Re: [ccp4bb] Resolution limit of index in XDS
I was a little provokative. A GUI with a viewer would actually be an excellent idea since it allows one to see what one is doing, which would be of great help for difficult data sets. Nevertheless, since XDS is part of many automated pipelines, the possibility to run XDS offline with a command file should not be touched. If IDXREF would take the INCLUDE_RESOLUTION_RANGE into account, I am sure this would improve the performance of XDS. Best regards and thank you for the work you put into XDS! Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kay Diederichs Sent: Thursday, March 21, 2013 10:02 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Resolution limit of index in XDS On Thu, 21 Mar 2013 08:28:27 +, herman.schreu...@sanofi.com wrote: >Dear Tim, > >It could be that COLSPOT does not rely on experimental setup parameters. >However, XDS must have reasonably close starting values for distance, direct >beam position etc., otherwise the autoindexing would fail, so the information >to calculate an approximate TRUSTED_REGION is available. TRUSTED_REGION and INCLUDE_RESOLUTION_RANGE are orthogonal concepts; both are input by the user and not calculated by the program. > >For good data, a limited spot range usually works as well. However, for the >weakly diffracting bad crystals with ice rings, salt spots, multiple >diffraction patterns etc., one often needs the full range and often needs >several tries with different parameters before indexing is successful. Since >it is only cpu-time, it is the least of my worries and, as you mention, it is >not bad to be forced to think once in a while instead of just clicking buttons >in GUI's. Nevertheless I plan to release a GUI for xds soon; among other things, this enables to visualize and change TRUSTED_REGION and INCLUDE_RESOLUTION_RANGE . best, Kay > >Best regards, >Herman > > > >-Original Message- >From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] >Sent: Wednesday, March 20, 2013 11:17 PM >To: Schreuder, Herman R&D/DE >Cc: CCP4BB@JISCMAIL.AC.UK >Subject: Re: [ccp4bb] Resolution limit of index in XDS > >-BEGIN PGP SIGNED MESSAGE- >Hash: SHA1 > >Dear Herman, > >the short answer might be that at the stage of COLSPOT the term 'resolution' >has a limited meaning because COLSPOT does not rely on the experimental setup >like distance and beam direction, so the term 'resolution limit' is >conceptually not applicable at this stage. > >Indexing does often not require the full data set, you can reduce the >"SPOT_RANGE" if you are worried about processing time, or by a multi-CPU >machine. > >One of the great advantages of XDS is that it asks you to think at a level >higher than the average MS-Windows user while processing your data, so the >effort to figure out the three numbers to set the TRUSTED_REGION is in line >with the philosphy of XDS as I understand it. > >But you are right, I do not have access to the source of XDS and I am not the >person to address a request to. > >Kind regards, >Tim > >On 03/20/2013 10:29 AM, herman.schreu...@sanofi.com wrote: >> Dear Tim, but probably I should adres this to Kai Diederichs, >> >> not including the resolution cutoff in COLSPOT and IDXREF is a >> feature of XDS I do not understand at all. For most cases, it may not >> matter since only the strong spots are used, but what are the advantages? >> >> In fact there are disadvantages, especially when dealing with poorly >> diffracting difficult data sets: -when a crystallographer imposes a >> resolution limit, there are usually good reasons for it. >> -outside the resolution limit, there may be ice rings or >> contaminating salt spots, which make the autoindexing fail. -when >> processing 900 frame Pilatus data sets, running COLSPOT on the >> complete detector surface takes significantly longer then running it >> only on the center region. >> >> Of course, one could fudge a resolution cutoff by translating >> resolution into pixels and then calculating a TRUSTED_REGION, or >> manually editing the SPOT.XDS file, but this is a lot of extra and in >> my view unneccessary work. >> >> I would really consider using the resolution cutoff for COLSPOT as >> well. >> >> Best, Herman >> >> >> -Original Message- From: CCP4 bulletin board >> [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent: >> Tuesday, March 19, 2013 11:06 PM To: CCP4BB@JISCMAIL.AC.UK Subject: >> Re: [ccp4bb] Resolution limit of index in XDS >> >> Dear Niu, >> >> indexing relies on strong
Re: [ccp4bb] Resolution limit of index in XDS
On Thu, 21 Mar 2013 08:28:27 +, herman.schreu...@sanofi.com wrote: >Dear Tim, > >It could be that COLSPOT does not rely on experimental setup parameters. >However, XDS must have reasonably close starting values for distance, direct >beam position etc., otherwise the autoindexing would fail, so the information >to calculate an approximate TRUSTED_REGION is available. TRUSTED_REGION and INCLUDE_RESOLUTION_RANGE are orthogonal concepts; both are input by the user and not calculated by the program. > >For good data, a limited spot range usually works as well. However, for the >weakly diffracting bad crystals with ice rings, salt spots, multiple >diffraction patterns etc., one often needs the full range and often needs >several tries with different parameters before indexing is successful. Since >it is only cpu-time, it is the least of my worries and, as you mention, it is >not bad to be forced to think once in a while instead of just clicking buttons >in GUI's. Nevertheless I plan to release