all chains). Because
> > from the CNS tutorial I follow the way to fit my search model into my
> > data.hkl as a dimer but It is a tertamer. Then after fitting the dimer
> > I follow the same way { translation. inp --> merge_structure. inp -->
> > shift_molecules. inp} to fit the next monomer into the dimer but
> > unfortunately it is failing at the stage of merge molecules as
> > trimer.The coordinates assigned, which seems totally rubbish
> >
> > ATOM 1 CB ALA 1.000. 000.000 1.00 0.00 A
> > etc...
> > (omitted the total chain: all are same coordinates and occupancy and B
> > factor)
> > and for B chain
> >
> > ATOM 2555 CB ALA 1.000. 000.000 1.00 0.00 B
> > etc...
> > (omitted the total chain: all are same coordinates and occupancy and B
> > factor)
> > and for C chain
> >
> > ATOM 5109 CB ALA1 32.637 74.346 146.854 1.00 20.00
> > C etc..
> > (Omitted the total chain: all are taking a reasonable values)
> >
> > Will you please help me with these problems. Thank you very much for
> > your attention and suggestions in advance.
> >
> > Your Sincerely
> > Debajyoti Dutta
> >
> >
> >
> >
> >
> > Rediff Shopping
>--
>Edwin Pozharski, PhD, Assistant Professor
>University of Maryland, Baltimore
>--
>When the Way is forgotten duty and justice appear;
>Then knowledge and wisdom are born along with hypocrisy.
>When harmonious relationships dissolve then respect and devotion arise;
>When a nation falls to chaos then loyalty and patriotism are born.
>-- / Lao Tse /
>
>
>
[ccp4bb] PhD fellowship in structural biology at Department of Medicinal Chemistry, University of Copenhagen
For more information please follow link and look at the project number 11: http://www.farma.ku.dk/index.php?id=5587 information on research group: www.farma.ku.dk/br Professor Michael Gajhede Biostructural research Department of Medicinal Chemistry University of Copenhagen +45 35336407
Re: [ccp4bb] pdbset bug - seqres record
> It seems to me that posting in ccp4bb is one of the correct ways to > report a problem. Am I wrong? The other option is to send it to > [EMAIL PROTECTED], but I assume that this address is subscribed to ccp4bb > anyway. > > Ed. Herewith the official line: The correct way of reporting problems is to send to [EMAIL PROTECTED] or [EMAIL PROTECTED] (these are aliases of each other) which goes to the developers at Daresbury. We have a rota set up to deal with these. Of course, we are also subscribed ourselves to ccp4bb, but given the deluge of emails coming in, it may or may not get dealt with. You can also bypass the official system by emailing individuals directly. That should work provided we are a) not on holiday, b) not in a meeting and c) sitting waiting for emails and not doing anything else. Cheers ;-) Martyn -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: [EMAIL PROTECTED] * * Fax: +44 1925 603825Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***
Re: [ccp4bb] pdbset bug - seqres record
Pete,
I don't think so. The pdbset output does not match the SEQRES
definition in PDB format version 2.3 and I didn't find any changes in
the upstream versions. Plus, the pdbset output does not match the
SEQRES record in the pdb-file downloaded from PDB, and it's unlikely
that format was changed without applying those changes to files in the
database.
It seems to me that posting in ccp4bb is one of the correct ways to
report a problem. Am I wrong? The other option is to send it to
[EMAIL PROTECTED], but I assume that this address is subscribed to ccp4bb
anyway.
Ed.
On Thu, 2008-07-10 at 14:42 -0700, Dunten, Pete W. wrote:
> Is this just a consequence of old/new conventions for the SEQRES records?
> If so, send a feature request to ccp4, asking for an option to be added to
> pdbset.
>
> Pete
>
> -Original Message-
> From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Ed Pozharski
> Sent: Thursday, July 10, 2008 2:31 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] pdbset bug - seqres record
>
> There is a bug in pdbset: when you output a sequence (using "SEQU PDB"), the
> residue names are shifted to the left by one position. Here is how it looks
> like:
>
> In PDB-file downloaded from the PDB:
> SEQRES 5 A 171 ALA THR CYS ...
> PDBSET output:
> SEQRES 5 A 171 ALA THR CYS ...
>
>
> I looked in the fortran code (CCP4 6.0.2) and it appears that this line:
>
> 6601 format ('SEQRES',i4,1x,a1,1x,i4,1x,13a4)
>
> should be corrected like this
>
> 6601 format ('SEQRES',i4,1x,a1,1x,i4,2x,13a4)
>
> I stumbled upon this when trying to insert SEQRES records into a pdb-file for
> processing in hydropro. Don't know if it's important anywhere else, but
> hydropro can't read the sequence if it's shifted.
