From grazulis at ibt.lt Tue Apr 23 08:39:55 2024 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=C5=BEulis?=) Date: Tue, 23 Apr 2024 08:39:55 +0300 Subject: [Cod-bugs] Fwd: Cod-bugs post from sakurabayashi26@sanken.osaka-u.ac.jp requires approval In-Reply-To: References: Message-ID: Dear COD team, I am Shuhei Sakurabayashi in Osaka University, Japan. I am currently trying to deposit the microED crystal structure of an organic compound onto COD. In the validation step, the following error occurred, and I cannot proceed. The following errors were detected in file [ND.cif]: Data block nd: data item '_refine_ls_R_factor_gt' value '0.2149' is > 0.2. data item '_refine_ls_wR_factor_ref' value '0.5835' is > 0.45. Can I proceed to the next step by adding a comment or something? Best regards, Shuhei Sakurabayashi -------- Forwarded Message -------- Subject: Cod-bugs post from sakurabayashi26 at sanken.osaka-u.ac.jp requires approval Date: Tue, 23 Apr 2024 04:03:18 +0300 From: cod-bugs-owner at lists.crystallography.net To: cod-bugs-owner at lists.crystallography.net As list administrator, your authorization is requested for the following mailing list posting: List: Cod-bugs at lists.crystallography.net From: sakurabayashi26 at sanken.osaka-u.ac.jp Subject: Deposition of microED crystal structure on COD Reason: Post by non-member to a members-only list At your convenience, visit: http://lists.crystallography.net/cgi-bin/mailman/admindb/cod-bugs to approve or deny the request. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded message was scrubbed... From: Subject: Deposition of microED crystal structure on COD Date: Tue, 23 Apr 2024 10:03:05 +0900 Size: 8880 URL: -------------- next part -------------- An embedded message was scrubbed... From: cod-bugs-request at lists.crystallography.net Subject: confirm c101ca738cbcff2d02223efc3152efc276273141 Date: Tue, 23 Apr 2024 04:03:18 +0300 Size: 772 URL: From grazulis at ibt.lt Tue Apr 23 09:04:05 2024 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=C5=BEulis?=) Date: Tue, 23 Apr 2024 09:04:05 +0300 Subject: [Cod-bugs] Fwd: Cod-bugs post from sakurabayashi26@sanken.osaka-u.ac.jp requires approval In-Reply-To: References:

Message-ID: Dear dr. Sakurabayashi thank you for depositing your data to the COD! Indeed, we should relax Rf requirements for the MicroED structures, but for now, please proceed as follows: 1. please comment out the '_refine_ls_R_factor_gt' and the '_refine_ls_wR_factor_ref' lines (data items) in you submitted file; you can do this in the COD deposition site editor. Please save these lines on you computer in a separate file; 2. your submission should be then ready for deposition ("green"). Please deposit it and send us: ?? a) the COD ID of the deposited structure; ?? b) the saved '_refine_ls_R_factor_gt' and the '_refine_ls_wR_factor_ref' lines (data items; We will reinsert them into your deposited file with the appropriate comment. You should also be able to reinsert them in the COD data editing Web window if you would like to do so. HTH, Sincerely yours, Saulius On 2024-04-23 08:39, Saulius Gra?ulis wrote: > > Dear COD team, > > I am Shuhei Sakurabayashi in Osaka University, Japan. > > I am currently trying to deposit the microED crystal structure of an > organic compound onto COD. > > In the validation step, the following error occurred, and I cannot > proceed. > > The following errors were detected in file [ND.cif]: > Data block nd: > data item '_refine_ls_R_factor_gt' value '0.2149' is > 0.2. > data item '_refine_ls_wR_factor_ref' value '0.5835' is > 0.45. > > Can I proceed to the next step by adding a comment or something? > > Best regards, > Shuhei