Re: [ccp4bb] strange MR problem
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear , Can you clearify what you mean by the sentence "when i tried to use the MR solution generated in phenix with the mtz file from ccp4 the model shows a lot of clashes"? I do not understand what you need the mtz file for in order the check for clashes. At 3A you may have serious model bias and one or both of the solutions may not be correct. The best would be to try and fit the second protein (by MR, or if only the sequence is known, try e.g. buccaneer). If your R/Rfree eventually drop below, say, 40%, you are probably on the right track. Tim On 12/13/2011 05:26 AM, intekhab alam wrote: > Hi All > > I have a 3.0A dataset of a protein-protein complex. I used one of the > protein structure solved previously as a template and used phaser in CCP4 > as well as in phenix. I used the sca file in phenix which gave a solution > with 6 monomers in ASU which are packed as a hexamer. In ccp4 phaser i used > the converted .mtz file which gave 6 molecules in ASU but with a different > packing. In both the cases map fits well in the model and there is some > extra density that may correspond to second protein partner of the complex > molecule. when i tried to use the MR solution generated in phenix with the > mtz file from ccp4 the model shows a lot of clashes. > > what kind of approach should i take so as to resolve this ambiguity. > > Regards - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO5x2YUxlJ7aRr7hoRAsp3AKC7ljNgMNuLHASo8TTQ3157GMzsowCeN/sq yJMgPbBDS/+j8obfudpxFFo= =SAle -END PGP SIGNATURE-
Re: [ccp4bb] artificial tetramer
I am a bit puzzled - do you know the direction of the rotation axis which can be converted to polar phi/psi angles, a mid point you want to rotate about, and the distance of the centre of mass of your molecule from that point, from which you could find the tranlation shift? If so I could design a script for pdbset rotat polar phi psi 90 tran tx1 ty1 tz1 Then rotat polar phi psi 180 tran tx2 ty2 tz2 And rotat polar phi psi -90 tran tx3 ty3 tz3 You would have to reassemble the tetramer from the 4 copies. Eleanor On 12/12/2011 07:49 PM, Fred wrote: Hi List, I would like to build an artificial tetramer from a monomer PBD file. All that I have is the coordinates it self with CRYST/CELL information cards. The artificial 4-fold axis has an arbitrary orientation into the cell. I mean, its not parallel to any crystallographic axis and have to be at a certain distance of the molecule. This sounds conceptually simple, but I would like to do that in batch mode for hundreds of PDB's. Could someone, please, tell me the easiest way/program to do that? Thanks in advance, Fred
Re: [ccp4bb] artificial tetramer
Do you mean just any tetramer? If so, Why not use an existing one - eg haemoglobin.. Eleanor On 12/12/2011 09:42 PM, Fred wrote: I only want to produce an artificial tetramer. Em 12-12-2011 19:41, Jacob Keller escreveu: Can you clarify your reason for doing this? JPK On Mon, Dec 12, 2011 at 3:36 PM, Fred wrote: Hi James, In my first post "arbitrary orientation into the cell" only means not parallel to any crystallographic axis, which would simplify things very much. I want to apply the 4-fold axis to the protein coordinates. If I have a cell and therefore an origin, I can take a point at any distance of the origin, pass a vector/axis through it and take the 3 others molecules by symmetry. That's trivial, given the point, the orientation and the property of the rotation. Don't know which program to use. Regards, Fred Em 12-12-2011 19:18, James Stroud escreveu: This is not trivial. Assuming an arbitrary origin, the simplest 4-fold symmetry operation (4-fold rotation) has 5 free parameters (translation along the symmetry axis is irrelevant). The biggest problem is determining the values for these parameters. For example, once you apply the symmetry, your molecule may clash with its symmetry mates or not even contact them. And even if you solve this latter problem automatically (which is not trivial because of irregularity), that leaves a net of 3 parameters describing the orientation of the protomer. James On Dec 12, 2011, at 1:34 PM, Fred wrote: Hi Tim, Thanks for your message and sorry if I wasn't clear. I don't have neither the axis orientation nor the rotation matrix. I would like to create them but don't know how and which program to use. Theoretically a have to create a axis (vector) at some distance of the molecule into the cell and give it the 4-fold propriety. Quite simple, but don't which program to use. Regards, Fred Em 12-12-2011 18:23, Tim Gruene escreveu: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Fred, if you know the rotation matrix, you can use pdbset with its 'rotate' keyword. It is not clear to me whether or not you have the rotation matrix or how you define rotation. Cheers, Tim On 12/12/2011 08:49 PM, Fred wrote: Hi List, I would like to build an artificial tetramer from a monomer PBD file. All that I have is the coordinates it self with CRYST/CELL information cards. The artificial 4-fold axis has an arbitrary orientation into the cell. I mean, its not parallel to any crystallographic axis and have to be at a certain distance of the molecule. This sounds conceptually simple, but I would like to do that in batch mode for hundreds of PDB's. Could someone, please, tell me the easiest way/program to do that? Thanks in advance, Fred - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO5mKwUxlJ7aRr7hoRAsyuAKDfnH50sG/EuKiFz7tCzgTUtnZrdQCg3zSn cqs8GHOu5M3JQahA/CofR1k= =tDUj -END PGP SIGNATURE-
