Re: [ccp4bb] packing test PHASER

2014-06-17 Thread Randy Read
I agree that looking at the packing is a good idea, but I also agree that having the wrong space group is a likely possible explanation. That’s the most common scenario when there are many clashing solutions with high TFZ scores. Randy Read On 17 Jun 2014, at 15:52, Roger Rowlett wrote: > In

Re: [ccp4bb] packing test PHASER

2014-06-17 Thread Ed Pozharski
/2014 10:52 AM (GMT-05:00) To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] packing test PHASER Increase the number of allowed clashes in Phaser, re-run it then look at the packing of the solution found and identify the source of the clashes. Possibilities for the clash issue include: Wrong

Re: [ccp4bb] packing test PHASER

2014-06-17 Thread Roger Rowlett
Increase the number of allowed clashes in Phaser, re-run it then look at the packing of the solution found and identify the source of the clashes. Possibilities for the clash issue include: 1. Wrong space group 2. Flexible loops or termini in search model not present or differently arranged

[ccp4bb] packing test PHASER

2014-06-17 Thread Almudena Ponce Salvatierra
Dear ccp4 users, I get the following message from Phaser when I do a molecular replacement with two ensembles. One of the ensembles is placed but the second one is not placed, and then it says this: Solutions with Z-scores greater than 13.0 (the threshold indicating a definite solution) were rej

[ccp4bb] packing diagrammes

2009-08-27 Thread Anita Lewit-Bentley
Dear all, thanks to everybody who offered their experience and hints. The most convenient way of preparing a packing diagramme, at least for me, was via PyMol as suggested by Michael Klein (see below). One can do something similar with the CCP4 graphics package, but for some reason the pro

Re: [ccp4bb] packing diagrammes

2009-08-26 Thread Phoebe Rice
I'd use MAMA to make an extremely simplified mask (either based on a couple of nicely-positioned spheres, or excessively smoothed) and they display it with its symmetry mates. Original message >Date: Wed, 26 Aug 2009 11:48:57 +0200 >From: Anita Lewit-Bentley >Su

Re: [ccp4bb] packing diagrammes

2009-08-26 Thread Jack Tanner
The cns script neighbours.inp might be useful for this purpose. From: AntonioLeung Reply-To: AntonioLeung Date: Wed, 26 Aug 2009 21:46:26 +0800 To: Subject: Re: [ccp4bb] packing diagrammes Hi, Pymol may do this work, use"Action-->generate-->symmetry mates" ---

Re: [ccp4bb] packing diagrammes

2009-08-26 Thread AntonioLeung
Hi, Pymol may do this work, use"Action-->generate-->symmetry mates" -- Original -- From: "Anita Lewit-Bentley"; Date: Wed, Aug 26, 2009 05:48 PM To: "CCP4BB"; Subject: [ccp4bb] packing diagrammes

[ccp4bb] packing diagrammes

2009-08-26 Thread Anita Lewit-Bentley
Dear all, does anyone know of a programme that would allow the graphical representation of the packing of protein molecules in a crystal? Ideally one would like to represent the protein as an elipsoid (or similar relatively simple shape) corresponding to its volume, over a few unit cells

Re: [ccp4bb] Packing broke for 2nd molecule in phaser?

2008-06-24 Thread Shane Atwell
92121 phone: (858) 228-1622 fax: (858) 457-5362 [EMAIL PROTECTED] -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Shane Atwell Sent: Friday, June 20, 2008 1:21 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Packing broke for 2nd molecule in phaser? I&#

Re: [ccp4bb] Packing broke for 2nd molecule in phaser?

2008-06-20 Thread Shane Atwell
That was "SEARCH ENSEmble mol2 NUM1" at the end. Bad editing. -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Shane Atwell Sent: Friday, June 20, 2008 1:21 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Packing broke for 2nd molecule in ph

[ccp4bb] Packing broke for 2nd molecule in phaser?

2008-06-20 Thread Shane Atwell
I'm attempting a difficult molecular replacement using phaser and low resolution data (3.5A). There's almost certainly only one molecule in the asymmetric unit. Since the entire structure of a homologous multidomain protein doesn't work, I've broken it down in domains and have been attempting to fi

Re: [ccp4bb] packing

2007-06-29 Thread Tassos Papageorgiou
Dear all, Thank you for your replies so far. I feel I should have been more precise in my original question. There is a dimer in the asymmetric unit and we end up with two different dimers after molecular replacement (the monomer-monomer interface is completely different). Each solution refines wi

Re: [ccp4bb] packing

2007-06-29 Thread Wim Burmeister
Tassos Papageorgiou wrote: Dear all, I am looking for examples of different packing arrangements in crystals of the same protein with similar unit cell parameters and space group (eg the protein adopts different packing although the crystals remain the same both in unit cell dimensions and space

[ccp4bb] packing

2007-06-29 Thread Tassos Papageorgiou
Dear all, I am looking for examples of different packing arrangements in crystals of the same protein with similar unit cell parameters and space group (eg the protein adopts different packing although the crystals remain the same both in unit cell dimensions and space group). Can this happen, for