Re: ccp4bb on new site

2007-01-22 Thread Kolstoe S.E.
In which case is this new server the best place to host the list? Simon -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Kjeldgaard Morten Sent: 22 January 2007 07:30 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: ccp4bb on new site Unfortunately, It appears

[ccp4bb] LIMS

2007-01-26 Thread Kolstoe S.E.
Dear all, Does anyone have any suggestions about the best LIMS software to use for keeping track of a project that is generating quite a few structures? Is the CCP4 one available yet? Simon -- Dr. Simon Kolstoe, Research Fellow School of Biological Sci

Re: [ccp4bb] Removal of cold gas layer for cryocooling

2007-02-01 Thread Kolstoe S.E.
I've used a home-made guillotine type contraption to accelerate crystals through the gas layer and into the liquid N2. A bit disconcerting when you watch your crystal plunge rapidly into your cryo-dish but it works well. Alternatively plunging into liquid ethane works better for flash freezing a

Re: [ccp4bb] MTZ to Shel-X?

2007-03-01 Thread Kolstoe S.E.
Yes I have always been annoyed by that. I tend to use sftools to trim and then rename the columns I want followed by mtz2various with something along the lines of "labin FP=F SIGFP=SIGF FREE=FreeR" and then finally edit the resulting text file to remove the header and all the "FREE"'s as you did. I

[ccp4bb] Refmac and B factors

2007-05-09 Thread Kolstoe S.E.
Dear all, I have a structure at fairly low resolution that I am trying to refine with Refmac. I do not want to refine B factors so have arbitrarily set them all to 20 and then run refmac in the ccp4i GUI after deselecting the "refine temperature factors" box. However, when I look at the resultin

Re: [ccp4bb] Refmac and B factors

2007-05-10 Thread Kolstoe S.E.
@jiscmail.ac.uk/msg01224.html Good luck, Eva 2007/5/9, Kolstoe S.E. <[EMAIL PROTECTED]>: Dear all, I have a structure at fairly low resolution that I am trying to refine with Refmac. I do not want to refine B factors so have arbitrarily set them a

Re: [ccp4bb] CCP4 GUI

2007-05-10 Thread Kolstoe S.E.
The most useful aspect of the ccp4i GUI is its automatic generation of com files. However, I would prefer the GUI to output a .com file into my working directory (rather than the obscure location they are saved to now) every time I run a program so that I can then tinker with it and add any extra k

[ccp4bb] Low resolution model building

2007-05-12 Thread Kolstoe S.E.
Dear ccp4bb, I am about to start model building a fairly low resolution structure (3A) with ten identical monomers in the asu, solved using MR. What I am thinking of doing is to build one monomer using some form of averaged NCS map, replicate and translate my one built monomer into the other ni

[ccp4bb] Google sketchup

2007-06-07 Thread Kolstoe S.E.
Has anyone tried to model crystal symmetry using google sketchup yet? I was about to have a go but thought that others might have got there first... if so has anyone done P6422? Simon

[ccp4bb] Squashed density

2007-06-27 Thread Kolstoe S.E.
Dear CCP4 message board, I am having a problem with electron density that looks as if it has been compressed along the Y axis. Density that would appear as a sphere looks like an ellipsoid, and the effect seems worse in some regions (typically where I am having problems building in a flexible loo

[ccp4bb] mr query

2007-08-08 Thread Kolstoe S.E.
Dear ccp4bb, In searching for a mr solution I ran both phaser and molrep, with both programs finding nice solutions in P21212 (cell 81.083 104.435 109.732 90.00 90.00 90.00, resolution 2.65A). For various reasons I refined the phaser and molrep solutions separately, and both behaved in exactl

Re: [ccp4bb] mr query

2007-08-09 Thread Kolstoe S.E.
lattice translation). However if you have only 1 mol/a.u. then this doesn't help - in which case I'm as baffled as you, sorry! Cheers -- Ian > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Kolstoe S.E. > Sent: 08 August 2007 16