Re: [ccp4bb] Some questions on tools for CCP4i2cloud: pdbset, pdbcur, coordconv, sftools
ATTACHED SOME CORRESPONDENCE WITH David Lawson re these issues/. Eleanor On Tue, 31 Aug 2021 at 10:29, Robbie Joosten wrote: > Hi everyone, > > Thank you for the replies so far on and off list, they are really helpful. > Feel free to keep them coming. > > Cheers, > Robbie > > > -Original Message- > > From: CCP4 bulletin board On Behalf Of Dirk > > Kostrewa > > Sent: Tuesday, August 31, 2021 10:24 > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: Re: [ccp4bb] Some questions on tools for CCP4i2cloud: pdbset, > > pdbcur, coordconv, sftools > > > > Dear Robbie, > > > > I use pdbset in scripts from time to time, mainly to generate symmetry > > equivalent copies. I use sftools on the command line more frequently, > > because it allows a lot of mathematical operations on data in mtz files. > > I also use sftools to produce lists of average data values against > > resolution (that I plot then with gnuplot). I can't recall having used > > coordconv at all. > > > > Best regards, > > > > Dirk. > > > > On 8/26/21 12:29 PM, Robbie Joosten wrote: > > > Dear CCP4 users, > > > > > > We (as in, the CCP4 developers) are investigating some (potentially) > > missing functionality in CCP4i2 and/or Cloud with respect to the programs > > pdbset, pdbcur, coordconv, and sftools. Some of these tools are quite old > > and may need to be replaced by other tools with similar functionality. > Could > > you answer a few questions: > > > > > > - Do you use any of these tools? > > > - If so, how often? (Few times a week, month, year, or less than once a > > year). > > > - Which functionality of program X do you use? > > > - Would you like a graphical interface to that functionality or are > you happy > > to use the command line? > > > > > > Personal example: > > > I use pdbset a few times a month, but only the "noise" function. I > don't > > need a graphical interface for it (because it is used in the context of > pdb- > > redo). I also use sftools, "reduce -> merge average" a few times a year. > Again, > > only from the command line. > > > > > > > > > Feel free to send your answers directly to me or to the bulletin board > if > > you want to start a discussion. Tips on alternative CCP4 tools to achieve > > similar effects are probably also interesting for other BB users. > > > > > > Cheers, > > > Robbie > > > > > > > > > > > > > > > > > ### > > # > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ > > > > -- > > > > *** > > Dirk Kostrewa > > Gene Center Munich > > Department of Biochemistry, AG Hopfner > > Ludwig-Maximilians-Universität München > > Feodor-Lynen-Str. 25 > > D-81377 Munich > > Germany > > Phone: +49-89-2180-76845 > > Fax:+49-89-2180-76998 > > E-mail: dirk.kostr...@lmu.de > > kostr...@genzentrum.lmu.de > > WWW:www.genzentrum.lmu.de > > *** > > > > ### > > # > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/WA-JISC.exe?SUBED1=CCP4BB=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/WA-JISC.exe?SUBED1=CCP4BB=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/ DaveLawson.docx Description: MS-Word 2007 document
Re: [ccp4bb] Some questions on tools for CCP4i2cloud: pdbset, pdbcur, coordconv, sftools
Hi everyone, Thank you for the replies so far on and off list, they are really helpful. Feel free to keep them coming. Cheers, Robbie > -Original Message- > From: CCP4 bulletin board On Behalf Of Dirk > Kostrewa > Sent: Tuesday, August 31, 2021 10:24 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Some questions on tools for CCP4i2cloud: pdbset, > pdbcur, coordconv, sftools > > Dear Robbie, > > I use pdbset in scripts from time to time, mainly to generate symmetry > equivalent copies. I use sftools on the command line more frequently, > because it allows a lot of mathematical operations on data in mtz files. > I also use sftools to produce lists of average data values against > resolution (that I plot then with gnuplot). I can't recall having used > coordconv at all. > > Best regards, > > Dirk. > > On 8/26/21 12:29 PM, Robbie Joosten wrote: > > Dear CCP4 users, > > > > We (as in, the CCP4 developers) are investigating some (potentially) > missing functionality in CCP4i2 and/or Cloud with respect to the programs > pdbset, pdbcur, coordconv, and sftools. Some of these tools are quite old > and may need to be replaced by other tools with similar functionality. Could > you answer a few questions: > > > > - Do you use any of these tools? > > - If so, how often? (Few times a week, month, year, or less than once a > year). > > - Which functionality of program X do you use? > > - Would you like a graphical interface to that functionality or are you > > happy > to use the command line? > > > > Personal example: > > I use pdbset a few times a month, but only the "noise" function. I don't > need a graphical interface for it (because it is used in the context of pdb- > redo). I also use sftools, "reduce -> merge average" a few times a year. > Again, > only from the command line. > > > > > > Feel free to send your answers directly to me or to the bulletin board if > you want to start a discussion. Tips on alternative CCP4 tools to achieve > similar effects are probably also interesting for other BB users. > > > > Cheers, > > Robbie > > > > > > > > > > > ### > # > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ > > -- > > *** > Dirk Kostrewa > Gene Center Munich > Department of Biochemistry, AG Hopfner > Ludwig-Maximilians-Universität München > Feodor-Lynen-Str. 25 > D-81377 Munich > Germany > Phone: +49-89-2180-76845 > Fax:+49-89-2180-76998 > E-mail: dirk.kostr...@lmu.de > kostr...@genzentrum.lmu.de > WWW:www.genzentrum.lmu.de > *** > > ### > # > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] Some questions on tools for CCP4i2cloud: pdbset, pdbcur, coordconv, sftools
Dear Robbie, I use pdbset in scripts from time to time, mainly to generate symmetry equivalent copies. I use sftools on the command line more frequently, because it allows a lot of mathematical operations on data in mtz files. I also use sftools to produce lists of average data values against resolution (that I plot then with gnuplot). I can't recall having used coordconv at all. Best regards, Dirk. On 8/26/21 12:29 PM, Robbie Joosten wrote: Dear CCP4 users, We (as in, the CCP4 developers) are investigating some (potentially) missing functionality in CCP4i2 and/or Cloud with respect to the programs pdbset, pdbcur, coordconv, and sftools. Some of these tools are quite old and may need to be replaced by other tools with similar functionality. Could you answer a few questions: - Do you use any of these tools? - If so, how often? (Few times a week, month, year, or less than once a year). - Which functionality of program X do you use? - Would you like a graphical interface to that functionality or are you happy to use the command line? Personal example: I use pdbset a few times a month, but only the "noise" function. I don't need a graphical interface for it (because it is used in the context of pdb-redo). I also use sftools, "reduce -> merge average" a few times a year. Again, only from the command line. Feel free to send your answers directly to me or to the bulletin board if you want to start a discussion. Tips on alternative CCP4 tools to achieve similar effects are probably also interesting for other BB users. Cheers, Robbie To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry, AG Hopfner Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76998 E-mail: dirk.kostr...@lmu.de kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] Some questions on tools for CCP4i2cloud: pdbset, pdbcur, coordconv, sftools
Hi Robbie I also use them quite regularly (less so coordconv, although I do use it), typically from the command line Thanks, Alejandro > On Aug 30, 2021, at 17:38, James Holton wrote: > > I use pdbset, coordconv and sftools a LOT. Usually for things no other > programs do, like converting to fractional coordinates, and performing math > operations on mtz data. Always from command line scripts. > > -James Holton > MAD Scientist > > On 8/26/2021 3:29 AM, Robbie Joosten wrote: >> Dear CCP4 users, >> >> We (as in, the CCP4 developers) are investigating some (potentially) missing >> functionality in CCP4i2 and/or Cloud with respect to the programs pdbset, >> pdbcur, coordconv, and sftools. Some of these tools are quite old and may >> need to be replaced by other tools with similar functionality. Could you >> answer a few questions: >> >> - Do you use any of these tools? >> - If so, how often? (Few times a week, month, year, or less than once a >> year). >> - Which functionality of program X do you use? >> - Would you like a graphical interface to that functionality or are you >> happy to use the command line? >> >> Personal example: >> I use pdbset a few times a month, but only the "noise" function. I don't >> need a graphical interface for it (because it is used in the context of >> pdb-redo). I also use sftools, "reduce -> merge average" a few times a year. >> Again, only from the command line. >> >> >> Feel free to send your answers directly to me or to the bulletin board if >> you want to start a discussion. Tips on alternative CCP4 tools to achieve >> similar effects are probably also interesting for other BB users. >> >> Cheers, >> Robbie >> >> >> >> >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/WA-JISC.exe?SUBED1=CCP4BB=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/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] Some questions on tools for CCP4i2cloud: pdbset, pdbcur, coordconv, sftools
I use pdbset, coordconv and sftools a LOT. Usually for things no other programs do, like converting to fractional coordinates, and performing math operations on mtz data. Always from command line scripts. -James Holton MAD Scientist On 8/26/2021 3:29 AM, Robbie Joosten wrote: Dear CCP4 users, We (as in, the CCP4 developers) are investigating some (potentially) missing functionality in CCP4i2 and/or Cloud with respect to the programs pdbset, pdbcur, coordconv, and sftools. Some of these tools are quite old and may need to be replaced by other tools with similar functionality. Could you answer a few questions: - Do you use any of these tools? - If so, how often? (Few times a week, month, year, or less than once a year). - Which functionality of program X do you use? - Would you like a graphical interface to that functionality or are you happy to use the command line? Personal example: I use pdbset a few times a month, but only the "noise" function. I don't need a graphical interface for it (because it is used in the context of pdb-redo). I also use sftools, "reduce -> merge average" a few times a year. Again, only from the command line. Feel free to send your answers directly to me or to the bulletin board if you want to start a discussion. Tips on alternative CCP4 tools to achieve similar effects are probably also interesting for other BB users. Cheers, Robbie To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] Some questions on tools for CCP4i2cloud: pdbset, pdbcur, coordconv, sftools
Dear Robbie, I don't use ccp4 regularly (since our structures are mainly small molecule structures), but when I do, I often use pdbset. I use it to remove het-atoms, or side chains, or water molecules, or reset the B-value. I also use sftools. I have a script for calculating Rcomplete with refmac. This script makes use of sftools in the preparation of the mtz-file. I use these tools, because they are command line tools - much faster than GUI based versions. Best wishes, Tim On Thu, 26 Aug 2021 10:29:22 + Robbie Joosten wrote: > Dear CCP4 users, > > We (as in, the CCP4 developers) are investigating some (potentially) > missing functionality in CCP4i2 and/or Cloud with respect to the > programs pdbset, pdbcur, coordconv, and sftools. Some of these tools > are quite old and may need to be replaced by other tools with similar > functionality. Could you answer a few questions: > > - Do you use any of these tools? > - If so, how often? (Few times a week, month, year, or less than once > a year). > - Which functionality of program X do you use? > - Would you like a graphical interface to that functionality or are > you happy to use the command line? > > Personal example: > I use pdbset a few times a month, but only the "noise" function. I > don't need a graphical interface for it (because it is used in the > context of pdb-redo). I also use sftools, "reduce -> merge average" a > few times a year. Again, only from the command line. > > > Feel free to send your answers directly to me or to the bulletin > board if you want to start a discussion. Tips on alternative CCP4 > tools to achieve similar effects are probably also interesting for > other BB users. > > Cheers, > Robbie > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ pgpenZJvWEENL.pgp Description: OpenPGP digital signature
[ccp4bb] Some questions on tools for CCP4i2cloud: pdbset, pdbcur, coordconv, sftools
Dear CCP4 users, We (as in, the CCP4 developers) are investigating some (potentially) missing functionality in CCP4i2 and/or Cloud with respect to the programs pdbset, pdbcur, coordconv, and sftools. Some of these tools are quite old and may need to be replaced by other tools with similar functionality. Could you answer a few questions: - Do you use any of these tools? - If so, how often? (Few times a week, month, year, or less than once a year). - Which functionality of program X do you use? - Would you like a graphical interface to that functionality or are you happy to use the command line? Personal example: I use pdbset a few times a month, but only the "noise" function. I don't need a graphical interface for it (because it is used in the context of pdb-redo). I also use sftools, "reduce -> merge average" a few times a year. Again, only from the command line. Feel free to send your answers directly to me or to the bulletin board if you want to start a discussion. Tips on alternative CCP4 tools to achieve similar effects are probably also interesting for other BB users. Cheers, Robbie To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
