Re: [ccp4bb] space groups not supported by Refmac5
Dear Phil, thank you very much for your thorough clarification. Best regards, Arefeh
Re: [ccp4bb] space groups not supported by Refmac5
Just to clarify this again: the question of standard settings for primitive orthorhombic space groups ( the I2/C2 choice) was raised by Ian Tickle in earlier discussions. He pointed out that the IUCr standard was to choose a b c for primitive orthorhombic irrespective of which axes are 2 or 2(1), and to choose either I2 or C2 to give the smaller beta angle his references http://nvl.nist.gov/pub/nistpubs/jres/106/6/j66mig.pdf http://nvl.nist.gov/pub/nistpubs/jres/107/4/j74mig.pdf This makes sense as you can generally make a b c at the indexing stage (unless some lengths are equal) before you know which axes are 2 or 2(1), and then you don't have to reindex later. For the I2/C2 choice, it is somewhat more convenient to have a less oblique axis system if you can. I made POINTLESS follow these conventions by default, but you do have a choice. These settings should then be referred to as the standard settings (ie abc, CELL-BASED in Pointless), and the alternative (SYMMETRY-BASED in Pointless) may be called reference settings (eg always P21 21 2 for space group 18). Most crystallographic software that we use is happy with non-reference space groups eg space group P2 21 2 : all CCP4 and Phenix programs are, as far as I know. The exceptions which don't work (and that I know about) are:- 1) Arp/warp: Victor Lamzin has I believe promised (Victor?) that the imminent new released version will work for these settings 2) Sharp: Clemens Vonrhein told me that he hoped the next release of Sharp would handle these cases I know this is a bit inconvenient at present, but I thought it a Good Thing to follow recognised conventions (and to force software developers to make their programs more general :-)) Phil Evans On 18 Aug 2009, at 12:48, Michele Lunelli wrote: Dear Arefeh, Arp/warp works with standard space groups, therefore you have to reindex P21221 to P21212. In this message from Anastassis Perrakis you can find some advice: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0709L=CCP4BBT=0F=S=P=100954 Michele Arefeh Seyedarabi wrote: Hi, I have a question; recently I have encountered a few space groups which are not supported by Refmac5. Examples include I2 and P21221. Both these space groups have been identified as the best solutions for the two different datasets I am working on using Pointless. However, I am faced with difficulties in Refmac5, and the program fails to complete when I select refinement cycles with Arp-waters...with the message saying 'space group not supported'. Any suggestions on how this problem could be overcome? Regards, Arefeh
Re: [ccp4bb] space groups not supported by Refmac5
It is Arp waters which doesnt support these space groups I believe.. REFMAC5 seems to accept everything.. And Arp-waters is pretty out of date - cot probably does a better job in positioned fully occupied waters. Eleanor David J. Schuller wrote: For the latter, P21221, you could reindex to get P21212, which is supported. - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu On Mon, 2009-08-17 at 17:37 +0100, Arefeh Seyedarabi wrote: Hi, I have a question; recently I have encountered a few space groups which are not supported by Refmac5. Examples include I2 and P21221. Both these space groups have been identified as the best solutions for the two different datasets I am working on using Pointless. However, I am faced with difficulties in Refmac5, and the program fails to complete when I select refinement cycles with Arp-waters...with the message saying 'space group not supported'. Any suggestions on how this problem could be overcome? Regards, Arefeh Arefeh Seyedarabi, PhD Postdoctoral research assistant School of Biological and Chemical sciences Queen Mary, University of London Mile End road London E1 4NS Based at Joseph Priestley Building G.35 020 78828480
Re: [ccp4bb] space groups not supported by Refmac5
Dear Arefeh, Arp/warp works with standard space groups, therefore you have to reindex P21221 to P21212. In this message from Anastassis Perrakis you can find some advice: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0709L=CCP4BBT=0F=S=P=100954 Michele Arefeh Seyedarabi wrote: Hi, I have a question; recently I have encountered a few space groups which are not supported by Refmac5. Examples include I2 and P21221. Both these space groups have been identified as the best solutions for the two different datasets I am working on using Pointless. However, I am faced with difficulties in Refmac5, and the program fails to complete when I select refinement cycles with Arp-waters...with the message saying 'space group not supported'. Any suggestions on how this problem could be overcome? Regards, Arefeh
Re: [ccp4bb] space groups not supported by Refmac5
Thank you all very much for your advice. I will reindex my data to P21212 in order to use Arp/Warp. Best regards, Arefeh Arefeh Seyedarabi, PhD Postdoctoral research assistant School of Biological and Chemical sciences Queen Mary, University of London Mile End road London E1 4NS Based at Joseph Priestley Building G.35 020 78828480
