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 number) then the peptides are treated more as small proteins for
crystallography. On a side I did just see that the structure of Lysozyme
in 50% ethanol was deposited in the PDB (not that lysozyme is a small
peptide).

Good Luck!

Gina 



-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Buz Barstow
Sent: Wednesday, May 25, 2011 8:04 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Peptide Crystallization

Dear all,

I am considering trying to crystallize a small peptide (around 15 amino
acids). The peptide is soluble in neutral water or buffer (pH 7.0) until
at least 10 mM (13 mg/mL), and adopts a turn conformation when bound to
Zn. 

What are your thoughts on attempting this?

If you think that it is worthwhile, what crystallization conditions
would you try? I am thinking of a sparse matrix screen using the Hampton
Crystal Screen 1 and 2 kits, using hanging drop crystallization in
Hampton Vdx trays.

Thanks! and all the best,

---Buz
Notice:  This e-mail message, together with any attachments, contains
information of Merck  Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates Direct contact information
for affiliates is available at 
http://www.merck.com/contact/contacts.html) that may be confidential,
proprietary copyrighted and/or legally privileged. It is intended solely
for the use of the individual or entity named on this message. If you are
not the intended recipient, and have received this message in error,
please notify us immediately by reply e-mail and then delete it from 
your system.


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 Ray Brown
Sent: Thu 10/03/2011 17:04
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] glycerol


Hi all,
 
I was intrigued by the recent question of whether glycerol had any adverse 
effects on the final purity of protein isolated by chromatography. Glycerol 
certainly helps to solubilize some proteins. Does anyone know of any negative 
effects of glycerol in protein purification, on protein crystal quality or use 
in cryocrystallography and on X-ray diffraction results?
 
Cheers.
 
Ray Brown 
Notice:  This e-mail message, together with any attachments, contains
information of Merck  Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates Direct contact information
for affiliates is available at 
http://www.merck.com/contact/contacts.html) that may be confidential,
proprietary copyrighted and/or legally privileged. It is intended solely
for the use of the individual or entity named on this message. If you are
not the intended recipient, and have received this message in error,
please notify us immediately by reply e-mail and then delete it from 
your system.


[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 Merck  Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates Direct contact information
for affiliates is available at 
http://www.merck.com/contact/contacts.html) that may be confidential,
proprietary copyrighted and/or legally privileged. It is intended solely
for the use of the individual or entity named on this message. If you are
not the intended recipient, and have received this message in error,
please notify us immediately by reply e-mail and then delete it from 
your system.


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, 2010 8:57 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] If it is a new structure?

Hi Liu,

If I understand your question correctly, youre asking how different  
do two structures need to be for one to be new'. If by new you  
mean a new fold, then the answer is NO. Your structure and the homolog  
have the same fold.

However, if your structure is the first structure of a protein in a  
new class, then your structure is a new insight for that reason (e.g.  
it is the first structure of a Unobtainium-metalloprotease).

If it is not the first structure of a protein from a new class, lets  
say a previous structure of Unobtainium-metalloprotease has been  
solved using H. sapiens' sequence, but your protein is the first D.  
melanogaster ortholog solved, then your structure is a new insight for  
that reason.

So, in a nut-shell, I guess what I am saying is that your protein is  
not a new fold, but is almost certainly new by some qualification,  
and you will know best what that qualification is. I hope that helps,  
cheers and happy holidays~

~Justin




 On 20/12/2010 10:49, Liu Zhao  wrote:
 The structure of my protein is as shown as the purple one. Another
one
 ,as shown as green,is homologous .But the structure of my protein
can't
 be obtained by using molecular replacement. And both structures have
 much different, especially in B chain. If my structure is a new one?
 thank you for help.
Notice:  This e-mail message, together with any attachments, contains
information of Merck  Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates Direct contact information
for affiliates is available at 
http://www.merck.com/contact/contacts.html) that may be confidential,
proprietary copyrighted and/or legally privileged. It is intended solely
for the use of the individual or entity named on this message. If you are
not the intended recipient, and have received this message in error,
please notify us immediately by reply e-mail and then delete it from 
your system.


