Re: [ccp4bb] tricky mr problem

We often use a "S-SAD" type data collection (there would be no need for enormous redundancy) which, if your model is correct, should show up the S positions in the same way as a Se-met would show up the Se positions. Good way of "validating" your model and a help to tracing. Cheers Andy

Re: [ccp4bb] tricky mr problem

>From my experience, my two cents: 1) Retain as much of the structure that fits the density well (no need to trim to poly ala completely), remove the rest and keep refining and adding on. You seem to have got the right solution. 2) Try simulated annealing and omit map calculations to improve on th

[ccp4bb] Docking models into low-res SAD map - summary

Many thanks for all the replies - I haven't yet tried all of them, but they all look worth following up on, much food for thought here: * Several people suggested SITUS COLORES, which I shall certainly try and had not heard of until now. * The program ESSENS, from the Uppsala software factory,

Re: [ccp4bb] Fwd: [ccp4bb] tricky mr problem

I've had good luck using the CCP4 DM program PARROT to improve poor initial MR maps with twinned data. (Based on some suggestions from this bb.) I think it works especially well if you have a lot of NCS symmetry, but it's worth a try, and doesn't take long. Cheers, ___

[ccp4bb] Fwd: [ccp4bb] tricky mr problem

I would try phase improvement, especially since you have two molecules per a.u. In other words averaging, solvent flattning, histogram matching. The best way is to start at low(er) resoltuion and extend to the highest resolution vailable. The best criterium for success is a improved and interpretab

Re: [ccp4bb] tricky mr problem

Rhys, Having worked on a number of these structures using both MR and SAD/MAD, my advice is to continue to make experimental phasing a priority since building into a poor density map at this resolution can take months to years to finish while building into a nice experimental map can take a few

Re: [ccp4bb] tricky mr problem

On Monday, 23 September, 2013 22:01:32 RHYS GRINTER wrote: > Hi all, > > I have been attempting to find a MR solution for a low resolution data set > (3.9A), with pretty poor merging stats of a 22 strand membrane beta barrel > I'm working on. > > I've created a trimmed poly-alanine from a struc

Re: [ccp4bb] tricky mr problem

Taking Tfz of 14.3 I assume that you have used Phaser, and according to what authors say, it is most probably the solution. Maybe map is not yet good, but you can try to refine using modern approaches for refinement of low resolution structures which are recently implemented in Refmac and Phenix.

[ccp4bb] tricky mr problem

Hi all, I have been attempting to find a MR solution for a low resolution data set (3.9A), with pretty poor merging stats of a 22 strand membrane beta barrel I'm working on. I've created a trimmed poly-alanine from a structure of 17% identity, that gives a solution with a Tfz of 14.3 with two

Re: [ccp4bb] tNCS: indexing and EP problems

Thanks for your answers, I realized too late that my question number 2 was misleading. I wondered in fact whether shelxd or another program could handle tNCS fine. Otherwise for my indexing concerns, I have been trying to feed xds with the unit cell parameters found by mosflm via the UNIT_CELL_C

[ccp4bb] השב: Re: [ccp4bb] tNCS: indexing and EP problems

Hi Nicolas, You may want to make sure that all other parameters in XDS are the same as in mosflm and particularly the origin. Otherwise, how does the xds indexing/integration look? Perhaps pointless will give a clue about the relation between the xds and mosflm cells/spacegroup? Cheers, Boaz

Re: [ccp4bb] tNCS: indexing and EP problems

>In difficult cases I use adxv to get an estimate for the cell >dimensions to judge whether or not XDS found the correct one. The new XDS gui can also serve for that these days, I guess. Boaz

Re: [ccp4bb] tNCS: indexing and EP problems

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Nicolas, shelxd is one answer to question 2 (http://shelx.uni-ac.gwdg.de/SHELX/shelxd_mm_keywords.php: PATS). I am sure there are others. You can provide the cell from mosflm to XDS. If you want XDS to find the cell without this information, the

Re: [ccp4bb] tNCS: indexing and EP problems

Hi, I'm not sure what you mean by 'configuring XDS the same way', do you mean that you tried to use the results from Mosflm as input to XDS? If not, it's worth trying. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 8410

Re: [ccp4bb] tNCS: indexing and EP problems

Hi Boaz, I'm looking for one or several XDS keyword(s) to configure, in order to find the same unit cell that Mosflm found. Thanks, Nicolas On 23/09/2013 15:04, Boaz Shaanan wrote: Hi, I'm not sure what you mean by 'configuring XDS the same way', do you mean that you tried to use the res

[ccp4bb] tNCS: indexing and EP problems

Dear experts, I am dealing at the moment with a case involving translated NCS copies of my asymmetric unit along one axis of the unit cell (3 clear non-origin peaks in the native Patterson). I could get Mosflm to find the corresponding big unit cell only after restricting the "max deviation

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