Re: [ccp4bb] (off-topic) Measurement of channel pore dimensions

Though I like our program HOLLOW for visualization, I think the tool for this job is MOLE (http://mole.chemi.muni.cz). You can use the online version to quickly generate two trajectories out from the center of the channel. MOLE has some mathematical advantages over HOLE or Caver. You then merge

[ccp4bb] Associate (W2) Professor Position at DESY

Dear Crystallographers, I would like to bring to your attention that the University of Düsseldorf and the Forschungszentrum Jülich (Germany) jointly have an opening for an (associate level / W2) faculty position. The group will be part of the newly established "Centre for Structural Systems Bi

Re: [ccp4bb] Can DM-skeletonisation specify the "join point cutoff" value?

The skeletonisation option in dm rarely produces any benefit. I wouldn't use it. Hailiang Zhang wrote: Hi all; It is described by "http://www.ccp4.ac.uk/html/dm_skeletonisation.html"; that the "skeletonisation" has two adjustable parameters (join point cutoff, and end point cutoff), but the DM

[ccp4bb] Trymethylamine n-oxide and PEG MME 2000

Dear All, recently I got some crystals using the following condition: 0.20 M trimethylamine n-oxide 0.1 M Tris-HCl pH 8.5 20% (w/v) PEG MME 2000 We have little experience with PEG MME and trimethylamine n-oxide, so I am wondering how likely they are to be protein and would welcome hearing about an

Re: [ccp4bb] protein aggregation

Dear Gauri This may be the saturation point of your protein and beyond this it will start precipitating in a particular buffer. Try to set the crystallization trial (if it is your application ) and select those condition in which you see clear drop. Change the purification buffer with that cond

Re: [ccp4bb] protein aggregation

- try limited proteolysis to see if you can chop off a disordered region - consider the fact that, although it purifies nicely, your protein may not be well-folded do you have a biochemical activity test? Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Bio

Re: [ccp4bb] protein aggregation

Try different detergents. Try 10% or more glycerol. Try adding ligands (if present/known). Try varying ionic strength and/or pH. Try giving more specifics so people on the board may be able to help you better. Bert On 3/23/11 1:51 PM, "gauri misra" wrote: The protein purifies nicely there is

Re: [ccp4bb] protein aggregation

The protein purifies nicely there is no problem in that. Just at the last step when it is concentrated it starts precipitating beyond a concentration of 1mg/ml. Already the purification buffers have the detergent. On Wed, Mar 23, 2011 at 1:44 PM, Kornelius Zeth < kornelius.z...@tuebingen.mpg.de> w

[ccp4bb] protein aggregation

Hi, What are the different methods to prevent protein aggregation while concentrating so as to increase the concentration of the protein? I have some idea of adding EDTA and charged amino acids like L-Arg and L-Glu. I would appreciate if the readers share their experiences. Thanks! Gauri

Re: [ccp4bb] (off-topic) Measurement of channel pore dimensions

Bert; I have found the online gui 3V to be very useful in calculating channel dimensions. It outputs the volume and surface area of the pore, along with a surface representation that can be visualized in Chimera or PyMOL. You can either specify a specific pore or search for pores within a giv

[ccp4bb] EU funded technician position at EMBL Grenoble

Hello, There is a technician position in my lab at EMBL Grenoble funded under the EU P-CUBE project to assist user access and perform associated R&D in high throughput protein technologies, notably in using robotics and random library screening for expression studies of challenging targets. The ful

Re: [ccp4bb] (off-topic) Measurement of channel pore dimensions

Dear Bert, You could try the program Hole from http://www.ncbi.nlm.nih.gov/pubmed/9195488 J Mol Graph. 1996 Dec;14(6):354-60, 376. HOLE: a program for the analysis of the pore dimensions of ion channel structural models. Smart OS

Re: [ccp4bb] while on the subject of stereo

Those must be older ones... The current Nvidia shutter glasses we use are about 50g. http://www.nvidia.co.uk/object/product_GeForce_3D_VisionKit_uk.html Christoph Jürgen Bosch wrote: I think the weight of the shutter glasses puts them off. Compared to the 30g or less of the Zalmans the shutt

Re: [ccp4bb] while on the subject of stereo

I think the weight of the shutter glasses puts them off. Compared to the 30g or less of the Zalmans the shutter glasses feel like bricks. I would estimate them to at least 270g. After one hour wearing them you feel them on your nose. Jürgen .. Jürgen Bosch Johns Hopkins Blo

Re: [ccp4bb] while on the subject of stereo

Hi Dave, We recently equipped a pool of 25 computers with Nvidia 3D shutter glasses, they're used in structural biology courses for undergraduate students of biochemistry . We teach mainly PyMOL, but (in an advanced course) also model building in COOT. Of course, we let the students decide w

Re: [ccp4bb] while on the subject of stereo

I never thought I would agree with Tassos :-) But same experience 3D and wiggling with a snaked ligand makes live so much easier. It helps to have a fast graphics card though. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry &

Re: [ccp4bb] (off-topic) Measurement of channel pore dimensions

Try the program Hollow. Or visit USF and find the cavity script. There's also Carver out there but I never got it really to work for my purposes, but it's been written for channels. Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochem

Re: [ccp4bb] (off-topic) Measurement of channel pore dimensions

On 3/23/11 9:02 AM, Van Den Berg, Bert wrote: Hello all, Does anyone know how to get values for pore sizes of membrane channels? I'm not interested in A x B angstrom values measured between atom centers and assuming a regular pore shape, but a "real-life" value of either surface area at the n

[ccp4bb] (off-topic) Measurement of channel pore dimensions

Hello all, Does anyone know how to get values for pore sizes of membrane channels? I'm not interested in A x B angstrom values measured between atom centers and assuming a regular pore shape, but a "real-life" value of either surface area at the narrowest point or the volume of a block centered

Re: [ccp4bb] while on the subject of stereo

To add my two cents, I am not at all a fun of stereo for routine use, but I appreciate it if I have to look at a long ligand bent 90 deg in the middle to bury in my protein, and all that at 3.0-3.5 A resolution ... So, I must have both types of brain damage that Jan refers to. No surprises