Re: [ccp4bb] Requesting old data sets
Hi Jürgen, I'd be willing to share my datasets obtained since 1999, which I have online. Older ones are on tape and it would be a significant effort to retrieve them, if at all possible. best, Kay
Re: [ccp4bb] SCALA keywords for merging Scalepack (no merge original index) data ?
Hi Phil, Usually with something like this I use: Data line--- bins 20 Data line--- resolution 2.80 Data line--- run 1 batch 1 to 900 Data line--- resolution run 1 high 2.80 Data line--- name run 1 project AUTOMATIC crystal DEFAULT dataset SAD Data line--- scales constant Data line--- exclude sdmin 2.0 Data line--- sdcorrection fixsdb noadjust norefine both 1.0 0.0 Data line--- anomalous on This was from xia2 merging data from XDS / XSCALE, but it should work. The sdcorrection card is to stop Scala adjusting the errors further. Best wishes, Graeme On 3 July 2012 16:43, Phil Jeffrey pjeff...@princeton.edu wrote: I'm not exactly a Scala veteran so am looking for advice as to what would be the best way to run Scala in the following scenario: * data integrated with Denzo * data scaled with Scalepack and output with NO MERGE ORIGINAL INDEX * .sca data imported into MTZ via Pointless Do I just use the SCALA keywords: run 1 all onlymerge anomalous off or would there be a better set of commands ? I've toyed with: sdcorrection norefine scales constant bfactor off reject merge 4 anomalous off which produces similar results. no merge original index data is already scaled and Lp-corrected so I want to avoid applying things twice. Thanks Phil Jeffrey Princeton
Re: [ccp4bb] getting larger protein crystals
Crushing the crustal in mother liquor and serial dilution and seeding may help in size improvement. On Wed, Jul 4, 2012 at 3:03 PM, REX PALMER rex.pal...@btinternet.comwrote: Does anyone have any new tips/methods for improving crystal size once the initial conditions have been established? Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com -- B. Anuradha Research scholar, CAS in crystallography and Biophysics, University of Madras.
[ccp4bb] hallo every body
hallo every body, i face problem with protein when i make gel filtration or concentrate my protein . i notice sever aggregation . i use only glycerol as additives to 50 mM TRIS and 150 mM NaCL ; PH 8 . my IP is 7.8 . any suggestions. best regards Amr
Re: [ccp4bb] hallo every body
check this article its quite useful http://www.ncbi.nlm.nih.gov/pubmed/12711344 On Wed, Jul 4, 2012 at 4:09 PM, amro selem amro_selem2...@yahoo.com wrote: hallo every body, i face problem with protein when i make gel filtration or concentrate my protein . i notice sever aggregation . i use only glycerol as additives to 50 mM TRIS and 150 mM NaCL ; PH 8 . my IP is 7.8 . any suggestions. best regards Amr -- B. Anuradha Research scholar, CAS in crystallography and Biophysics, University of Madras.
Re: [ccp4bb] SCALA keywords for merging Scalepack (no merge original index) data ?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Phil, why do you want to use scala to merge the data? I think the default output from scalepack is already merged, so by avoiding scala altogether you would also avoid making extra mistakes. Unless you want certain statistics or graphs from scala output. scalepack2mtz from ccp4i is usually my program of choice to convert sca-format to mtz and works really well. Cheers, Tim On 07/03/12 17:43, Phil Jeffrey wrote: I'm not exactly a Scala veteran so am looking for advice as to what would be the best way to run Scala in the following scenario: * data integrated with Denzo * data scaled with Scalepack and output with NO MERGE ORIGINAL INDEX * .sca data imported into MTZ via Pointless Do I just use the SCALA keywords: run 1 all onlymerge anomalous off or would there be a better set of commands ? I've toyed with: sdcorrection norefine scales constant bfactor off reject merge 4 anomalous off which produces similar results. no merge original index data is already scaled and Lp-corrected so I want to avoid applying things twice. Thanks Phil Jeffrey Princeton - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFP9C1TUxlJ7aRr7hoRAsdCAJoCD4NckLZcOE1KQtzLCDFiRnZhmACgmgmh uB2+ClJ56W0StsLRBi7fIEs= =m8p9 -END PGP SIGNATURE-
Re: [ccp4bb] getting larger protein crystals
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Rex, - - macroseeding - - microseeding - - further concentration by addition of precipitant to the reservoir - - changing crystallisation technique (hanging vs. sitting drops, crystallisation through membrane, batch crystallisation...) - - variation of protein concentration - - add an extra purification step before setting up crystals - - vary temperature . there is loads, depending on what you mean by 'establised'! Best Tim On 07/04/12 11:33, REX PALMER wrote: Does anyone have any new tips/methods for improving crystal size once the initial conditions have been established? Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFP9C5RUxlJ7aRr7hoRAiIYAKCmyqMa7m0scuzAm+RbzVxnSHh2wgCg+5c0 J19qlIQWz/h38HBqtjzGXcA= =A53z -END PGP SIGNATURE-
[ccp4bb] information received through the AFC: iycr2014
Dear colleagues, Information just received here through the AFC channels: the UN general assembly has declared that 2014 will be the international year of crystallography. Their statement (in French) as an attachment (sorry about including an attachment). F. Vellieux IYCr-FR.pdf Description: Adobe PDF document
Re: [ccp4bb] information received through the AFC: iycr2014
Et alors, what will this mean for us? Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Vellieux Frederic [frederic.velli...@ibs.fr] Sent: Wednesday, July 04, 2012 2:50 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] information received through the AFC: iycr2014 Dear colleagues, Information just received here through the AFC channels: the UN general assembly has declared that 2014 will be the international year of crystallography. Their statement (in French) as an attachment (sorry about including an attachment). F. Vellieux
Re: [ccp4bb] information received through the AFC: iycr2014