Re: [ccp4bb] PHENIX vs REFMAC refinement had me fooled
PHIC wont do any harm - you may need it for various reasons - I use it mostly as input for a DANO map to check out possible metal sites.. The reason for not using a refmac output mtz as input for the next run is 1) the refmac output Fobs has been scaled by the anisotropic scale so all subsequent scaling as you improve the model wold be relative.. 2) If there is any twinning detected the output "Fobs" have been corrected for this twin factor. 3) Obviously if you asked for refinement with phase restraints it would very unwise to set your input phase to the existing PHIC. However I think this is well nigh impossible without relabelling PHIC to some other column label - the mtz utilities would scream that you have an input label and an output label the same.. Eleanor factor On 12/13/2011 02:31 AM, Yuri Pompeu wrote: Hi Ed, I just had a chance of looking at your comment more closely. You are right it only uses PHIC if in refmacs set up you choose to refine "with prior phase information" -AFAIU. So what exactly is the info contained in the output refmacX.mtz besides map coefficients for COOT? If it is not just the raw xray data Fo, is it Fc only, or Fc that are filled in for missing Fo? I guess I am not really sure. I was under the impression that model´s PHIC would cause the problems, if they were present. Best,
Re: [ccp4bb] strange MR problem
csymmatch pdbin-ref my_favorite.pdb pdbin the-other.pdb -origin-hand This should move the-other.pdb to overlay my-favorite.pdb It WONT relabel the Chain IDs though.. Eleanor On 12/13/2011 04:26 AM, intekhab alam wrote: Hi All I have a 3.0A dataset of a protein-protein complex. I used one of the protein structure solved previously as a template and used phaser in CCP4 as well as in phenix. I used the sca file in phenix which gave a solution with 6 monomers in ASU which are packed as a hexamer. In ccp4 phaser i used the converted .mtz file which gave 6 molecules in ASU but with a different packing. In both the cases map fits well in the model and there is some extra density that may correspond to second protein partner of the complex molecule. when i tried to use the MR solution generated in phenix with the mtz file from ccp4 the model shows a lot of clashes. what kind of approach should i take so as to resolve this ambiguity. Regards
[ccp4bb] Early Stage Researcher (PhD Fellowship)
Dear ccp4bb on behalf of Ludvig Sollid, I would like to announce the following PhD studentships. "We are seeking to fill two fully funded PhD fellowships (Early Stage Researcher, SKO 1017, stipendiat) in the biochemistry and immunology of coeliac disease for the Marie Curie Initial Training Networks (ITN) Project TRANSPATH. The objective of TRANSPATH is to establish the molecular nature of the role of transglutaminases in a variety of human diseases including coeliac disease. TRANSPATH is funded by the European Framework Programme 7 Marie Curie Actions with the purpose of offering early-stage researchers the opportunity to improve their research skills, join established research teams and enhance their career prospects." see more information http://ec.europa.eu/euraxess/index.cfm/jobs/jobDetails/33752069 People with a structural biology background will have an advantage. cheers Preben
[ccp4bb] Experimental Postdoctoral Position in High Throughput Small Molecule Ligand Screening
Experimental Postdoctoral Position in High Throughput Small Molecule Ligand Screening Outstanding postdoctoral applicants to work jointly with Drs. Julia Kubakek, Mark Hay and Jeffrey Skolnick at the Georgia Institute of Technology are sought with the following qualifications: * Extensive experience in enzyme kinetics studies, enzyme purification or other aspects of protein biology and enzyme activity. Experience in handling multiple protein systems would be a plus. * A background in high throughput small molecule ligand screening is strongly preferred. * Experience with or a desire to learn computational biology and molecular modeling of protein-ligand interactions. * The ideal candidate is someone who gets satisfaction out of methods development and working through large data sets to see broad-scale patterns. To apply, please email your CV to : skoln...@gatech.edu
Re: [ccp4bb] PHENIX vs REFMAC refinement had me fooled