Sakurabayashi > > -------- Forwarded Message -------- > Subject: Cod-bugs post from sakurabayashi26 at sanken.osaka-u.ac.jp > requires approval > Date: Tue, 23 Apr 2024 04:03:18 +0300 > From: cod-bugs-owner at lists.crystallography.net > To: cod-bugs-owner at lists.crystallography.net > > > > As list administrator, your authorization is requested for the > following mailing list posting: > > List: Cod-bugs at lists.crystallography.net > From: sakurabayashi26 at sanken.osaka-u.ac.jp > Subject: Deposition of microED crystal structure on COD > Reason: Post by non-member to a members-only list > > At your convenience, visit: > > http://lists.crystallography.net/cgi-bin/mailman/admindb/cod-bugs > to approve or deny the request. > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > > > -- > This message has been scanned for viruses and > dangerous content by *MailScanner* , and is > believed to be clean. > > _______________________________________________ > Cod-bugs mailing list > Cod-bugs at lists.crystallography.net > http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs -- Dr. Saulius Gra?ulis Vilnius University Institute of Biotechnology, Saul?tekio al. 7 LT-10257 Vilnius, Lietuva (Lithuania) mobile: (+370-684)-49802, (+370-614)-36366 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: From sakurabayashi26 at sanken.osaka-u.ac.jp Tue Apr 23 12:33:11 2024 From: sakurabayashi26 at sanken.osaka-u.ac.jp (sakurabayashi26 at sanken.osaka-u.ac.jp) Date: Tue, 23 Apr 2024 18:33:11 +0900 Subject: [Cod-bugs] Fwd: Cod-bugs post from sakurabayashi26@sanken.osaka-u.ac.jp requires approval In-Reply-To: References:

Message-ID: <002b01da9561$41ee8d10$c5cba730$@sanken.osaka-u.ac.jp> Dear Dr. Saulius, ? Thank you for the reply. ? I commented out the line with ?;?, but it doesn't seem to work (errors still occur). Then, I replaced it with an arbitrary number to meet the criteria shown in the red errors. ? Now, I can see no errors (two yellow warnings), but the deposit button is not active yet (screenshot is attached). ? Sorry for bothering you, but I would appreciate if you could tell me how to handle this problem. ? Best, Shuhei Sakurabayashi ? ? From: Saulius Gra?ulis Sent: Tuesday, April 23, 2024 3:04 PM To: cod-bugs at lists.crystallography.net; sakurabayashi26 at sanken.osaka-u.ac.jp Subject: Re: [Cod-bugs] Fwd: Cod-bugs post from sakurabayashi26 at sanken.osaka-u.ac.jp requires approval ? Dear dr. Sakurabayashi ? thank you for depositing your data to the COD! ? Indeed, we should relax Rf requirements for the MicroED structures, but for now, please proceed as follows: ? 1. please comment out the '_refine_ls_R_factor_gt' and the '_refine_ls_wR_factor_ref' lines (data items) in you submitted file; you can do this in the COD deposition site editor. Please save these lines on you computer in a separate file; ? 2. your submission should be then ready for deposition ("green"). Please deposit it and send us: ? ? ? a) the COD ID of the deposited structure; ? ? b) the saved '_refine_ls_R_factor_gt' and the '_refine_ls_wR_factor_ref' lines (data items; ? We will reinsert them into your deposited file with the appropriate comment. You should also be able to reinsert them in the COD data editing Web window if you would like to do so. ? HTH, ? Sincerely yours, Saulius ? On 2024-04-23 08:39, Saulius Gra?ulis wrote: Dear COD team, I am Shuhei Sakurabayashi in Osaka University, Japan. I am currently trying to deposit the microED crystal structure of an organic compound onto COD. In the validation step, the following error occurred, and I cannot proceed. The following errors were detected in file [ND.cif]: Data block nd: data item '_refine_ls_R_factor_gt' value '0.2149' is > 0.2. data item '_refine_ls_wR_factor_ref' value '0.5835' is > 0.45. Can I proceed to the next step by adding a comment or something? Best regards, Shuhei Sakurabayashi -------- Forwarded Message -------- Subject: Cod-bugs post from sakurabayashi26 at sanken.osaka-u.ac.jp requires approval Date: Tue, 23 Apr 2024 04:03:18 +0300 From: cod-bugs-owner at lists.crystallography.net To: cod-bugs-owner at lists.crystallography.net As list administrator, your authorization is requested for the following mailing list posting: List: Cod-bugs at lists.crystallography.net From: sakurabayashi26 at sanken.osaka-u.ac.jp Subject: Deposition of microED crystal structure on COD Reason: Post by non-member to a members-only list At your convenience, visit: http://lists.crystallography.net/cgi-bin/mailman/admindb/cod-bugs to approve or deny the request. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 175481 bytes Desc: not available URL: From grazulis at ibt.lt Wed Apr 24 09:34:00 2024 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=C5=BEulis?=) Date: Wed, 24 Apr 2024 09:34:00 +0300 Subject: [Cod-bugs] Fwd: Cod-bugs post from sakurabayashi26@sanken.osaka-u.ac.jp requires approval In-Reply-To: <002b01da9561$41ee8d10$c5cba730$@sanken.osaka-u.ac.jp> References:

<002b01da9561$41ee8d10$c5cba730$@sanken.osaka-u.ac.jp> Message-ID: <60ceb527-d57d-4b4f-a09e-b2c773bbb397@ibt.lt> On 2024-04-23 12:33, sakurabayashi26 at sanken.osaka-u.ac.jp wrote: > > I commented out the line with ?;?, but it doesn't seem to work (errors > still occur). > The semicolon (';') is /not/ a comment symbol, it starts a text field that continues till the next semicolon at the beginning of the line! The comment symbol is a hash sign ('#'). So you can prepend the excluded lines with the ?#? or, for that matter, remove them altogether. > Then, I replaced it with an arbitrary number to meet the criteria > shown in the red errors. > From the data management perspective, it is better to have no data than to have incorrect data, and the arbitrary values you mention are apparently not correct. Alternatively, you can replace the values by a single dot ('.'); this means the value is irrelevant. Such tokens are permitted by the CIF and are interpreted as "the value is not relevant", which approximately reflects your situation. > Now, I can see no errors (two yellow warnings), but the deposit button > is not active yet (screenshot is attached). > > Sorry for bothering you, but I would appreciate if you could tell me > how to handle this problem. > I would suggest removing the lines containing '_refine_ls_R_factor_gt' and the '_refine_ls_wR_factor_ref', or prepend the, with the comment sign "#". The structure should be then ready for deposition. This procedure assumes that the numeric values for the '_refine_ls_R_factor_gt' and the '_refine_ls_wR_factor_ref' data items are on the same line as the data names ('_refine_ls_R_factor_gt' and the '_refine_ls_wR_factor_ref') themselves. After the deposition, please send us the newly obtained COD ID and the two commented (or removed) lines with the '_refine_ls_R_factor_gt' and the '_refine_ls_wR_factor_ref' data items. Sorry for this hassle, but we need to have the CIF syntax strictly correct for the COD, for the benefit of future automatic processing by you and others :) HTH, Saulius -- Dr. Saulius Gra?ulis Vilnius University Institute of Biotechnology, Saul?tekio al. 7 LT-10257 Vilnius, Lietuva (Lithuania) mobile: (+370-684)-49802, (+370-614)-36366 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: From grazulis at ibt.lt Wed Apr 24 09:38:04 2024 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=C5=BEulis?=) Date: Wed, 24 Apr 2024 09:38:04 +0300 Subject: [Cod-bugs] Fwd: Cod-bugs post from sakurabayashi26@sanken.osaka-u.ac.jp requires approval In-Reply-To: <004d01da95e2$e96d68a0$bc4839e0$@sanken.osaka-u.ac.jp> References:

<004d01da95e2$e96d68a0$bc4839e0$@sanken.osaka-u.ac.jp> Message-ID: <3fa9a062-4aca-455a-9894-b11c07d73aca@ibt.lt> Dear dr. Sakurabayashi, thank you for your message. I'm very glad that your deposition worked! On 2024-04-24 04:01, sakurabayashi26 at sanken.osaka-u.ac.jp wrote: > > Dear Dr. Saulius, > > Thank you for the reply. > > >1. please comment out the '_refine_ls_R_factor_gt' and the '_refine_ls_wR_factor_ref' lines > (data >items) in >you submitted file; you can do this in the COD > deposition site editor. Please save these >lines on you >computer in a > separate file; > > I just deposited the cif file with the two lines above commented out. > > Deposition seems to have worked. > > >2. your submission should be then ready for deposition ("green"). Please deposit it and send us: > > > > > >?? a) the COD ID of the deposited structure; > > >?? b) the saved '_refine_ls_R_factor_gt' and the '_refine_ls_wR_factor_ref' lines (data items; > > The COD ID is 3000497. > > Those two lines are shown below; > > _refine_ls_R_factor_gt???????????? 0.2149 > > _refine_ls_wR_factor_ref?????????? 0.5835 > > If necessary, please add the below comment as the reason of errors. > > This is a MicroED structure refined only kinematically. > > Thus, traditional X-ray crystallography thresholds are not adequate. > Excellent! I'll insert the values into your structure in the 'on-hold' repository. The values will be there when the structure is released. > If there are still any deficiencies regarding depositions, I would > appreciate it if you could let me know. > I'll let you know but for now everything seems OK! Sincerely yours, Saulius > Best regards, > > Shuhei Sakurabayashi > > *From:*Saulius Gra?ulis grazulis at ibt.lt > *Sent:* Tuesday, April 23, 2024 3:04 PM > *To:* cod-bugs at lists.crystallography.net; > sakurabayashi26 at sanken.osaka-u.ac.jp > *Subject:* Re: [Cod-bugs] Fwd: Cod-bugs post from > sakurabayashi26 at sanken.osaka-u.ac.jp requires approval > > Dear dr. Sakurabayashi > > thank you for depositing your data to the COD! > > Indeed, we should relax Rf requirements for the MicroED structures, > but for now, please proceed as follows: > > 1. please comment out the '_refine_ls_R_factor_gt' and the > '_refine_ls_wR_factor_ref' lines (data items) in you submitted file; > you can do this in the COD deposition site editor. Please save these > lines on you computer in a separate file; > > 2. your submission should be then ready for deposition ("green"). > Please deposit it and send us: > > ?? a) the COD ID of the deposited structure; > > ?? b) the saved '_refine_ls_R_factor_gt' and the > '_refine_ls_wR_factor_ref' lines (data items; > > We will reinsert them into your deposited file with the appropriate > comment. You should also be able to reinsert them in the COD data > editing Web window if you would like to do so. > > HTH, > > Sincerely yours, > Saulius > > > -- > This message has been scanned for viruses and > dangerous content by *MailScanner* , and is > believed to be clean. -- Dr. Saulius Gra?ulis Vilnius University Institute of Biotechnology, Saul?tekio al. 7 LT-10257 Vilnius, Lietuva (Lithuania) mobile: (+370-684)-49802, (+370-614)-36366 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: From grazulis at ibt.lt Wed Apr 24 15:04:24 2024 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=C5=BEulis?=) Date: Wed, 24 Apr 2024 15:04:24 +0300 Subject: [Cod-bugs] Fwd: Cod-bugs post from sakurabayashi26@sanken.osaka-u.ac.jp requires approval In-Reply-To: <3fa9a062-4aca-455a-9894-b11c07d73aca@ibt.lt> References:

<004d01da95e2$e96d68a0$bc4839e0$@sanken.osaka-u.ac.jp> <3fa9a062-4aca-455a-9894-b11c07d73aca@ibt.lt> Message-ID: Dear Dr. Sakurabayashi, I have inserted the data items form you mail (below) into the on-hold COD entry 3000497. You may want to verify at the https://www.crystallography.net/cod/manage_depositions.php Web page (after the login) that the changes correspond to you original intended antry. Sincerely yours, Saulius On 2024-04-24 09:38, Saulius Gra?ulis wrote: > Dear dr. Sakurabayashi, > > thank you for your message. I'm very glad that your deposition worked! > > On 2024-04-24 04:01, sakurabayashi26 at sanken.osaka-u.ac.jp wrote: >> >> Dear Dr. Saulius, >> >> Thank you for the reply. >> >> >1. please comment out the '_refine_ls_R_factor_gt' and the '_refine_ls_wR_factor_ref' lines >> (data >items) in >you submitted file; you can do this in the COD >> deposition site editor. Please save these >lines on you >computer in >> a separate file; >> >> I just deposited the cif file with the two lines above commented out. >> >> Deposition seems to have worked. >> >> >2. your submission should be then ready for deposition ("green"). Please deposit it and send us: >> >> > >> >> >?? a) the COD ID of the deposited structure; >> >> >?? b) the saved '_refine_ls_R_factor_gt' and the '_refine_ls_wR_factor_ref' lines (data items; >> >> The COD ID is 3000497. >> >> Those two lines are shown below; >> >> _refine_ls_R_factor_gt???????????? 0.2149 >> >> _refine_ls_wR_factor_ref?????????? 0.5835 >> >> If necessary, please add the below comment as the reason of errors. >> >> This is a MicroED structure refined only kinematically. >> >> Thus, traditional X-ray crystallography thresholds are not adequate. >> > Excellent! I'll insert the values into your structure in the 'on-hold' > repository. The values will be there when the structure is released. > >> If there are still any deficiencies regarding depositions, I would >> appreciate it if you could let me know. >> > I'll let you know but for now everything seems OK! > > Sincerely yours, > Saulius > >> Best regards, >> >> Shuhei Sakurabayashi >> >> *From:*Saulius Gra?ulis grazulis at ibt.lt >> *Sent:* Tuesday, April 23, 2024 3:04 PM >> *To:* cod-bugs at lists.crystallography.net; >> sakurabayashi26 at sanken.osaka-u.ac.jp >> *Subject:* Re: [Cod-bugs] Fwd: Cod-bugs post from >> sakurabayashi26 at sanken.osaka-u.ac.jp requires approval >> >> Dear dr. Sakurabayashi >> >> thank you for depositing your data to the COD! >> >> Indeed, we should relax Rf requirements for the MicroED structures, >> but for now, please proceed as follows: >> >> 1. please comment out the '_refine_ls_R_factor_gt' and the >> '_refine_ls_wR_factor_ref' lines (data items) in you submitted file; >> you can do this in the COD deposition site editor. Please save these >> lines on you computer in a separate file; >> >> 2. your submission should be then ready for deposition ("green"). >> Please deposit it and send us: >> >> ?? a) the COD ID of the deposited structure; >> >> ?? b) the saved '_refine_ls_R_factor_gt' and the >> '_refine_ls_wR_factor_ref' lines (data items; >> >> We will reinsert them into your deposited file with the appropriate >> comment. You should also be able to reinsert them in the COD data >> editing Web window if you would like to do so. >> >> HTH, >> >> Sincerely yours, >> Saulius >> >> >> -- >> This message has been scanned for viruses and >> dangerous content by *MailScanner* , >> and is >> believed to be clean. > > > -- > Dr. Saulius Gra?ulis > Vilnius University Institute of Biotechnology, Saul?tekio al. 7 > LT-10257 Vilnius, Lietuva (Lithuania) > mobile: (+370-684)-49802, (+370-614)-36366 > > -- > This message has been scanned for viruses and > dangerous content by *MailScanner* , and is > believed to be clean. > > _______________________________________________ > Cod-bugs mailing list > Cod-bugs at lists.crystallography.net > http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs -- Dr. Saulius Gra?ulis Vilnius University Institute of Biotechnology, Saul?tekio al. 7 LT-10257 Vilnius, Lietuva (Lithuania) mobile: (+370-684)-49802, (+370-614)-36366 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wojdyr at gmail.com Sat Apr 27 14:41:51 2024 From: wojdyr at gmail.com (Marcin Wojdyr) Date: Sat, 27 Apr 2024 13:41:51 +0200 Subject: [Cod-bugs] spacegroup name 'C 2 e b' Message-ID: Hello, I've been checking space group names, and I noticed that I can't read 'C 2 e b' which is used in COD. I see several space groups were renamed in 2015 to introduce 'e': https://github.com/cod-developers/cod-tools/commit/173879a3dc289f36b0cb343c9464bb9fdc19ecf4 but this one name differs from symbols used in cctbx and spglib that I've been using as a reference. So we have: C 2 c b - old C 2 c e - cctbx C 2 e b - cod-tools I didn't even try to understand the details of the space group naming, so I can't tell which name is correct. Any thoughts? Marcin -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. From grazulis at ibt.lt Sat Apr 27 15:15:42 2024 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=) Date: Sat, 27 Apr 2024 15:15:42 +0300 Subject: [Cod-bugs] spacegroup name 'C 2 e b' In-Reply-To: References: Message-ID: <7f61fded-97ee-f2a1-dd62-267658c64414@ibt.lt> Hi, Marcin, On 2024-04-27 14:41, Marcin Wojdyr wrote: > I've been checking space group names, and I noticed that I can't read > 'C 2 e b' which is used in COD. I see several space groups were > renamed in 2015 to introduce 'e': > https://github.com/cod-developers/cod-tools/commit/173879a3dc289f36b0cb343c9464bb9fdc19ecf4 > but this one name differs from symbols used in cctbx and spglib that > I've been using as a reference. > So we have: > C 2 c b - old > C 2 c e - cctbx > C 2 e b - cod-tools > I didn't even try to understand the details of the space group naming, > so I can't tell which name is correct. Any thoughts? > From what I see, this could be indeed a bug in our tables, the ITC Vol. A to which we all refer indeed mentions 'C 2 c e' and not the 'C 2 e b'. We'll have a look and harmonise the space group name with the Tables. I the meantime, may I suggest that you either use the Hall symbol ('C -2ac 2'), which seems to be correct for all 9 COD entries that mention 'C 2 e b' [1]. I have even a code (in Ada :) that parses the Hall symbol and returns symmetry operation matrices [2]. Alternatively, probably the most versatile way to describe symmetry is to use symmetry operation matrices described in the '_space_group_symop_operation_xyz' data item. All entries in [1] seem to have these data items. Sorry for the inconvenience! Sincerely, Saulius Refs: [1] COD entries with the 'C 2 e b' H-M space group symbol: > mysql -u cod_reader -h sql.crystallography.net cod -e 'select file, > sgNumber, sg, sgHall, svnrevision, date from data where sg = "C 2 e b" > order by file' > +---------+----------+---------+----------+-------------+------------+ > | file??? | sgNumber | sg????? | sgHall?? | svnrevision | date?????? | > +---------+----------+---------+----------+-------------+------------+ > | 4003235 |?????? 41 | C 2 e b | C -2ac 2 |????? 231452 | 2020-10-21 | > | 4127236 |?????? 41 | C 2 e b | C -2ac 2 |????? 223200 | 2020-10-21 | > | 4131512 |?????? 41 | C 2 e b | C -2ac 2 |????? 