Re: [ccp4bb] Hi

I would suggest biopython. http://combichem.blogspot.com/2013/08/aligning-pdb-structures-with-biopython.html On Tue, May 26, 2015 at 10:25 AM, Dimitry Rodionov d.rodio...@gmail.com wrote: Dear Vijay, Your problem sounds like a job for LigAlign: http://www.pymolwiki.org/index.php/LigAlign

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

Isn't the only criteria for EDS that calculated R (by EDS) is +/- 5% of reported R? On Thu, Apr 23, 2015 at 12:35 PM, Misbah ud Din Ahmad misba.ah...@gmail.com wrote: Dear Gert, I just did that and I wonder how these structures end there !!! @ Sabine: I was talking about Ramachandran

Re: [ccp4bb] extracting PHENIX structures

I did the same search as above (Patrick). I am confused how with SHELX you can get 320 (when using SOFTWARE) and then when using TEXT only 130. I get the same no's. If the word SHELX exists as follows SOFTWARE USED: SHELX the same word (SHELX) will be picked up when we do a text search as well

Re: [ccp4bb] AW: [ccp4bb] RMSD between structures of homologous proteins

Thanks to the mailing list I came across this: http://www.ncbi.nlm.nih.gov/pubmed/24167157 The C code to compute is available on the link mentioned in the paper. Best wishes, George On Wed, Aug 13, 2014 at 8:01 AM, Eugene Krissinel eugene.krissi...@stfc.ac.uk wrote: It is probably

[ccp4bb] AMoRe

Hi, Has anyone tried the tutorial on the CCP4 website for AMoRe? http://www.ccp4.ac.uk/examples/tutorial/html/mr-tutorial-amore.html I am trying to learn how to use the package in CCP4 and it fails and I am wondering if the tutorial has become outdated? Thank you, George

[ccp4bb] DATAMAN/RAVE alternatives

Hi, I was looking at the Kleywegt et al paper from 2004 'The Uppsala Electron Density Sever' and I was trying to follow the steps outlined in the paper (section 3) 'Generating the maps' I found RAVE/DATAMAN on the Uppsala s/w factory but for my OS X (10.7.5) it seems it is no longer supported.

Re: [ccp4bb] DATAMAN/RAVE alternatives

, George Devaniranjan devaniran...@gmail.com wrote: Hi, I was looking at the Kleywegt et al paper from 2004 'The Uppsala Electron Density Sever' and I was trying to follow the steps outlined in the paper (section 3) 'Generating the maps' I found RAVE/DATAMAN on the Uppsala s/w factory but for my

Re: [ccp4bb] EDSTATS for an extracted fragment

Thank you Gerard for your suggestion. I will look into the paper you suggested and MAPMAN too. I am idealizing fragments of PDB and while this would not agree when compared with the well refined structure, my goal really is seeing if these ideal fragments can still be identifiable when I look

[ccp4bb] EDSTATS for an extracted fragment

HI, I want to calculate real-space R factor/RSCC and such parameters using EDSTATS in CCP4 but only for a selected fragment that has been extracted and then modified (changed the Phi and Psi) from the native. I have the original MTZ and MAP. Is it even possible to calculate these values

Re: [ccp4bb] EDSTATS for an extracted fragment

calculated from the PDB file supplied. If you have changed the PDB file then the original MTZ/MAP files will no longer be suitable. This means you have to supply exactly the same complete PDB file that you used to run the refinement job. Cheers -- Ian On 10 June 2014 19:52, George

Re: [ccp4bb] EDSTATS for an extracted fragment

, Jun 10, 2014 at 8:04 PM, Ethan A Merritt merr...@u.washington.edu wrote: On Tuesday, 10 June, 2014 19:13:57 George Devaniranjan wrote: Thank you Ian. To clarify, I actually want to compare the new PDB file to the old MTZ file to see how well the residues fit. This is why I mentioned that I

[ccp4bb] : MTZ for a protein fragment and R factors, Masking and Maps

Hi, First off I am pretty new to CCP4/X-ray crystallography so please bear with me as I try to explain my question. I was looking at a protein structure from the PDB (let's say 1aho.pdb). I have the corresponding MTZ file. I wanted to calculate the R-factor for some selected residues (lets say