Re: [ccp4bb] Electostatic surface at various pH

Hi John, I would probably use Pdb2pqr, to assign charges and radii for the atoms at different pHs, and then APBS integrated in Pymol software for visualization: http://kryptonite.nbcr.net/pdb2pqr/ http://www.poissonboltzmann.org/apbs/ Hope this helps, Florian On Aug 19, 2011, at 2:35 PM,

Re: [ccp4bb] Electostatic surface at various pH

John, You can use APBS in conjunction with PDB2PQR and PROPKA (all available from the ABPS website) for the calculations and Pymol for visualization. Good luck Carsten -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of john peter Sent: Friday, Augus

[ccp4bb] Electostatic surface at various pH

Hi All, Apologies for this slight off topic, however this could very well be the best bulletin board to seek help. I need to calculate the electrostatic surface and make surface figures for a protein at various pHs, say 4.0, 7.0 & 9.0. I'm doing this kind of wok for the first time. Could you su

Re: [ccp4bb] Off topic_protein degradation.

Another option is DTNB (aka Ellman's Reagent). This compound reacts with free thiols and produces a yellow color. The reaction is stoichiometric, so if you have access to a very basic spectrophotometer and know your protein concentration you can quantify the free thiols quite easily. Basic pH d

[ccp4bb] phaser openmp

Dear all, it would be really great if someone could point out to me how to enable the openmp option for phaser during the compilation of the latest ccp4 release. The system will be a SUSE 11.3 64bit using gcc. Cheers, Jochen ---

Re: [ccp4bb] crystal Packing

A really simple trick is to dilute your drops. This has worked to suppress excessive nucleation for us many times, and nearly always increases crystal size. For example, instead of setting drops with 1 uL of protein and 1 uL of well solution, try setting the drop

Re: [ccp4bb] crystal Packing

Dear Eswar, You could try to slow down crystallization somehow. There are several ways to accomplish this: 1) increase drop size 2) add small amounts of glycerol (1-5% v/v) 3) cover the reservoir solution with paraffin or silicon oil or a mixture of both in order to reduce the vapor-diffusion rate

Re: [ccp4bb] Sequence Alignment Question- Thank you everyone

Thanks everyone, for the help. -- Yuri Pompeu

Re: [ccp4bb] Off topic_protein degradation.

If you are unsure about whether the disulfides have formed treat a small amount of protein with N-ethylmaleimide. If the disulfides have not formed, when you perform mass spec on the protein you should see an increase of mass of 125Da for each exposed cysteine.

[ccp4bb] Diamond MX BAG Training - November 2011

To all Diamond MX BAG Users, Diamond Light Source will be holding the next training day for MX BAG Users on Wednesday 2nd November 2011. The aim of the day is to provide BAG users with sufficient training to be able to operate any of the Diamond MX beamlines efficiently and get the most benefit

[ccp4bb] Neat and tidy Re: [ccp4bb] more Computer encryption matters

That is neat and tidy! I don't suppose you know if Windows 7 might have such a facility? Anyway it's a good tip and I will start looking in that direction, Thanks, John Prof John R Helliwell DSc On 19 Aug 2011, at 09:05, Phil Evans wrote: > With OSX 10.6 Snow Leopard, you can FileVault your s

[ccp4bb] Application deadline for MX-beamtime at HZB-BESSY is approaching soon at September 1, 2011 !

Next MX-proposal application deadline: September 1, 2011 is approaching See also: http://www.bessy.de/boat/ We kindly invite new MX-proposals for beamtime applications for the next beamtime period. In order to apply for beamtime, please register at the HZB on-line

Re: [ccp4bb] Off topic_protein degradation.

BioSAXS can also tell you if the protein is folded or not, but in either case, you may want to purify on site since degradation is so fast. Many BioSAXS beamlines (including ours at MacCHESS) now have SEC systems on site. Richard Gillilan MacCHESS Cornell University On Aug 19, 2011, at 3:55 A

[ccp4bb] ccp4 at IUCr2011

Shameless advertising, but... CCP4 will have a booth, No. 47, and posters at the IUCr meeting in Madrid next week. So, I hope to see you there Charles

Re: [ccp4bb] Sequence Alignment Question

Jalview is another option. http://www.jalview.org/ Sent from my HTC - Reply message - From: "Yuri" Date: Fri, Aug 19, 2011 00:31 Subject: [ccp4bb] Sequence Alignment Question To: UID 23435 BODY[1]<0> {238} Hello Everyone, A little off topic but, what is a good way to show (publicatio

Re: [ccp4bb] Sequence Alignment Question‏

Another quite powerful tool is ESPript ( http://espript.ibcp.fr/ESPript/ESPript/ ), which takes e.g. clustalw outputs and allows various manipulations (change of colors, add text, secondary structures, etc.) Matthias From: CCP4 bulletin board [CCP4BB@JI

Re: [ccp4bb] more Computer encryption matters

With OSX 10.6 Snow Leopard, you can FileVault your sensitive home directory, but put all your non-sensitive compute || i/o-intensive files outside your home directory (eg in /Users/Stuff) I don't know whether you can do this in 10.7 Lion Phil On 18 Aug 2011, at 22:50, William G. Scott wrote:

Re: [ccp4bb] Off topic_protein degradation.

Dear Bei, The first question to ask is not whether there is spontaneous disulfide bond breakage, but whether the correct disulfide bonds have been made in the first place. Extreme protease sensitivity could point to an unfolded/misfolded protein. If you know some protein NMR people, you could ask

Re: [ccp4bb] Sequence Alignment Question

Re sequence alignment, For those TeXnically inclined, TeXshade produces beautiful alignment figures. (Steep TeX learning curve, I have an example script if anyone wants one). http://www.ctan.org/pkg/texshade James -- Dr. James W. Murray David Phillips Research Fellow Division of Molecular Bio