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 > Data, time, & regional formatting (hidden on the right) > Additional data, time, & regional settings > Change data, time, or number formats > Additional settings Only "decimal symbol" and "Digit grouping symbol" need to be set to . and , respectively. Cheers, Robbie > -----Original Message----- > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Eugene > Krissinel > Sent: Friday, May 29, 2020 12:47 > To: CCP4BB@JISCMAIL.AC.UK > Subject: 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 it if you go > to > the previous Coot job report, scroll down to "Output Structure", press > "Display" and scroll down a bit. > > This effect is known to be peculiar to WinCoot -- have you used Windows > machine to run Coot in job 179? And had you used a different machine to > run Coot in job 169, which produced output file in correct format? > > The only way to cope with the situation, known to me, is to ensure that your > Windows machine uses US/English locale settings. This takes tweaking > Language settings in Windows Control Panel and rebooting the machine. > Regrettably, you will have to repeat job 179 in new locale. If it contains > particularly valuable results that are difficult to reproduce, let me know > and I > will advise you of the rescue procedure. > > Admittedly, you are by far not the only one who encounters this problem, > which appears in all locales with float point formats different from > US/English. Therefore, I cc WinCoot developer on this email (they are aware > anyway, and are working on the issue), as well as CCP4 BB list, where you > placed your request initially, for other CCP4 users to be aware of this > feature. And there is an obvious homework for us here at CCP4. > > Once again, many thanks for your report. Please unshare this project now > (simply remove my login name where you have put it for sharing before). > > Kind regards, > > Eugene > > > On Fri, May 29, 2020 at 9:52 AM Nadine Gerlach <ngerl...@marum.de > <mailto:ngerl...@marum.de> > wrote: > > > Hey Eugene, > > actually this happend not just for one project of mine, but I shared > one project with you now. Scroll down to the last refmac run after model > building with coot. I just tried it again but it is still the same result. > > Thanks for the help!! > > Nadine > > > > > > Am 28.05.2020 um 19:28 schrieb Eugene Krissinel: > > > Dear Nadine, > > We would need more information on what happens. You can > share your project with me and I can have a look at it. To share the project, > open it, then push Main Manu button in top-left corner, choose "Share" and > set my login name (eugene), then confirm to me by e-mail. Your data and > project will be treated as confidential. > > Many thanks for writing to us (use c...@ccp4.ac.uk > <mailto:c...@ccp4.ac.uk> rather than BB list for this type of queries please) > > Eugene > > > ---------- Forwarded message --------- > From: Nadine Gerlach <ngerl...@marum.de > <mailto:ngerl...@marum.de> > > Date: Thu, 28 May 2020 at 14:21 > Subject: Refmac error > To: <ccp4bb-requ...@jiscmail.ac.uk <mailto:CCP4BB- > requ...@jiscmail.ac.uk> > > > > > > Hey everybody, > > I am running refmac in CCP4 ccloud after Coot and I get this > error message: > > *** error running refmac5: Error in command.call > Return code: 512 > > Any held is really appreaciated! > > Best wishes, > Nadine > -- > Nadine Gerlach > PhD candidate > MPG MARUM Bridge Group Marine Glycobiology > MARUM, University Bremen & Max Planck Institute for > Marine Microbiology > Tel: +49 421 218-65758 > Email: ngerlach@mpi-bremen.de <http://men.de> , > ngerl...@marum.de <mailto:ngerl...@marum.de> > MARUM Pavillon room 1110 > Leobener Straße > 28359 Bremen, Germany > > This email and any attachments are intended solely for the > use of the named recipients. If you are not the intended recipient you must > not use, disclose, copy or distribute this email or any of its attachments and > should notify the sender immediately and delete this email from your > system. UK Research and Innovation (UKRI) has taken every reasonable > precaution to minimise risk of this email or any attachments containing > viruses or malware but the recipient should carry out its own virus and > malware checks before opening the attachments. UKRI does not accept any > liability for any losses or damages which the recipient may sustain due to > presence of any viruses. Opinions, conclusions or other information in this > message and attachments that are not related directly to UKRI business are > solely those of the author and do not represent the views of UKRI. > > -- > Nadine Gerlach > PhD candidate > MPG MARUM Bridge Group Marine Glycobiology > MARUM, University Bremen & Max Planck Institute for Marine > Microbiology > Tel: +49 421 218-65758 > Email: ngerlach@mpi-bremen.de <http://men.de> , > ngerl...@marum.de <mailto:ngerl...@marum.de> > MARUM Pavillon room 1110 > Leobener Straße > 28359 Bremen, Germany > > > ________________________________ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
