[ccp4bb] CCP4 Study Weekend 2015

The CCP4 Study Weekend (7 - 9 January 2015) East Midlands Conference Centre, University of Nottingham Wednesday 7 - MX User Meeting Thursday 8 / Friday 9 - CCP4 Study Weekend "Advances in Experimental Phasing" We cordially invite you to participate in this year's Study Weekend at the the Eas

[ccp4bb] Postdoc in Barcelona

*/Postdoctoral position in protein biochemistry/molecular biology/* A senior postdoctoral position is available to work on peptidases, their inhibitors and their complexes. The hosting place is the Proteolysis Lab of the Molecular Biology Institute of Barcelona (IBMB) from the Spanish Research

[ccp4bb] Bond lengths and angles used by Molprobity for ANP (AMPPNP)

Does anyone know if Molprobity has recently changed the standard bond lengths and angles that it uses ? Molprobity is reporting errors in the C4-C5 bond length and the C5-C4-N3 bond angle (deviations of 8-10 sigma) for AMPPNP (monomer code ANP) for a new structure refined with Refmac. I then

[ccp4bb] Selenium in AreaImol

I want to have a quantitative estimate for the accessible solvent area for a Selenocysteine residue in a tripeptide, gly-Sec-gly. AreaImol doesn't recognize Selenium, at least in the version I'm using (6.1.1). The online documentation for Areaimol doesn't include the text Selenium. Do newer vers

[ccp4bb] Technician / Research assistant at the technology platform ŒProtein Crystallography Core Facility¹ of EPFL (Switzerland)

The technology platform ‘Protein Crystallography Core Facility’ (http://pcrycf.epfl.ch) of Life Sciences Faculty is opening a fixed-term position for a highly motivated Technician / Research assistant The mission of the platform is to provide instrumentation and expertise

Re: [ccp4bb] Bond lengths and angles used by Molprobity for ANP (AMPPNP)

On Monday, 15 September 2014 03:24:19 PM Andrew Leslie wrote: > Does anyone know if Molprobity has recently changed the standard bond lengths > and angles that it uses ? > > Molprobity is reporting errors in the C4-C5 bond length and the C5-C4-N3 bond > angle (deviations of 8-10 sigma) for AMP

Re: [ccp4bb] Bond lengths and angles used by Molprobity for ANP (AMPPNP)

Isn't Molprobity too tight anyway for high resolution structures? I have often (for proteins) found it highlighting "outliers" when in fact that is what the density shows.Isn't it a trade off between molprobity and what the measurements show, especially at high resolutions?-Original Messag

Re: [ccp4bb] Bond lengths and angles used by Molprobity for ANP (AMPPNP)

Hi Andrew, the ccp4 ANP.cif entry for C4'-C5' is 1.528A, but both the Phenix and Grade cif list 1.508A. The distance in 2JDI is 1.53, so if molprobity relies on one of the latter two sources, this might be the source of the flag. Also some shelxl dictionary lists 1.509A, so it's 3:1 for the flag b

Re: [ccp4bb] Bond lengths and angles used by Molprobity for ANP (AMPPNP)

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 In general the word "outlier" should not be read as "error". It simply means that this thing is interesting. You have to judge, based on all information at hand, if it is interesting because it is rare or because it is wrong. It is true that

Re: [ccp4bb] Bond lengths and angles used by Molprobity for ANP (AMPPNP)

On 15 Sep 2014, at 15:24, Andrew Leslie wrote: > This would suggest that the standard dictionary that Molprobity uses has > changed, but I cannot find any reference to this on the Molprobity pages. > > I would be very grateful if anyone can throw some light on

Re: [ccp4bb] Bond lengths and angles used by Molprobity for ANP (AMPPNP)

Dear Huw, Many thanks for this information. I had seen the notice about Molprobity using CCTBX validation metrics, but I mistakenly thought that Phenix used the CCP4 monomer library, which I think was true once but is clearly no longer the case. Given the very small sigma values associated wit

Re: [ccp4bb] Bond lengths and angles used by Molprobity for ANP (AMPPNP)

Andrew, GRADE gives: ANP C5 C4aromatic 1.388 0.011 ANP C5 C4 C3 126.8 0.7 i.e. essentially the same as Phenix, so I would go with that. The CCP4 values definitely could do with a re-examination: I've never heard of a "double bond" with a length of 1.49, an

Re: [ccp4bb] Bond lengths and angles used by Molprobity for ANP (AMPPNP)

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 9/15/2014 9:42 AM, Andrew Leslie wrote: > Dear Huw, > > Many thanks for this information. I had seen the notice about > Molprobity using CCTBX validation metrics, but I mistakenly thought > that Phenix used the CCP4 monomer library, which I think

Re: [ccp4bb] Bond lengths and angles used by Molprobity for ANP (AMPPNP)

On 15/09/14 18:05, Dale Tronrud wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 9/15/2014 9:42 AM, Andrew Leslie wrote: Dear Huw, Many thanks for this information. I had seen the notice about Molprobity using CCTBX validation metrics, but I mistakenly thought that Phenix used the CCP

Re: [ccp4bb] ligand mismathces in pdb deposit

The problem keeps during the deposition! I tried to replace all 'HEM' atoms with the pdb published before and run refinement. The mismatch is still there. Here is a picture cut from pdb deposition website. The 3 letter of my heme is 'HEM' which is exactly the 'PROTOPORPHYRIN IX CONTAINING FE '.

Re: [ccp4bb] ligand mismathces in pdb deposit

Forgot the picture! Here is it! From: Paul Emsley [pems...@mrc-lmb.cam.ac.uk] Sent: Sunday, September 14, 2014 6:16 PM To: Wang, Bing Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] ligand mismathces in pdb deposit On 12/09/14 23:28, Wang, Bing wrote: > Hi

Re: [ccp4bb] ligand mismathces in pdb deposit

Hi Bing, This is the result of the new PDB deposition system being buggy. I had a similar problem with imidazole recently. This is the solution given to me by the PDB annotators. >Please choose from the instance page: >type of ligand: heterogen, >then give alternate ligand ID as IMD, (in your c

Re: [ccp4bb] Bond lengths and angles used by Molprobity for ANP (AMPPNP)

On 15 September 2014 17:48, Ian Tickle wrote: > > > ANP C5 C4 C3 126.8 0.7 > > Oops sorry, typo: > ANP C5 C4 N3 126.8 0.7 I.

Re: [ccp4bb] ligand mismathces in pdb deposit

Thank you very one here! Got fixed from Katherine's solution! You guys are really helpful! Bing From: Katherine Sippel [katherine.sip...@gmail.com] Sent: Monday, September 15, 2014 3:17 PM To: Wang, Bing Cc: ccp4bb Subject: Re: [ccp4bb] ligand mismathces in pdb de