>
> --
> Ed Pozharski <[EMAIL PROTECTED]>
> University of Maryland - Baltimore
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
-- / Lao Tse /
[ccp4bb] REMINDER: Ninth International School on the Crystallography of Biological Macromolecules
*** ONLY TWO WEEKS TO GO! *** There are only two weeks left to register for the Ninth International School on the Crystallography of Biological Macromolecules Como (Italy), 29th September – 3rd October 2008. The School is one of the premier forums i Europe for dissemination of developments in macromolecular crystallography methodology. For more details and to register, please visit the web page: www.crystallographyschool.org DEADLINES Registration: 24th July Accommodation: 25th July Abstracts: 28th August PRELIMINARY PROGRAMME AND REGISTRATION The meeting will last from after lunch (not provided) on Monday September 29th, 2008, to after lunch (provided) on Friday October 3rd. A strictly limited number of Ph.D. students will be eligible for financial support. Those wishing to apply for such subsidy should submit a short CV and motivation at the time of application. Poster and oral presentation abstracts should also be submitted before 28th August for inclusion in the abstract book. PURPOSE AND ORGANIZATION OF THE SCHOOL The school will be open to a maximum of 200 participants and will focus on the application of X-ray crystallographic methods to the study of proteins and nucleic acids, with emphasis on the latest developments. The program will include lectures on protein expression and purification, crystallization, data collection and processing, synchrotrons, phasing (MAD/SAD and molecular replacement), phase improvement, model building, refinement, analysis and validation of structural data. These methods sections will be complemented with seminars about new structures. Several contributions will come from participants who are encouraged to propose a title for a poster or oral contribution in their application. LOCATION The school will be held at Società del Casino, Como, Italy. (http://www.societadelcasino.com/ ), which is located literally in the centre of Como, next to the cathedral. Como can be reached comfortably by train (30-40 min. from Milan; 3-4 hours from Zurich and Basel) or by car via the A9-E36 motorway. There will be a conference dinner att Villa Geno (http://www.villageno.it ). INVITED LECTURERS INCLUDE Imre Berger (EMBL Grenoble), Ian Berry (Oxford University), Gleb Bourenkov (EMBL Hamburg), Dominique Bourgeois (ESRF), Florian Brueckner (Gene Center Munich), Marek Brzozowski (York University), Martin Caffrey (University of Limerick), Liz Carpenter (Diamond Light Source), Kevin Cowtan (York University), Zbigniew Dauter (Argonne National Laboratory), Simon Davis (Oxford University), Valeria de Marco (NKI, Amsterdam), Raimund Dutzler (University of Zürich), Hans Eklund (Swedish Agricultural University, Uppsala), Paul Emsley (Oxford University), Robert Esnouf (Oxford University), Stephen Graham (Oxford University), Tim Grüne (Göttingen University), Udo Heinemann (PSF Berlin), Michael Hennig (Hoffmann laRoche), Rod Hubbard (Versalis), Mariusz Jaskolski (Adam Mickiewicz University, Poznan), Wolfgang Kabsch (MPI Heidelberg), Claude Lecomte (Université Henri Poincaré, Nancy), Andrew Leslie (MRC LMB, Cambridge), Joseph Luft (Hauptmann- Woodward Institute, Buffalo), Natalia Markova (iNovacia, Stockholm), Garib Murshudov (York University), Frank Niesen (SGC Oxford), Poul Nissen (Århus University), Martin Noble (Oxford University), Santosh Panjikar (EMBL Hamburg), Navraj Pannu (Leiden University), Chris Phillips (Pfizer), Simon Phillips (Leeds University), Randy Read (Cambridge University), Marc Ruff (IGBMC, Strasbourg), Elisabeth Sauer- Eriksson (Umeå University), Gebhard Schertler (MRC LMB, Cambridge), Clemens Schulze-Briese (SLS, Villigen), Irmgard Sinning (Heidelberg University), Bente Vestergaard (Copenhagen University), Gert Vriend (Nijmegen University), Martin Walsh (MRC France, ESRF), Martyn Winn (STFC Daresbury Lab), Peter Zwart (Lawrence Berkeley Laboratory)
[ccp4bb] PhD Student Position in Structural Biology
PhD student position in structural biology A PhD student position in structural biology is open and presently available at the University of Hamburg, Institute of Biochemistry and Molecular Biology. The research project in which the candidate will be integrated is in collaboration with a research group from the Center for Structural Genomics of the University of Sao Jose de Rio Preto, Brazil. It is entitled “Applied snake venom proteomics/Venomics” and funded by the GermanResearch Foundation (DFG). The main goal of this project is to determine the proteomic compositions of selected snake, insect and spider venoms and the structural and functional characterization of the novel proteins. The project will be important for the production of specific antivenoms with increased efficacy and development of novel drugs for the therapy of cardiovascular diseases, stroke, arthritis and allergy. The activities of the successful candidate will include isolation and purification or cloning and expression of novel proteins from snake and insect venoms, crystallization and X-ray structure analysis to high resolution. The position would be ideal for applicants having a diploma or master's degree in biochemistry, chemistry, biophysics. A good understanding of protein biochemistry and molecular biology is supportive and a strong interest in protein crystallography is a plus. The hosting laboratory of the University is on the DESY Campus. Letters of application including a CV, and 1-2 references should be sent by e-mail to: [EMAIL PROTECTED] or as hardcopy to the address below. In case further information is required, contact the same e-mail address. Prof. Ch. Betzel Universityof Hamburg Instituteof Biochemistryand Molecularbiology Laboratory for Structural Biology of Infection and Inflammation c/o DESY, Build. 22a Notkestr. 85 22603 Hamburg Dr. Dessi Georgieva Laboratorium für Strukturbiologie von Infektion und Entzündung DESY; Geb. 22a Notkestrasse 85 22607 Hamburg, GERMANY Tel.: +49-40-8998-4749 Fax: +49-40-8998-4747 __ Gesendet von Yahoo! Mail. Dem pfiffigeren Posteingang. http://de.overview.mail.yahoo.com
Re: [ccp4bb] Anion binding sites in proteins
Dear Albert, please have a look at dx.doi.org/10.1007/s11010-008-9826-1 Good luck! Karsten --- Dr. Karsten Niefind Institute of Biochemistry Department of Chemistry University of Cologne Zuelpicher Strasse 47 D-50674 Cologne tel.: +49/221/470-6444 fax: +49/221/470-5092