a GUI for xds soon; among other things, this enables to visualize and change TRUSTED_REGION and INCLUDE_RESOLUTION_RANGE . best, Kay > >Best regards, >Herman > > > >-Original Message- >From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] >Sent: Wednesday, March 20, 2013 11:17 PM >To: Schreuder, Herman R&D/DE >Cc: CCP4BB@JISCMAIL.AC.UK >Subject: Re: [ccp4bb] Resolution limit of index in XDS > >-BEGIN PGP SIGNED MESSAGE- >Hash: SHA1 > >Dear Herman, > >the short answer might be that at the stage of COLSPOT the term 'resolution' >has a limited meaning because COLSPOT does not rely on the experimental setup >like distance and beam direction, so the term 'resolution limit' is >conceptually not applicable at this stage. > >Indexing does often not require the full data set, you can reduce the >"SPOT_RANGE" if you are worried about processing time, or by a multi-CPU >machine. > >One of the great advantages of XDS is that it asks you to think at a level >higher than the average MS-Windows user while processing your data, so the >effort to figure out the three numbers to set the TRUSTED_REGION is in line >with the philosphy of XDS as I understand it. > >But you are right, I do not have access to the source of XDS and I am not the >person to address a request to. > >Kind regards, >Tim > >On 03/20/2013 10:29 AM, herman.schreu...@sanofi.com wrote: >> Dear Tim, but probably I should adres this to Kai Diederichs, >> >> not including the resolution cutoff in COLSPOT and IDXREF is a feature >> of XDS I do not understand at all. For most cases, it may not matter >> since only the strong spots are used, but what are the advantages? >> >> In fact there are disadvantages, especially when dealing with poorly >> diffracting difficult data sets: -when a crystallographer imposes a >> resolution limit, there are usually good reasons for it. >> -outside the resolution limit, there may be ice rings or contaminating >> salt spots, which make the autoindexing fail. -when processing 900 >> frame Pilatus data sets, running COLSPOT on the complete detector >> surface takes significantly longer then running it only on the center >> region. >> >> Of course, one could fudge a resolution cutoff by translating >> resolution into pixels and then calculating a TRUSTED_REGION, or >> manually editing the SPOT.XDS file, but this is a lot of extra and in >> my view unneccessary work. >> >> I would really consider using the resolution cutoff for COLSPOT as >> well. >> >> Best, Herman >> >> >> -Original Message- From: CCP4 bulletin board >> [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent: >> Tuesday, March 19, 2013 11:06 PM To: CCP4BB@JISCMAIL.AC.UK Subject: >> Re: [ccp4bb] Resolution limit of index in XDS >> >> Dear Niu, >> >> indexing relies on strong reflections only, that is (in very >> brieft) why INCLUDE_RESOLUTION_RANGE indeed does not affect the >> relections collected in COLSPOT which in turn are used by IDXREF. >> You can work around this, however, by making use of TRUSTED_REGION and >> set it to e.g. 0.7 or 0.6 (you can use adxv to translate resolution >> into pixel and then calculate the fraction you need to set the second >> number in TRUSTED_REGION to (or the first if you want to exclude the >> inner resolution reflections - I remember one data set where this was >> essential for indexing - DNA was involved >> there) >> >> Best, Tim >> >> On 03/19/2013 08:53 PM, Niu Tou wrote: >>
Re: [ccp4bb] Resolution limit of index in XDS
Dear Herman, some pros and cons are documented at http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Wishlist#Would_be_nice_to_have , and the workaround is at http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Ice_rings . These XDSwiki articles are old, and nobody has contributed to the discussion since 2007 (after all, is is a Wiki!), so there has not been much reason for a change. Tim is right in that usage of INCLUDE_RESOLUTION_RANGE does not fit well at the COLSPOT stage, since COLSPOT "knows" nothing about wavelength, distance, pixel size and so on. If there is agreement among XDS users that IDXREF should take INCLUDE_RESOLUTION_RANGE into account, there is a good chance that the next version of XDS will do that. best, Kay On Wed, 20 Mar 2013 09:29:47 +, herman.schreu...@sanofi.com wrote: >Dear Tim, but probably I should adres this to Kai Diederichs, > >not including the resolution cutoff in COLSPOT and IDXREF is a feature of XDS >I do not understand at all. For most cases, it may not matter since only the >strong spots are used, but what are the advantages? > >In fact there are disadvantages, especially when dealing with poorly >diffracting difficult data sets: >-when a crystallographer imposes a resolution limit, there are usually good >reasons for it. >-outside the resolution limit, there may be ice rings or contaminating salt >spots, which make the autoindexing fail. >-when processing 900 frame Pilatus data sets, running COLSPOT on the complete >detector surface takes significantly longer then running it only on the center >region. > >Of course, one could fudge a resolution cutoff by translating resolution into >pixels and then calculating a TRUSTED_REGION, or manually editing the SPOT.XDS >file, but this is a lot of extra and in my view unneccessary work. > >I would really consider using the resolution cutoff for COLSPOT as well. > >Best, >Herman > > >-Original Message- >From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim >Gruene >Sent: Tuesday, March 19, 2013 11:06 PM >To: CCP4BB@JISCMAIL.AC.UK >Subject: Re: [ccp4bb] Resolution