Re: [ccp4bb] Twinned data

2010-10-04 Thread Clayton, Gina Martyn
Hi there


Thank you for the advice regarding my twin data (mostly sent off the
board).

Seems I didn't put enough info in the email sorry for that!

The resolution is 2.6Ang.
My first thought was that the crystal was a fragment of the full length
protein. 
The crystals are undergoing mass spec (the proteins itself appears
stable using DLS etc)...
I did try molecular replacement in the different space groups prior to
detwin with variants of my search model.
Truncate for the centric moments of E show a value close to 1.5 (perfect
twin is 1.5)
H test for twinning close -lkh is close to 0.5
Pseudo twin fraction is given as 0.43
The unmerged data processed in p1 are selected as p21 by Pointless and
P421/3 if given as unmerged in p21.


Thankfully I have new crystals now...

Gina













-Original Message-
From: George M. Sheldrick [mailto:gshe...@shelx.uni-ac.gwdg.de] 
Sent: 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% is too low, the most likely explanation
is that it is not twinned but that the protein is smaller than the one 
you are expecting. With an unknown sequence and no experimental phase 
information such as SAD or MAD, your only hope would be Arcimboldo, but 
that requires data to about 2A or better (you don't mention the 
resolution). As an even longer shot, you could search the PDB for
matching cells and space groups.

George

Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582


On Fri, 1 Oct 2010, Clayton, Gina Martyn wrote:

 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 the
unit
 cell as 16% I discovered the data are merohedrally twinned with twin
 fraction given as 0.1. 
 
 I reprocessed the data as p1, p2 p21, c2221 (Rsymm etc indicates wrong
 space group, Mats Coeff 16%) p4 etc. In p2 the (pseudo) twin fraction
is
 given as 0.43 (Mats Coeff 60% solvent 2.7 mol/ASU). 
 
 I ran Detwin (ccp4) on the p2 p21 data with alternate operators as
 indicated by Xtriage in Phenix.   I have had no molecular replacement
 solution i.e. Molrep rotational searches are not giving peaks and
Phaser
 has not found a solution (nor with alternates of the search model).
 
 Does anyone have any suggestions/best paper to consult etc based on
 their experience of twinned data (aside from sort the crystals out...)
 or should I throw in the towell?
 
 Thanks in advance for any information and advice
 
 Gina
 
 
 
 
 Notice:  This e-mail message, together with any attachments, contains
 information of Merck  Co., Inc. (One Merck Drive, Whitehouse Station,
 New Jersey, USA 08889), and/or its affiliates Direct contact
information
 for affiliates is available at 
 http://www.merck.com/contact/contacts.html) that may be confidential,
 proprietary copyrighted and/or legally privileged. It is intended
solely
 for the use of the individual or entity named on this message. If you
are
 not the intended recipient, and have received this message in error,
 please notify us immediately by reply e-mail and then delete it from 
 your system.
 
 
Notice:  This e-mail message, together with any attachments, contains
information of Merck  Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates Direct contact information
for affiliates is available at 
http://www.merck.com/contact/contacts.html) that may be confidential,
proprietary copyrighted and/or legally privileged. It is intended solely
for the use of the individual or entity named on this message. If you are
not the intended recipient, and have received this message in error,
please notify us immediately by reply e-mail and then delete it from 
your system.


Re: [ccp4bb] Twinned data

2010-10-04 Thread Clayton, Gina Martyn
 
Hi Boaz
 
thanks for the advice -  Yes your suggestions are very useful thank you! 
 
 
I actually have not tried Phaser with the P4 data  so I will give that a shot. 
Curiously Pointless selects P21 from P4 and P421/3 from P21...
I tried MolRep in P1 but Phaser failed to find any solution though perhaps I 
did not pursue it enough...
I think it is entirely possible that the space group I have , as in your 
example, may be something other than P21 etc
Never tried Zanadu sounds interesting I'll take a look...
 
