Re: [ccp4bb] sequence format conversion
Hello, The tool is called awk. There is also another tool called Perl, but I won't recommend it. Regards, F. On 05/08/2012 04:02 PM, K Singh wrote: Dear All I was looking for a script or an informatics tool enabling me to change the sequence from FASTA format to something like following: FASTA FORMAT abcdefghijklmnopqrstuvwxyz to 1 abcde fghij 11 klmno pqrst 21 uvwxy z Many thanks in advance Regards Kris
Re: [ccp4bb] ShelXL and Coot
Hi Kalyan, If you are unable to read the .res file then I suspect that you had and END without an HKLF. Thanks to Tim this problem has been fixed now (r4161) if you're feeling adventurous. As for the PDB file, yes indeed, Coot will choke if you try to feed it atoms without residue names. Some of the Coot tools depend on standard residue names, this maybe why things are not working for you (devil's in the details). Paul. On 07/05/12 10:06, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Kalyan, the reason why you cannot read in the .res-file is that you don't have RESI-cards. They are required by coot. For the same reason your PDB-file does not contain any information that would allow coot to refine the coordinates. As far as I know coot does not create restraints from the .res-file, hence you need to give your structure residue names for which cif-files exist with constraints. However, I since you are working on such a small structure at atomic resolution I suggest you use Christian Huebschle's shelxle instead of coot as GUI for shelxl refinement. You find it at http://ewald.ac.chemie.uni-goettingen.de/shelx/eingabe.php Best, Tim On 05/07/12 05:38, Kalyan wrote: Hi George: I am facing the same problem reading .pdb file generated from shelxl in coot. I have tried inserting the space group name in the CRYST1 record but still unable to read the file. COOT is able to read the .res and .fcf file and I can see the map but COOT is not allowing me to build the molecule from .res file. I am trying to refine the solution obtained from direct methods using SHELXS. What are the parameters that I need to change in the .res or .pdb file to be able to modify and build the molecule in the first place. Do I have to replace 'Q' with 'C' or some other changes, and then how will I connect the atoms in COOT? The appearance of the part of the .pdb file is shown below (space group name is manually inserted). CRYST1 21.139 51.900 31.090 90.00 104.69 90.00 P 1 21/a 1 1 SCALE1 0.047306 0.00 0.012400 0.00 SCALE2 0.00 0.019268 0.00 0.00 SCALE3 0.00 0.00 0.033251 0.00 ATOM 1 S1 0 -0.215 21.413 10.717 1.000 4.73 ATOM 2 S2 0 0.551 21.040 12.581 1.000 4.64 ATOM 3 S3 0 1.526 18.258 7.542 1.000 5.05 ATOM 4 S4 0 0.802 16.539 8.374 1.000 4.95 ATOM 5 S5 0 11.171 22.546 8.376 1.000 5.35 ATOM 6 S6 0 9.747 22.514 6.903 1.000 5.85 ATOM 7 Q2 0 -1.517 23.108 -2.742 1.000 0.41 ATOM 8 Q3 0 -5.977 20.216 -0.493 1.000 1.03 ATOM 9 Q4 0 13.309 15.857 11.911 1.000 1.63 ATOM 10 Q6 0 -2.030 15.341 9.819 1.000 2.42 ATOM 11 Q7 0 0.489 22.190 6.739 1.000 2.46 ATOM 12 Q8 0 -1.247 24.612 5.096 1.000 2.29 ATOM 13 Q9 0 4.588 21.769 11.905 1.000 2.41 ATOM 14 Q10 0 -3.731 19.433 12.713 1.000 2.78 ATOM 15 Q11 0 7.498 18.251 9.847 1.000 2.39 ATOM 16 Q12 0 3.703 20.519 8.595 1.000 2.22 ATOM 17 Q13 0 0.926 24.359 15.407 1.000 2.33 Thanks, Kalyan - -- - -- 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/ iD8DBQFPp5CJUxlJ7aRr7hoRAut9AKCwBvWucGGdz9sfqRnlymWePgjs7gCg2Ewk BwWxLB0dWfOmj6cr/Shpuqs= =8jcn -END PGP SIGNATURE-
Re: [ccp4bb] sequence format conversion