On Tue, 2011-12-13 at 02:31 +, Yuri Pompeu wrote: > Hi Ed, > I just had a chance of looking at your comment more closely. > You are right it only uses PHIC if in refmacs set up you choose to refine > "with prior phase information" -AFAIU. > So what exactly is the info contained in the output refmacX.mtz besides map > coefficients for COOT? If it is not just the raw xray data Fo, is it Fc only, > or Fc that are filled in for missing Fo? > I guess I am not really sure. I was under the impression that model´s PHIC > would cause the problems, if they were present. > Best, The columns in a standard refmac output mtz file are H K L FreeR_flag - self-evident F SIGF - these are modified compared to the input. AFAIU, some of the scaling is applied to the Fo's as a matter of programming elegance. Naturally, this makes using them for future refinement cycles problematic. FC PHIC - these are Fc's from the atoms present in the model FC_ALL PHIC_ALL - full Fc's, i.e including the solvent contribution FWT PHWT DELFWT PHDELWT - this is what you called the "map coefficients for COOT", although this is historically incorrect since refmac produced this output before coot was born FOM - figure-of-merit As for filling-in missing reflections, it is always on. Not to rekindle another Hegelian fire, but the idea is that the missing reflections should always be filled in because Fc's are definitely better estimates of Fo's than zeros. HTH, Ed. -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs
[ccp4bb] Beckman Biosys 2000
I was just contacted by a group looking for install disks for the Biosys program used to run the old Biosys2000 FPLC from Beckman. I don't have the install disks anymore (we eventually bludgeoned our Biosys to death, and then set it on fire, if I recall--it was always very unreliable). However, if anyone does, by some miracle, have these disks, and feels like being a good Samaritan (just in time for the winter holidays!), then please contact this person directly: Jean-Baptiste Reiser . Cheers, Pat Loll --- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.l...@drexelmed.edu
[ccp4bb] postdoc position at the Univ of Milan
Dear BB readers, at the University of Milan in the Dept. of Biomol. Sciences we are currently looking for a motivated candidate for a 3-year Postdoctoral position in the lab of Prof. Bolognesi, under my supervision. The contract will start sometimes this spring (most likely March-April). The project will be focusing on crystallographic and biophysical studies of Beta-2 microglobulin, a human protein forming pathogical amyloid fibrils. Crystallization and biophysical characterization of mutants, oligomers in order to understand the b2m fibril formation will be the focus of the project. Strong background in crystallography is necessary and experience in protein expression and purification is very welcome. Fluent English is required. If you want to know more about the project and my research, you can check: http://users.unimi.it/stericagno/default.html and/or contact me directly (sterica...@gmail.com) if you want to know more about Bolognesi's group check: http://users.unimi.it/biolstru/Home.html Any interested candidate should send a short CV and two references to this address sterica...@gmail.com I'll be at the CCP4 week end in the beginning of January in case someone is interested in a chat... Regards Stefano
Re: [ccp4bb] PHENIX vs REFMAC refinement had me fooled
A small but potentially important correction: FC_ALL PHIC_ALL from REFMAC are indeed the calculated structure factor of the coordinates+bulk_solvent, but AFTER multiplying by the likelihood coefficient "D" (as in 2*m*Fo-D*Fc ). So, if you subtract ( FC_ALL PHIC_ALL ) from ( FC PHIC ) you will NOT get the bulk solvent contribution alone. AFAIK there is no way to obtain just the bulk solvent contribution from REFMAC. -James Holton MAD Scientist On 12/13/2011 6:24 AM, Ed Pozharski wrote: On Tue, 2011-12-13 at 02:31 +, Yuri Pompeu wrote: Hi Ed, I just had a chance of looking at your comment more closely. You are right it only uses PHIC if in refmacs set up you choose to refine "with prior phase information" -AFAIU. So what exactly is the info contained in the output refmacX.mtz besides map coefficients for COOT? If it is not just the raw xray data Fo, is it Fc only, or Fc that are filled in for missing Fo? I guess I am not really sure. I was under the impression that model´s PHIC would cause the problems, if they were present. Best, The columns in a standard refmac output mtz file are H K L FreeR_flag - self-evident F SIGF - these are modified compared to the input. AFAIU, some of the scaling is applied to the Fo's as a matter of programming elegance. Naturally, this makes using them for future refinement cycles problematic. FC PHIC - these are Fc's from the atoms present in the model FC_ALL PHIC_ALL - full Fc's, i.e including the solvent contribution FWT PHWT DELFWT PHDELWT - this is what you called the "map coefficients for COOT", although this is historically incorrect since refmac produced this output before coot was born FOM - figure-of-merit As for filling-in missing reflections, it is always on. Not to rekindle another Hegelian fire, but the idea is that the missing reflections should always be filled in because Fc's are definitely better estimates of Fo's than zeros. HTH, Ed.
