Re: [ccp4bb] Who invented PDB format?

### ### ### ### CCP4 6.3: COORDCONVversion 6.3 : 17/09/08## #

Re: [ccp4bb] Who invented PDB format?

bash or any other shell script using http://www.ccp4.ac.uk/html/coordconv.html Probably moleman2 http://xray.bmc.uu.se/usf/moleman_man.html can handle your request too. Jürgen On Jan 7, 2013, at 12:48 AM, Teri Arman wrote: Fractional Coordiantes to Orthogonal Coordinates and Vice Versa Hi, I n

Re: [ccp4bb] Who invented PDB format?

Fractional Coordiantes to Orthogonal Coordinates and Vice Versa Hi, I need help, how can I make coordiates of 100 of PDBs of different space groups to fractional coordiantes and vice versa. I do not find CCP4 do it? A program of fortran or C codes with possible suggestion may be helpful. Thank yo

Re: [ccp4bb] "Difference" set of contacts

CCP4 now has QtPISA, where the output is prettier than at the EBI :) Eugene On 6 Jan 2013, at 12:42, Eleanor Dodson wrote: > pisa at the ebi will do this very nicely. > > Upload your pdb files. > > PISA is part of the CCP4 distribution too, but the EBI output is prettier > Eleanor > > On 4 Ja

Re: [ccp4bb] pymol help?

Hi, Make sure your mouse mode is set to 3-button editing mode ! *How to move stuff around in PyMOL?* To move molecules around one have to activate 3-button editing mouse mode. Easiest way to do it is to click on "Mouse Mode - 3-Button Viewing" in the lower right corner of the main window. Then y

[ccp4bb] pymol help?

I am trying to manually move a molecule (pdb) onto another molecule (pdb) in pymol. I opened molecules separately. When I use the middle button on my mouse both move together, as if one object. I will appreciate any help. Thanks Debasish

Re: [ccp4bb] Who invented PDB format?

As a person who wears two hats- "we- the crystallographers" and "they- the bioinformaticians" it is interesting to see that the world can be divided by one of the most trivial issues- coordinate formats! Enjoying the debate :) Shekhar On Sun, Jan 6, 2013 at 8:02 PM, Boaz Shaanan wrote: > Dear

Re: [ccp4bb] Who invented PDB format?

Dear Ian, thank you for enlightening my ignorance! So George, maybe PDB coordinates will be accepted by chemical crystallographers? Doing this also them will develop something as nice as bioinformatics! :-) FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Mol

Re: [ccp4bb] Who invented PDB format?

Dear George, "Those folks" (bioinformaticiens ?) are not interested in inter-molecular contacts, as far as I'm aware so they can't bothered less by the orthogonal coordinates used in pdb files.     Cheers, Boaz   Boaz Shaanan, Ph.D. Dep

Re: [ccp4bb] Who invented PDB format?

While it is certainly a simple coding job to convert back and forth between orthogonal and fractional coordinates there is perhaps something lost in the former and that is the notion of a molecule embedded in a crystal structure. Generally speaking, it's the latter that we determine. George may

Re: [ccp4bb] Who invented PDB format?

The original PDB format that was used for the first 100 or so entries carried both fractional and orthogonal coordinates. That format used 132 column lines which was awkward on some computers. When we designed what is now known as PDB format we decided to use 72 columns for data plus sequencing

Re: [ccp4bb] Who invented PDB format?

> ... anyhow all calculations during refinement are in fractional coordinates ... Not necessarily: I can only speak for the RESTRAIN program for restrained refinement that I was involved in developing (the first use of TLS in macromolecular refinement), and at no point were co-ordinates converted

Re: [ccp4bb] "Difference" set of contacts

pisa at the ebi will do this very nicely. Upload your pdb files. PISA is part of the CCP4 distribution too, but the EBI output is prettier Eleanor On 4 Jan 2013, at 22:11, Brad Bennett wrote: > Hi all- > I have 2 PDB files of the same protein (in slightly different states) and I > want to outp

Re: [ccp4bb] Who invented PDB format?

Well, for bioinformatitions the only benefit is that they can calculate distances without going into trigonometric functions. However, angles even in cartesian PDB system will require trigonometry. Fractional coordinates are more difficult, as even distance calculations require trigonometry an

Re: [ccp4bb] Who invented PDB format?

Chemical crystallographers have always used fractional coordinates, it makes it so much easier to handle symmetry, special positions etc. But if the PDB hadn't used orthogonal coordinates, bioinformatics might never have taken off. George On 01/06/2013 09:34 AM, Eleanor Dodson wrote: Some of us

Re: [ccp4bb] Who invented PDB format?

Some of us resisted using an orthogonal format for coordinates, arguing that the output from a crystal structure should refer to crystal axes. And since symmetry was a crystal property it was important that we could "see" it easily. The PDB format won out, but I still use coordconv a lot to t