Re: [ccp4bb] : Crystallographic Programs on AMD computers

Edward A. Berry wrote: Kay Diederichs wrote: the CPU (AMD versus Intel) does not play any role for crystallographic computing, but you'll have to decide whether you want to install the 64bit or the 32bit version of RHEL4. 32bit programs run a bit faster on a 64bit operating system, and with

Re: [ccp4bb] oxidised cys

A possible modification for cysteine that adds extra density is S-(dimethylarsenic) cysteine (CAS). Requires DTT and cacodylate buffer conditions however. And does not crosslink so far as I know. Has been seen in a number of structures from cacodylate conditions - eg. one of the Xrcc4 struc

Re: [ccp4bb] Unusual Difference Fourier near Methionines

When I experienced strong difference density near methionines, It could be explained by an alternative conformation of the residue... greetings, david Original-Nachricht Datum: Fri, 13 Apr 2007 09:51:09 - Von: Ethayathulla Abdulsamath <[EMAIL PROTECTED]> An: [EMAIL PROTECT

Re: [ccp4bb] Additive screens

Some comments on Hampton additive screen for CCP4 BB: We use the Hampton 96-condition additive screen routinely with our nanolitre dispensing robots (Cartesian 8-channel microsys) and often find it gives an improvement in crystal quality. We get it as the individual tubes because to make best us

Re: [ccp4bb] Unusual Difference Fourier near Methionines

Dear Ethayathulla , did you solve the structure by SeMet MAD or some other way? Sometimes you get strange densities around the ends of methionine side chains (around the S/Se) when switching from SeMet data to native. Cheers Ed __ T.Edwards Ph.D. Astbury Centre for Structural

Re: [ccp4bb] Unusual Difference Fourier near Methionines

This appears to be a symmetry threefold axis. These areas are notoriously prone to have density artefacts. Also it looks like your terminal carbons are pointing in the opposite way, and the entire end of Met is slightly shifted as a result. You may never be able to fit this area to your satisfactio

Re: [ccp4bb] Unusual Difference Fourier near Methionines

I think the SD-CE is pointing the wrong way. And they look much too close. I would rotate them and re-refine Eleanor PS - any noise on the 3 fold axis will be multiplied by a factor of 3 Ethayathulla Abdulsamath wrote: Dear all I am doing one structure at 2.6A resolution where I found unu

Re: [ccp4bb] oxidised cys

Dear John I think this is a thiol-specific reaction - where it has happened to Cys residues the Met residues appear normal. I wondered if anyone had ever used this on purpose as a heavy atom derivative. Arsenic has quite a good anomalous signal too I think. All the best

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Re: [ccp4bb] oxidised cys

It worked well for me, on the selenium edge. Back-soaking out the remaining cacodylate was necessary to find the sites. Choe's group have used this fruitfully: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=pubmed&term=greenwald+butler+choe&tool=fuzzy&ot=Greenwald+Bultler+Choe Meign

[ccp4bb] Groundhog Day syndrome?

We've seem to be experiencing the 'Groundhog Day' syndrome again, and no I didn't hit 'Send' accidentally! -- Ian > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Ian Tickle > Sent: 10 April 2007 11:21 > To: [EMAIL PROTECTED] > Subject: Re: [ccp4bb]

Re: [ccp4bb] Unusual Difference Fourier near Methionines

Dear Dr. Thomas It's not SAD/MAD data I have solved it using molrep only. I will try alternate positions for met and see the density again. Thanx to all for valuable suggestions Ethayathulla   On Fri, 13 Apr 2007 Thomas Edwards wrote : > >Dear Ethayathulla , > >did you solve the structure b

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[ccp4bb] Twin refinement with SHELXL

Dear All, I have 1.4 A data and a molecular replacement solution for a crystal indexed as C2, with beta approximately equal to 90. Refinement with refmac is progressing poorly, and intensity statistics (Truncate) and other twinning tests (xtriage) suggest pseudo-merohedral twinning with a twin f

[ccp4bb] Re-calculating polar/apolar ASA at the interface

Hi all, Another solution to calculate the polar vs. non-polar portions of the ASA at the interface is, as suggested by Susan Crennel, to use the server: http://www.biochem.ucl.ac.uk/bsm/PP/server/ (actually before posting my question I tried that server which I used before, but I received