Re: [ccp4bb] artificial tetramer
Dear CCP4bb list, Thank you very much all of you who have answered my post. I'm really sorry if I was unclear. Such operation is so unusual that I could be able to express myself appropriately. From quick reading some replies (James Stroud and Guillaume Ponchel), it seems is possible do build artificial tetramers with Coot. Several problems have been raised like clashes, unusual interfaces and so on. A second step would be to take Coot's rotation and translation matrix and apply it to all pdb's in batch mode with pdbset. All pdb's are superposed by a common sequence region, which also will be part of the tetramer interface. I'll try to make things work. Once more, sorry for any inconvenience and thank you very much. Kind regards, Fred
[ccp4bb] symmetry for ages 6 and up
Hi all, For those who teach xtallography - we found some plastic turtles that can be snapped together in an amazing variety of space groups. Worked well in a workshop for our students, so I thought I'd share the shopping tip. They're called Reptangles, and we got them from Amazon. http://www.amazon.com/Fat-Brain-Toys-FA042-1-Reptangles/dp/B00392NSQ4 Have fun! Phoebe = Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp
Re: [ccp4bb] symmetry for ages 6 and up
whoa - now that looks like fun! Amazon just made some money off of me. Thanks for sharing! Steve -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Phoebe Rice Sent: Tuesday, December 13, 2011 5:53 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] symmetry for ages 6 and up Hi all, For those who teach xtallography - we found some plastic turtles that can be snapped together in an amazing variety of space groups. Worked well in a workshop for our students, so I thought I'd share the shopping tip. They're called Reptangles, and we got them from Amazon. http://www.amazon.com/Fat-Brain-Toys-FA042-1-Reptangles/dp/B00392NSQ4 Have fun! Phoebe = Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
Re: [ccp4bb] symmetry for ages 6 and up
reminds me of these symmetric 2D P3 lizards: http://www.worldofescher.com/store/Z51.html I bought the RGB-coloured set/puzzle after visiting an Escher exhibition and sometimes use them in crystallography/symmetry teaching. Nice to make the students assemble them and then decide on the symmetry operator, unit cell and asymmetric unit. Quoting Phoebe Rice: Hi all, For those who teach xtallography - we found some plastic turtles that can be snapped together in an amazing variety of space groups. Worked well in a workshop for our students, so I thought I'd share the shopping tip. They're called Reptangles, and we got them from Amazon. http://www.amazon.com/Fat-Brain-Toys-FA042-1-Reptangles/dp/B00392NSQ4 Have fun! Phoebe = Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoléculas Centro Nacional de Biotecnología - CSIC c/Darwin 3, Campus Cantoblanco 28049 Madrid tel. 91 585 4616 email: mjvanra...@cnb.csic.es
Re: [ccp4bb] symmetry for ages 6 and up
Does anyone know where one can acquire some Penrose tiles? I think they'd be great toys as well, and drive you a little bonkers. Maybe a kitchen/bathroom floor made from them? Jacob On Tue, Dec 13, 2011 at 5:03 PM, VAN RAAIJ , MARK JOHAN wrote: > reminds me of these symmetric 2D P3 lizards: > http://www.worldofescher.com/store/Z51.html > I bought the RGB-coloured set/puzzle after visiting an Escher exhibition and > sometimes use them in crystallography/symmetry teaching. > Nice to make the students assemble them and then decide on the symmetry > operator, unit cell and asymmetric unit. > > > Quoting Phoebe Rice: > >> Hi all, >> For those who teach xtallography - we found some plastic turtles that can >> be snapped together in an amazing variety of space groups. Worked well in a >> workshop for our students, so I thought I'd share the shopping tip. They're >> called Reptangles, and we got them from Amazon. >> >> http://www.amazon.com/Fat-Brain-Toys-FA042-1-Reptangles/dp/B00392NSQ4 >> >> Have fun! >> >> Phoebe >> >> = >> Phoebe A. Rice >> Dept. of Biochemistry & Molecular Biology >> The University of Chicago >> phone 773 834 1723 >> >> http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 >> http://www.rsc.org/shop/books/2008/9780854042722.asp >> > > > > Mark J van Raaij > Laboratorio M-4 > Dpto de Estructura de Macromoléculas > Centro Nacional de Biotecnología - CSIC > c/Darwin 3, Campus Cantoblanco > 28049 Madrid > tel. 91 585 4616 > email: mjvanra...@cnb.csic.es -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] symmetry for ages 6 and up
(oops, previous mail got sent before I wanted) the turtles would be really nice to extend things into 3D. great find, Mark Quoting Phoebe Rice: Hi all, For those who teach xtallography - we found some plastic turtles that can be snapped together in an amazing variety of space groups. Worked well in a workshop for our students, so I thought I'd share the shopping tip. They're called Reptangles, and we got them from Amazon. http://www.amazon.com/Fat-Brain-Toys-FA042-1-Reptangles/dp/B00392NSQ4 Have fun! Phoebe = Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoléculas Centro Nacional de Biotecnología - CSIC c/Darwin 3, Campus Cantoblanco 28049 Madrid tel. 91 585 4616 email: mjvanra...@cnb.csic.es
Re: [ccp4bb] symmetry for ages 6 and up