241703 | 2020-10-21 | > | 4518546 |?????? 41 | C 2 e b | C -2ac 2 |????? 263581 | 2021-04-04 | > | 7060405 |?????? 41 | C 2 e b | C -2ac 2 |????? 263802 | 2021-04-05 | > | 7225528 |?????? 41 | C 2 e b | C -2ac 2 |????? 183458 | 2020-10-21 | > | 7237089 |?????? 41 | C 2 e b | C -2ac 2 |????? 236814 | 2020-10-21 | > | 7238091 |?????? 41 | C 2 e b | C -2ac 2 |????? 244064 | 2020-10-21 | > | 7701682 |?????? 41 | C 2 e b | C -2ac 2 |????? 223334 | 2020-10-21 | > +---------+----------+---------+----------+-------------+------------+ [2] Gra?ulis, S. (2022) A program and library to decode Hall crystallographic space group symbols. GitHub. URL: https://github.com/sauliusg/decode-Hall-symbol [accessed 2024-04-27T15:08+03:00]. -- Dr. Saulius Gra?ulis Vilnius University Institute of Biotechnology, Saul?tekio al. 7 LT-10257 Vilnius, Lietuva (Lithuania) fax: (+370-5)-2234367 / phone (office): (+370-5)-2234353 mobile: (+370-684)-49802, (+370-614)-36366 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- A non-text attachment was scrubbed... Name: grazulis.vcf Type: text/vcard Size: 4 bytes Desc: not available URL: From wojdyr at gmail.com Sun Apr 28 21:37:30 2024 From: wojdyr at gmail.com (Marcin Wojdyr) Date: Sun, 28 Apr 2024 20:37:30 +0200 Subject: [Cod-bugs] spacegroup name 'C 2 e b' In-Reply-To: <7f61fded-97ee-f2a1-dd62-267658c64414@ibt.lt> References: <7f61fded-97ee-f2a1-dd62-267658c64414@ibt.lt> Message-ID: Hi Saulius, > I the meantime, may I suggest that you either use the Hall symbol ('C > -2ac 2'), which seems to be correct for all 9 COD entries that mention > 'C 2 e b' [1]. I have even a code (in Ada :) that parses the Hall symbol > and returns symmetry operation matrices [2]. Alternatively, probably the > most versatile way to describe symmetry is to use symmetry operation > matrices described in the '_space_group_symop_operation_xyz' data item. > All entries in [1] seem to have these data items. That's actually why I was checking the space groups. I was trying to find out what's the best order for reading a space group. On one hand, Hall symbols are unambiguous, but on the other hand if they are less popular, there is a bigger chance that someone changes H-M in a file and forgets to change Hall. At least that's my thinking. I also have code for parsing Hall symbols, although I'm missing software for doing the opposite (symops -> Hall symbol). In particular, for getting canonical Hall symbols. ITC vol. B mentions an unambiguous method of selecting the Hall symbols by sorting operations into "a strictly prescribed order based on the shape of their Seitz matrices", and then it refers for details to a website that's no longer available. Cctbx docs mention that they used Xtal 3.7 to generate Hall symbols, but I haven't sorted out how to use Xtal. Best, Marcin -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. From valmar.sobrinho at ifrn.edu.br Sun Apr 28 03:57:27 2024 From: valmar.sobrinho at ifrn.edu.br (Valmar da Silva Severiano Sobrinho) Date: Sun, 28 Apr 2024 00:57:27 +0000 Subject: [Cod-bugs] Problems using the database Message-ID: <7e85a8e6307a4cf0adc624ab2f99d6f8@ifrn.edu.br> Hello Dear, I downloaded all the cif files with the COD database and intend to use them in my research (for 'svn' method), but all these files simply cannot be used as a search database since they are not in a format accepted by analysis software. If I use QualX and want to use its database it needs a ".sq" file for the database, if I use Xpert Highscore it needs a ".hsrdb" file. How can I use COD in my work for phase identification? Valmar da Silva S. Sobrinho. Physics Professor - IFRN - Brazil. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: