[ccp4bb] dissolving peptides !

Hello everybody, I have a 16 mer peptide which is predicted to be positively charged alpha helix and has 50% of its sequence hydrophobic. Could any one recommend the best way to dissolve it, and then it can be used for crystallization trials. thanks -- rashmi

Re: [ccp4bb] Fwd: creating a metal plane model to fit a protein.

Well - try the coordinate utility recommended by Martyn Winn to convert cif to pdb coord_format xyzin ./1ivo.cif xyzout 1ivo.pdb eof END eof Then pdbset xyzin 1ivo.pdb xyzout 1ivo-sym.pdb symgen -x,y,z (or whatever sym op you want) end This will generate symmetry copy of your coordinates as

[ccp4bb] Scaling question

Dear CCP4bb, I was wondering if someone could tell me how mosflm and scala deal with overloaded reflections. From my understanding mosflm extrapolates the overloaded peaks but then scala throws them out completely - is this right? If so am I right to not worry about contamination from

Re: [ccp4bb] Scaling question

Hello Simon, if I remember correctly, mosflm only estimates overloads if you explicitly ask for it - which you should NOT do especially since you do have a low resolution pass. (from the documentation at http://www.mrc-lmb.cam.ac.uk/harry/mosflm/mosflm_user_guide.html : Note that you MUST

[ccp4bb] GPU computing

Hi All, I am wondering anyone is looking into GPU computing on structural refinement? I see VMD supports GPU computing already, how about other programs such as CCP4 and Phenix Thanks, Tongqing Tongqing Zhou, Ph.D. Staff Scientist Structural Biology Section Vaccine Research Center,

[ccp4bb] Pcube User meeting

Dear Colleagues, I would like to draw your attention to the upcoming Pcube-user meeting (September 8-9, 2010 in Grenoble). You are probably aware that the EU-founded Pcube project provides open access to several supportive technologies for macromolecular crystallography, ranging from fragment

Re: [ccp4bb] Scaling question

Mosflm integrates them (profile-fitted overloads) but flags them. Pointless uses them for systematic absence tests. Scala by default ignores them, but you can include them if you want: this is not normally recommended since they are pretty inaccurate (look in the Excluded data tab of

Re: [ccp4bb] GPU computing

I looked at it and concluded that our FFTs are on the whole too short for it to be worthwhile, and a lot of calculations aren't FFT bound anyway. An awful lot of our stuff is simply not very slow. Also, GPU computing at the moment is crippled for many problems by the bandwidth bottleneck and

Re: [ccp4bb] insect cell media

We have happily made a transition last year from using Invitrogen's SFM medium and cellfectin to Insect-Xpress (Lonza) and polyethyleneimine for transfection. We are moving several protein targets to large-scale cultures and would consider cost-cutting alternatives. For example, Invitrogen and

Re: [ccp4bb] insect cell media

Hi, well, actually this is availalbe as powder (HYClone), as it says on the page.. (we have it made in our media kitchen on a regular basis, but not for huge scale... so i dont know about the prices..)

Re: [ccp4bb] dissolving peptides !

Rashmi, You can try 1%DMSO and also acetonitrile but the former is preferable. Gauri On Mon, Jun 7, 2010 at 3:04 AM, rashmi panigrahi rashmi.panigrah...@gmail.com wrote: Hello everybody, I have a 16 mer peptide which is predicted to be positively charged alpha helix and has 50% of its

Re: [ccp4bb] Scaling question

Dear Simon, mosflm does indeed estimate the intensity of overloaded reflections, and these are rejected by default in SCALA, but you can choose to include them using the appropriate keywords (ACCEPT OVERLOADS). The number of overloads in the MTZ file, and the number

[ccp4bb] Ligand weak density in SHELXL

Dear all, I solved the structure of an enzyme at resolution of 1.1A with a bound substrate using Refmac5 and Coot for refinement/building. I have a very nice density for my ligand and a very good structure, as judged by Molprobity analysis. Now I'm using SHELXL to finish refinement but most

Re: [ccp4bb] GPU computing

Most of what Kevin says applies equally well to Phenix - refinement is a relatively complex series of calculations, much less inherently parallel than what VMD is using GPUs for. There are many other things we could do to speed up calculations that would probably be more useful and more

Re: [ccp4bb] insect cell media

I mentioned to to Chris already, but we use nothing but HyClone SFX-Insect powder. We make 20-30 L batches, sterilize with a large peristaltic pump and a disposable Millipak filter from Millipore. We never have contamination problems that are due to preparing our own media from powder. We buy

Re: [ccp4bb] Ligand weak density in SHELXL

Dear Fatima, just a couple of things you may consider: - you can let shelxl refine the occupancy by assigning a free variable to the whole ligand - did you refine the structure anisotropically? At this resolution you certainly should. - maybe you made a mistake converting the files from

Re: [ccp4bb] Ligand weak density in SHELXL

Dear Tim, Thanks for your advice. I am refining my structure anisotropically. If, as you suggested, I did something wrong converting files to use in SHELXL I would expect that the whole structure to have problems or am I wrong? And how can I assign a free variable to the whole ligand?

[ccp4bb] MR on low resolution soaking data.

Dear colleagues, We are now trying to soak some ligands into a protein, which is about 60kd in size and the structure has been solved before. But the molecular replacement cannot give a right solution. Below is some contrast of the data: Native 2A P212121 monomer Soaked4A

Re: [ccp4bb] MR on low resolution soaking data.

since the ligands bare being soaked into a known solved structure, why is MR necessary? Why not just start out with some rigid body refinement of the native structure to account for possible slight differences in the cell dimensions? --

Re: [ccp4bb] insect cell media

For large amount of media, it's actually cheaper to buy liquid media in bags when factor in the cost of labor and water. MilliQ water may not be low endotoxin. --Chun -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Nathaniel Clark Sent: Monday,

Re: [ccp4bb] MR on low resolution soaking data.

You haven't given much detail to work with so I can only guess about your problem. A Wilson B of 20 for a 4 A data set is ridiculous, but the uncertainty in the Wilson B calculation at 4 A is enormous, so what might be a more reasonable statement would be to say your Wilson B calculates to 20

[ccp4bb] New Version of the Protein Geometry Database Operational

A new version of the Protein Geometry Database (PGD) has just been released. This version includes - The ability to compose queries and analyze the behavior of side chain chi angles. - Structures released in the wwPDB up to April 8, 2010 consisting of roughly 18,000 nonredundant protein