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Re: [ccp4bb] Peptide on two-fold axis - was:[ccp4bb] PEG molecule crossing a two-fold crystallographic symmetry axis |
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CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: Peptide on two-fold axis - was: PEG molecule crossing a two-fold crystallographic symmetry axis From: Kris Tesh Kris {- dot -} Tesh {- at -} RIGAKU {- dot -} COM Date: 2009-05-01 A trick that small molecule crystallographers use is to make a packing diagram where the volume includes both molecules A and B, or maybe even two of each. In this case, it would display all of C (or maybe even 2 of C either twisted back on itself (symmetry element near molecule C) or extending on the along or opposite side of A or B, both of occupancy 0.5). So, I would look at what your display radius or unit cell parameters shows...and try to extend it. Kris --------------------------------- Kris F. Tesh, Ph D Director, Macromolecular Products Rigaku Americas Corporation 9009 New Trails Drive The Woodlands, TX 77381 USA 001 281 362 2300 x 144 From: lidefeng To: CCP4BB@JISCMAIL.AC.UK Date: 05/01/2009 07:51 AM Subject: Re: [ccp4bb] Peptide on two-fold axis - was:[ccp4bb] PEG molecule crossing a two-fold crystallographic symmetry axis Dear Herman.Schreuder, Perhaps there is some misunderstanding about my question. There is one molecule in the asymmetric unit (showed as symbos A). After the 2nd crystallographic symmetric operation, another molecule appears (symbol B). However, the density show that there is one peptide chain cross the 2nd axis (symbol C). If we give chain C occupancy of 0.5, only 50% of chain C belongs to molecules A and B, respectively. In another word, , it looks like one half of chain C belongs to molecule A and the other belongs to B. It means that one half of chain C belongs to molecule A disappear, so do that belongs to molecule B. 2nd axis AAAAAA BBBBBB AAAAAA BBBBBB AA BB / CCCCCCC CCCCCCC Your sincerely ????????De-Feng Li ????????lidefeng@moon.ibp.ac.cn ??????????2009-05-01 Defeng Li, Dr., Email: lidefeng@moon.ibp.ac.cn National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China ======= 2009-04-30 14:52:00 You writed in your letter?======= >Dear Feng-Li, > >The other half occupancy peptide is generated by crystallographic symmetry (the twofold), you need only to build one. To check that everything fits properly, you should switch on the crystallographic symmetry in coot. (Draw -> Cell & Symmetry). > >Good luck! >Herman > > >-----Original Message----- >From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of lidefeng >Sent: Thursday, April 30, 2009 3:44 AM >To: CCP4BB@JISCMAIL.AC.UK >Subject: Re: [ccp4bb] Peptide on two-fold axis - was:[ccp4bb] PEG molecule crossing a two-fold crystallographic symmetry axis > >Dear Tim Gruene, > > But how to illustrate the other one half occupancy of peptide? Disorder ? > > > Your sincerely > De-Feng Li > lidefeng@moon.ibp.ac.cn > 2009-04-30 > >Defeng Li, Dr., >Email: lidefeng@moon.ibp.ac.cn >National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, >15 Datun Road, Chaoyang District, >Beijing 100101, China > > >======= 2009-04-29 10:55:00 You writed in your letter：======= > >>Hello De-Feng Li, >> >>first of all sorry for changing the subject: I think starting a new >>thread from an existing one may hamper people who are going to search >>the archives in the future, therefore it is good practice to give it >>its separate subject line, even though it certainly is be very closely >>related. >> >>In your case you can refine two peptides each with an occupancy of 0.5, >>one for each direction. >> >>Tim >>-- >>Tim Gruene >>Institut fuer anorganische Chemie >>Tammannstr. 4 >>D-37077 Goettingen >> >>GPG Key ID = A46BEE1A >> >> >>On Wed, 29 Apr 2009, lidefeng wrote: >> >>> Hi everyone, >>> >>> Following Chandrika's question, what should I do if one peptide chain crosses a two-fold crystallographic symmetry axis? >>> The peptide is not symmetric and the sidechain of one Se-Met (two after CS operation) is determined and conformed by MAD. >>> >>> Your sincerely >>> ????????De-Feng Li >>> ????????lidefeng@moon.ibp.ac.cn >>> ??????????2009-04-29 >>> >>> Defeng Li, Dr., >>> Email: lidefeng@moon.ibp.ac.cn >>> National Laboratory of Biomacromolecules, Institute of Biophysics, >>> Chinese Academy of Sciences, >>> 15 Datun Road, Chaoyang District, >>> Beijing 100101, China >>> >>> >>> ======= 2009-04-29 17:02:00 You writed in your letter?======= >>> >>>> Hello everyone, >>>> >>>> My protein crystallised in the spacegroup P6522 with one protein molecule in the asymmetric unit. I have a PEG molecule from the crystallization condition which crosses a two-fold crystallographic symmetry axis. PEG is symmetric hence this does not violate the crystal symmetry. However, this situation causes two problems which I need to solve : >>>> >>>> First, How can I refine this structure ? I am using Phenix. Is there a way to remove van der Waals repulsion between one half occupancy PEG and its crystallographic symmetry mate ? >>>> >>>> Second, how do I submit this structure to PDB ? Do I include a full PEG molecule at half occupancy even though one half is related to the other via crystallographic symmetry ? >>>> >>>> Thanks, >>>> Chandrika >>> >>> ======================================================== >>> >>> > >======================================================== > ======================================================== CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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