limit of index in XDS > >-BEGIN PGP SIGNED MESSAGE- >Hash: SHA1 > >Dear Niu, > >indexing relies on strong reflections only, that is (in very brieft) why >INCLUDE_RESOLUTION_RANGE indeed does not affect the relections collected in >COLSPOT which in turn are used by IDXREF. You can work around this, however, >by making use of TRUSTED_REGION and set it to e.g. 0.7 or 0.6 (you can use >adxv to translate resolution into pixel and then calculate the fraction you >need to set the second number in TRUSTED_REGION to (or the first if you want >to exclude the inner resolution reflections - I remember one data set where >this was essential for indexing - DNA was involved there) > >Best, >Tim > >On 03/19/2013 08:53 PM, Niu Tou wrote: >> Dear All, >> >> Is there any command can set the resolution limit for index step in >> XDS? I only found a keyword INCLUDE_RESOLUTION_RANGE, but it looks to >> be a definition of resolution range after index step as it >> says: >> >> INCLUDE_RESOLUTION_RANGE=20.0 0.0 !Angstroem; used by >> DEFPIX,INTEGRATE,CORRECT >> >> Thanks! Niu >> > >- -- >Dr Tim Gruene >Institut fuer anorganische Chemie >Tammannstr. 4 >D-37077 Goettingen > >GPG Key ID = A46BEE1A >-BEGIN PGP SIGNATURE- >Version: GnuPG v1.4.12 (GNU/Linux) >Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > >iD8DBQFRSOFJUxlJ7aRr7hoRAo6TAKC+BePgeODbDyngO7N8vCE4CnjxmQCfS5cP >srShHNz1sDK0EMHSbE3fDwA= >=kAwf >-END PGP SIGNATURE-
Re: [ccp4bb] Resolution limit of index in XDS
Dear Tim, It could be that COLSPOT does not rely on experimental setup parameters. However, XDS must have reasonably close starting values for distance, direct beam position etc., otherwise the autoindexing would fail, so the information to calculate an approximate TRUSTED_REGION is available. For good data, a limited spot range usually works as well. However, for the weakly diffracting bad crystals with ice rings, salt spots, multiple diffraction patterns etc., one often needs the full range and often needs several tries with different parameters before indexing is successful. Since it is only cpu-time, it is the least of my worries and, as you mention, it is not bad to be forced to think once in a while instead of just clicking buttons in GUI's. Best regards, Herman -Original Message- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Sent: Wednesday, March 20, 2013 11:17 PM To: Schreuder, Herman R&D/DE Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Resolution limit of index in XDS -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Herman, the short answer might be that at the stage of COLSPOT the term 'resolution' has a limited meaning because COLSPOT does not rely on the experimental setup like distance and beam direction, so the term 'resolution limit' is conceptually not applicable at this stage. Indexing does often not require the full data set, you can reduce the "SPOT_RANGE" if you are worried about processing time, or by a multi-CPU machine. One of the great advantages of XDS is that it asks you to think at a level higher than the average MS-Windows user while processing your data, so the effort to figure out the three numbers to set the TRUSTED_REGION is in line with the philosphy of XDS as I understand it. But you are right, I do not have access to the source of XDS and I am not the person to address a request to. Kind regards, Tim On 03/20/2013 10:29 AM, herman.schreu...@sanofi.com wrote: > Dear Tim, but probably I should adres this to Kai Diederichs, > > not including the resolution cutoff in COLSPOT and IDXREF is a feature > of XDS I do not understand at all. For most cases, it may not matter > since only the strong spots are used, but what are the advantages? > > In fact there are disadvantages, especially when dealing with poorly > diffracting difficult data sets: -when a crystallographer imposes a > resolution limit, there are usually good reasons for it. > -outside the resolution limit, there may be ice rings or contaminating > salt spots, which make the autoindexing fail. -when processing 900 > frame Pilatus data sets, running COLSPOT on the complete detector > surface takes significantly longer then running it only on the center > region. > > Of course, one could fudge a resolution cutoff by translating > resolution into pixels and then calculating a TRUSTED_REGION, or > manually editing the SPOT.XDS file, but this is a lot of extra and in > my view unneccessary work. > > I would really consider using the resolution cutoff for COLSPOT as > well. > > Best, Herman > > > -Original Message- From: CCP4 bulletin board > [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent: > Tuesday, March 19, 2013 11:06 PM To: CCP4BB@JISCMAIL.AC.UK Subject: > Re: [ccp4bb] Resolution limit of index in XDS > > Dear Niu, > > indexing relies on strong reflections only, that is (in very > brieft) why INCLUDE_RESOLUTION_RANGE indeed does not affect the > relections collected in COLSPOT which in turn are used by IDXREF. > You can work around this, however, by making use of TRUSTED_REGION and > set it to e.g. 0.7 or 0.6 (you can use adxv to translate resolution > into pixel and then calculate the fraction you need to set the second > number in TRUSTED_REGION to (or the first if you want to exclude the > inner resolution reflections - I remember one data set where this was > essential for indexing - DNA was involved > there) > > Best, Tim > > On 03/19/2013 08:53 PM, Niu Tou wrote: >> Dear All, > >> Is there any command can set the resolution limit for index step in >> XDS? I only found a keyword INCLUDE_RESOLUTION_RANGE, but it looks to >> be a definition of resolution range after index step as it says: > >> INCLUDE_RESOLUTION_RANGE=20.0 0.0 !Angstroem; used by >> DEFPIX,INTEGRATE,CORRECT > >> Thanks! Niu > > > - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRSjVtUxlJ7aRr7hoRApZhAJ9RFBs8D9NGjgLY3KOoNHhNtdOWggCgj7U0 zY7jEFDYZfl0Umb9E1Bzs1U= =+HjR -END PGP SIGNATURE-
