Re: [ccp4bb] Reindexing Orthorhombic

James Stroud wrote: ... What is the operation to reindex such that real space is rotated 180 about z? These are in P212121. Isn't that the 21 along z in your orthorhomic space group? Just apply it to your MR solution instead, and add an affine normaliser if needed to superpose the

Re: [ccp4bb] build fragment library from pdb based on a specific geometry

The most general solution to this problem boils down to one of graph isomorphism: http://en.wikipedia.org/wiki/Graph_isomorphism James On Apr 16, 2009, at 8:13 PM, rui wrote: Dear all, I want to pull out the sugar binding proteins from the pdb, however, there are so many different

[ccp4bb] Pointless not Painless

Below is my log file. The crux of the output is Reindexed space group is not in library. Given the output, I think it should still be p212121. The log makes no mention as to which space group is actually missing, only that it has been reindexed. I take it that the symops listed describe

[ccp4bb] Taking account of Density modification in Refmac

My basic question is how do you get refmac to take account of denisty modfication of the mtz file. Do you have to explicitly tell it to do this? Is it done by inputting hendrickson-lattman coefficients or something? cheers Andy

Re: [ccp4bb] build fragment library from pdb based on a specific geometry

hi Rui RCSB run a facility called Ligand-Expo (formerly Ligand-Depot.) You sketch a fragment of a ligand and it runs a graph search on the ligands in the PDB. http://ligand-expo.rcsb.org/ chiralities are not specified so it is perfect for your sugar query best wishes Pete Quoting rui

Re: [ccp4bb] Taking account of Density modification in Refmac

Hi Andy, Density modification should mean that you have some phases for your structure. As far as I know you can ask refmac to take experimental phases into account. What exactly are you trying to do? Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG

Re: [ccp4bb] Reindexing Orthorhombic

If you were lazy you'd just run phaser ;-) -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Fri, 17 Apr 2009, James Stroud wrote: Update: The pounding I am beginning to feel in my head is reminiscent of a pounding I felt while

Re: [ccp4bb] Reindexing Orthorhombic

Update: The pounding I am beginning to feel in my head is reminiscent of a pounding I felt while working in p43212 a while ago. I think this is an alternate origin issue. Now I just need to figure out how to redefine the origin. James On Apr 16, 2009, at 9:38 PM, James Stroud wrote:

Re: [ccp4bb] Taking account of Density modification in Refmac

Hi Tim, I have a solution of a structure from MR without using DM. I have performed DM and now want to see if this improves my refinement compared to not using DM. cheers andy 2009/4/17 Tim Gruene t...@shelx.uni-ac.gwdg.de: Hi Andy, Density modification should mean that you have some phases

[ccp4bb] close Cl contacts and poor Cl density

Hello, Does anyone have any insights into close intermolecular contacts involving Cl atoms in crystal structures? There may be some basis for close contacts (~ 2.5Å) in the phenomenon so-called halogen bonding [ref-1] but this does not explain close C-Cl contacts observed in some structures for

Re: [ccp4bb] Reindexing Orthorhombic

Dear James, yes, this reminds me of a problem long time ago: since the origin in P212121 is defined as the midpoint of non-intersecting screw axes (I hope that's right - I don't have the tables at hand), you have to add (1/4*a,1/4*c,1/4*b) after re-indexing, if I'm not mistaken. Best

[ccp4bb] Refmac dictionary problem

Dear ccp4bb, I've finally gotten around to updating my ccp4 to version 6.1.1 with the default refmac 5.5.0072 that comes with this from the ccp4 downloads site. I am working on relatively high resolution structures with a number of alternate conformers for certain amino acids which I put

Re: [ccp4bb] close Cl contacts and poor Cl density

How about disorder and/or partial occupancy? B-factors of the Thr and Cl seem pretty high compared to the rest of the structure. Hydrolysis during (possibly weeks/months of) crystallisation is another option. Check the pH and presence of nucleophiles. cheers, Hans Mike Gretes schreef: Hello,

Re: [ccp4bb] Reindexing Orthorhombic

when reindexing p212121 with -h,l,k, you get P 21 21 21 (a+1/4,b-1/4,c-1/4) so you should subtract 1/4 from x and add a quarter to y and z. some tools in the cctbx are available that make this go easy (reindexing and moving things back to a standard setting). Reruning phaser might be the least

Re: [ccp4bb] build fragment library from pdb based on a specific geometry

There are a number of useful tools at glycoscience.de http://www.dkfz.de/spec/glycosciences.de/tools/index.php Unfortunately, none of them may be **exactly** what you are looking for... pdb2linucs - extracts carbohydrate information from pdb files (definitely not a trivial task considering

Re: [ccp4bb] Refmac dictionary problem

Thanks to Robbie Joosten who suggested updating to refmac 5.5.0090 which seems to be happy with alternate conformation again. I thought it was probably worth mentioning on the list that the ccp4 bundled refmac has this bug. Simon On 17 Apr 2009, at 14:07, Simon Kolstoe wrote: Dear

[ccp4bb] In CCP4 6.1.1 import_scaled isn't reading a dataset_name?

Despite setting a dataset name in the dialog box, i get the following in the log file. $TEXT:Warning: $$ comment $$ WARNING: PROJECTNAME not assigned $$ $TEXT:Warning: $$ comment $$ WARNING: CRYSTALNAME not assigned $$ $TEXT:Warning: $$ comment $$ WARNING: DATASETNAME not

Re: [ccp4bb] Reindexing Orthorhombic

James, If you still have the raw images on line, you can use a new feature in LABELIT to take care of matching the 2nd dataset indexing solution against the isomorphous atomic model from data set 1, and then re-integrate. Usage: labelit.index data set 2 first image data set 2 90-degree

Re: [ccp4bb] Calculation of angle between two helix of different subunits

Check out also this paper. --- Comput Biol Chem. 2008 Oct;32(5):370-4. Epub 2008 Jul 7. Determination of helix orientations in proteins. Tatulian SA. Biomolecular Science Center, University of Central Florida, 12722 Research Parkway, Orlando, FL 32826, USA. statu...@mail.ucf.edu

Re: [ccp4bb] Reindexing Orthorhombic

For the sake of completeness I also thought that the REFERENCE_DATA_SET card in XDS does the same thing. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Fri, 17 Apr 2009, Nicholas K. Sauter wrote: James, If you still have the