 
We have new crystals... I was wanting to solve the twinned data to get some 
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 data


Hi  Gina, 

I've had a similar situation and here are some suggestions/ ideas:

1) You could try to run Phaser on the the data processed as P4 BEFORE 
detwinning and ask it to try all the possible space groups including the P422 
and related ones.

2) Before step 1 or in parallel or following it, I would run the P4 processed 
data (again NOT detwinned) through pointless and/or xtriage to see whether they 
can give some indications for better choice of space group.

3) In my case, only running Phaser in P1 gave me a solution (the data were 
initially processed as P4 but I reprocessed them in P1 for that purpose). It's 
worth you trying too.

4)  Eventually, I ran the P1 model (8 mols.) and data in  Zanuda (on the York 
site) and that gave me a new space group choice (P21212). When I ran Phaser in 
this space group (after reprocessing the data again) it also gave a good 
solution which I'm now refining (with twinning) either in Phenix or refmac but 
without detwinning, since the program do this for you internally (I'm sure 
about refmac and assume it's the same in Phenix).

I hope you'll find some of this helpful.

   Cheers,

 Boaz 

- Original Message -
From: Clayton, Gina Martyn gina_clay...@merck.com
Date: Friday, October 1, 2010 21:28
Subject: [ccp4bb] Twinned data
To: CCP4BB@JISCMAIL.AC.UK

 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 
 the unit
 cell as 16% I discovered the data are merohedrally twinned with twin
 fraction given as 0.1. 
 
 I reprocessed the data as p1, p2 p21, c2221 (Rsymm etc indicates wrong
 space group, Mats Coeff 16%) p4 etc. In p2 the (pseudo) twin 
 fraction is
 given as 0.43 (Mats Coeff 60% solvent 2.7 mol/ASU). 
 
 I ran Detwin (ccp4) on the p2 p21 data with alternate operators as
 indicated by Xtriage in Phenix.   I have had no 
 molecular replacement
 solution i.e. Molrep rotational searches are not giving peaks 
 and Phaser
 has not found a solution (nor with alternates of the search model).
 
 Does anyone have any suggestions/best paper to consult etc based on
 their experience of twinned data (aside from sort the crystals out...)
 or should I throw in the towell?
 
 Thanks in advance for any information and advice
 
 Gina
 
 
 
 
 Notice:  This e-mail message, together with any 
 attachments, contains
 information of Merck  Co., Inc. (One Merck Drive, Whitehouse Station,
 New Jersey, USA 08889), and/or its affiliates Direct contact 
 informationfor affiliates is available at 
 http://www.merck.com/contact/contacts.html) that may be confidential,
 proprietary copyrighted and/or legally privileged. It is 
 intended solely
 for the use of the individual or entity named on this message. 
 If you are
 not the intended recipient, and have received this message in error,
 please notify us immediately by reply e-mail and then delete it 
 from 
 your system.
 


Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
Phone: 972-8-647-2220 ; Fax: 646-1710
Skype: boaz.shaanan

‎ 
Notice:  This e-mail message, together with any attachments, contains
information of Merck  Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates Direct contact information
for affiliates is available at 
http://www.merck.com/contact/contacts.html) that may be confidential,
proprietary copyrighted and/or legally privileged. It is intended solely
for the use of the individual or entity named on this message. If you are
not the intended recipient, and have received this message in error,
please notify us immediately by reply e-mail and then delete it from 
your system.


[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 the unit
cell as 16% I discovered the data are merohedrally twinned with twin
fraction given as 0.1. 

I reprocessed the data as p1, p2 p21, c2221 (Rsymm etc indicates wrong
space group, Mats Coeff 16%) p4 etc. In p2 the (pseudo) twin fraction is
given as 0.43 (Mats Coeff 60% solvent 2.7 mol/ASU). 

I ran Detwin (ccp4) on the p2 p21 data with alternate operators as
indicated by Xtriage in Phenix.   I have had no molecular replacement
solution i.e. Molrep rotational searches are not giving peaks and Phaser
has not found a solution (nor with alternates of the search model).

Does anyone have any suggestions/best paper to consult etc based on
their experience of twinned data (aside from sort the crystals out...)
or should I throw in the towell?

