Re: [ccp4bb] Easy way to generate symmetry-related protein chains? (summary)

Yes, "Save Symmetry Coordinates" in COOT is a very easy way. To avoid text editing, you can first reload the pdb and use the "Copy Fragment ..." under Extensions/Modeling to get the desired chains. Then use the "Merge Molecules" under Calculate to assemble. Yong -Original Message- Fr

Re: [ccp4bb] Easy way to generate symmetry-related protein chains? (summary)

It seems the easiest way is to "Save Symmetry Coordinates" in COOT and then assemble the desired chains in a text editor. > Extensions -> Modelling -> Symm Shift Reference Chain Here. is present if you build COOT yourself, but is not in the pre-built releases (for now). Mark J van Raaij Dpto de

[ccp4bb] In Situ Serial Crystallography Workshop at SLS

In Situ Serial Crystallography Workshop http://indico.psi.ch/event/issx Swiss Light Source, Paul Scherrer Institut, Switzerland Nov. 17-19, 2015 This workshop is dedicated to the presentation of a novel in meso in situ serial crystallography (IMISX) method (Huang et al. 2015 ActaD), which comb

Re: [ccp4bb] Easy way to generate symmetry-related protein chains?

If you mean generation of pdb coordinates of specific symmetry chains (not just viewing) then you can do this with the symexp command in pymol. Select the desired symmetry partners and save as pdb. You may want to edit duplicate chain id labels in coot or a text editor. Roger Rowlett On May 22, 20

Re: [ccp4bb] Easy way to generate symmetry-related protein chains?

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Mark, you can 'File -> Save Symmetry Coordinates' and reload the PDB file. In my Coot 0.8.2-pre, revision 5628, Extensions -> Modelling -> Symm Shift Reference Chain Here is available works. Cheers, Tim On 05/22/2015 02:24 PM, Mark J van Raai

Re: [ccp4bb] Easy way to generate symmetry-related protein chains?

Hi Mark, If the structure has been deposited in the PDB you can download the "biological assembly" - even works for viruses, cheers, Matt. On 22/05/2015 14:24, Mark J van Raaij wrote: Just wondering if there is an easy way to generate symmetry-related chains, necessary for instance to join

[ccp4bb] Easy way to generate symmetry-related protein chains?

Just wondering if there is an easy way to generate symmetry-related chains, necessary for instance to join protein chains into the biologically relevant multimers. What I do now is look up the correct symmetry and translation operator in COOT or PYMOL and input that in PDBSET, but there may be e

Re: [ccp4bb] X-rays and matter (the particle-wave picture)

Dear Murpholino, Interaction of waves and matter always involve the particle-wave duality. Some pocesses are easier described using particles, others by using the wave concept. The X-ray photon, or rather the X-ray wavelet, has only a small chance of "hitting" atoms in the crystal. We will use

Re: [ccp4bb] Heme D restraints

There are a set of restraints available in the ccp4 area: $CLIBD/monomers/d/DHE.cif I attach them Eleanor On 22 May 2015 at 10:33, Schara Safarian wrote: > Hey Everyone, > > I am having trouble generating a adequate cif restraint file for a heme d > ligand. > I have tried to do a couple of thing

[ccp4bb] Heme D restraints

Hey Everyone,I am having trouble generating a adequate cif restraint file for a heme d ligand.I have tried to do a couple of things now, but either the restraint file is simply wrong (Phenix suite) or the output is generating a restraint file without a complexed Fe atom (CCP4).Additionally I have u

Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Point group

You do know even that if the pointgroup is P422 the the SPACEgroup can by P 4 2 2 or P 41 21 2 or P43 21 2 or P41 22 or .. Lots of possibilities! Eleanor Although you R factors look good.. On 22 May 2015 at 08:13, wrote: > So both space groups most likely describe the same crystal packi

Re: [ccp4bb] X-rays and matter (the particle-wave picture)

It seems to me important here to remind that this wave-particle duality is not limited to photons. Electrons and neutrons of course, but also atoms and even molecules have to be considered. To illustrate this, and since it is Friday, shall I propose some nice reading for the week-end :

[ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Point group

So both space groups most likely describe the same crystal packing. In this case I would choose the highest symmetry which still gives good refinement results. Best, Herman Von: dhaval patel [mailto:pateldhaval...@gmail.com] Gesendet: Freitag, 22. Mai 2015 09:09 An: Schreuder, Herman R&D/DE

Re: [ccp4bb] X-rays and matter (the particle-wave picture)

Hi Fellows, Zbi's response has addressed refs and the technical complexities that arise when describing the scattering process on a microscopic QM basis. I shall tell you why I decided to provide this probabilistic QM interpretation. First, a probabilistic approach to empirical science is the

Re: [ccp4bb] AW: [ccp4bb] Point group

Dear Herman Thanks for reply. My molecule is generally found to be tetramer. In P212121 space group cell content analysis shows 4molecules in asymmetric unit and in P4212 it shows two molecules in asymmetric unit. Dhaval Patel PhD Student, Bioinformatics & Structural Biology Indian Institute of A

[ccp4bb] AW: [ccp4bb] Point group

Dear Dhaval, In principle, it does not matter how you describe the packing of the molecules in your crystal. E.g. you can refine a P212121 structure in space group P212121 with one molecule in the asymmetric unit, or in P1 with 4 molecules in the asymmetric unit. In the latter case, these 4 mol