Re: [ccp4bb] R pim and Rmeans

Hi Frank, of course R_pim is just one number and it may not be discriminatory enough to decide when to stop including images. But I can say from my own experience that R_pim will not drop forever. I have seen data sets with R_pim values of 0.5% to 2.0 A or better resolution, but never R_pim

Re: [ccp4bb] R pim and Rmeans

There are useful plots from scala showing various measures v frame number. I usually look at those and do some hand waving to decide where the increasing R_xs indicate you are measuring nothing, or measuring something different from the first frames because of radiation damage Eleanor Frank

Re: [ccp4bb] R pim and Rmeans

Hi Frank, maybe this is an opportunity to state that there is indeed a way to assess radiation damage by looking at an R-factor plot, but that R-factor is R_d [1], not R_pim. The formula and some explanation is in the CCP4 wiki at

Re: [ccp4bb] refmac 5.5.0068 error

Dear Michael, ARP/wARP should recognise this refmac version with no problem. Before typing './install.sh' just do 'refmac5 -i' to check that refmac is executed fine and CCP4 environment is setup. If the problem remains please get back to us with details on the ARP/wARP version number and

[ccp4bb] plate survey

Hi Community, I would like to do a little survey on popular 2-3 drop per 96 well plates, and the pros and cons of these plates. I know that the new Cornings, the MRC and the Intelliplates are used often in the labs I visit (we use 2 drop MRC plates mostly). Perhaps you can comment on optical

Re: [ccp4bb] Summary - torsion angle restraints in REFMAC

On the Ligand tab (upper left of web page), at left you'll see PDB (model coordinates) and PDB (ideal coordinates). The Ideal coords really are idealized, including a very different torsion between the two ring systems in this ligand. The Model coords seem correct (one of the two in the asymmetric

Re: [ccp4bb] Restrictions in ccp4-6.1 ?

The current value of maxbat in scala_/parameters.fh is 5000 Mind you, according to CVS this was increased from 1000 to 5000 in 1999! sortmtz and reindex also have MBATCH=5000. There's no restriction in the library itself. Cheers Martyn -Original Message- From: CCP4 bulletin board on

[ccp4bb] generating omit maps

Hi Everyone, Can anyone tell me a relatively easy way to generate an omit density map for a ligand? I know that CNS can do this, but I was wondering if there's a CCP4 related program to generate omit maps. Thanks, Kathleen

Re: [ccp4bb] generating omit maps

Subject: generating omit maps From: Kathleen Frey [EMAIL PROTECTED] Reply-To: Kathleen Frey [EMAIL PROTECTED] Date: Wed, 10 Dec 2008 10:30:47 -0500 Hi Everyone, Can anyone tell me a relatively easy way to generate an omit density map for a ligand? I know that CNS can do this, but I was

Re: [ccp4bb] generating omit maps

as a small variation on this, I would first finish the protein, and then include ligands, working from larger to smaller (ATP = citrate = glycerol = sulphates = waters). Sometimes several waters (from automated solvent building) in place of a bona fide ligand (or a glycerol for example)

Re: [ccp4bb] generating omit maps

On Dec 10, 2008, at 9:52 AM, Mark J. van Raaij wrote: as a small variation on this, I would first finish the protein, and then include ligands, working from larger to smaller (ATP = citrate = glycerol = sulphates = waters). Sometimes several waters (from automated solvent building) in

Re: [ccp4bb] generating omit maps

Let me also follow up on this point. I also agree that the ligand should be added very late in the refinement/model-building procedure. I also encourage people in my group to create a subdirectory BEFORE_LIGANDS into which they put the current PDB and map (or mtz) files prior to adding the

Re: [ccp4bb] generating omit maps

Kathleen - The easiest way is to simply remove the ligand from the coordinates and refine for a few cycles. Whether that is particularly meaningful is another question. Better would be to remove the ligand coordinates, shake the remaining coordinates (i.e., randomly displace them by a

Re: [ccp4bb] R pim and Rmeans

Yup, there is that. It doesn't help make the decision, though, of how much to include. And the other problem is it requires higher redundancy than I usually have when living on the edge of completeness vs death. (It's not multiplicity-weighted, is it?) (It's other problem is that it is

[ccp4bb] definition of I Sigma I

Hi, does anyone have a definition of I Sigma I please. Any definitions that i have found are not very informative for novices. thanks andy

Re: [ccp4bb] definition of I Sigma I

Hi - I Sigma I means nothing. I/sigma(I) is the average intensity of a group of reflections divided by the average standard deviation (sigma) of the same group of reflections. Usually its reported per resolution shell, groups of reflections within thin shells of resolution. I/sigma(I)

[ccp4bb] Ref for B-factor Underlying Phenomenon

Hello Crystallographers, does anybody have a good reference dealing with interpretations of what B-factors (anisotropic or otherwise) really signify? In other words, a systematic addressing of all of the possible underlying molecular/crystal/data-collection phenomena which the B-factor

[ccp4bb] Summary: Modeling residues with very poor density

Thank you Afonine, Hans, Kumar, Deliang, Mark, Jose, Tim, Eleanor and Ed for sharing your thoughts. Here is a summary of the responses I received- 1. One should try to model residues based on 2Fo-Fc maps contoured at 1.0 sigma level. Structures of mobile regions/loops can sometimes be

Re: [ccp4bb] Ref for B-factor Underlying Phenomenon

The original reference is Debye, P. (1914) Ann. d. Physik 43, 49, which is in German. Waller's paper came later and the forgotten paper wich did the math rigorously was Ott, H. (1935) Ann. d. Physik 23, 169. The best description I have seen in English was in chapter 1 section 3 of: James R. W.