Re: [ccp4bb] Resolution limit of index in XDS
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Herman, the short answer might be that at the stage of COLSPOT the term 'resolution' has a limited meaning because COLSPOT does not rely on the experimental setup like distance and beam direction, so the term 'resolution limit' is conceptually not applicable at this stage. Indexing does often not require the full data set, you can reduce the "SPOT_RANGE" if you are worried about processing time, or by a multi-CPU machine. One of the great advantages of XDS is that it asks you to think at a level higher than the average MS-Windows user while processing your data, so the effort to figure out the three numbers to set the TRUSTED_REGION is in line with the philosphy of XDS as I understand it. But you are right, I do not have access to the source of XDS and I am not the person to address a request to. Kind regards, Tim On 03/20/2013 10:29 AM, herman.schreu...@sanofi.com wrote: > Dear Tim, but probably I should adres this to Kai Diederichs, > > not including the resolution cutoff in COLSPOT and IDXREF is a > feature of XDS I do not understand at all. For most cases, it may > not matter since only the strong spots are used, but what are the > advantages? > > In fact there are disadvantages, especially when dealing with > poorly diffracting difficult data sets: -when a crystallographer > imposes a resolution limit, there are usually good reasons for it. > -outside the resolution limit, there may be ice rings or > contaminating salt spots, which make the autoindexing fail. -when > processing 900 frame Pilatus data sets, running COLSPOT on the > complete detector surface takes significantly longer then running > it only on the center region. > > Of course, one could fudge a resolution cutoff by translating > resolution into pixels and then calculating a TRUSTED_REGION, or > manually editing the SPOT.XDS file, but this is a lot of extra and > in my view unneccessary work. > > I would really consider using the resolution cutoff for COLSPOT as > well. > > Best, Herman > > > -Original Message- From: CCP4 bulletin board > [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent: > Tuesday, March 19, 2013 11:06 PM To: CCP4BB@JISCMAIL.AC.UK Subject: > Re: [ccp4bb] Resolution limit of index in XDS > > Dear Niu, > > indexing relies on strong reflections only, that is (in very > brieft) why INCLUDE_RESOLUTION_RANGE indeed does not affect the > relections collected in COLSPOT which in turn are used by IDXREF. > You can work around this, however, by making use of TRUSTED_REGION > and set it to e.g. 0.7 or 0.6 (you can use adxv to translate > resolution into pixel and then calculate the fraction you need to > set the second number in TRUSTED_REGION to (or the first if you > want to exclude the inner resolution reflections - I remember one > data set where this was essential for indexing - DNA was involved > there) > > Best, Tim > > On 03/19/2013 08:53 PM, Niu Tou wrote: >> Dear All, > >> Is there any command can set the resolution limit for index step >> in XDS? I only found a keyword INCLUDE_RESOLUTION_RANGE, but it >> looks to be a definition of resolution range after index step as >> it says: > >> INCLUDE_RESOLUTION_RANGE=20.0 0.0 !Angstroem; used by >> DEFPIX,INTEGRATE,CORRECT > >> Thanks! Niu > > > - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRSjVtUxlJ7aRr7hoRApZhAJ9RFBs8D9NGjgLY3KOoNHhNtdOWggCgj7U0 zY7jEFDYZfl0Umb9E1Bzs1U= =+HjR -END PGP SIGNATURE-
Re: [ccp4bb] Resolution limit of index in XDS
Dear Tim, but probably I should adres this to Kai Diederichs, not including the resolution cutoff in COLSPOT and IDXREF is a feature of XDS I do not understand at all. For most cases, it may not matter since only the strong spots are used, but what are the advantages? In fact there are disadvantages, especially when dealing with poorly diffracting difficult data sets: -when a crystallographer imposes a resolution limit, there are usually good reasons for it. -outside the resolution limit, there may be ice rings or contaminating salt spots, which make the autoindexing fail. -when processing 900 frame Pilatus data sets, running COLSPOT on the complete detector surface takes significantly longer then running it only on the center region. Of course, one could fudge a resolution cutoff by translating resolution into pixels and then calculating a TRUSTED_REGION, or manually editing the SPOT.XDS file, but this is a lot of extra and in my view unneccessary work. I would really consider using the resolution cutoff for COLSPOT as well. Best, Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent: Tuesday, March 19, 2013 11:06 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Resolution limit of index in XDS -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Niu, indexing relies on strong reflections only, that is (in very brieft) why INCLUDE_RESOLUTION_RANGE indeed does not affect the relections collected in COLSPOT which in turn are used by IDXREF. You can work around this, however, by making use of TRUSTED_REGION and set it to e.g. 0.7 or 0.6 (you can use adxv to translate resolution into pixel and then calculate the fraction you need to set the second number in TRUSTED_REGION to (or the first if you want to exclude the inner resolution reflections - I remember one data set where this was essential for indexing - DNA was involved there) Best, Tim On 03/19/2013 08:53 PM, Niu Tou wrote: > Dear All, > > Is there any command can set the resolution limit for index step in > XDS? I only found a keyword INCLUDE_RESOLUTION_RANGE, but it looks to > be a definition of resolution range after index step as it > says: > > INCLUDE_RESOLUTION_RANGE=20.0 0.0 !Angstroem; used by > DEFPIX,INTEGRATE,CORRECT > > Thanks! Niu > - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRSOFJUxlJ7aRr7hoRAo6TAKC+BePgeODbDyngO7N8vCE4CnjxmQCfS5cP srShHNz1sDK0EMHSbE3fDwA= =kAwf -END PGP SIGNATURE-