Thanks in advance for any information and advice

Gina




Notice:  This e-mail message, together with any attachments, contains
information of Merck  Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates Direct contact information
for affiliates is available at 
http://www.merck.com/contact/contacts.html) that may be confidential,
proprietary copyrighted and/or legally privileged. It is intended solely
for the use of the individual or entity named on this message. If you are
not the intended recipient, and have received this message in error,
please notify us immediately by reply e-mail and then delete it from 
your system.


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!
Gina
 



From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
atul kumar
Sent: Friday, June 18, 2010 5:14 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] model refinement (corrections, apologies!)


Dear all

Thanks for your replies.  And thanks to all those who noticed that I had
posted wrong unit cell dimensions for P3221 (which I picked from the
header of the template pdb).

My space group is P3221 (unit cell 54.8 54.8 100.1 90 90 120).  

Data quality appears fine.  I/sigI=4.9; Rmerge=0.088; Completeness=99.9
(outershell values are: 2.3; 0.333; 99.9 respectively)

As mentioned above, I solved the structure by molecular replacement and
there appears to be no twinning.  There are no major unmodelled
densities.  A couple of small blobs are present, which I think may be
glycerol or some other  molecule from my crystallization buffer but I
still need to model these.  Other than that, there are no major issues.
I was just wondering if the present R-factor values seem alright for a
1.9 ang data, which many of you have suggested it does?

Thanks again.   Any other suggestions/comments are still welcome. 

Atul



On Fri, Jun 18, 2010 at 7:39 AM, atul kumar atulsingh21...@gmail.com
wrote:


Dear all

I am trying to solve structure of data set at 1.9 A,r merge
9.3,it belongs to space group P3221 unit cell 160.78 157.32 135.62 90.0
90.0 90.0,i has no NCS ,i did tls refinement as well but after water
addition the r factor and r free is stucked at 22 and 25
respectively.suggestions are requested for the same.
 
regards
 

Atul Kumar


Notice:  This e-mail message, together with any attachments, contains
information of Merck  Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates Direct contact information
for affiliates is available at 
http://www.merck.com/contact/contacts.html) that may be confidential,
proprietary copyrighted and/or legally privileged. It is intended solely
for the use of the individual or entity named on this message. If you are
not the intended recipient, and have received this message in error,
please notify us immediately by reply e-mail and then delete it from 
your system.


[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
ramachandran regions during their activity, but that the strained high
energy state is relevant to the enzyme activity?

If I get enough responses I will list them and post them back up.

Thanks so much in advance

Gina

Notice:  This e-mail message, together with any attachments, contains
information of Merck  Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates Direct contact information
for affiliates is available at 
http://www.merck.com/contact/contacts.html) that may be confidential,
proprietary copyrighted and/or legally privileged. It is intended solely
for the use of the individual or entity named on this message. If you are
not the intended recipient, and have received this message in error,
please notify us immediately by reply e-mail and then delete it from 
your system.


[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 tried the
script from the Wiki site, but Pymol will not accept the 4 rgb colours.
Does anyone have an idea how I can colour with 4 colours (but not
rainbow too confusing).


Thanks in advance for any help

Best
Gina
 
Notice:  This e-mail message, together with any attachments, contains 
information of Merck  Co., Inc. (One Merck Drive, Whitehouse Station, New 
Jersey, USA 08889), and/or its affiliates Direct contact information for 
affiliates is available at http://www.merck.com/contact/contacts.html) that may 
be confidential, proprietary copyrighted and/or legally privileged. It is 
intended solely for the use of the individual or entity named on this message. 
If you are not the intended recipient, and have received this message in error, 
please notify us immediately by reply e-mail and then delete it from your 
system.


Re: [ccp4bb] B factor Coloring in Pymol

2010-03-31 Thread Clayton, Gina Martyn
Hi Ron

Mmmm...

not really but thanks for the info:)

I have my Bfactor column assigned in percent conservation so the B value
ranges from 
say 30% to 100%. I want to colour my molecule accordingly. Pymol allows
B factor 
colouring but seems only to allow 3 colour choices. It used to allow 4
colour choices say WYOR
I was wondering if any one had an idea how I could trick Pymol into
accepting say 4 colours.

