[ccp4bb] Question about stereo on LCD monitor

Dear CCP4BB users, Sorry, for non-CCP4 question. I'm looking for any freeware program for molecule model building, especially for perfect matching RNA duplex. Could you help me? I found some programs with options of de novo protein chain building, but without options of DNA/RNA chain building.

[ccp4bb] Software for RNA model building

Sorry, for mistake in the title of my last post. Please ingnore it. Dear CCP4BB users, Sorry, for non-CCP4 question. I'm looking for any freeware program for molecule model building, especially for perfect matching RNA duplex. Could you help me? I found some programs with options of de novo

Re: [ccp4bb] Software for RNA model building

Dear Rafal, The program 'Coot' or (X)3DNA can easily do this for you. Regards Kristof On 12 May 2009, at 10:05, Rafal Dolot wrote: Sorry, for mistake in the title of my last post. Please ingnore it. Dear CCP4BB users, Sorry, for non-CCP4 question. I'm looking for any freeware program

Re: [ccp4bb] Software for RNA model building

I dare say that make-na can do it even easier (no need to install anything): http://structure.usc.edu/make-na/server.html It is for *very* simple stuff though. James On May 12, 2009, at 1:11 AM, Kristof Van Hecke wrote: Dear Rafal, The program 'Coot' or (X)3DNA can easily do this for

Re: [ccp4bb] phasing with se-met at low resolution

On Mon, May 11, 2009 at 05:22:25PM -0500, Pete Meyer wrote: P.S. I would also appreciate the specific query type for searching the PDB on the web for phasing method (MR, MAD, SAD, MIR, etc.). They seem to have everything under the sun searchable, but I cannot find this one. Last time I

[ccp4bb] Crystal Screen Optimization Server

Hi all, I’ve written a GUI to calculate 2D gradients for crystal screen optimization that people might find useful (much like a web 2.0 version of Hampton’s “Make Tray” utility). It’s intended to write scripts for a liquid handling robot our lab uses, but I’ve set up a public version up that

Re: [ccp4bb] SUMMARY:vSystem virtual machine recommendation for crystallography?

Hello Everyone, Thank you for the replies to my questions regarding system virtual machine software. I have organized the replies into subheadings and summarized the comments below. The original question was: I would like to install a system virtual machine to run Ubuntu Linux as a

Re: [ccp4bb] phasing with se-met at low resolution

measuring anomalous differences has nothing to do with resolution. measuring anomalous differences has nothing to do with Rmerge. measuring anomalous differences has EVERYTHING to do with signal and noise. (as does measuring anything else) If your average anomalous difference is going to be

Re: [ccp4bb] phasing with se-met at low resolution

Dear James, On Tue, May 12, 2009 at 11:26:55AM -0700, James Holton wrote: However, do not get too excited if this resolution limit is 6 A. Although 6 A phases are better than no phases at all, have you ever LOOKED at a 6 A map? It can be very hard to tell if it is protein or not, even

Re: [ccp4bb] phasing with se-met at low resolution

Thanks, I do understand all of that. I gave some Rmerge and resolution values to give some idea about errors and noise expected in the data, and an idea for up to what resolution phases would be good. And if such low resolution phases ever yield a meaningful model. Both measures are flawed

Re: [ccp4bb] phasing with se-met at low resolution

Dear Engin, On Tue, May 12, 2009 at 12:20:31PM -0700, Engin Ozkan wrote: The take home message for me was that noone agrees on the best data collection strategy No - since you have to factor in at least half a dozen parameters: unfortunately there is no silver bullet :-( Another point is the

Re: [ccp4bb] phasing with se-met at low resolution

However, do not get too excited if this resolution limit is 6 A. Although 6 A phases are better than no phases at all, have you ever LOOKED at a 6 A map? It can be very hard to tell if it is protein or not, even with perfect phases and all the right hand choices, etc. If the map is a 6

Re: [ccp4bb] phasing with se-met at low resolution

Dear James, I don't understand why measuring anomalous differences has nothing to do with resolution. Heavy atoms scatter anomalously because the inner shell electrons of the heavy atom cannot be considered to be free anymore as was assumed for normal Thomson scattering. As a result the atomic

Re: [ccp4bb] phasing with se-met at low resolution

Dear Raja, FOR  HIGH ANGLE REFLECTIONS ANOMALOUS DATA BECOMES IMPORTANT.   Raja  this is the theoretical point of view. As James pointed out, in real life the intensities of reflections at high resolution becomes comparable to the noise level so that the accuracy of which the reflections

[ccp4bb] Mercaptoethanol

Hi. We are trying to prepare heavy atom derivatives of a protein in which a surface residue was mutated to cysteine. Mass spectrometry of the purified cysteine mutant showed an additional peak with a molecular mass that correspond to a mercaptoethanol-bound cysteine mutant. I am

[ccp4bb] question on Akta Prime

Dear colleagues, I have an Akta Prime. I have always had problem with the reproducibility of the peak heights of the various peaks. Recently the pump is breaking. Does anyone have an idea what can cause the pump to break? It is more than once. Jackie Vitali

Re: [ccp4bb] Mercaptoethanol

Hi Bill: Thanks for the prompt reply. I will try purifying the protein without mercaptoethanol. Wataru On 2009/05/13, at 11:42, William G. Scott wrote: HI Wataru: I think it makes an R-S-S-R' bond, so the disulfide will prevent the heavy atom from binding, unless exchange is rapid.