Ta Now dear My deadline for this grant is on the second I will try to get a rewritten simplified version to you before tomorrow morning. When I do PLEASE look it over and see if you can write in anything else wrt modelling - at present its not written in year 1 Also general check and approval Thanks kid jacq
On 30/5/20, 09:06, "CCP4 bulletin board on behalf of CCP4BB automatic digest system" <[email protected] on behalf of [email protected]> wrote: There are 10 messages totaling 2125 lines in this issue. Topics of the day: 1. visual mask editor - why (2) 2. Strange Pseudosymmetry Effects (2) 3. Fwd: Refmac error (2) 4. Job Offer at INNOVATION CAMPUS BERLIN in Computational Chemistry 5. PDB file header lines... (3) ######################################################################## 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/ ---------------------------------------------------------------------- Date: Fri, 29 May 2020 00:02:11 -0700 From: Pavel Afonine <[email protected]> Subject: Re: 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 above: what we (or you) are missing? Pavel On Thu, May 28, 2020 at 11:17 AM Bernhard Rupp <[email protected]> wrote: > Maybe I should explain an example: Say coot detects an unmodelled blob > (maybe a ligand). Now, I would like to do > > a number of things without biasing towards a model. Like comparing these > map regions, excluding > > intrusion of a solvent mask, etc. > > > > Now could coot for example just generate a mask around what it already > knows are blobs? > > Possible useful items could be a solvent mask not including that regions, > or a density map > > that includes only features with a certain boundary around that blob. > > > > I pilfered some kludges together from different sources, but let’s just > say inelegant would be a compliment. > > > > Best, BR > > ------------------------ > > Brief question: Does something like a visual density mask editor exist? > > Thx, BR > > ------------------------------------------------------ > > Bernhard Rupp > > http://www.hofkristallamt.org/ > > [email protected] > > +1 925 209 7429 > > +43 676 571 0536 > > ------------------------------------------------------ > > Many plausible ideas vanish > > at the presence of thought > > ------------------------------------------------------ > > > > ------------------------------ > > 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/ ------------------------------ Date: Fri, 29 May 2020 09:34:23 +0100 From: Harry Powell - CCP4BB <[email protected]> Subject: Re: 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 with plenty of time to search through old boxes… Harry > On 28 May 2020, at 21:04, Tim Gruene <[email protected]> wrote: > Dear Eddie, dear all > > According to ftp://ftp.ccp4.ac.uk/ccp4/newsletter/jun_95/, this article > appeare in Newsletter June 95. It is mentioned in the table of contents, > "Correction on perfection: primary extinction correction in protein > crystallography" by Polykarpov and Sawyer. > Unfortunately, the article itself is not there > > Extinction is not the same as the dynamic effects that James mentioned, > but this seems the closest match. > > Would anyone have a copy they can share with me? > > Thanks a lot! > > Best, > > Tim ######################################################################## 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/ ------------------------------ Date: Fri, 29 May 2020 10:49:03 +0100 From: Eleanor Dodson <[email protected]> Subject: Re: 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] <x1> <x2> <y1> <y2> <z1> <z2>**Set the output map extent as `extend'. <x1>-<z2> are given in grid units or in fractional coordinates. It is possible to automatically extend to the CCP4 default asymmetric unit, or a whole unit cell, by specifying `XYZLIM ASU' or `XYZLIM CELL'. It is also possible to extend the map to match another map (given as MAPLIM) by specifiying `XYZLIM MATCH'. The default is to keep the extent of the input map.* On Fri, 29 May 2020 at 08:03, Pavel Afonine <[email protected]> wrote: > 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 above: what we (or you) are missing? > > Pavel > > On Thu, May 28, 2020 at 11:17 AM Bernhard Rupp <[email protected]> > wrote: > >> Maybe I should explain an example: Say coot detects an unmodelled blob >> (maybe a ligand). Now, I would like to do >> >> a number of things without biasing towards a model. Like comparing these >> map regions, excluding >> >> intrusion of a solvent mask, etc. >> >> >> >> Now could coot for example just generate a mask around what it already >> knows are blobs? >> >> Possible useful items could be a solvent mask not including that regions, >> or a density map >> >> that includes only features with a certain boundary around that blob. >> >> >> >> I pilfered some kludges together from different sources, but let’s just >> say inelegant would be a compliment. >> >> >> >> Best, BR >> >> ------------------------ >> >> Brief question: Does something like a visual density mask editor exist? >> >> Thx, BR >> >> ------------------------------------------------------ >> >> Bernhard Rupp >> >> http://www.hofkristallamt.org/ >> >> [email protected] >> >> +1 925 209 7429 >> >> +43 676 571 0536 >> >> ------------------------------------------------------ >> >> Many plausible ideas vanish >> >> at the presence of thought >> >> ------------------------------------------------------ >> >> >> >> ------------------------------ >> >> 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 > ######################################################################## 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/ ------------------------------ Date: Fri, 29 May 2020 11:46:52 +0100 From: Eugene Krissinel <[email protected]> Subject: Re: 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 <[email protected]> 