Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0

2011-04-04 Thread Quyen Hoang
This could be my last post ... I am now leaving mercury It's surface was safe and free Meet a mystical gryphon and some alien mosquitos They gave me some protein crystals Which tried to shoot like 007 Missed them all but the heaven Will try again with my new X8 Which 007 would surely hate Now app

Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0

2011-04-01 Thread George T. DeTitta
ty_Alphabetically.php?faculty_id=123 > http://www.rsc.org/shop/books/2008/9780854042722.asp > > > Original message >>Date: Thu, 31 Mar 2011 23:06:47 -0700 >>From: CCP4 bulletin board (on behalf of Ethan Merritt >>) >>Subject: [ccp4bb] Crystallogr

Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0

2011-04-01 Thread Jacob Keller
rsc.org/shop/books/2008/9780854042722.asp > > > Original message >>Date: Thu, 31 Mar 2011 23:06:47 -0700 >>From: CCP4 bulletin board (on behalf of Ethan Merritt >>) >>Subject: [ccp4bb] Crystallographic Breakthrough  -  DarkMatter Version 1.0 >>To:

Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0

2011-04-01 Thread Phoebe Rice
.org/shop/books/2008/9780854042722.asp Original message >Date: Thu, 31 Mar 2011 23:06:47 -0700 >From: CCP4 bulletin board (on behalf of Ethan Merritt >) >Subject: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0 >To: CCP4BB@JISCMAIL.AC.UK > >Hi to

Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0

2011-04-01 Thread Jacob Keller
Well, actually you probably haven't subtracted the "dark R" value from your final R. This and other values are available in a "dark folder" on your hard drive, which is impossible to see/read, but which contains a lot of important information which will make your structure have a much higher impact

Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0

2011-04-01 Thread Quyen Hoang
Will this affect my reprocessing of the data with D*TREK on my journey to XPLORE the planets MERCURY and rPLUTO in my ENDEAVOUR to find and BUSTER some CRYSTALS with my on-board TNT into XPOWDER? I am still trying to GRASP the idea of AUTODOCKing on precise HKL locations based on the SHARP bu

Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0

2011-04-01 Thread Ed Pozharski
Oh, that is where those pesky inhibitors I couldn't find were hiding... On Thu, 2011-03-31 at 23:06 -0700, Ethan Merritt wrote: > Given recent discussion and in particular James Holton's suggestion > that > the problem of disordered sidechains is a problem akin to the > difficulty > of describin

Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0

2011-04-01 Thread Edward A. Berry
Do you have a list of dark-matter-aware PDB refinement programs? Adding dark matter and refining in TNT or Xplor gives me exactly the same R as without. Furthermore the final refined files have lost the dark matter as far as I can see. This leads me to believe these programs are completely ignorin

Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0

2011-04-01 Thread Dirk Kostrewa
Hi Ethan, many thanks for that - your Dark Matter really (en)lightened my day! I wonder, how many pdb records in the future will contain the corresponding remark lines that your incredible perl script produces :-) Best regards, Dirk. Am 01.04.11 08:06, schrieb Ethan Merritt: Hi to all on c

Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0

2011-04-01 Thread Jürgen Bosch
I assume TLS is supported or do we have to wait for version 1.1 ? When will you have a 10.7 (lion) standalone version compiled ? Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Resea

Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0

2011-04-01 Thread Mark J van Raaij
The program appears a bit black-box to me, could you provide more details (today of course). Mark Sent from my HTC - Reply message - From: "Robbie Joosten" Date: Fri, Apr 1, 2011 11:04 Subject: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0 To: Hi Ethan

Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0

2011-04-01 Thread Pedro M. Matias
Well played, Ethan! At 07:06 01-04-2011, Ethan Merritt wrote: Hi to all on ccp4bb: What better day to announce the availability of a breakthrough technique in macromolecular crystallography? Given recent discussion and in particular James Holton's suggestion that the problem of disordered side

Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0

2011-04-01 Thread Pedro M. Matias
Have you noticed the date ? It's April 1! At 10:31 01-04-2011, Frank von Delft wrote: I'm pretty sure Coot has been displaying it all along. In the early days it displayed it much better, I must say, which is why it tended to crash. Maybe the next version of coot as well as pymol/ Raster3D

Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0

2011-04-01 Thread Frank von Delft
I'm pretty sure Coot has been displaying it all along. In the early days it displayed it much better, I must say, which is why it tended to crash. Maybe the next version of coot as well as pymol/ Raster3D could also display virtual particles. This would really flashily push the quality of ou

Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0

2011-04-01 Thread Tim Gruene
Maybe the next version of coot as well as pymol/ Raster3D could also display virtual particles. This would really flashily push the quality of our models, especially on the title pages of the electronic versions of journals. There could even be a special July-14th-mode (http://de.wikipedia.org/w/in

Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0

2011-04-01 Thread Flip Hoedemaeker
Dear Ethan, I would really really like to enhance all my PDB files, but I am concerned I will create a black hole in my hard drive. I hope you can convince me of the safety of your tool, thx Flip On 4/1/2011 8:06, Ethan Merritt wrote: Hi to all on ccp4bb: What better day to announce the av

Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0

2011-04-01 Thread Robbie Joosten
lographic Breakthrough - DarkMatter Version 1.0 > To: CCP4BB@JISCMAIL.AC.UK > > Hi to all on ccp4bb: > > What better day to announce the availability of a breakthrough technique > in macromolecular crystallography? > > Given recent discussion and in particular James Holton&#

[ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0

2011-03-31 Thread Ethan Merritt
Hi to all on ccp4bb: What better day to announce the availability of a breakthrough technique in macromolecular crystallography? Given recent discussion and in particular James Holton's suggestion that the problem of disordered sidechains is a problem akin to the difficulty of describing dark mat