Sorry if I was not clearer in the previous.

Thanks again advance.
Gina


-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Rob Nicholls
Sent: Wednesday, March 31, 2010 3:14 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] B factor Coloring in Pymol

Hi,

I'm aware of two ways to do this:

by writing the colour as a word, e.g:
color white, (mypdbfile//A/*/*)
which will colour a whole chain.

Or by using rgb colours, e.g:
set_color 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 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 tried the
 script from the Wiki site, but Pymol will not accept the 4 rgb  
 colours.
 Does anyone have an idea how I can colour with 4 colours (but not
 rainbow too confusing).


 Thanks in advance for any help

 Best
 Gina

 Notice:  This e-mail message, together with any attachments,  
 contains information of Merck  Co., Inc. (One Merck Drive,  
 Whitehouse Station, New Jersey, USA 08889), and/or its affiliates  
 Direct contact information for affiliates is available at
http://www.merck.com/contact/contacts.html) 
  that may be confidential, proprietary copyrighted and/or legally  
 privileged. It is intended solely for the use of the individual or  
 entity named on this message. If you are not the intended recipient,  
 and have received this message in error, please notify us  
 immediately by reply e-mail and then delete it from your system.
Notice:  This e-mail message, together with any attachments, contains 
information of Merck  Co., Inc. (One Merck Drive, Whitehouse Station, New 
Jersey, USA 08889), and/or its affiliates Direct contact information for 
affiliates is available at http://www.merck.com/contact/contacts.html) that may 
be confidential, proprietary copyrighted and/or legally privileged. It is 
intended solely for the use of the individual or entity named on this message. 
If you are not the intended recipient, and have received this message in error, 
please notify us immediately by reply e-mail and then delete it from your 
system.


Re: [ccp4bb] B factor Coloring in Pymol

2010-03-31 Thread Clayton, Gina Martyn
Hi Robert

That seems like a great suggestion! I will give it a shot and let CCP4BB
know if it works


Thanks
Gina
 

-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Robert Campbell
Sent: Wednesday, March 31, 2010 4:29 PM
To: CCP4BB@JISCMAIL.AC.UK
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 colours - say white, yellow, orange, red.  However it
 seems that Pymol now only allows 3 colours to be used - I tried the
 script from the Wiki site, but Pymol will not accept the 4 rgb
colours.
 Does anyone have an idea how I can colour with 4 colours (but not
 rainbow too confusing).

Say, your b-factor values range from 0-10, and your object is called
protein, then you could do:

color white, protein
color yellow, protein  b  2.5
color orange, protein  b  5.0
color red, protein  b  7.5

If you want to automate that process, then you need to write a script
that
determines, the b-factor limits for the 4 colours based on the b-factors
present in your structure.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821Fax: 613-533-2497
robert.campb...@queensu.ca
http://pldserver1.biochem.queensu.ca/~rlc
Notice:  This e-mail message, together with any attachments, contains 
information of Merck  Co., Inc. (One Merck Drive, Whitehouse Station, New 
Jersey, USA 08889), and/or its affiliates Direct contact information for 
affiliates is available at http://www.merck.com/contact/contacts.html) that may 
be confidential, proprietary copyrighted and/or legally privileged. It is 
intended solely for the use of the individual or entity named on this message. 
If you are not the intended recipient, and have received this message in error, 
please notify us immediately by reply e-mail and then delete it from your 
system.


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 Coloring in Pymol

Hi Robert

That seems like a great suggestion! I will give it a shot and let CCP4BB
know if it works


Thanks
Gina
 

-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Robert Campbell
Sent: Wednesday, March 31, 2010 4:29 PM
To: CCP4BB@JISCMAIL.AC.UK
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 colours - say white, yellow, orange, red.  However it
 seems that Pymol now only allows 3 colours to be used - I tried the
 script from the Wiki site, but Pymol will not accept the 4 rgb
colours.
 Does anyone have an idea how I can colour with 4 colours (but not
 rainbow too confusing).

Say, your b-factor values range from 0-10, and your object is called
protein, then you could do:

color white, protein
color yellow, protein  b  2.5
color orange, protein  b  5.0
color red, protein  b  7.5

If you want to automate that process, then you need to write a script
that
determines, the b-factor limits for the 4 colours based on the b-factors
present in your structure.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821Fax: 613-533-2497
robert.campb...@queensu.ca
http://pldserver1.biochem.queensu.ca/~rlc
Notice:  This e-mail message, together with any attachments, contains
information of Merck  Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates Direct contact information
for affiliates is available at
http://www.merck.com/contact/contacts.html) that may be confidential,
proprietary copyrighted and/or legally privileged. It is intended solely
for the use of the individual or entity named on this message. If you
are not the intended recipient, and have received this message in error,
please notify us immediately by reply e-mail and then delete it from
your system.
Notice:  This e-mail message, together with any attachments, contains 
information of Merck  Co., Inc. (One Merck Drive, Whitehouse Station, New 
Jersey, USA 08889), and/or its affiliates Direct contact information for 
affiliates is available at http://www.merck.com/contact/contacts.html) that may 
be confidential, proprietary copyrighted and/or legally privileged. It is 
intended solely for the use of the individual or entity named on this message. 
If you are not the intended recipient, and have received this message in error, 
please notify us immediately by reply e-mail and then delete it from your 
system.


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 RT system very useful.

Good luck!



-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Ezra Peisach
Sent: Wednesday, January 27, 2010 7:41 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Crystal rescue

MiTeGen (www.mitegen.com) sells a RT device  - plastic capillary to put 
over loop... I do not know how well it would work for a long data 
collection - but people here have used it to evaluate their crystals

Ezra


On 1/27/2010 3:58 AM, Flip Hoedemaeker wrote:
 Zhiyi,

 You can use a thin cap over your cryo loop, just put a drop of mother 
 liquor in the top, place over the loop and make it airtight at the 
 base.  Not sure who sells these things though, I guess you can make it

 from a capillary too. Then remove the cryo stream or put it at a temp 
 above freezing, say 253K.

 Flip

 Zhiyi Wei wrote:
 Thanks for so many quick responses!

 Actually, I have test several different cryo-protectants, including
 glycerol, EG, and PEG400. I did not see much differences between
these
 cryo conditions. So, I choose glycerol.

 I would like to test my crystals in RT. But I don't know how to do
 this. Just mount crystal to the X-ray machine without cryo stream? Or
 I should use capillaries?

 Zhiyi

 On Wed, Jan 27, 2010 at 5:45 AM, Kelly Daughtry kddau...@bu.edu
wrote:
 Tascimate can be used as the cryo as well. I have had experience
with
 crystals in similar condition and moved the crystals to a 20%
 increased Tascimate solution and they froze well.

 I agree with Ezra, room temperature mount your crystal before
 freezing. It is the only way to know the true problem.


 Kelly
 ***
 Kelly Daughtry
 PhD Candidate
 Department of Physiology and Biophysics
 Boston University School of Medicine
 590 Commonwealth Ave
 R 390
 Boston MA, 02215
 (P) 617-358-5548
 ***



 On Tue, Jan 26, 2010 at 1:25 PM, Marcus Winter
 marcus.win...@oxford-diffraction.com wrote:
 Dear Zhiyi,


 Ezra is exactly right, of course.  The Oxford Diffraction PX
Scanner
 system can assess the diffraction qualities of (putative) protein
 crystals in situ - in the crystallisation plate.  So, directly, you
 would discover if your 'big and beautiful' crystals actually
diffract
 well... in their mother liquor under ambient conditions and before
the
 addition of any cryo-protect.  Do you have a friend or neighbour
with
 a PX Scanner ?  If not, please feel most welcome to contact
 Oxford Diffraction: we would be pleased to assist if at all
possible.