Surely a sequence analysis tools are the easiest way to do it. I'd recommend EMBOSS (open source and runs nicely on most platforms - the ccp4 of sequence analysis for me at least) http://emboss.sourceforge.net/ Seqret (SEQuence RETurn) program: seqret -out test.seq -osformat gcg test.fasta Marko PS. fasta format needs as a first line with (optional) description in the input file. And not sure what amino acids b and j would get converted to :-) On Tue, 8 May 2012, Francois Berenger wrote: More seriously, there is the babel command from Open Babel in case the second format you show has a known name. On 05/08/2012 04:46 PM, Francois Berenger wrote: Hello, The tool is called awk. There is also another tool called Perl, but I won't recommend it. Regards, F. On 05/08/2012 04:02 PM, K Singh wrote: Dear All I was looking for a script or an informatics tool enabling me to change the sequence from FASTA format to something like following: FASTA FORMAT abcdefghijklmnopqrstuvwxyz to 1 abcde fghij 11 klmno pqrst 21 uvwxy z Many thanks in advance Regards Kris _ Marko Hyvonen Department of Biochemistry, University of Cambridge ma...@cryst.bioc.cam.ac.uk http://www-cryst.bioc.cam.ac.uk/groups/hyvonen tel:+44-(0)1223-766 044 mobile: +44-(0)7796-174 877 fax:+44-(0)1223-766 002 --
Re: [ccp4bb] sequence format conversion
On Tue, 2012-05-08 at 09:22 +0100, Marko Hyvonen wrote: PS. fasta format needs as a first line with (optional) description in the input file. And not sure what amino acids b and j would get converted to :-) A good tool should leave b as is: it is ASX (the standard ambiguity code for ASP or ASN). j, o and u are a different matter :-) Regards, Peter. -- Peter Keller Tel.: +44 (0)1223 353033 Global Phasing Ltd., Fax.: +44 (0)1223 366889 Sheraton House, Castle Park, Cambridge CB3 0AX United Kingdom
[ccp4bb] reminder: CCP-EM positions now available
A reminder that the deadline for these positions is this Friday (11 May 2012). If you have any questions, or problems with the application procedure, please contact me off-list. Martyn --- Dear Colleagues, We have been awarded a Partnership grant by the MRC to provide computational support for UK scientists using electron cryo-microscopy for structural biology. One of the major aims is to create a Collaborative Computational Project, CCP-EM, by analogy with similar successful projects in macromolecular crystallography (CCP4) and biological nuclear magnetic resonance spectroscopy (CCPN). We seek two excellent and motivated computational scientists to support the Partnership grant and the CCP-EM project. These posts will have a wide variety of responsibilities, including writing community code, improving the useability of existing code, providing training, and supporting individual scientists. The first post will focus on technical aspects, building community tools and improving the programs available. The second post will focus more on the scientific requirements of the community. The posts are located at the Research Complex at Harwell (near Oxford), alongside the core group of CCP4, but the postholders will be expected to travel throughout the UK and interact with international groups to support the collaboration. Applications must be made through the RCUK Shared Services recruitment portal https://ext.ssc.rcuk.ac.uk/ using the references IRC50385 and IRC50666. Further information is available there. Informal enquiries may be made to Martyn Winn (martyn.winn at stfc.ac.uk). Best wishes, Martyn Winn, Richard Henderson, Alan Roseman, Peter Rosenthal, Helen Saibil and Ardan Patwardhan -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk* * Fax: +44 1925 603634Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***
Re: [ccp4bb] sequence format conversion
A good tool should leave b as is: it is ASX (the standard ambiguity code for ASP or ASN). j, o and u are a different matter :-) http://www.uniprot.org/manual/non_std Selenocyteine [sic!] and pyrrolysine are represented in the sequence using the one-letter codes U for selenocysteine and O for pyrrolysine --Gerard ** Gerard J. Kleywegt http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ** Little known gastromathematical curiosity: let z be the radius and a the thickness of a pizza. Then the volume of that pizza is equal to pi*z*z*a ! **
Re: [ccp4bb] saxs on xtals