Thank you for the info. It looks great for teaching or for just having fun. Carlos R. Escalante Ph.D Assistant Professor Department of Physiology and Biophysics VCU School of Medicine 1220 East Broad Street MMRB 2-040 Richmond, VA 23219 cescala...@vcu.edu (804)628-1202 On 12/13/11 5:53 PM, Phoebe Rice wrote: Hi all, For those who teach xtallography - we found some plastic turtles that can be snapped together in an amazing variety of space groups. Worked well in a workshop for our students, so I thought I'd share the shopping tip. They're called Reptangles, and we got them from Amazon. http://www.amazon.com/Fat-Brain-Toys-FA042-1-Reptangles/dp/B00392NSQ4 Have fun! Phoebe = Phoebe A. Rice Dept. of Biochemistry& Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp
Re: [ccp4bb] symmetry for ages 6 and up
If you go to froogle.google.com you will find that you can buy these at a noticeably lower price than at amazon.com, at least for people in the USA - just search for Reptangles. Frances = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = On Tue, 13 Dec 2011, Phoebe Rice wrote: Hi all, For those who teach xtallography - we found some plastic turtles that can be snapped together in an amazing variety of space groups. Worked well in a workshop for our students, so I thought I'd share the shopping tip. They're called Reptangles, and we got them from Amazon. http://www.amazon.com/Fat-Brain-Toys-FA042-1-Reptangles/dp/B00392NSQ4 Have fun! Phoebe = Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp
Re: [ccp4bb] symmetry for ages 6 and up
we have a whole street made of them... welcome to Helsinki... t. On Dec 14, 2011, at 1:10 AM, Jacob Keller wrote: > Does anyone know where one can acquire some Penrose tiles? I think > they'd be great toys as well, and drive you a little bonkers. Maybe a > kitchen/bathroom floor made from them? > > Jacob > > On Tue, Dec 13, 2011 at 5:03 PM, VAN RAAIJ , MARK JOHAN > wrote: >> reminds me of these symmetric 2D P3 lizards: >> http://www.worldofescher.com/store/Z51.html >> I bought the RGB-coloured set/puzzle after visiting an Escher exhibition and >> sometimes use them in crystallography/symmetry teaching. >> Nice to make the students assemble them and then decide on the symmetry >> operator, unit cell and asymmetric unit. >> >> >> Quoting Phoebe Rice: >> >>> Hi all, >>> For those who teach xtallography - we found some plastic turtles that can >>> be snapped together in an amazing variety of space groups. Worked well in a >>> workshop for our students, so I thought I'd share the shopping tip. They're >>> called Reptangles, and we got them from Amazon. >>> >>> http://www.amazon.com/Fat-Brain-Toys-FA042-1-Reptangles/dp/B00392NSQ4 >>> >>> Have fun! >>> >>> Phoebe >>> >>> = >>> Phoebe A. Rice >>> Dept. of Biochemistry & Molecular Biology >>> The University of Chicago >>> phone 773 834 1723 >>> >>> http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 >>> http://www.rsc.org/shop/books/2008/9780854042722.asp >>> >> >> >> >> Mark J van Raaij >> Laboratorio M-4 >> Dpto de Estructura de Macromoléculas >> Centro Nacional de Biotecnología - CSIC >> c/Darwin 3, Campus Cantoblanco >> 28049 Madrid >> tel. 91 585 4616 >> email: mjvanra...@cnb.csic.es > > > > -- > *** > Jacob Pearson Keller > Northwestern University > Medical Scientist Training Program > email: j-kell...@northwestern.edu > *** > Tommi Kajander, Ph.D., Docent Structural Biology and Biophysics Institute of Biotechnology University of Helsinki Viikinkaari 1 (P.O. Box 65) 00014 Helsinki Finland p. +358-9-19158903 tommi.kajan...@helsinki.fi
[ccp4bb] very strange lattice: high anisotropy, 78% solvent content and maybe merohedral twinning
I am looking at a highly unusual crystal lattice right now and can't figure out what is going on, so I decided to ask the experts. I recently got data on a oligomeric protein with many highly correlated NCS units (4.0A resolution, linear R-sym is 0.16-0.21 in I4, I422, F222, C2 and 0.12 in P1) with severe anisotropic diffraction (according to diffraction anisotropy server, the F/sigma drops below 3 at a=6.1 b=6.1 c=never, suggested isotropic B-sharpening -125A^2) This lattice has a problem. The apparent unit cell is rather huge (roughly 180 180 620 / 90 90 90) The unit cell dimensions are almost perfectly I4 and the presence of systematic absent reflections >50 I/s in I41 and I4122 suggest no screw axis. I used a very closely related structure solved at 4.2A as molecular replacement model and got a solution from the anisotropy corrected data in I422 space group with two oligomers in the asymmetric unit cell. Confidence of the MR "solution" is quite high since (a)the MR replacement put one model one NCS raster off the "true" position resulting in a clash with the second one in an empty region of the map and additional electron density on the other side which corresponds perfectly to the wrongly positioned monomer, and (b) after rotating the model in the "right" position I could refine the structure to R-work=0.31. R-free=0.35 in one run of rigid body refinement followed by NCS restrained simulated annealing refinement (phenix.refine), which is in my opinion really good at such an early stage of refinement given the low overall resolution and even lower completeness of strong reflections in a and b due to high anisotropy (observables to atoms ratio is about 3:1) . I can even see clear density for some of the bulky sidechains which were not included in the model. Now here is the baffling thing. The unit cell is almost empty with an apparent solvent