Seems that toothpaste (if my translation of 'dentifrice' is correct) figures high on the agenda! -- Ian On 4 July 2012 13:01, Boaz Shaanan bshaa...@exchange.bgu.ac.il wrote: Et alors, what will this mean for us? Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Vellieux Frederic [frederic.velli...@ibs.fr] Sent: Wednesday, July 04, 2012 2:50 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] information received through the AFC: iycr2014 Dear colleagues, Information just received here through the AFC channels: the UN general assembly has declared that 2014 will be the international year of crystallography. Their statement (in French) as an attachment (sorry about including an attachment). F. Vellieux
Re: [ccp4bb] information received through the AFC: iycr2014
The press release in English: http://www.un.org/News/Press/docs/2012/ga11262.doc.htm Boaz: perhaps the crystallography congresses and events taking place in 2014 will be attended by UN peacekeeping force members as well (with their blue helmets) ? F.V. Boaz Shaanan wrote: Et alors, what will this mean for us? Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710
Re: [ccp4bb] information received through the AFC: iycr2014
English version: http://www.un.org/ga/search/view_doc.asp?symbol=A/66/L.51 David On 07/04/2012 01:50 PM, Vellieux Frederic wrote: Dear colleagues, Information just received here through the AFC channels: the UN general assembly has declared that 2014 will be the international year of crystallography. Their statement (in French) as an attachment (sorry about including an attachment). F. Vellieux
Re: [ccp4bb] information received through the AFC: iycr2014
And perhaps all crystallographers will have to wear those blue hats during conferences or even during data collection sessions at syncrhotrons. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Vellieux Frederic [frederic.velli...@ibs.fr] Sent: Wednesday, July 04, 2012 3:03 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] information received through the AFC: iycr2014 The press release in English: http://www.un.org/News/Press/docs/2012/ga11262.doc.htm Boaz: perhaps the crystallography congresses and events taking place in 2014 will be attended by UN peacekeeping force members as well (with their blue helmets) ? F.V. Boaz Shaanan wrote: Et alors, what will this mean for us? Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710
Re: [ccp4bb] information received through the AFC: iycr2014
On 07/04/12 08:03, Vellieux Frederic wrote: The press release in English: http://www.un.org/News/Press/docs/2012/ga11262.doc.htm Boaz: perhaps the crystallography congresses and events taking place in 2014 will be attended by UN peacekeeping force members as well (with their blue helmets) ? Powder blue, one might say. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] information received through the AFC: iycr2014
Do you mean we should crush the helmets and solve the structure of the resulting powder blue coloured powder by crystallographic methods ? Sounds like a good proposal to be put forward to the UN to help them get rid of their used helmets ! David Schuller wrote: On 07/04/12 08:03, Vellieux Frederic wrote: The press release in English: http://www.un.org/News/Press/docs/2012/ga11262.doc.htm Boaz: perhaps the crystallography congresses and events taking place in 2014 will be attended by UN peacekeeping force members as well (with their blue helmets) ? Powder blue, one might say.
Re: [ccp4bb] SCALA keywords for merging Scalepack (no merge original index) data ?
Hi Tim, While I use Scalepack2mtz (not from the gui) all the time, Scalepack has the unfortunate feature that once Rsym 1.0 it gets reported as 0.0. Now that I'm exploring higher resolution limits along the lines of the recent Karplus and Diederichs paper (Science Vol. 336, pp. 1030-33 (2012)) I actually want a real number for this. Additionally: Scala reports Rmeas and Rpim but Scalepack does not Scala reports CC_IMEAN which I see from Materials and Methods in the Karplus Diederichs paper is the same as CC1/2. Since I do intend on exploiting data for which Rsym 1, at least for this quite redundant F432 dataset I'm working with, I think these extra statistics are very useful. Thanks Phil From: Tim Gruene [t...@shelx.uni-ac.gwdg.de] Hi Phil, why do you want to use scala to merge the data?
Re: [ccp4bb] SCALA keywords for merging Scalepack (no merge original index) data ?
I use the GUI with most of the defaults , and just ask for SCALES constant And anomalous on of course but that is by default in SCALA .. Eleanor On 3 Jul 2012, at 16:43, Phil Jeffrey wrote: I'm not exactly a Scala veteran so am looking for advice as to what would be the best way to run Scala in the following scenario: * data integrated with Denzo * data scaled with Scalepack and output with NO MERGE ORIGINAL INDEX * .sca data imported into MTZ via Pointless Do I just use the SCALA keywords: run 1 all onlymerge anomalous off or would there be a better set of commands ? I've toyed with: sdcorrection norefine scales constant bfactor off reject merge 4 anomalous off which produces similar results. no merge original index data is already scaled and Lp-corrected so I want to avoid applying things twice. Thanks Phil Jeffrey Princeton
Re: [ccp4bb] getting larger protein crystals
Rex,
\begin{shameless self-advertizing}
Once upon a time we did a systematic study how to optimize crystal size. The
study was done with knowledge of the protein solubility (which is not normally
available, of course) and we showed that you can still do it when you do not
have this information.
Perhaps worth reading. The paper does not end with a shocking conclusion, but
more or less with if you do a systematic study, you can improve crystal
volume.
http://www.springerlink.com/content/16133650m43x013g/?MUD=MP
\end{shamelss self-advertizing}
Mark
-Original Message-
From: REX PALMER rex.pal...@btinternet.com
To: CCP4BB CCP4BB@JISCMAIL.AC.UK
Sent: Wed, Jul 4, 2012 3:55 am
Subject: [ccp4bb] getting larger protein crystals
Does anyone have any new tips/methods for improving crystal size once the
initial conditions have been established?
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
