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 wrote: > Dear Vijay, > > Your problem sounds like a job for LigAlign: > http://www.pymolwiki.org/index.php/LigAlign > > Regards, > Dm

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 wrote: > Dear Gert, > I just did that and I wonder how these structures end there !!! > > @ Sabine: I was talking about Ramachandran outliers. I had learnt th

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 wel

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 Gesamt/

[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I am trying to learn how to use the package in CCP4 and it fails and I am wondering if the tutorial has become outdated?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

Re: [ccp4bb] DATAMAN/RAVE alternatives

40 AM, 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'

[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] 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 lo

Re: [ccp4bb] EDSTATS for an extracted fragment

On Tue, Jun 10, 2014 at 8:04 PM, Ethan A Merritt 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 ment

Re: [ccp4bb] EDSTATS for an extracted fragment

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 Devaniranjan >> wrote: >> >>> HI, >>> >>>

[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 witho

[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 1