content of >78%. The molecules cluster around the c-axis and at the origin with an empty gap in a and b of at least 15A and up to 165A(!) in the longest dimension. There is no sign of electron density that would indicate a missing protein in that region and ~98% of my model is already accounted for by the density in the 2Fo-Fc map, making a contact of disordered protein regions across the ASUs unlikely. In fact, the protein density is well defined at the closest gap and no mainchain atom is unaccounted for in that region. The oligomer has a magnitude of ~105A x 70A. I heavily doubt that a crystal lattice with such little contacts and holes as huge as these can exist and therefore think that: (a) the R-factors are misleading me to think the solution is correct and complete (b) I must have been doing something really wrong Since proteins from this family have a well established history of producing twinned crystals I had a look at that possibility. Analyzing the anisotropy corrected I4 data for twinning (Padilla & Yeates method) revealed a 2-fold twin law with a twin fraction of 0.42 which would make the discrimination between an almost perfectly merohedral twin in I4 and a (non twinned ?) I422 extremely difficult (to me). MR with anisotropy corrected I4 data gave the same crystal packing and hence the same void solvent region. MR in lower point groups was not successful so far although I haven't pursued that idea vigorously. The same data in I422 has no indication for twinning and in C2 three 2-fold twin laws. Anomalous data is not easily available since those crystals grow in about one year and getting another crystal is also not very likely because this IS "the other crystal". I am clueless now on how to proceed here and would appreciate advice from experienced crystallographers on what to try first. Am I worrying too much about the packing? Is it even possible to have such an enormously huge solvent region in a protein crystal? What is the recommended protocol when dealing with many and very strongly correlated NCS units, putative twinning and severe anisotropy all at the same time? Stefan Gajewski
Re: [ccp4bb] very strange lattice: high anisotropy, 78% solvent content and maybe merohedral twinning
Hi Stefan, 1) just out of curiosity I wrote a tiny script using CCTBX that estimates solvent content via bulk-solvent mask, and quickly run this script for all PDB structures for which I could re-calculate the R-work within 5% from published value. Also, this script extracted the solvent content values reported in PDB file header. Here is what I get: Histogram of solvent contents (estimated via mask): Solvent content Number of structures 5.980 - 14.482 : 11 14.482 - 22.984 : 109 22.984 - 31.486 : 396 31.486 - 39.988 : 3590 39.988 - 48.490 : 11442 48.490 - 56.992 : 11707 56.992 - 65.494 : 6524 65.494 - 73.996 : 2561 73.996 - 82.498 : 510 82.498 - 91.000 : 19 Histogram of solvent contents (extracted from REMARK records): Solvent content Number of structures 6.000 - 14.300 : 91 14.300 - 22.600 : 550 22.600 - 30.900 : 2046 30.900 - 39.200 : 6487 39.200 - 47.500 : 9566 47.500 - 55.800 : 9050 55.800 - 64.100 : 5853 64.100 - 72.400 : 2420 72.400 - 80.700 : 720 80.700 - 89.000 : 86 So, your 78% is not that uncommon although it is at the high(ish) end. 2) Does Xtriage suggest twinning? If so what happens if you refine with the twin law? 3) Make sure you look at both, 2mFo-DFc with and without missing Fobs filled with DFc (depending on completeness of your data that may make a big difference). Pavel On Tue, Dec 13, 2011 at 8:47 PM, Stefan Gajewski wrote: > I am looking at a highly unusual crystal lattice right now and can't > figure out what is going on, so I decided to ask the experts. > > I recently got data on a oligomeric protein with many highly correlated > NCS units (4.0A resolution, linear R-sym is 0.16-0.21 in I4, I422, F222, C2 > and 0.12 in P1) with severe anisotropic diffraction (according to > diffraction anisotropy server, the F/sigma drops below 3 at a=6.1 b=6.1 > c=never, suggested isotropic B-sharpening -125A^2) This lattice has a > problem. The apparent unit cell is rather huge (roughly 180 180 620 / 90 90 > 90) > > The unit cell dimensions are almost perfectly I4 and the presence of > systematic absent reflections >50 I/s in I41 and I4122 suggest no screw > axis. I used a very closely related structure solved at 4.2A as molecular > replacement model and got a solution from the anisotropy corrected data in > I422 space group with two oligomers in the asymmetric unit cell. > > Confidence of the MR "solution" is quite high since (a)the MR replacement > put one model one NCS raster off the "true" position resulting in a clash > with the second one in an empty region of the map and additional electron > density on the other side which corresponds perfectly to the wrongly > positioned monomer, and (b) after rotating the model in the "right" > position I could refine the structure to R-work=0.31. R-free=0.35 in one > run of rigid body refinement followed by NCS restrained simulated annealing > refinement (phenix.refine), which is in my opinion really good at such an > early stage of refinement given the low overall resolution and even lower > completeness of strong reflections in a and b due to high anisotropy > (observables to atoms ratio is about 3:1) . I can even see clear density > for some of the bulky sidechains which were