 Good Luck and Best Wishes,

 Marcus Winter.

 www.oxford-diffraction.com




 -Original Message-
 From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf
Of
 Ezra Peisach
 Sent: 26 January 2010 16:01
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: Re: [ccp4bb] Crystal rescue

 First you need to establish if it is your cryo conditions or the
 crystals.  Depending where you are - they might have the equipment 
 to do

 a wet mount - without freezing.  Yes the crystal will not last -
but
 then you know if the problem is in the
 crystal.  If it is - you need better crystals.  If it is the cryo -

 you
 need to work on that.  Tacsimate is mixture of alot of different
 compounds - but the smears are too close together to be a small
salt
 crystal on top...

 Good luck,

 Ezra

 On 1/26/2010 10:42 AM, Zhiyi Wei wrote:
 Dear all,

 I got a problem with my crystals. I have two total different
proteins
 that both can be crystallized in the condition with PEG3350 and
 Tacsimate
 (although the concentrations are different) with different shapes.

 The
 crystals look big and beautiful. However, when I test them in
 synchrotron,
 both of these two types of crystals showed poor diffractions. As
 showed in
 the attached diffraction image, the diffraction is up to ~4 A but
 smear in
 one direction while8 A in the other direction. The interesting
thing
 is
 that the diffraction pattern is similar for all crystals (from two
 different
 proteins) that I tested without exception although they belong to
 different
 space groups. So, I wonder whether these kind of pattern is caused
by
 Tacsimate (I don't know what it is) and how to rescue these
crystals.
 Any
 suggestions or comments?

 Thanks a lot!

 Best,
 Zhiyi


Notice:  This e-mail message, together with any attachments, contains 
information of Merck  Co., Inc. (One Merck Drive, Whitehouse Station, New 
Jersey, USA 08889), and/or its affiliates Direct contact information for 
affiliates is available at http://www.merck.com/contact/contacts.html) that may 
be confidential, proprietary copyrighted and/or legally 

[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 useful and 
interesting (thanks!). 

In no particular order

1. Anion binding sites in protein structures.Chakrabarti P.
J Mol Biol. 1993 Nov 20;234(2):463-82.

2. On the routine use of soft X-rays in macromolecular crystallography. Part 
IV. Efficient determination of anomalous substructures in biomacromolecules 
using longer X-ray wavelengths.
Mueller-Dieckmann C, Panjikar S, Schmidt A, Mueller S, Kuper J, Geerlof A, 
Wilmanns M, Singh RK, Tucker PA, Weiss MS.
Acta Crystallogr D Biol Crystallogr. 2007 Mar;63(Pt 3):366-80. Epub 2007 Feb 21.

3. Structural effects of monovalent anions on polymorphic lysozyme crystals.
Vaney MC, Broutin I, Retailleau P, Douangamath A, Lafont S, Hamiaux C, Prangé 
T, Ducruix A, Riès-Kautt M.
Acta Crystallogr D Biol Crystallogr. 2001 Jul;57(Pt 7):929-40. Epub 2001 Jun 21.

4. Data mining of metal ion environments present in protein structures.
Zheng H, Chruszcz M, Lasota P, Lebioda L, Minor W.
J Inorg Biochem. 2008 Sep;102(9):1765-76. Epub 2008 May 28.

5. Use of complementary cation and anion heavy-atom salt derivatives to solve 
the structure of cytochrome P450 46A1.
White MA, Mast N, Bjorkhem I, Johnson EF, Stout CD, Pikuleva IA.
Acta Crystallogr D Biol Crystallogr. 2008 May;64(Pt 5):487-95. Epub 2008 Apr 19.

6. Direct interaction between a human digestive protease and the mucoadhesive 
poly(acrylic acid).
Pallarès I, Fernández D, Comellas-Bigler M, Fernández-Recio J, Ventura S, 
Avilés FX, Bode W, Vendrell J.
Acta Crystallogr D Biol Crystallogr. 2008 Jul;D64(Pt 7):784-91. Epub 2008 Jun 
18.

7. The Oligomeric states of Haloarcula marismortui malate dehydrogenase are 
modulated by solvent components as shown by crystallographic and biochemical 
studies.
Irimia A, Ebel C, Madern D, Richard SB, Cosenza LW, Zaccaï G, Vellieux FM.
J Mol Biol. 2003 Feb 21;326(3):859-73.

