Re: [ccp4bb] Question about the electron density maps (.ccp4) in PDBe

Hi, > Unfortunately not all structure > factor programs will give you that F000. > phenix.f000 will give you F(0,0,0) value based on atomic model alone or atomic model plus bulk-solvent. Pavel To unsubscribe from the CCP

Re: [ccp4bb] Electron scattering factors for SHELXL

Hi, > Or, alternatively, if anyone has used a different program to refine small > molecule structures determined by ED, we would be happy to hear about that > program too. > phenix.refine has an option to use electron scattering factors. I can provide further assistance off-list or on phenix mai

[ccp4bb] Electron scattering factors for SHELXL

Greetings all, We have solved a small molecule structure using electron diffraction and would like to refine the structure with SHELXL. Coming from a macromolecular background, this is our first experience with SHELXL, and we are not exactly sure how to proceed. The first thing to do seems t

Re: [ccp4bb] Change dimer assembly in ASU

Dear Ezequiel, There is nothing special about which particular symmetry copies a molecular replacement program chooses, so there is no good reason to stick to those symmetry copies. On the other hand, there are very good reasons to present a molecule that is as close as possible to what is bio

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Re: [ccp4bb] (EXTERNAL) Re: [ccp4bb] Question about the electron density maps (.ccp4) in PDBe

Also check if the mean value of the map over the ASU is zero. If so, the map was probably calculated without the 0,0,0 term of the Fourier series, so zero does not represent zero density but rather the mean density. On 03/04/2019 12:43 PM, Ian Tickle wrote: Hi Sen If you multiply the electro

Re: [ccp4bb] Question about the electron density maps (.ccp4) in PDBe

Dear Sen, I may be unaware of special features of these maps, but if they are computed in conventional ways, they lack an F000 term. Therefore the average value of the 2mFo-DFc map is zero, just as if it was a difference map. This may explain why you do not find all the electrons you would be

Re: [ccp4bb] Racemic crystallography and structure solving problem

Thank You Pierre! I will have a look and let you know. Regards Prasun From: LEGRAND Pierre Sent: 04 March 2019 16:33:56 To: Prasun Kumar; CCP4BB@JISCMAIL.AC.UK Subject: RE:[ccp4bb] Racemic crystallography and structure solving problem Hi Prasum, In such cas

[ccp4bb] Change dimer assembly in ASU

Dear CCP4bb community: My crystal is a heterodimeric complex. I solved the structure using MR with a related structure (containig the dimer), using a highly automated pipeline. However, the MR solution is not the dimer of biological relevance. The experimentally validated dimer is formed between

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Re: [ccp4bb] Racemic crystallography and structure solving problem

Hi Prasum, In such case, with xia2 you could try to add the option: small_molecule=true. This will enable the consideration of centrosymmetric spacegourps. Or you can try in pointless the options: CHIRALITY NONCHIRAL or CENTROSYMMETRIC Your spacegroup could be P-1 (#2). Good luck, Pierre __

[ccp4bb] Question about the electron density maps (.ccp4) in PDBe

Hi all, I have been using the electron density maps available on the PDBe website to run some analysis. And I run into this question that I hope that I can get some help from the community. In the ccp4 format, the electron density is represented as a 3-d array map, with each number corresponds to

[ccp4bb] Racemic crystallography and structure solving problem

Hi All: I have performed racemic crystallography and got crystals that diffracted. The automatic processing softwares, XIA2 DIALS, (available in Diamond, UK) gives the space group as P1 and cell dimension 42.78 52.16 54.49 114.11 92.16 92.31. Challanges start from here: 1) How much

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