Re: [ccp4bb] Multiple conformations of disulfide-linked cysteines

Thank you for the prompt replies! I was able to resolve the issue by specifying an 'SS' id in the 'LINK' record for the individual conformers. (see Garib's post below) > From: CCP4 bulletin board on behalf of Garib Murshudov > Sent: Mon 3/8/2010 5:21 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re

[ccp4bb] python install issues?

Hi, I'm simultaneously installing ccp4 on a MacBook Pro running Snow Leopard and on a MacPro running Leopard. On both machines, the command: source /sw*/bin/init.csh (where /sw* is either /sw64 on the machine running 10.6, or /sw on the machine running 10.5) gives the error: ***

[ccp4bb] LSQ line fit given a set of atomic coordinates

Dear all, I know this can be done with any statistics program, or even by handbut, just for practical reasons and having to deal with a bunch of pdb's, is there any (CCP4...or eventually other) program containing an embedded feature to calculate the best straight line fitting into a chose

Re: [ccp4bb] Multiple conformations of disulfide-linked cysteines

On Monday 08 March 2010 14:11:00 Jim Fairman wrote: > I have a similar situation so I am also curious for the answer. Refmac will > always try to form a disulfide bond with both conformers for me as well. From the current PDB reference document

Re: [ccp4bb] Multiple conformations of disulfide-linked cysteines

Quoting Andrew Purkiss-Trew : Quoting "Critton, David" : Dear CCP4BB, I am building a protein structure containing a pair of cysteines linked via disulfide bond. This disulfide bond (i.e. the cysteine S-gamma atoms) refines well at 2/3 occupancy, however the electron density suggests th

Re: [ccp4bb] Multiple conformations of disulfide-linked cysteines

Quoting "Critton, David" : Dear CCP4BB, I am building a protein structure containing a pair of cysteines linked via disulfide bond. This disulfide bond (i.e. the cysteine S-gamma atoms) refines well at 2/3 occupancy, however the electron density suggests that these cysteines each adopt a

Re: [ccp4bb] Multiple conformations of disulfide-linked cysteines

Automatically yes. But you can force it to use only one conformation. You need to use link record instead of ssbond (they are essentially same). To do this you need to put link records just before cryst1 card. Examples of link record are in: http://www.ysbl.york.ac.uk/refmac/data/template_l

Re: [ccp4bb] Multiple conformations of disulfide-linked cysteines

The SSBOND record format cannot take alternate id's. However, refmac allows using LINK records (or LINKR in the newer versions) which support alternate id designations with the link id set to "SS" to refine disulfide bonds with alternates. See http://www.ccp4.ac.uk/html/refmac5/files/coordinates

Re: [ccp4bb] Multiple conformations of disulfide-linked cysteines

I have a similar situation so I am also curious for the answer. Refmac will always try to form a disulfide bond with both conformers for me as well. On Mon, Mar 8, 2010 at 4:55 PM, Critton, David wrote: > Dear CCP4BB, > > I am building a protein structure containing a pair of cysteines linked vi

Re: [ccp4bb] Don't understand output of refmac with "tlso addu" option

On Monday 08 March 2010 09:28:15 Ethan Merritt wrote: > I'm trying to come to grips with the recent PDB policy for depositing > files which have the TLS model expanded out into individual ANISOU > records. Up until now I've been using tlsextract/tlsanl to prepare > such files, but now I've just tr

[ccp4bb] Multiple conformations of disulfide-linked cysteines

Dear CCP4BB, I am building a protein structure containing a pair of cysteines linked via disulfide bond. This disulfide bond (i.e. the cysteine S-gamma atoms) refines well at 2/3 occupancy, however the electron density suggests that these cysteines each adopt a second, unlinked conformation (pr

Re: [ccp4bb] crystallization of a macromolecular complex

Hi Jan-- What is the composition of your protein buffer? Thanks! annie Annie Hassell Glaxo Smithkline 5 Moore Drive RTP, NC 27709 919/483-3228 919/483-0368 (FAX) annie.m.hass...@gsk.com "Jan Rash" Sent by: "CCP4 bulletin board" 05-Mar-2010 09:02 Please respond to "Jan Rash" To CCP

[ccp4bb] older version of CCP4 Program Suite vs newer!

Dear All, I wonder if anyone has come across the differences seen between the statistics obtained from scala output files using CCP4 Program Suite 6.0.2 CCP4Interface 1.4.4.2 versus CCP4 Program Suite 6.1.2 CCP4Interface 2.0.5 (which is obviously a more recent version). The reason I ask is that

[ccp4bb] Don't understand output of refmac with "tlso addu" option

I'm trying to come to grips with the recent PDB policy for depositing files which have the TLS model expanded out into individual ANISOU records. Up until now I've been using tlsextract/tlsanl to prepare such files, but now I've just tried using the new refmac option TLSO ADDU and I'm confused. M

[ccp4bb] Setting default PDB viewer to PyMOL in CCP4i

Dear CCP4 developers and all, CCP4i of CCP4 version 6.1.3 can set the default PDB viewer to PyMOL (Default Viewers section in Preferences dialog). I have not noticed this function in previous versions. But viewing PDB file with PyMOL fails. It shows message dialog "ERROR could not start PyMol". S

Re: [ccp4bb] Need help for phasing using Tantalum bromide cluster

Le 06/03/2010 00:52, Dhirendra K Simanshu a écrit : I try answering your question without knowing exactly what has already been sent to CCP4BB. Sorry, if I duplicate previous answers. We have a good practice with bromine as an anomalous scatterer for solving nucleic acids structures. In fact,

[ccp4bb] Head of X-ray service facility

*Ben-Gurion University of the Negev (BGU) and the National Institute for Biotechnology in the Negev (NIBN) are looking for X-ray crystallographer for their macromolecular X-ray crystallography unit.* * * *Job description* The Head of our service macromolecular X-ray crystallography facility, is

Re: [ccp4bb] solve structure by molecular replacement

The best check for what to expect in an asymmetric unit is to run matthews. It works out the volume of your asymmetric unit, the volume your molecule should occupy ( based on mol. wt or number of residues) and indicates whether you could fit one, two and so on molecules into the cells asymmetr

Re: [ccp4bb] anomalous phase extension to native data

I assume the native and Se-met are isomorphous and indexed on the same convention? pOINTLESS will check the indexing convention for you. Then you must use cad to merge the native and the phased data. I am not sure of PHENIX output but you need an mtz file with h k l Fnat etc F-Semet ... PHI FO