Re: [ccp4bb] Resolution limit of index in XDS
Hello, The way I do it is by manually editing the SPOT.XDS file (generated by the COLSPOT step). Spots are arranged by order of decreasing intensity in that file. So if you do down the file, select an appropriate intensity cutoff and then remove all spots below that value, it will have the effect of selecting a resolution cutoff (think of the plot of vs. resolution) but you won't know what cutoff this corresponds to unless you do a careful analysis of the resulting SPOT.XDS file. HTH, Fred. On 19/03/13 20:53, Niu Tou wrote: Dear All, Is there any command can set the resolution limit for index step in XDS? I only found a keyword INCLUDE_RESOLUTION_RANGE, but it looks to be a definition of resolution range after index step as it says: INCLUDE_RESOLUTION_RANGE=20.0 0.0 !Angstroem; used by DEFPIX,INTEGRATE,CORRECT Thanks! Niu -- Fred. Vellieux (B.Sc., Ph.D., hdr) ouvrier de la recherche IBS / ELMA 41 rue Jules Horowitz F-38027 Grenoble Cedex 01 Tel: +33 438789605 Fax: +33 438785494
Re: [ccp4bb] Resolution limit of index in XDS
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Niu, indexing relies on strong reflections only, that is (in very brieft) why INCLUDE_RESOLUTION_RANGE indeed does not affect the relections collected in COLSPOT which in turn are used by IDXREF. You can work around this, however, by making use of TRUSTED_REGION and set it to e.g. 0.7 or 0.6 (you can use adxv to translate resolution into pixel and then calculate the fraction you need to set the second number in TRUSTED_REGION to (or the first if you want to exclude the inner resolution reflections - I remember one data set where this was essential for indexing - DNA was involved there) Best, Tim On 03/19/2013 08:53 PM, Niu Tou wrote: > Dear All, > > Is there any command can set the resolution limit for index step in > XDS? I only found a keyword INCLUDE_RESOLUTION_RANGE, but it looks > to be a definition of resolution range after index step as it > says: > > INCLUDE_RESOLUTION_RANGE=20.0 0.0 !Angstroem; used by > DEFPIX,INTEGRATE,CORRECT > > Thanks! Niu > - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRSOFJUxlJ7aRr7hoRAo6TAKC+BePgeODbDyngO7N8vCE4CnjxmQCfS5cP srShHNz1sDK0EMHSbE3fDwA= =kAwf -END PGP SIGNATURE-
[ccp4bb] Resolution limit of index in XDS
Dear All, Is there any command can set the resolution limit for index step in XDS? I only found a keyword INCLUDE_RESOLUTION_RANGE, but it looks to be a definition of resolution range after index step as it says: INCLUDE_RESOLUTION_RANGE=20.0 0.0 !Angstroem; used by DEFPIX,INTEGRATE,CORRECT Thanks! Niu
Re: [ccp4bb] resolution limit
Hi Narayan, there's nothing wrong with using data with I/sigmaI 2.5, Rsym 224.3 % for multiplicity 7.8 and completeness 98.2 %. However, when you discarded frames you might have made the data worse - one should only reject data if they deviate systematically (e.g. from radiation damage). Weak data should not be rejected, and Rmerge is the wrong measure to judge about data quality. best, Kay On Wed, 18 Jul 2012 02:41:48 -0700, narayan viswam wrote: >Hello CCP4ers, > > In my data, the highest reolution shell 2.8-3.0 A has I/sigmaI 2.5 & Rsym >224.3 % for multiplicity 7.8 and completeness 98.2 %. I solved the >structure by MAD & refined it to Rfree 27.3 %. Ths crystal belongs to P622 >space group and it is not twinned. The water content is 68%. I loweredthe > multiplicity to 4.1 by excluding few images but still the Rsym is > 200 % >and I/sigmaI > 2.0. My rudimentary crystallography knowledge makes me >believe it's quite Ok to use data upto 2.8 A and report the statistics. >Could I request people's views. Thanks very much. >Narayan >
Re: [ccp4bb] resolution limit
I was [too] obliquely alluding to this thread... http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg27056.html JPK On Wed, Jul 18, 2012 at 12:32 PM, Edwin Pozharski wrote: > http://www.ysbl.york.ac.uk/ccp4bb/2001/msg00383.html > > > > > Rsym...what's that? > > > > JPK > > > > On Wed, Jul 18, 2012 at 9:12 AM, Edwin Pozharski > > wrote: > > > >> As has been shown recently (and discussed on this board), Rsym is not > >> the > >> best measure of data quality (if any measure at all): > >> > >> http://www.sciencemag.org/content/336/6084/1030.abstract > >> > >> > >> > >> > narayan viswam wrote: > >> >> Hello CCP4ers, > >> >> In my data, the highest reolution shell 2.8-3.0 A has I/sigmaI 2.5 & > >> >> Rsym 224.3 % > >> >> for multiplicity 7.8 and completeness 98.2 %. I solved the structure > >> by > >> >> MAD & refined it > >> >> to Rfree 27.3 %. Ths crystal belongs to P622 space group and it is > >> not > >> >> twinned. The water > >> >> content is 68%. I loweredthe multiplicity to 4.1 by excluding few > >> >> images but still the > >> >> Rsym