Re: [ccp4bb] manipulation of water molecules in pdb files

The old fashioned water tidy will try to assign matching (non-standard) names to matching H2Os which is useful for analysis of structural waters, but cannot be deposited. I think coot has a tool to move waters to be near the protein but maybe that isn't all you want. Why not start deposition

Re: [ccp4bb] refinement of ligands

What do you mean - running REFMAC directly on the output file? Are you sure you have the same space group given in the mtz file and the PDB file? If the MR has placed your structure in P32 say, nd the input mtz has SG P31, you need to change the mtz header to include the now-known SG. There

[ccp4bb] refmac5.7 refine pesudo-translational symmetry

Dear all, Can I use the twin refinement to refine the pesudo-translational symmetry dataset? Thanks a lot for your help. Best wishes, Qixu Cai

Re: [ccp4bb] refmac5.7 refine pesudo-translational symmetry

My understanding is that ML functions in the presence of pseudo-translational symmetry are suboptimal (see a very short discussion in Acta Cryst. (2011). D67, 355–367. Acta Cryst. (2008). D64, 99–107 is also a good reading). Having said that if your crystal/dataset exhibits twinning on top of

Re: [ccp4bb] refmac5.7 refine pesudo-translational symmetry

It's a P212121 dataset. I have used phaser to find four solution in ASU. This is the phaser log file: PEUDO-TRANSLATIONAL NCS VECTOR -- Space Group : P 21 21 21

Re: [ccp4bb] refmac5.7 refine pesudo-translational symmetry

Hi, The second Patterson peak is twice the first (considering lattice translations, where 1 is equivalent to 0 modulo 1), and then if you triple the first vector you'll get minus the first vector (again considering lattice translations, i.e. 3/4 is equal to 1 - 1/4 which is equivalent to

[ccp4bb] value of observed criterion sigma

Dear all i have two basic queries 1) i have processed my data in HKL 2000 and during pdb submission i need to know the value of observed criterion sigma (F) and observed criterion sigma (I). 2) during entering data in category resolution shell whether one needs to mention the statistics of

Re: [ccp4bb] Space group R32 and H32

Dear Ian, Yes, the expression lattice mode I used is synonymous with centring type. The choice of a rhombohedral vs. a hexagonal cell would be a choice of centring type, whereas the choice of obverse vs. reverse would be a choice of setting. A clear operational difference between the two is

[ccp4bb] Master in Crystallography and Crystallisation?

Hi folks First off, apologies to all who are not members of the BCA, since this is a question for the BCA members amongst you - I asked BCA to send out an advert for this course, and their admin people say they have done so - but I haven't received it, so I was wondering if anyone had got it?

Re: [ccp4bb] Summary for scale out data

Hi Uma, The scale.log file contains all of those values. They're all near the bottom of the file. Also, once you refine your structure, refmac will print out most of those numbers in the .pdb file. --- Greg

Re: [ccp4bb] Summary for scale out data

Hi Uma, In HKL2000, if you go to Report menu (near to Help menu) you will see the option for generation of tables. Hope this helps. With regards S. Karthikeyan On 7/31/2012 6:57 PM, Uma Ratu wrote: Dear All: I process my data using HKL2000. After scale, the program generates several

Re: [ccp4bb] value of observed criterion sigma

HKL2000 does not have an observed criterion sigma (F) since Scalepack deals with intensities. Leave that entry blank. Scalepack uses observed criterion sigma (I) = -3 On question #2 you always want to quote the statistics (completeness, Rsym, I/sigI etc) for the highest resolution shell but

[ccp4bb] rigidbody group in refmac5

Dear all, When we are running the rigidbody refinement of refmac5, if we do not assign the rigidbody group in CCP4i GUI, what's the default rigidbody group in refmac5? Is it a rigidbody for each chain? Thanks a lot.

[ccp4bb] FW: Principal Scientist, Crystallography at Takeda California (San Diego)

Resending for posting. From: Marshman, David (TSD) Sent: Tuesday, July 31, 2012 9:00 AM To: ccp4bb@jiscmail.ac.uk Subject: Principal Scientist, Crystallography at Takeda California (San Diego) Principal Scientist, Crystallography at Takeda California (San Diego) Summary Plays a

[ccp4bb] July 2012 Computational Crystallography Newsletter

Folks The latest issue of the Computational Crystallography Newsletter is available on-line at http://www.phenix-online.org/newsletter for download. The articles are of general interest to protein crystallographers and are listed below. Enjoy Nigel Moriarty Articles --- cctbx tools

Re: [ccp4bb] manipulation of water molecules in pdb files

Thank you all for quick replies. The issue has been solved by using sortwater and a little manual editing. Using PDBe could be a easier way. Next time I may try it. Best, Zhiyi On 7/31/12, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: The old fashioned water tidy will try to assign matching

Re: [ccp4bb] rigidbody group in refmac5

Dear Lakshmanan Govindasamy, I cannot find the related information in refmac5 document. Could you please help me? Thanks. Qixu Cai Email: caiq...@gmail.com School of Life Sciences, Xiamen University, Fujian, China **from thunderbird** On 08/01/2012 04:43 AM, Lakshmanan Govindasamy wrote: