Re: [ccp4bb] just how bad can phases be and still help

On Thu, 6 Sep 2007, William Scott wrote: I think the reason it works is because the lack of closure error is nearly random and the signal is not interesting notion Low initial FOM in many senses are good [..] because density modification has more latitude my understanding was that density m

Re: [ccp4bb] few organophophates coordiantes

Dear Sam The HIC-Up website link is http://xray.bmc.uu.se/hicup/ Hope it will help you Vijay Kumar, SRF Protein science and Engg. Division IMTECH, Sector -39A, Chandigarh INDIA U Sam <[EMAIL PROTECTED]> wrote Hi, Thanks for the reply to my earlier query.

Re: [ccp4bb] just how bad can phases be and still help

Hi Bryan: I think the question is hard to answer because the idea of "bad" phases is not particularly well-understood (at least by me). Good phases give you a nice map. "Weak phases" give you a map that is weakly interpretable, but often can be improved by solvent flattening, NCS averaging, and

[ccp4bb] just how bad can phases be and still help

general question - perhaps the fundamental question - for anyone who had "weak/poor/bad" phases from some source, that were later actually used to solve a structure when combined w/ another source - HOW bad were the worst phases on their own, in terms of resolution, FOM, CC, e-density, (any ot

[ccp4bb] The X6A workbench - Fall session

The X6A workbench - Advanced Strucutral Biology Tools at the National Synchrotron Light Source scheduled for September 25 through 28 Is a hands-on course for those interested in getting acquainted with Synchrotron Radiation methods in structural biology. The course provides a comprehensive vie

Re: [ccp4bb] xplot84driver problems

Hi, Yes, I made the files on the Intel Mac. I've sent one to Charles Ballard for testing. They do also work wih pltdev. I agree about the antediluvial origins of xplot84driver, but for lack of anything better... Derek On Sep 6, 2007, at 17:15, [EMAIL PROTECTED] wrote: Did you make you

[ccp4bb]

Somebody out there (preferentially in the US) who is willing to sell his/her used MAR imaging plate. It should be in good working condition. Please contact me directly (not the ccp4bb). Best Marius Dr.habil. Marius Schmidt Asst. Professor University of Wisconsin-Milwaukee Department of Physics

Re: [ccp4bb] xplot84driver problems

The file format is definitely machine byte order dependent. (see $CDOC/plot84.doc) A few years ago I was toying with the idea of making library code deal with swapping if need be... Never did it though William Scott wrote: Did you make your plt file on the intel mac? I've noticed that one

Re: [ccp4bb] xplot84driver problems

Did you make your plt file on the intel mac? I've noticed that ones I made on ppc give that error on my otherwise functional xplot84driver (in the fink package). I tried byte-swapping with dd but to no avail. I guess this is still the cutting edge of 1984 software? Bill On Thu, 6 Sep 2007 15

[ccp4bb] glycosidic bonds for refmac library

Hello everyone, I have a couple of structures which contain oligomeric sugars in different conformations. Is there any general way of defining a glycosidic bond for the refmac library - instead of creating .cif files for every single ligand-structure ? Thank you very much in advance Eike

[ccp4bb] combining various SAD phases

Hi, i would be interested in hints about what would be the best way to combine & improve SAD phases from two (or several) non-isomorphous crystals, i can only get reasonable phases from SHARP so far i think. (the other set is very poor but has some signal there) one back as HLs into sharp? or d

[ccp4bb] xplot84driver problems

Hi, I've installed CCP4 on an Intel Mac running Mac OS X 10.4.10 using the binary installer from the automatic download page. Everything works fine and dandy except xplot84driver. This currently means I have to convert every plot file on the command line using pltdev then use Preview to v

Re: [ccp4bb] How to obtain specific chain protein structures without ligand?

You would have to edit the command script for PDBSET (From GUI - Run and View com file, then modify it..) There are options to select CHAIN A and protein only. etc etc Eleanor Antony Oliver wrote: You could simply hand-edit the PDB file to remove the offending ligand. Regards, Tony. H

Re: [ccp4bb] How many twinned crystals?

Not an expert on integration at all, but is this true for mosaic crystals when spots overlap rather messily? Eleanor George M. Sheldrick wrote: Since processing non-merohedrally twinned crystals became routine in small-molecule crystallography, the number of such twins has increased dramatical

[ccp4bb] ESRF Rolling access beamtime

Dear all, The ESRF is pleased to remind you about the procedure for applying for rolling access beamtime on its MX beamlines. The rolling access procedure is designed to improve access to ESRF MX beam-lines and encourage the use of ESRF facilities by smaller groups working in the MX field. Thi

Re: [ccp4bb] Best program to find whether a crystal is twinned ?

Within CCP4 SFCHECK and TRUNCATE provide an analysis the PHENIX Xtriage is excellent.. See http://www.ccp4.ac.uk/dist/html/twinning.html Eleanor Jobichen Chacko wrote: Dear All, Can you please inform me the programs available to find whether a crystal is twinned and also the data reduction

Re: [ccp4bb] How many twinned crystals?

Crystals with messy spots smeared out in one direction with sometimes more than one maximum are probably better described as split crystals rather than twins, but if the splitting of the spots is clear enough the same procedures can be used to integrate them. George Prof. George M. Sheldrick F

Re: [ccp4bb] Resid for occupancy

Vu Thai wrote: Hi, I have a protein that binds nucleotides, and in my structure, it appears that the binding pocket is partial occupied by ADP and AMP; the beta phosphate of ADP is transfered to another molecule. I want to refine the structure with both ADP and AMP modeled in the sight and manu