is > 200 % and I/sigmaI > 2.0. My rudimentary crystallography > >> >> knowledge makes me > >> >> believe it's quite Ok to use data upto 2.8 A and report the > >> statistics. > >> >> Could I request > >> >> people's views. Thanks very much. > >> >> Narayan > >> > > >> > After refinement, what is R-free in the last shell? If it is > >> significantly > >> > better > >> > than random, say around .4 or less, that could be taken as evidence > >> that > >> > there > >> > is data in the last shell. > >> > Also check the error model- Rsym >2 sort of implies the error is > >> greater > >> > than > >> > the signal, so I/sigI 2 seems surprising. > >> > eab > >> > > >> > >> > >> -- > >> Edwin Pozharski, PhD > >> University of Maryland, Baltimore > > > > > > > > > > -- > > *** > > Jacob Pearson Keller > > Northwestern University > > Medical Scientist Training Program > > email: j-kell...@northwestern.edu > > *** > > > > > -- > Edwin Pozharski, PhD > University of Maryland, Baltimore > -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] resolution limit
http://www.ysbl.york.ac.uk/ccp4bb/2001/msg00383.html > Rsym...what's that? > > JPK > > On Wed, Jul 18, 2012 at 9:12 AM, Edwin Pozharski > wrote: > >> As has been shown recently (and discussed on this board), Rsym is not >> the >> best measure of data quality (if any measure at all): >> >> http://www.sciencemag.org/content/336/6084/1030.abstract >> >> >> >> > narayan viswam wrote: >> >> Hello CCP4ers, >> >> In my data, the highest reolution shell 2.8-3.0 A has I/sigmaI 2.5 & >> >> Rsym 224.3 % >> >> for multiplicity 7.8 and completeness 98.2 %. I solved the structure >> by >> >> MAD & refined it >> >> to Rfree 27.3 %. Ths crystal belongs to P622 space group and it is >> not >> >> twinned. The water >> >> content is 68%. I loweredthe multiplicity to 4.1 by excluding few >> >> images but still the >> >> Rsym is > 200 % and I/sigmaI > 2.0. My rudimentary crystallography >> >> knowledge makes me >> >> believe it's quite Ok to use data upto 2.8 A and report the >> statistics. >> >> Could I request >> >> people's views. Thanks very much. >> >> Narayan >> > >> > After refinement, what is R-free in the last shell? If it is >> significantly >> > better >> > than random, say around .4 or less, that could be taken as evidence >> that >> > there >> > is data in the last shell. >> > Also check the error model- Rsym >2 sort of implies the error is >> greater >> > than >> > the signal, so I/sigI 2 seems surprising. >> > eab >> > >> >> >> -- >> Edwin Pozharski, PhD >> University of Maryland, Baltimore > > > > > -- > *** > Jacob Pearson Keller > Northwestern University > Medical Scientist Training Program > email: j-kell...@northwestern.edu > *** > -- Edwin Pozharski, PhD University of Maryland, Baltimore
Re: [ccp4bb] resolution limit
Rsym...what's that? JPK On Wed, Jul 18, 2012 at 9:12 AM, Edwin Pozharski wrote: > As has been shown recently (and discussed on this board), Rsym is not the > best measure of data quality (if any measure at all): > > http://www.sciencemag.org/content/336/6084/1030.abstract > > > > > narayan viswam wrote: > >> Hello CCP4ers, > >> In my data, the highest reolution shell 2.8-3.0 A has I/sigmaI 2.5 & > >> Rsym 224.3 % > >> for multiplicity 7.8 and completeness 98.2 %. I solved the structure by > >> MAD & refined it > >> to Rfree 27.3 %. Ths crystal belongs to P622 space group and it is not > >> twinned. The water > >> content is 68%. I loweredthe multiplicity to 4.1 by excluding few > >> images but still the > >> Rsym is > 200 % and I/sigmaI > 2.0. My rudimentary crystallography > >> knowledge makes me > >> believe it's quite Ok to use data upto 2.8 A and report the statistics. > >> Could I request > >> people's views. Thanks very much. > >> Narayan > > > > After refinement, what is R-free in the last shell? If it is > significantly > > better > > than random, say around .4 or less, that could be taken as evidence that > > there > > is data in the last shell. > > Also check the error model- Rsym >2 sort of implies the error is greater > > than > > the signal, so I/sigI 2 seems surprising. > > eab > > > > > -- > Edwin Pozharski, PhD > University of Maryland, Baltimore -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] resolution limit
As has been shown recently (and discussed on this board), Rsym is not the best measure of data quality (if any measure at all): http://www.sciencemag.org/content/336/6084/1030.abstract > narayan viswam wrote: >> Hello CCP4ers, >> In my data, the highest reolution shell 2.8-3.0 A has I/sigmaI 2.5 & >> Rsym 224.3 % >> for multiplicity 7.8 and completeness 98.2 %. I solved the structure by >> MAD & refined it >> to Rfree 27.3 %. Ths crystal belongs to P622 space group and it is not >> twinned. The water >> content is 68%. I loweredthe multiplicity to 4.1 by excluding few >> images but still the >> Rsym is > 200 % and I/sigmaI > 2.0. My rudimentary crystallography >> knowledge makes me >> believe it's quite Ok to use data upto 2.8 A and report the statistics. >> Could I request >> people's views. Thanks very much. >> Narayan > > After refinement, what is R-free in the last shell? If it is significantly > better > than random, say around .4 or less, that could be taken as evidence that > there > is data in the last shell. > Also check the error model- Rsym >2 sort of implies the error is greater > than > the signal, so I/sigI 2 seems surprising. > eab > -- Edwin Pozharski, PhD University of Maryland, Baltimore
Re: [ccp4bb] resolution limit
