Re: [ccp4bb] Rhodamine in FPLC

[Tomas Malinauskas]

Dear Reza,
I used hydrogen peroxide (~0.1-2%?) to remove rhodamine stuck on
Superdex columns. "Pink" columns turned "white" after this kind of
treatment.
Hope that helps,
Tomas

On Fri, Jun 9, 2017 at 10:43 PM, Reza Khayat  wrote:
> Hi,
>
> Sorry for the non crystallography question. We're using Rhodamine for 
> labeling some material that we need to run through our FPLC. It seems that 
> the Rhodamine is getting stuck to the PEEK tubing. Anyone has experience with 
> successfully removing the Rhodamine from the tubing? Thanks.
>
> Best wishes,
> Reza
>
> Reza Khayat, PhD
> Assistant Professor
> City College of New York
> Department of Chemistry
> New York, NY 10031

[ccp4bb] Rhodamine in FPLC

[Reza Khayat]

Hi,

Sorry for the non crystallography question. We're using Rhodamine for labeling 
some material that we need to run through our FPLC. It seems that the Rhodamine 
is getting stuck to the PEEK tubing. Anyone has experience with successfully 
removing the Rhodamine from the tubing? Thanks.

Best wishes,
Reza

Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031

Re: [ccp4bb] preparing DL-Malic acid stock solution

[Sebastiano Pasqualato]

Dear Janet,
thanks for the excellent tip! It worked like charme!
I think the reason why our solution turned milky was that we were adding NaOH 
pellets without controlling the temperature, and possibly its increase caused 
the (seemingly irreversible) transition to the “porridge” state.
Your method allowed to get a solution which remained clear, despite the 
increase in temperature.
Thanks again!
I have also to thank Edward A. Berry, Diana R. Tomchick and Edward E. Pryor for 
the answers to my post and the valuable information.
Have a nice weekend,
ciao,
Sebastiano


> On 9 Jun 2017, at 01:35, Janet Newman  wrote:
> 
> The way I have done it (and it was sort of fun in a mad scientist way) was to 
> mix up solid DL-malic acid and sodium hydroxide in the right amounts and add 
> water as needed.  This generates  of heat, but gets around the 
> solubility minimum which is impossible to get out of:
> 
> I mixed 40.23 g of DL-malic acid powder (MW=134.1) with 24g of NaOH pellets 
> (MW=40) in a large beaker with a stirrer bar.  Put the beaker in a larger 
> container of ice, and put that on a stirrer in the cold room. Add 80 mL H20 
> to the beaker containing the chemicals, stand back - lots of heat evolved.
> when everything has quietened down, make up to 100 mL with water (we filtered 
> through a 0.22 um filter).
> 
> Cheers, Janet
> 
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Edward 
> A. Berry
> Sent: Friday, 9 June 2017 2:53 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] preparing DL-Malic acid stock solution
> 
> (di)Sodium D,L-malate is available from Sigma-Aldrich (# CDS023113) and
> probably dissolves to give a 3M solution which is slightly alkaline.
> If pK2 is 5.1, then an insignificant amt of malic acid should bring the
> pH down to 7 (If you have to add a significant amount, just add more
> water to dilute to a final conc of 3M Malate + Malic acid)
> 
> 
> On 06/08/2017 12:32 PM, Diana Tomchick wrote:
>> As the pKa1 of malic acid is 3.4, it may be that the partially neutralized 
>> malic acid salt is less soluble than the acid or the fully neutralized salt.
>> 
>> The pKa2 of malic acid is 5.1.
>> 
>> Contact the people at Hampton Research
>> 
>> https://www.hamptonresearch.com/contact_us.aspx
>> 
>> and ask them. They sell it as a 3.0 M solution, pH neutralized to 7.0.
>> 
>> It is possible that you need to fully neutralize it before it turns clear, 
>> or that you may also need to gently heat it.
>> 
>> Diana
>> 
>> **
>> Diana R. Tomchick
>> Professor
>> Departments of Biophysics and Biochemistry
>> University of Texas Southwestern Medical Center
>> 5323 Harry Hines Blvd.
>> Rm. ND10.214A
>> Dallas, TX 75390-8816
>> diana.tomch...@utsouthwestern.edu 
>> (214) 645-6383 (phone)
>> (214) 645-6353 (fax)
>> 
>> On Jun 8, 2017, at 9:54 AM, Sebastiano Pasqualato 
>> > 
>> wrote:
>> 
>> 
>> Dear all,
>> we’ve recently having trouble preparing a 3 M stock solution of DL-Malic 
>> Acid, pH 7 (which we had, so it’s doable!).
>> When we reach pH 3 - 4 the solution turns milky white and does not goes back 
>> to a clear solution even when the pH is raised.
>> Does anybody have any advice on how to get a clear solution? Has anyone gone 
>> through the same?
>> Thanks in advance,
>> ciao,
>> Sebastiano
>> 
>> 
>> --
>> *Sebastiano Pasqualato, PhD*
>> Crystallography Unit
>> Department of Experimental Oncology
>> European Institute of Oncology
>> IFOM-IEO Campus
>> via Adamello, 16
>> 20139 - Milano
>> Italy
>> 
>> tel +39 02 9437 5167
>> fax +39 02 9437 5990
>> web http://is.gd/IEOXtalUnit
>> 
>> 
>> 
>> --
>> 
>> UTSouthwestern
>> 
>> Medical Center
>> 
>> The future of medicine, today.
>> 

[ccp4bb] Parsing error monomer library jLigand

[Becker, Stefan]

Hi all,

I installed the newest version of ccp4 package using the setup manager. When I 
launch jLigand from within Coot I get the error message "Cannot parse the 
standard monomer library". We checked if all paths and permissions are 
correctly set and couldn´t find any mistake. Also repeating the installation 
did not work. The system is running ubuntu 12.04 LTS.

Would anyone have a suggestion how to solve the problem?

Thanks in advance.

Stefan

[ccp4bb] new version of XDS

[Kay Diederichs]

Dear all,

a new version for academic users of XDS has been posted. The major changes are:

- a CLUSTER_NODES keyword that lets you use several machines in a flexible and 
easy way
- (bug fix) Eiger data can (again) be read, preferentially using Dectris' 
Neggia library
- new RELRAD keyword that allows to get better background estimates (i.e. 
better data for weak reflections) for very weak exposures (there is also a 
RELBET keyword but this has a minor influence it seems)

best,

Kay