Re: [ccp4bb] space groups not supported by Refmac5
For the latter, P21221, you could reindex to get P21212, which is supported. - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu On Mon, 2009-08-17 at 17:37 +0100, Arefeh Seyedarabi wrote: Hi, I have a question; recently I have encountered a few space groups which are not supported by Refmac5. Examples include I2 and P21221. Both these space groups have been identified as the best solutions for the two different datasets I am working on using Pointless. However, I am faced with difficulties in Refmac5, and the program fails to complete when I select refinement cycles with Arp-waters...with the message saying 'space group not supported'. Any suggestions on how this problem could be overcome? Regards, Arefeh Arefeh Seyedarabi, PhD Postdoctoral research assistant School of Biological and Chemical sciences Queen Mary, University of London Mile End road London E1 4NS Based at Joseph Priestley Building G.35 020 78828480
Re: [ccp4bb] space groups not supported by Refmac5
On Monday 17 August 2009 09:37:40 Arefeh Seyedarabi wrote: Hi, I have a question; recently I have encountered a few space groups which are not supported by Refmac5. Examples include I2 and P21221. This is not correct. Refmac is perfectly happy with these settings, although there are some glitches to be careful of when you eventually get to the point of data deposition. (See earlier thread about mtz2various mangling the spacegroup description when converting to *.cif). Both these space groups have been identified as the best solutions for the two different datasets I am working on using Pointless. However, I am faced with difficulties in Refmac5, and the program fails to complete when I select refinement cycles with Arp-waters...with the message saying 'space group not supported'. Ah. Perhaps this is a message from Arp/wArp? I don't know. But having recently refined several I2 structures in refmac, I can attest that it works fine in recent versions. Ethan -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742
Re: [ccp4bb] space groups not supported by Refmac5
Hi, Following mail (retrived from ccp4bb archieve) may help for intechanging the cell axis. HTH S.Karthikeyan == I have a CCP4 script for this: http://bl831.als.lbl.gov/~jamesh/elves/scripts/reindex.com If you run the script like this: reindex.com yourdata.mtz P22121 Then you will get a file called reindexed.mtz that has the space group P21212 with the cell permuted so that the shortest edge is b. Specifying P21221 will give you P21212 with the shortest edge at c, and P21212 will give you the shortest edge at a, like it is supposed to be. Like George said, this way you are always working in a cannonical space group so you will have much less portability issues between programs. -James Holton MAD Scientist = For the latter, P21221, you could reindex to get P21212, which is supported. - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu On Mon, 2009-08-17 at 17:37 +0100, Arefeh Seyedarabi wrote: Hi, I have a question; recently I have encountered a few space groups which are not supported by Refmac5. Examples include I2 and P21221. Both these space groups have been identified as the best solutions for the two different datasets I am working on using Pointless. However, I am faced with difficulties in Refmac5, and the program fails to complete when I select refinement cycles with Arp-waters...with the message saying 'space group not supported'. Any suggestions on how this problem could be overcome? Regards, Arefeh Arefeh Seyedarabi, PhD Postdoctoral research assistant School of Biological and Chemical sciences Queen Mary, University of London Mile End road London E1 4NS Based at Joseph Priestley Building G.35 020 78828480
Re: [ccp4bb] space groups not supported by Refmac5
Yeah, I2 works indeed just fine (for me, right now). Andreas Ethan Merritt wrote: On Monday 17 August 2009 09:37:40 Arefeh Seyedarabi wrote: Hi, I have a question; recently I have encountered a few space groups which are not supported by Refmac5. Examples include I2 and P21221. This is not correct. Refmac is perfectly happy with these settings, although there are some glitches to be careful of when you eventually get to the point of data deposition. (See earlier thread about mtz2various mangling the spacegroup description when converting to *.cif). Both these space groups have been identified as the best solutions for the two different datasets I am working on using Pointless. However, I am faced with difficulties in Refmac5, and the program fails to complete when I select refinement cycles with Arp-waters...with the message saying 'space group not supported'. Ah. Perhaps this is a message from Arp/wArp? I don't know. But having recently refined several I2 structures in refmac, I can attest that it works fine in recent versions. Ethan -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