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 [email protected] rather than BB list > for this type of queries please) > > Eugene > > > ---------- Forwarded message --------- > From: Nadine Gerlach <[email protected]> > Date: Thu, 28 May 2020 at 14:21 > Subject: Refmac error > To: <[email protected]> > > > 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, [email protected] > 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, [email protected] > 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. ######################################################################## 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/ ------------------------------ Date: Fri, 29 May 2020 11:11:54 +0000 From: Robbie Joosten <[email protected]> Subject: Re: 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 > 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 <[email protected]> On Behalf Of Eugene > Krissinel > Sent: Friday, May 29, 2020 12:47 > To: [email protected] > 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 <[email protected] > <mailto:[email protected]> > 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 [email protected] > <mailto:[email protected]> rather than BB list for this type of queries please) > > Eugene > > > ---------- Forwarded message --------- > From: Nadine Gerlach <[email protected] > <mailto:[email protected]> > > Date: Thu, 28 May 2020 at 14:21 > Subject: Refmac error > To: <[email protected] <mailto:CCP4BB- > [email protected]> > > > > > > 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> , > [email protected] <mailto:[email protected]> > 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> , > [email protected] <mailto:[email protected]> > 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/ ------------------------------ Date: Fri, 29 May 2020 11:32:56 +0000 From: Martina Schaefer <[email protected]> Subject: 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 information and how to apply can be found here: https://nuvisan.odoo.com/de_DE/jobs/detail/director-computational-chemistry-m-f-d-673 Nuvisan INNOVATION CAMPUS BERLIN is a newly founded contract research organization with approximately 400 employees belonging to the Nuvisan group. We offer a dynamic and inspiring working environment in the heart of Berlin. ICB has a long history of experience in pharma research and the combination with Nuvisan as an international service provider for clinical studies, laboratory services and contract manufacturing offers an attractive working environment. Best Regards, Martina Freundliche Grüße / Best regards, Dr. Martina Schaefer Structural Biology 3 //////////////////// Bayer AG Research & Development, Pharmaceuticals Structural Biology Building S116, 323 13342 Berlin, Germany Tel: +49 30 468192089 Fax: +49 30 46816707 Mobile: +49 152 08821830 E-mail: [email protected] Web: http://www.bayer.com Datenschutzhinweise<https://www.bayer.de/de/datenschutzhinweise-fuer-ausgewaehlte-verarbeitungstaetigkeiten.aspx> // Data privacy information<https://www.bayer.com/en/data-privacy-information-for-specific-processing-activities.aspx> /// Vorstand: Werner Baumann, Vorsitzender | Liam Condon, Wolfgang Nickl, Stefan Oelrich, Heiko Schipper /// Vorsitzender des Aufsichtsrats: Norbert Winkeljohann /// Sitz der Gesellschaft: Leverkusen | Amtsgericht Köln, HRB 48248 ######################################################################## 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/ ------------------------------ Date: Fri, 29 May 2020 15:57:13 +0100 From: Harry Powell - CCP4BB <[email protected]> Subject: 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 this down to “MODEL” lines in the file headers. I’ve tested this most in QTMG, so the following may not be true for Coot. If I change this line so that it has “M ”, “MO ”, “MOD ”, MODE ”, “MODEL1 ”, “MODEL22 ”, “MODEL678 ” or even “MODEL^&* ” instead of “MODEL ” then all looks hunky-dory. I thought - “aha - there’s something about 5 characters” - so I tried replacing “MODEL ” with “TRUMP ” and “BIDEN ” and the files read okay, so it does look very specific. I’m sure there’s a simple answer to this (is there a “FM” I could read?), but I haven’t found one yet. Can anyone on the BB help out? Harry ######################################################################## 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/ ------------------------------ Date: Fri, 29 May 2020 15:02:26 +0000 From: Robbie Joosten <[email protected]> Subject: Re: 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 either ignored or a parser will throw an error. Cheers, Robbie > -----Original Message----- > From: CCP4 bulletin board <[email protected]> On Behalf Of Harry > Powell - CCP4BB > Sent: Friday, May 29, 2020 16:57 > To: [email protected] > Subject: [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 this down to “MODEL” lines in the file headers. > > I’ve tested this most in QTMG, so the following may not be true for Coot. If I > change this line so that it has “M ”, “MO ”, “MOD ”, MODE ”, “MODEL1 ”, > “MODEL22 ”, “MODEL678 ” or even “MODEL^&* ” instead of “MODEL ” then > all looks hunky-dory. > > I thought - “aha - there’s something about 5 characters” - so I tried replacing > “MODEL ” with “TRUMP ” and “BIDEN ” and the files read okay, so it does > look very specific. > > I’m sure there’s a simple answer to this (is there a “FM” I could read?), but I > haven’t found one yet. Can anyone on the BB help out? > > Harry > > ############################################################### > ######### > > 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/ ######################################################################## 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/ ------------------------------ Date: Fri, 29 May 2020 16:07:21 +0100 From: Harry Powell - CCP4BB <[email protected]> Subject: Re: 