[ccp4bb] Database with protein experimental pKa values, with possibility to search for Cysteines and .pdb structure
Hello all, this might not be the appropriate place, but I was wondering if anyone knows of a database with protein experimental pKa values, with possibility to search for Cysteines and .pdb structures. PINT: Protein-protein Interactions Thermodynamic Database seems to be down. The question arose on the pymol mailing list, and I thought I give it a shot here. Many thanks for any pointers! Best, Thomas
Re: [ccp4bb] Fw: Re: [ccp4bb] Solidarity with Japan
http://japan.person-finder.appspot.com/?lang=en The latest numbers I read is that they have 140,000 records, unfortunately there is no information about TAKENAKA Akio available yet. Best wishes, Thomas On Wed, Mar 16, 2011 at 21:17, Philippe DUMAS p.du...@ibmc-cnrs.unistra.frwrote: Le 16/03/2011 17:59, REX PALMER a écrit : Would it be possible to get information through the CCP4BB about colleagues who do not answer mails ? I'd like to have news about TAKENAKA Akio, Faculty of Pharmacy, Iwaki Meisei University, Tokyo Institute of Technology. Thank you if somebody can transmit the information. Philippe Dumas I was very relieved to learn that my friend and colleague Hideaki Niwa who took his MSc and PhD with me at Birkbeck is safe and well in Japan. I believe that International the Red Cross is doing great work out there and need all the help they can get. You can donate by going to the link below: http://clicks.aweber.com/y/ct/?l=7vf_Vm=1adA9w4Zgg1yh1b=_szL3OnaO1I3NyRX06YTVA Rex Palmer Birkbeck College
Re: [ccp4bb] First images of proteins and viruses caught with an X-ray laser
Thank you for clarifying this James. Those details are indeed often lost/misinterpreted when the paper is discussed in journal club, so your comment was especially helpful. Best wishes, Thomas On Wed, Feb 9, 2011 at 20:38, James Holton jmhol...@lbl.gov wrote: As one of the people involved (I'm author #74 out of 88 on PMID 21293373), I can tell you that about half of the three million snapshots were blank, but we wanted to be honest about the number that were collected, as well as the minimum number that were needed to get a useful data set. The blank images were on purpose, since the nanocrystals were diluted so that there would be relatively few double-hits. As many of you know, multiple lattices crash autoindexing algorithms! Whether or not a blank image or a failed autoindexing run qualifies as conforming to our existing model or not I suppose is a matter of semantics. But yes, I suppose some details do get lost between the actual work and the press release! In case anyone wants to look at the data, it has been deposited in the PDB under 3PCQ, and the detailed processing methods published under PMID: 20389587. -James Holton MAD Scientist On 2/9/2011 10:38 AM, Thomas Juettemann wrote: http://www.nanowerk.com/news/newsid=20045.php http://home.slac.stanford.edu/pressreleases/2011/20110202.htm I think it is pretty exciting, although they only take the few datasets that conform to their existing model: The team combined 10,000 of the three million snapshots they took to come up with a good match for the known molecular structure of Photosystem I.
Re: [ccp4bb] Structures determined: breakdown of methods
Is this: http://www.pdb.org/pdb/statistics/holdings.do what you are looking for? On Sat, Jan 15, 2011 at 21:28, REX PALMER rex.pal...@btinternet.com wrote: Does anyone know of a statistical breakdown of successful protein structure determinations in terms of the method used? Rex Palmer Birkbeck College
Re: [ccp4bb] pdb formats
It trains you to only use files created by MS Windows and complain if you get files that use another standard. As usual, follow the money... On Tue, Dec 14, 2010 at 14:45, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Why, by the way, is the default text editor in windows, notepad, such a lousy text editor? (Sounds like a riddle, I guess, but is really a question...) JPK On Tue, Dec 14, 2010 at 6:02 AM, Ian Tickle ianj...@gmail.com wrote: Rex, as Tim says, the PDB format has always been 1 atom per line. But which program are you using to display the PDB file? Some MS-Win programs (Notepad is one that springs to mind) don't recognise Unix-style line-breaks (i.e. newline char) and display the file as one continuous string. If that's what's happened try displaying the file using a different editor. Cheers -- Ian On Tue, Dec 14, 2010 at 11:34 AM, REX PALMER rex.pal...@btinternet.com wrote: Does anyone know if it is possible to transform the continuous (compacted) pdf format ino the older version where each atom occupies a single line (and vice versa). Rex Palmer Birkbeck College -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Milch and Minor
I certainly did not email it to him! On Mon, Oct 18, 2010 at 19:05, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com wrote: Dear All, my J Appl Cryst collection does not extend far enough to unearth J. Appl. Cryst. (1974). 7, 502-505 [ doi:10.1107/S0021889874010284 ] The indexing of single-crystal X-ray rotation photographs J. R. Milch and T. C. Minor perhaps someone has a pdf and would certainly not email it to me ;-) Many thx, BR - Bernhard Rupp, Hofkristallrat a.D. 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ -- Der einzigartige chillout-mix in der Hofkristall-lounge --
Re: [ccp4bb] Beginning crystallography text
This book worked great for me: http://www.amazon.com/Crystallography-Made-Crystal-Clear-Third/dp/0125870736/ref=sr_1_3?ie=UTF8s=booksqid=1278618216sr=1-3 Cheers, Thomas On Thu, Jul 8, 2010 at 12:35, Peter Hsu hsuu...@u.washington.edu wrote: Hi all, I haven't gotten past the phase of growing the crystal, but I'd certainly still like to learn the actual theories of crystallography. Can anyone recommend a good beginner to mid-level text on macromolecular crystallography? Thanks, Peter