narayan viswam wrote: Hello CCP4ers, In my data, the highest reolution shell 2.8-3.0 A has I/sigmaI 2.5 & Rsym 224.3 % for multiplicity 7.8 and completeness 98.2 %. I solved the structure by MAD & refined it to Rfree 27.3 %. Ths crystal belongs to P622 space group and it is not twinned. The water content is 68%. I loweredthe multiplicity to 4.1 by excluding few images but still the Rsym is > 200 % and I/sigmaI > 2.0. My rudimentary crystallography knowledge makes me believe it's quite Ok to use data upto 2.8 A and report the statistics. Could I request people's views. Thanks very much. Narayan After refinement, what is R-free in the last shell? If it is significantly better than random, say around .4 or less, that could be taken as evidence that there is data in the last shell. Also check the error model- Rsym >2 sort of implies the error is greater than the signal, so I/sigI 2 seems surprising. eab
Re: [ccp4bb] resolution limit
Hi Narayan My only comment would be that P622 is a fairly uncommon space group (currently 43 PDB entries excl homologs), but obviously that doesn't mean it's wrong - just worth double-checking! Just out of interest what's the CC(1/2) statistic for your highest shell? Personally I specify more bins than the default (e.g. 20 instead of 10) so that the highest resolution bin would be somewhat narrower than yours. I would also prefer that the binning is done by equal steps in d*^3 rather than d*^2 as many programs do since this gives a more even spread of reflections in the bins and gives an even narrower binning at the high res end (though it does tend to lump all the low res data into 1 bin!). Cheers -- Ian On 18 July 2012 10:41, narayan viswam wrote: > > > Hello CCP4ers, > > In my data, the highest reolution shell 2.8-3.0 A has I/sigmaI 2.5 & Rsym > 224.3 % for multiplicity 7.8 and completeness 98.2 %. I solved the structure > by MAD & refined it to Rfree 27.3 %. Ths crystal belongs to P622 space group > and it is not twinned. The water content is 68%. I loweredthe multiplicity > to 4.1 by excluding few images but still the Rsym is > 200 % and I/sigmaI > > 2.0. My rudimentary crystallography knowledge makes me believe it's quite Ok > to use data upto 2.8 A and report the statistics. Could I request people's > views. Thanks very much. > Narayan
[ccp4bb] resolution limit
Hello CCP4ers, In my data, the highest reolution shell 2.8-3.0 A has I/sigmaI 2.5 & Rsym 224.3 % for multiplicity 7.8 and completeness 98.2 %. I solved the structure by MAD & refined it to Rfree 27.3 %. Ths crystal belongs to P622 space group and it is not twinned. The water content is 68%. I loweredthe multiplicity to 4.1 by excluding few images but still the Rsym is > 200 % and I/sigmaI > 2.0. My rudimentary crystallography knowledge makes me believe it's quite Ok to use data upto 2.8 A and report the statistics. Could I request people's views. Thanks very much. Narayan
Re: [ccp4bb] resolution limit stuck in Refmac5
Hi Jon On 30 Oct 2010, at 00:46, Tom Huxford wrote: Hi all, I'm working with good quality relatively complete x-ray diffraction data collected to a resolution limit 2.6 Å from a crystal of a protein with a small molecule ligand bound. I ran MR from 10-4 Å and then did maximum likelihood rigid body refinement in Refmac5 against data from 50-3.5 Å. Now I would like to run restrained refinement from 50-3 Å. The reason for doing this is that, in order to minimize the divergence between R-cryst and R-free during refinement my advisor who, by the way, is forwarding this e-mail for me (and editing it so please don't bash him too mercilessly) suggested I first build in the ligand and newly positioned polypeptide loops and refine against data at a lower resolution limit before opening it up to all the available data. I personally would not first build in the ligand and refine against low res data... Assuming the ligand is what you're after, I would: (a) leave the ligand out of the time being (b) refine the model using all data (c) build the ligand in (d) refine the model using all data I'm not clear why doing restrained refinement using limited data first should help.. Apparently this has worked well for him in the past (and it has!). The problem is that I'm to the point where I'd like to extend the resolution down to 3 Å during restrained refinement but even if I set the range from 50-3 Å in the ccp4i window refinement only happens from 50-3.5 Å. If I take a step back and do the rigid body refinement from 50-3 Å and then carry out restrained refinement from 50-3 Å it works fine. Why would the limits imposed by rigid body refinement cause the subsequent restrained refinement to be stuck at the rigid body refinement's resolution limits? Are you using the original reflection file? Best Roberto Thanks for any thoughts, Jon Fleming Graduate Student Structural Biochemistry Laboratory (Huxford Lab) Department of Chemistry & Biochemistry San Diego State University --- Dr. Roberto Steiner Randall Division of Cell and Molecular Biophysics New Hunt's House King's College London Guy's Campus London, SE1 1UL Phone +44 (0)20-7848-8216 Fax +44 (0)20-7848-6435 e-mail roberto.stei...@kcl.ac.uk
Re: [ccp4bb] resolution limit stuck in Refmac5
