Re: [ccp4bb] Peptide Crystallization

2011-05-25 Thread Clayton, Gina Martyn
You could also consider organic solvents (or a mix) for crystallisation trials too. If you scan through the literature you will find that small peptides have in the past been treated as small molecules in terms of crystallization. Once the peptide gets over say 20 amino acids (not the exact

Re: [ccp4bb] glycerol

2011-03-10 Thread Clayton, Gina Martyn
Hi Ray I have seen glycerol at less than 5% in the protein buffer prevent crystal growth completely and when removed from the buffer has resulted in very nice crystal growth of the glycerol free protein. Best Gina From: CCP4 bulletin board on behalf of

[ccp4bb] Myristate

2011-03-02 Thread Clayton, Gina Martyn
Hi there Sort of off topic... Does anyone know of a good resource/literature which demonstrates the pKa and other physical chemistry of Myristate and other fatty acids? Thanks for any info in advance Gina Notice: This e-mail message, together with any attachments, contains information of

Re: [ccp4bb] If it is a new structure?

2010-12-20 Thread Clayton, Gina Martyn
Hi Liu Looks like (on the images you show) that you have a nice conformational difference for some of the helices between the 2 structures... Happy Hols Gina -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Justin Hall Sent: Monday, December 20,

Re: [ccp4bb] Twinned data

2010-10-04 Thread Clayton, Gina Martyn
: Friday, October 01, 2010 6:35 PM To: Clayton, Gina Martyn Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Twinned data If you really have the systematic absences for P41 or P43 then you must have (at least) four molecules in the cell, twinning cannot reduce this. Since a solvent content of 16

Re: [ccp4bb] Twinned data

2010-10-04 Thread Clayton, Gina Martyn
initial info etc and as a crystallography problem/exercise not having come across it yet... thanks again Best Gina From: Boaz Shaanan [mailto:bshaa...@bgu.ac.il] Sent: Friday, October 01, 2010 5:18 PM To: Clayton, Gina Martyn Subject: Re: [ccp4bb] Twinned

[ccp4bb] Twinned data

2010-10-01 Thread Clayton, Gina Martyn
Hi there Just wondering if anyone has any suggestions how I can deal, if possible, with the following situation -. My first encounter with twinned data... which initially indexed as p43/p41 cell dimensions 58.4 58.4 61 90 90 90. Having seen the Matthews Coefficient for the solvent content of

Re: [ccp4bb] model refinement

2010-06-18 Thread Clayton, Gina Martyn
Not sure if anyone has mentioned this but for example what sort of maps are you using for your refinement. Have you tried density modification, or simulated annealing and or omit maps. These can really be useful for finding parts of your model that are not consistent with the data. Good luck!

[ccp4bb] Catalytic residues in active sites

2010-05-25 Thread Clayton, Gina Martyn
Hi there I wonder if anyone can recommend a good review/paper describing crystal structures that show high energy residues in active sites. By that I mean residues that may be in a strained conformation and rotate between conformations, such that they may even switch into unfavoured

[ccp4bb] B factor Coloring in Pymol

2010-03-31 Thread Clayton, Gina Martyn
Dear Everyone Slightly off topic... I am trying to colour a structure by B factor in Pymol. More specifically I am colouring conserved residues (value in b factor). I want to use 4 colours - say white, yellow, orange, red. However it seems that Pymol now only allows 3 colours to be used - I

Re: [ccp4bb] B factor Coloring in Pymol

2010-03-31 Thread Clayton, Gina Martyn
newcolor0 = [1,1,1]; color newcolor0, (mypdbfile//A/2/*) which will colour individual residues (residue 2 in this case) Pymol should accept a script containing such lines. Hope that helps, Rob On 31 Mar 2010, at 15:00, Clayton, Gina Martyn wrote: Dear Everyone Slightly off topic... I am

Re: [ccp4bb] B factor Coloring in Pymol

2010-03-31 Thread Clayton, Gina Martyn
Subject: Re: [ccp4bb] B factor Coloring in Pymol Hi Gina, On Wed, 31 Mar 2010 15:00:34 -0400 Clayton, Gina Martyn gina_clay...@merck.com wrote: I am trying to colour a structure by B factor in Pymol. More specifically I am colouring conserved residues (value in b factor). I want to use 4

Re: [ccp4bb] B factor Coloring in Pymol

2010-03-31 Thread Clayton, Gina Martyn
Hi All Seems Roberts suggestion has worked. Thank you Robert Best Gina -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Clayton, Gina Martyn Sent: Wednesday, March 31, 2010 4:34 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] B factor

Re: [ccp4bb] Crystal rescue

2010-01-27 Thread Clayton, Gina Martyn
MiTeGen have instructions on their website for using their system. In practice I usually put a little silicon grease at the base of the capillary as sometimes the capillaries fall off plus you need reasonable steady hand eye coordination to put the capillary over the loop...I have found MiTeGen

[ccp4bb] Re Anions in Protein Structures

2010-01-25 Thread Clayton, Gina Martyn
Hi CCP4ers As requested I have compiled the list of responses I got regarding anions in protein structures. I did not receive a huge number (wrong time of day perhaps..) but I do think that the list below covers the various aspects (specific examples as well as various studies) and was very

[ccp4bb] Anions in protein structures

2010-01-05 Thread Clayton, Gina Martyn
Dear CCP4ers Can anyone recommend their favourite paper, or review, that discusses anions in protein structures. Thanks in advance and Happy New Year Gina Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse

[ccp4bb] Van der Waals contacts

2009-07-14 Thread Clayton, Gina Martyn
Hi CCP4ers Perhaps I am hashing over old news.but We are having a discussion about Van Der Waals contacts and effective contacts i.e. the real distance of a VDW bump between say a CH and a CH group which sometimes is described as between a C and a C as i.e. 2x 1.6A and ending about 4A but

Re: [ccp4bb] Lipid content/removal

2009-07-07 Thread Clayton, Gina Martyn
Also MALDI-TOF can be used to help identify the lipid (with standards). I vaguely remember one would extract the lipid, from the protein, using organic solvents then apply that to the MS. When I did it (about 10 years ago) I used non plastic vials and a Hamilton syringe so as not to contaminate