Re: [ccp4bb] Strange Pseudosymmetry Effects

Hello Eddie, I believe this article from Robert Huber and coauthors was the first to discuss dynamical effects in a protein crystal:- Acta Cryst. (1980). B*36* , 621-627 Greetings, John On Thu, May 28, 2020 at 4:44

Re: [ccp4bb] PDB file header lines...

Hi Robbie Many thanks. I should tell the owners of the prediction server that they’re writing non-compliant files, in that case. So “BIDEN” is not compliant but “TRUMP” is? He’d like that… H > On 29 May 2020, at 16:02, Robbie Joosten wrote: > > Hi Harry, > > You need this: > http://www.wwp

Re: [ccp4bb] PDB file header lines...

Hi Harry, You need this: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#MODEL Essentially you have to make sure a MODEL has a number and a closing tag. It is read as a real PDB record so you have to make sure it is correct BIDEN is not PDB compliant and will be eith

[ccp4bb] PDB file header lines...

Hi Is there something about “MODEL ” lines (i.e. five characters followed by a space) in PDB files that is completely beyond the pale? I’ve got some PDB files from a protein structure prediction server based in the US that Coot fails to read and that cause QTMG to crash on my Mac. I’ve tracked

[ccp4bb] Job Offer at INNOVATION CAMPUS BERLIN in Computational Chemistry

Dear colleagues, Nuvisan ICB in Berlin is offering a permanent position as Director of Computational Chemistry in Berlin, Germany. Your tasks will include build-up and lead the Computational Chemistry team working in interdisciplinary teams to advance drug-discovery projects. Further informatio

Re: [ccp4bb] Fwd: Refmac error

Hi Eugene, We recently had this with a student as well and at least in PDB format the files are salvageable by doing a simple search and replace from , to . Rather than going completely American, you can also just change the number format. In Windows 10 this is Settings > Time & Language > Dat

Re: [ccp4bb] Fwd: Refmac error

Dear Nadine, Many thanks for sharing your project with me on CCP4 Cloud. The reason for Refmac failure is absolutely clear: the previous Coot job exported PDB file, using commas (wie im besten Deutsch) instead of periods (as we would expect in best English) for all float-point numbers. You can see

Re: [ccp4bb] visual mask editor - why

Wont mapmask do that? Find the fraction coordinate of the blob extent then carve that section out of the map? Eleanor >From documentation: *XYZLIM [ASU] [CELL] [MATCH] **Set the output map extent as `extend'. - are given in grid units or in fractional coordinates. It is possible to automatic

Re: [ccp4bb] Strange Pseudosymmetry Effects

Hi Tim You could send out an SOS to some of the other authors in the same issue, who might have kept a copy - several are “regular" posters on this forum, e.g. Sacha Urzhumtsev Gerard Kleywegt Eleanor Dodson There’s a good chance they’ll be stuck at home at the moment

Re: [ccp4bb] visual mask editor - why

Hi Bernhard, "Like comparing these map regions, excluding intrusion of a solvent mask, etc.": You didn't say much about the context.. So I'd say Polder map approach comes to mind first based on these keywords. Next is "map comparison" ( https://doi.org/10.1107/S1399004714016289). If none of the