I guess you are using as input mtz the output mtz from the previous cycle? This will be limited to the requested previous resolution.. it is good practice to always use as input the full data - eg mystuff-scala.mtz output from the scala/ctruncate step.. If the input file has the full resolution then your requested limits should be respected.. Unlike your supervisor I would probably have run the rigid body refinement against limited data then gone straight to using thefull resolution available - restrained refinement of B factors works better the higher the resolution, and provides a very useful way of smudging out errors. Wrong bits often have B factors which go through the roof, and it is then very obvious in the maps But there are many ways to kill a goose, and ditto for refinement strategy.. Eleanor On 10/30/2010 01:46 AM, Tom Huxford wrote: Hi all, I'm working with good quality relatively complete x-ray diffraction data collected to a resolution limit 2.6 Å from a crystal of a protein with a small molecule ligand bound. I ran MR from 10-4 Å and then did maximum likelihood rigid body refinement in Refmac5 against data from 50-3.5 Å. Now I would like to run restrained refinement from 50-3 Å. The reason for doing this is that, in order to minimize the divergence between R-cryst and R-free during refinement my advisor who, by the way, is forwarding this e-mail for me (and editing it so please don't bash him too mercilessly) suggested I first build in the ligand and newly positioned polypeptide loops and refine against data at a lower resolution limit before opening it up to all the available data. Apparently this has worked well for him in the past (and it has!). The problem is that I'm to the point where I'd like to extend the resolution down to 3 Å during restrained refinement but even if I set the range from 50-3 Å in the ccp4i window refinement only happens from 50-3.5 Å. If I take a step back and do the rigid body refinement from 50-3 Å and then carry out restrained refinement from 50-3 Å it works fine. Why would the limits imposed by rigid body refinement cause the subsequent restrained refinement to be stuck at the rigid body refinement's resolution limits? Thanks for any thoughts, Jon Fleming Graduate Student Structural Biochemistry Laboratory (Huxford Lab) Department of Chemistry & Biochemistry San Diego State University
Re: [ccp4bb] resolution limit stuck in Refmac5
On Fri, Oct 29, 2010 at 5:46 PM, Tom Huxford wrote: > I'm working with good quality relatively complete x-ray diffraction data > collected to a resolution limit 2.6 Å from a crystal of a protein with a > small molecule ligand bound. I ran MR from 10-4 Å and then did maximum > likelihood rigid body refinement in Refmac5 against data from 50-3.5 Å. Now > I would like to run restrained refinement from 50-3 Å. The reason for doing > this is that, in order to minimize the divergence between R-cryst and R-free > during refinement my advisor who, by the way, is forwarding this e-mail for > me (and editing it so please don't bash him too mercilessly) suggested I > first build in the ligand and newly positioned polypeptide loops and refine > against data at a lower resolution limit before opening it up to all the > available data. Apparently this has worked well for him in the past (and it > has!). The problem is that I'm to the point where I'd like to extend the > resolution down to 3 Å during restrained refinement but even if I set the > range from 50-3 Å in the ccp4i window refinement only happens from 50-3.5 > Å. If I take a step back and do the rigid body refinement from 50-3 Å and > then carry out restrained refinement from 50-3 Å it works fine. Why would > the limits imposed by rigid body refinement cause the subsequent restrained > refinement to be stuck at the rigid body refinement's resolution limits? > Did you refine against the file output by Refmac after rigid-body refinement, instead of using the original reflections? -Nat
[ccp4bb] resolution limit stuck in Refmac5
Hi all, I'm working with good quality relatively complete x-ray diffraction data collected to a resolution limit 2.6 Å from a crystal of a protein with a small molecule ligand bound. I ran MR from 10-4 Å and then did maximum likelihood rigid body refinement in Refmac5 against data from 50-3.5 Å. Now I would like to run restrained refinement from 50-3 Å. The reason for doing this is that, in order to minimize the divergence between R-cryst and R-free during refinement my advisor who, by the way, is forwarding this e-mail for me (and editing it so please don't bash him too mercilessly) suggested I first build in the ligand and newly positioned polypeptide loops and refine against data at a lower resolution limit before opening it up to all the available data. Apparently this has worked well for him in the past (and it has!). The problem is that I'm to the point where I'd like to extend the resolution down to 3 Å during restrained refinement but even if I set the range from 50-3 Å in the ccp4i window refinement only happens from 50-3.5 Å. If I take a step back and do the rigid body refinement from 50-3 Å and then carry out restrained refinement from 50-3 Å it works fine. Why would the limits imposed by rigid body refinement cause the subsequent restrained refinement to be stuck at the rigid body refinement's resolution limits? Thanks for any thoughts, Jon Fleming Graduate Student Structural Biochemistry Laboratory (Huxford Lab) Department of Chemistry & Biochemistry San Diego State University
[ccp4bb] Resolution limit for Molecular Replacement
Hi All, I read some literature for phasing by molecular replacement performed with reflections upto 3.5 Angstroms. Can anybody tell me why? I would prefer deleting low resolutions so as to reduce contribution from the solvent that might affect RF search and obtaining a solution. Your responses to this question would also be highly appreciated. Thanks, Rajan
