Re: [ccp4bb] Weird MR result

On Thursday, 14 November, 2013 18:58:27 Niu Tou wrote: > Dear Phil, > > I used PHASER to do the task. I have double checked and both files have > the same prefix, so they are from the same output. I have also checked the > headers again, they have the same spacegroup. Actually I was trying to > s

[ccp4bb] I want to dock/align an EM envelope (MRC) into a DM averaging and/or solvent envelope (MSK).

Is there a single tool or suite of tools that addresses this? Or a CCP4 workflow if need be. Thanks! F - Francis E. Reyes PhD 215 UCB University of Colorado at Boulder

Re: [ccp4bb] Weird MR result

Dear Phil, I used PHASER to do the task. I have double checked and both files have the same prefix, so they are from the same output. I have also checked the headers again, they have the same spacegroup. Actually I was trying to search for two different molecules but only one was found. The space

Re: [ccp4bb] Weird MR result

Hello Niu, Do you have pseudo translation. It could echo of another molecule that might be in correct orientation. Regards Garib On 14 Nov 2013, at 22:47, Phil Jeffrey wrote: > Hello Niu, > > 1. We need extra information. What program did you use ? What's the > similarity (e.g. % identit

Re: [ccp4bb] [CCP4] Converting ShelX .phs to mtz

Hi Yury, Your idea seemed to work well, however I now have 50% completeness in phi and 100% completeness in Intensities. I am not sure where I am going wrong. H K L IMEAN FOM PHI SIGIMEAN > Hi Yarrow, > > You may consider producing mtz file from your original .sca or .hkl file > first. Then tak

Re: [ccp4bb] Weird MR result

Hello Niu, 1. We need extra information. What program did you use ? What's the similarity (e.g. % identity) of your model. What's your space group ? Did you try ALL the space groups in your point group in ALL the permutations (e.g. in primitive orthorhombic there are 8 possibilities). 1a

Re: [ccp4bb] shelx anamalous data

I'm not sure why you want to do that. If you wish to look at a map or poly-Ala trace from SHELXE, just read the .pdb and then .phs files into Coot directly. If you want to use them to make pictures with PYMOL, use Tim Gruene's SHELX2map. For further information please go to the SHELX homepage (

[ccp4bb] shelx anamalous data

I'm sorry, I have not used shelx before and didn't realize in my last post that the anamolous data is kept separate. I am planning on converting both the mysad.phs and mysad.pha to mtz files and then merge them. However, I am not sure of the column lables in mysad.pha. Does anyone know how to get

[ccp4bb] Converting ShelX .phs to mtz

Hello CCP4 users, I seem to be loosing data (50%) when converting shelX .phs reflelection file to mtz format using F2MTZ. I think it has something to do with loosing my anamolous data. Is it possible to merge the anamolous data before conversion or to tell F2MTZ to include it. These are my labels

[ccp4bb] [CCP4] Converting ShelX .phs to mtz

Hello CCP4 users, I seem to be loosing data (50%) when converting shelX .phs reflelection file to mtz format using F2MTZ. I think it has something to do with loosing my anamolous data. Is it possible to merge the anamolous data before conversion or to tell F2MTZ to include it. These are my labels

[ccp4bb] Submissions for next CCN newsletter

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission in the January 2014 issue is 15 December 2013 but if you can send me an email we can make exceptions so you can use the holiday break to work on your drafts. The Computational Cry

Re: [ccp4bb] observed criterion sigma

To add one more nugget, in your pdb you might see a REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.36 or some such thing. Ignore it (I am not sure why this isn't closer to zero, but that must be a result of French/Wilson). This is *not* your observed criterion for sigma for F's, although I

Re: [ccp4bb] observed criterion sigma

Dear Faisal - HKL2000 (Denzo/Scalepack) use I greater than -3 sigma (that's NEGATIVE 3) as the observed criterion, so that's what you would put down for this entry. There is another place where you're asked to provide an observed criterion for F's used during refinement. I always put down 0

Re: [ccp4bb] observed criterion sigma

As I understand it this refers to the decision whether an observation is valid or not, and the default value in HKL suite is -3 sigma (note the negative sign). The denzo/scalepack manual explains that while it is important not to exclude observations that are slightly negative due to random erro

[ccp4bb] Postdoc positions (SGC, Diamond): fragments into crystals

Hello, I have 3 open postdoc positions, to work on technologies around fragment screening in crystals, which is what my (joint) research team at Diamond (beamline I04-1) and SGC (PX group) is trying to make simple and accessible. Details of the project are on my website

[ccp4bb] A POSTDOCTORAL RESEARCHER IN MACROMOLECULAR MODELING

Dear All, On behalf of prof. Adrian Goldman, I would like to post a job opening position (please, see below). Best wishes, Robert A postdoctoral researcher position in macromolecular modeling will be available at the University of Helsinki (Department of Biosciences) from 1.1.2014, until 30.06.

Re: [ccp4bb] observed criterion sigma

Dear Mark et al., In small molecule crystallography one always refines against ALL data up to a specified resolution, usually 0.83A or better. Failure to do this generates a category A CheckCIF alert! However one is expected to give both the R-value for all data and a R-value for I < 2sigma(I). Th

Re: [ccp4bb] observed criterion sigma

I think it used to be "default" in denzo/scalepack. Or perhaps it was used to calculate statistics, but not to exclude reflections...I do remember having to "switch it off". On 14 Nov 2013, at 12:29, Phil Evans wrote: > Always deprecated, hopefully never common! > > > > On 14 Nov 2013, a

Re: [ccp4bb] observed criterion sigma

Always deprecated, hopefully never common! On 14 Nov 2013, at 11:27, Mark J van Raaij wrote: > It used to be common to only include reflections for which I > x sigma(I) in > refinement, with x often being 3. > However, nowadays this is not considered good practise, as reflections with > smal

Re: [ccp4bb] observed criterion sigma

It used to be common to only include reflections for which I > x sigma(I) in refinement, with x often being 3. However, nowadays this is not considered good practise, as reflections with small Is are likely to have I < 3 sigma(I), but are also important for refinement. In small molecule crystal

[ccp4bb] observed criterion sigma

Dear all I request you to please explain the "Observed criterion sigma" value required during pdb deposition. Does it depends on the methods of data integration and scaling ? if yes then what are the values for the data processed through scalepack2mtz (HKL2000) and scala (mosflm).. -- Regards F