Re: [ccp4bb] How to align a sequence to a know profile
Does chainsaw not the opposite? Pruning a coordinate file based on non-conserved residues identified in a MSA? Yuan has a MSA of known structures and a sequence he wants to add to it. I am always keen to learn about alignment programs, it would be great to know how to use chainsaw for this problem. On Tue, Jun 1, 2010 at 02:20, Eleanor Dodson c...@ysbl.york.ac.uk wrote: chainsaw does just that eleanor 商元 wrote: Hello, everyone, I've a protein sequence of known domain. Based on structure alignment, I've got a alignment of those with known structures. Then how to add my sequence to the alignment?Any suggestions? Regards, Yuan SHANG
Re: [ccp4bb] How to align a sequence to a know profile
Dear Yuan, the MUSCLE program can do that for you. It is capable of doing profile-profile and profile-sequence alignments. http://www.drive5.com/muscle/muscle_userguide3.8.html#_Toc260497021 Section 2.10 of the manual should be what you want. Cheers, Thomas On Mon, May 31, 2010 at 01:46, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear Yuan SHANG, you can use Jalview do create and edit an alignment with your sequence. Jalview is available at http://www.jalview.org/, and I quite liked it when I worked with it. Tim On Mon, May 31, 2010 at 04:29:48PM +0800, 商元 wrote: Hello, everyone, I've a protein sequence of known domain. Based on structure alignment, I've got a alignment of those with known structures. Then how to add my sequence to the alignment?Any suggestions? Regards, Yuan SHANG -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.9 (GNU/Linux) iD8DBQFMA3djUxlJ7aRr7hoRArVqAJsGxH8tcPIzwtzpeGFSB7yNGWLBNACg3wbj 5hpD2QWQG6h3X6ySCViGxDc= =0qUC -END PGP SIGNATURE-
Re: [ccp4bb] Alignment software
Another alignment tool worth to keep an eye on is this one: http://foldit.wikia.com/wiki/Alignment_Tool They are still debugging, but the plan is to release a standalone version after CASP9. Or at least a version that runs in a standalone FoldIt version. On Tue, May 25, 2010 at 15:18, Victor Alves vdal...@fmv.utl.pt wrote: Hi Charlie I am so sorry I assumed development had halted, but I'm glad one of the authors of ALINE has stepped in to restore the truth, and even more that ALINE is still being taken care of. Hopefully those needed funds will materialize, for your sake and also for the benefit of all the scientific community. I will e-mail you some suggestions. Cheers, Victor Alves __ VICTOR DIOGO ALVES, DVM PhD Professor Auxiliar Faculdade de Medicina Veterinária UTL - Lisboa __ -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Charlie Bond Sent: terça-feira, 25 de Maio de 2010 4:48 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Alignment software Hi Victor, Thanks for recommending ALINE. It is not exactly true that development has stopped. It is just glacially slow as funding for such utilities is not easily obtained! Recommendations for improvements (to improve that potential) are well-received and a keen user can write their own plug-ins to achieve new functionality. Cheers, Charlie Victor Alves wrote: Hi Mohd You can also check: ALINE (An Extensible WYSIWYG Protein Sequence Alignment Editor for Publication Quality Figures) http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/ It’s quite nice and has a lot of potential, although unfortunately it seems that development of the software as stopped :-( Cheers Victor Alves *From:* CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] *On Behalf Of *Salameh, Mohd A., Ph.D. *Sent:* sexta-feira, 21 de Maio de 2010 16:11 *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] Alignment software Dear All, I’m trying to prepare an alignment figure of 2 proteins that highlight conserved and similar residues and probably secondary structures; I will greatly appreciate it if anybody can recommend a software that I can use. Thanks, Mohd -- Charlie Bond Professorial Fellow University of Western Australia School of Biomedical, Biomolecular and Chemical Sciences M310 35 Stirling Highway Crawley WA 6009 Australia charles.b...@uwa.edu.au +61 8 6488 4406
Re: [ccp4bb] automise ncont
Many thanks for all answers, it is greatly appreciated.
Best wishes,
Thomas
On Thu, Apr 29, 2010 at 09:50, Ian Tickle ianj...@gmail.com wrote:
On Thu, Apr 29, 2010 at 4:25 PM, Edward A. Berry ber...@upstate.edu wrote:
Command-line param like XYZIN don't seem to be shell variables,
but can be set by variables:
bin/ncont XYZIN $XYZIN eofncont${XYZIN}.log
Actually command line parameters for CCP4 programs are indeed also
shell variables, though they first have to be exported to the
environment so they can be picked up by the program.
So for example:
setenv XYZIN input.pdb
setenv XYZOUT output.pdb
program_name EOF
..
EOF
produces exactly the same result as:
program_name XYZIN input.pdb XYZOUT output.pdb EOF
..
EOF
If the variable is specified both in the environment and on the
command line, then the latter is always used. What happens is that
when say 'XYZIN input.pdb' is read from the command line (or it could
be from anywhere), the function that processes the command line does
an internal 'setenv XYZIN input.pdb' (thus overwriting any previous
setting of XYZIN). Then whenever the value of the XYZIN variable is
needed, say to open a file, the value is read back from the
environment by the file-opening function.
-- Ian
[ccp4bb] automise ncont
Dear all, I am pretty new to the CCP4 suite. I am trying to automise the execution and parsing of ncont. Could someone advise me how (if possible) to pass parameters to the program? I am trying to do something like bin/ncont XYZIN 1FNT_BJ.pdb source /*/B target /*/J maxdist 6.0 and have the output redirected into a file. Thank you for your time! Best wishes, Thomas