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 <[email protected]> wrote: > > 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 either ignored or a parser will throw an error. > > Cheers, > Robbie > >> -----Original Message----- >> From: CCP4 bulletin board <[email protected]> On Behalf Of Harry >> Powell - CCP4BB >> Sent: Friday, May 29, 2020 16:57 >> To: [email protected] >> Subject: [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 this down to “MODEL” lines in the file headers. >> >> I’ve tested this most in QTMG, so the following may not be true for Coot. If I >> change this line so that it has “M ”, “MO ”, “MOD ”, MODE ”, “MODEL1 ”, >> “MODEL22 ”, “MODEL678 ” or even “MODEL^&* ” instead of “MODEL ” then >> all looks hunky-dory. >> >> I thought - “aha - there’s something about 5 characters” - so I tried replacing >> “MODEL ” with “TRUMP ” and “BIDEN ” and the files read okay, so it does >> look very specific. >> >> I’m sure there’s a simple answer to this (is there a “FM” I could read?), but I >> haven’t found one yet. Can anyone on the BB help out? >> >> Harry >> >> ############################################################### >> ######### >> >> 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/ ######################################################################## 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/ ------------------------------ Date: Fri, 29 May 2020 16:47:36 +0100 From: John R Helliwell <[email protected]> Subject: Re: 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. <https://journals.iucr.org/b> (1980). B*36* <https://journals.iucr.org/b/contents/backissues.html>, 621-627 Greetings, John On Thu, May 28, 2020 at 4:44 PM Edward Snell <[email protected]> wrote: > This jogged my memory of a CCP4 newsletter article many years ago covering > kinematical versus dynamic scattering in protein crystals and offering a > correction that could be used. I think it was Lindsay Sawyer and Igor > Polikarpov in the late 90’s. I apologize if I have the authors wrong but I > thought it was a commentary well ahead of its time and with modern sources > and low noise detectors, I am wondering if anyone has revisited this? > Protein crystals are remarkably high quality until you cryocool them. > Serial methods combined with instrument capabilities may rate a revisit to > the use of the kinematical approximation versus application of dynamical > theories? Certainly the computational power is available. > > > > Just my 2 cents for the day. > > > > Best, > > > > Eddie > > > > > > Edward Snell Ph.D. > > > > Director of the NSF BioXFEL Science and Technology Center > > President and CEO Hauptman-Woodward Medical Research Institute > > BioInnovations Chaired Professorship, University at Buffalo, SUNY > > 700 Ellicott Street, Buffalo, NY 14203-1102 > > hwi.buffalo.edu > > Phone: (716) 898 8631 Fax: (716) 898 8660 > > Skype: eddie.snell Email: [email protected] > > Webpage: https://hwi.buffalo.edu/scientist-directory/snell/ > > [image: hwilogo] > > Heisenberg was probably here! > > > > > > > > *From:* CCP4 bulletin board <[email protected]> *On Behalf Of *James > Holton > *Sent:* Thursday, May 28, 2020 11:34 AM > *To:* [email protected] > *Subject:* Re: [ccp4bb] Strange Pseudosymmetry Effects > > > > Be careful with electron diffraction and apparent absence violations. It > is possible these weak spots are simply due to multiple scattering. If so, > you would see them relatively stronger with larger crystals,but much weaker > relative to the strong reflections when the crystal is smaller. Do you? > > -James Holton > MAD Scientist > > On 5/27/2020 6:49 PM, Jessica Bruhn wrote: > > Hello, > > > > I am wondering if pseudosymmetry can cause weak reflections that mimic the > doubling of one unit cell axis' length. Has anyone seen something like this > before? > > > > I am processing data from a small molecule sample collected with electron > diffraction from multiple crystals. For the b axis, it is not clear if the > length should be 10A or 20A. There are spots with the correct spacing for > b=20A, but every other spot seems weaker than the spots along k if I choose > b=10A (this extends beyond (0,k,0)). I am unable to phase the b=20 data. I > have solved this structure in P1 with b=10 and found four molecules in the > ASU and in P212121 with b=10 resulting in one molecule in the ASU. In P1, > three of the four molecules adopt the same conformation, but the fourth > molecule is in an alternate conformation that causes only ~1/2 of the > molecule to be consistent with the first three. In P212121 I see density > for part of this alternative conformation, but the full molecule in this > alternate conformation cannot pack properly in P212121. Based on these > results and some orthogonal data, I think I should refine the solution in > P1 with b=10. Does it seem reasonable that pseudosymmetry is causing these > weak reflections along k hinting at a doubling of the b axis? > > > > Thanks in advance! > > > > Best, > > Jessica > > > > -- > > Jessica Bruhn, Ph.D > > Principal Scientist > > NanoImaging Services, Inc. > > 4940 Carroll Canyon Road, Suite 115 > > San Diego, CA 92121 > > Phone #: (888) 675-8261 > > www.nanoimagingservices.com > > > ------------------------------ > > 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 > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > -- Professor John R Helliwell DSc ######################################################################## 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/ ------------------------------ End of CCP4BB Digest - 28 May 2020 to 29 May 2020 (#2020-148) ************************************************************* _______________________________________________ The information in this email is confidential and intended solely for the addressee. 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