Dear Maria
have you collected the crystals before they dissolve and washed them, then
either dissolved them in SDS PAGE buffer and ran them on an SDS PAGE gel (for
say a western blot) or capillary mounted them, then shot them on the x-ray set
to determine if they are protein or small
I second Michael's situation. I am stuck with getting the old SGI system to
work in this case - . So many thanks for the info Michael I will let you know
if that works out.
Hi Bill I have not seen the Zalman for sale at the price you give of $270. I
looked around a while ago for a good
Hi there
we are trying to install Coot onto one of our old SGIs and so we installed Coot
0.0.33 (IRIX). However when starting Coot, such as in the Coot (install)
directory, we get an error message stating thatlib libgcc_s.so is required
but can not be found. We have the sgi freeware gcc_lib
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
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
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
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information of
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,
: 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
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
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
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!
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
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
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
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
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
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
Dear CCP4ers
Can anyone recommend their favourite paper, or review, that discusses
anions in protein structures.
Thanks in advance and Happy New Year
Gina
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information of Merck Co., Inc. (One Merck Drive, Whitehouse
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
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
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