8. Is the bond-valence method able to identify metal atoms in protein 
structures?
Müller P, Köpke S, Sheldrick GM.
Acta Crystallogr D Biol Crystallogr. 2003 Jan;59(Pt 1):32-7. Epub 2002 Dec 19.


Best
Gina
Notice:  This e-mail message, together with any attachments, contains 
information of Merck  Co., Inc. (One Merck Drive, Whitehouse Station, New 
Jersey, USA 08889), and/or its affiliates Direct contact information for 
affiliates is available at http://www.merck.com/contact/contacts.html) that may 
be confidential, proprietary copyrighted and/or legally privileged. It is 
intended solely for the use of the individual or entity named on this message. 
If you are not the intended recipient, and have received this message in error, 
please notify us immediately by reply e-mail and then delete it from your 
system.


[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 Station, New 
Jersey, USA 08889), and/or its affiliates Direct contact information for 
affiliates is available at http://www.merck.com/contact/contacts.html) that may 
be confidential, proprietary copyrighted and/or legally privileged. It is 
intended solely for the use of the individual or entity named on this message. 
If you are not the intended recipient, and have received this message in error, 
please notify us immediately by reply e-mail and then delete it from your 
system.


[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 not including hydrogen.

Some programs list contacts, to say a ligand, as far as 6A apart and
some of the simulation programs use that distance too for contacts for
protein protein interactions. 

Does anyone know of a good paper that discusses the effective distance
or has a comment on where a VDW force may begin and end or it's
effective distance - though some say it never truly ends  just
approaches zero...


G



Notice:  This e-mail message, together with any attachments, contains
information of Merck  Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates (which may be known
outside the United States as Merck Frosst, Merck Sharp  Dohme or
MSD and in Japan, as Banyu - direct contact information for affiliates is
available at http://www.merck.com/contact/contacts.html) that may be
confidential, proprietary copyrighted and/or legally privileged. It is
intended solely for the use of the individual or entity named on this
message. If you are not the intended recipient, and have received this
message in error, please notify us immediately by reply e-mail and
then delete it from your system.


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 the sample with plastics.

Hope that's useful!

Gina


-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Soisson, Stephen
Sent: Tuesday, July 07, 2009 2:01 PM
To: 
Subject: Re: [ccp4bb] Lipid content/removal

Activated charcoal (see serum albumin structure references) can remove
fatty acids.

Good luck-

Steve 

-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Jacob Keller
Sent: Tuesday, July 07, 2009 1:01 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Lipid content/removal

Dear Crystallographers,

does anybody know of a simple, fast way to determine whether a protein 
sample contains lipid, and roughly to determine the quantity? As
corollary, 
does anybody know of a quick way to extract/remove the putative lipid?
In my 
case, I am working with an extremely robust/stable soluble protein which
may 
contain bacterial lipids.

Thanks for your consideration,

Jacob Keller


***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: j-kell...@northwestern.edu
***
Notice:  This e-mail message, together with any attachments, contains
information of Merck  Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates (which may be known
outside the United States as Merck Frosst, Merck Sharp  Dohme or
MSD and in Japan, as Banyu - direct contact information for affiliates
is
available at http://www.merck.com/contact/contacts.html) that may be
confidential, proprietary copyrighted and/or legally privileged. It is
intended solely for the use of the individual or entity named on this
message. If you are not the intended recipient, and have received this
message in error, please notify us immediately by reply e-mail and
then delete it from your system.
Notice:  This e-mail message, together with any attachments, contains
information of Merck  Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates (which may be known
outside the United States as Merck Frosst, Merck Sharp  Dohme or
MSD and in Japan, as Banyu - direct contact information for affiliates is
available at http://www.merck.com/contact/contacts.html) that may be
confidential, proprietary copyrighted and/or legally privileged. It is
intended solely for the use of the individual or entity named on this
message. If you are not the intended recipient, and have received this
message in error, please notify us immediately by reply e-mail and
then delete it from your system.