not included in the model. > > Now here is the baffling thing. The unit cell is almost empty with an > apparent solvent content of >78%. The molecules cluster around the c-axis > and at the origin with an empty gap in a and b of at least 15A and up to > 165A(!) in the longest dimension. There is no sign of electron density that > would indicate a missing protein in that region and ~98% of my model is > already accounted for by the density in the 2Fo-Fc map, making a contact of > disordered protein regions across the ASUs unlikely. In fact, the protein > density is well defined at the closest gap and no mainchain atom is > unaccounted for in that region. The oligomer has a magnitude of ~105A x > 70A. I heavily doubt that a crystal lattice with such little contacts and > holes as huge as these can exist and therefore think that: > > (a) the R-factors are misleading me to think the solution is correct and > complete > (b) I must have been doing something really wrong > > Since proteins from this family have a well established history of > producing twinned crystals I had a look at that possibility. Analyzing the > anisotropy corrected I4 data for twinning (Padilla & Yeates method) > revealed a 2-fold twin law with a twin fraction of 0.42 which would make > the discrimination between an almost perfectly merohedral twin in I4 and a > (non twinned ?) I422 extremely difficult (to me). MR with anisotropy > corrected I4 data gave the same crystal packing and hence the same void > solvent region. MR in lower point groups was not successful so far although > I haven't pursued that idea vigorously.
Re: [ccp4bb] very strange lattice: high anisotropy, 78% solvent content and maybe merohedral twinning
If you have air in the packing that's worrysome. If symmetry mates don't make crystal contacts you are in trouble. Have you checked a simple selfrotation function in your currently favored space group ? Do you have sufficient data collected to start out in P1 or C2 ? Then I would start there and systematically look at selfrotation functions in those space groups. Also check the native Patterson for translational NCS. 4 A is not great for stable refinement of cell parameters, which program did you use and which parameters did you fix? Did you use main.ncs=true in the SA approach ? Pointless or xtriage ? Why does it take a year to grow those crystals ? Out of curiosity, how did you collect on this crystal without overlapping reflections ? Good luck, Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Dec 13, 2011, at 23:57, "Stefan Gajewski" wrote: > I am looking at a highly unusual crystal lattice right now and can't figure > out what is going on, so I decided to ask the experts. > > I recently got data on a oligomeric protein with many highly correlated NCS > units (4.0A resolution, linear R-sym is 0.16-0.21 in I4, I422, F222, C2 and > 0.12 in P1) with severe anisotropic diffraction (according to diffraction > anisotropy server, the F/sigma drops below 3 at a=6.1 b=6.1 c=never, > suggested isotropic B-sharpening -125A^2) This lattice has a problem. The > apparent unit cell is rather huge (roughly 180 180 620 / 90 90 90) > > The unit cell dimensions are almost perfectly I4 and the presence of > systematic absent reflections >50 I/s in I41 and I4122 suggest no screw axis. > I used a very closely related structure solved at 4.2A as molecular > replacement model and got a solution from the anisotropy corrected data in > I422 space group with two oligomers in the asymmetric unit cell. > > Confidence of the MR "solution" is quite high since (a)the MR replacement put > one model one NCS raster off the "true" position resulting in a clash with > the second one in an empty region of the map and additional electron density > on the other side which corresponds perfectly to the wrongly positioned > monomer, and (b) after rotating the model in the "right" position I could > refine the structure to R-work=0.31. R-free=0.35 in one run of rigid body > refinement followed by NCS restrained simulated annealing refinement > (phenix.refine), which is in my opinion really good at such an early stage of > refinement given the low overall resolution and even lower completeness of > strong reflections in a and b due to high anisotropy (observables to atoms > ratio is about 3:1) . I can even see clear density for some of the bulky > sidechains which were not included in the model. > > Now here is the baffling thing. The unit cell is almost empty with an > apparent solvent content of >78%. The molecules cluster around the c-axis and > at the origin with an empty gap in a and b of at least 15A and up to 165A(!) > in the longest dimension. There is no sign of electron density that would > indicate a missing protein in that region and ~98% of my model is already > accounted for by the density in the 2Fo-Fc map, making a contact of > disordered protein regions across the ASUs unlikely. In fact, the protein > density is well defined at the closest gap and no mainchain atom is > unaccounted for in that region. The oligomer has a magnitude of ~105A x 70A. > I heavily doubt that a crystal lattice with such little contacts and holes as > huge as these can exist and therefore think that: > > (a) the R-factors are misleading me to think the solution is correct and > complete > (b) I must have been doing something really wrong > > Since proteins from this family have a well established history of producing > twinned crystals I had a look at that possibility. Analyzing the anisotropy > corrected I4 data for twinning (Padilla & Yeates method) revealed a 2-fold > twin law with a twin fraction of 0.42 which would make the discrimination > between an almost perfectly merohedral twin in I4 and a (non twinned ?) I422 > extremely difficult (to me). MR with anisotropy corrected I4 data gave the > same crystal packing and hence the same void solvent region. MR in lower > point groups was not successful so far although I haven't pursued that idea > vigorously. The same data in I422 has no indication for twinning and in C2 > three 2-fold twin laws. > > Anomalous data is not easily available since those crystals grow in about one > year and getting another crystal is also not very likely because this IS "the > other crystal". > > I am clueless now on how to proceed here and would appreciate advi
Re: [ccp4bb] very strange lattice: high anisotropy, 78% solvent content and maybe merohedral twinning
Don't forget that if you have poorly resolved spots due to the long axis, the intensity statistics may falsely seem to indicate twinning, since weak spots may be contaminated by neighbouring strong ones Phil On 14 Dec 2011, at 04:47, Stefan Gajewski wrote: > I am looking at a highly unusual crystal lattice right now and can't figure > out what is going on, so I decided to ask the experts. > > I recently got data on a oligomeric protein with many highly correlated NCS > units (4.0A resolution, linear R-sym is 0.16-0.21 in I4, I422, F222, C2 and > 0.12 in P1) with severe anisotropic diffraction (according to diffraction > anisotropy server, the F/sigma drops below 3 at a=6.1 b=6.1 c=never, > suggested isotropic B-sharpening -125A^2) This lattice has a problem. The > apparent unit cell is rather huge (roughly 180 180 620 / 90 90 90) > > The unit cell dimensions are almost perfectly I4 and the presence of > systematic absent reflections >50 I/s in I41 and I4122 suggest no screw axis. > I used a very closely related structure solved at 4.2A as molecular > replacement model and got a solution from the anisotropy corrected data in > I422 space group with two oligomers in the asymmetric unit cell. > > Confidence of the MR "solution" is quite high since (a)the MR replacement put > one model one NCS raster off the "true" position resulting in a clash with > the second one in an empty region of the map and additional electron density > on the other side which corresponds perfectly to the wrongly positioned > monomer, and (b) after rotating the model in the "right" position I could > refine the structure to R-work=0.31. R-free=0.35 in one run of rigid body > refinement followed by NCS restrained simulated annealing refinement > (phenix.refine), which is in my opinion really good at such an early stage of > refinement given the low overall resolution and even lower completeness of > strong reflections in a and b due to high anisotropy (observables to atoms > ratio is about 3:1) . I can even see clear density for some of the bulky > sidechains which were not included in the model. > > Now here is the baffling thing. The unit cell is almost empty with an > apparent solvent content of >78%. The molecules cluster around the c-axis and > at the origin with an empty gap in a and b of at least 15A and up to 165A(!) > in the longest dimension. There is no sign of electron density that would > indicate a missing protein in that region and ~98% of my model is already > accounted for by the density in the 2Fo-Fc map, making a contact of > disordered protein regions across the ASUs unlikely. In fact, the protein > density is well defined at the closest gap and no mainchain atom is > unaccounted for in that region. The oligomer has a magnitude of ~105A x 70A. > I heavily doubt that a crystal lattice with such little contacts and holes as > huge as these can exist and therefore think that: > > (a) the R-factors are misleading me to think the solution is correct and > complete > (b) I must have been doing something really wrong > > Since proteins from this family have a well established history of producing > twinned crystals I had a look at that possibility. Analyzing the anisotropy > corrected I4 data for twinning (Padilla & Yeates method) revealed a 2-fold > twin law with a twin fraction of 0.42 which would make the discrimination > between an almost perfectly merohedral twin in I4 and a (non twinned ?) I422 > extremely difficult (to me). MR with anisotropy corrected I4 data gave the > same crystal packing and hence the same void solvent region. MR in lower > point groups was not successful so far although I haven't pursued that idea > vigorously. The same data in I422 has no indication for twinning and in C2 > three 2-fold twin laws. > > Anomalous data is not easily available since those crystals grow in about one > year and getting another crystal is also not very likely because this IS "the > other crystal". > > I am clueless now on how to proceed here and would appreciate advice from > experienced crystallographers on what to try first. > > Am I worrying too much about the packing? > Is it even possible to have such an enormously huge solvent region in a > protein crystal? > What is the recommended protocol when dealing with many and very strongly > correlated NCS units, putative twinning and severe anisotropy all at the same > time? > > Stefan Gajewski