Anna Are the nanoparticles expected to be single crystals? Magnetite has Fd3m space group with a 8.4A lattice (just looked it up). This should give some diffraction features such as broad spots (broadened because of the small particle size) or rings (if there is no alignment between the nanoparticles). Have you looked for such effects in the diffraction patterns which you already have from the single crystals? Colin From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of anna anna Sent: 07 May 2012 17:30 To: ccp4bb Subject: [ccp4bb] saxs on xtals Dear all, I'd like some suggestions/opinions about the sense of an experiment proposed by a collaborator expert in saxs. In few words, he wants to collect SAXS data on a suspension of protein xtals to investigate low resolution periodicity of the xtal (more details below). The experiment requires a very huge number of xtals to obtain the circles typical of saxs and it is very time-consuming to me (I know nothing about saxs, I have only to prepare the sample). I proposed to measure a single rotating xtal (like in XRD) but he told they don't have a goniometer on saxs beamline. Here is my concern: does it make sense to measure many xtals together? Don't we lose information with respect to single xtal? And, most of all, what can I see by saxs that I can't see by waxs?? Sorry for the almost off-topic question but I think that only someone who knows both the techniques can help me!! Some detail for who is intrigued by my story: we prepared doped magnetite nanoparticles using ferritin as bioreactor. I crystallized this spheres filled with metal and solved the structure at 3.7A but I can see only the protein shell while there is no density inside, even if I know that the nanoparticles are there. A simple explanation is that the particles are free to move in the cavity(note that the diameter of the nanoparticle is shorter then the inner diameter of the protein shell), ie are disordered, and do not contribute to diffraction, in fact, to my knowledge, nobody have ever seen the metal core inside ferritin or dps proteins. However, since they are magnetic particles they must see each other through the protein wall, ie they can't be completely free to move in the cavity. Maybe, but this is just my opinion, I don't see the particle because the period of the particle in the xtal is different/longer than the period of the protein shell. Anyway, we are interested in the relative distance between the magnetic particles in the xtal to study the effects of magnetostatic interactions in nanoparticles 3D arrays. We are going to do this by saxs since, they told me, lower resolution is useful in studying this long range periodicity (the diameter of ferritin is about 120A) but it seems fool to me using a suspension of so many xtals to obtain a scattering curve while I could collect diffraction images from a single xtal!!! I know that saxs is used when you don't have xtals but if you have xtals, ie your system is ordered, xtallography is much more powerful!! Another question: how can I handle my diffraction data at 3.7A resolution to look for nanoparticles? Should I try a lower symmetry? Maybe the anomalous signal? Have you any reference for a similar case? Thank you very much!! anna
Re: [ccp4bb] saxs on xtals
Dear Anna, I know that you already have gotten replies from some top experts, but your intriguing problem brought up some issues I have run across in the past. First, from you experience with single crystal diffraction, your results are not that much different from those seen in virus structures where the nucleic acid structure is averaged out. As the nucleic acid doesn't (and mostly can't) adopt the symmetry of the protein shell, the crystallization process alone does the averaging. Just because that ferritin and magnetite have cubic symmetry elements, if they don't line up, the magnetite structure can be averaged out upon crystallization. So, working at lower symmetry may not help, unless there is some directional correlation of the magnetite symmetry and position with the crystal axes. But try P1 and see what happens. A second comment is why not try neutron scattering (SANS or single crystal neutron diffraction), particularly as you can match out the protein with D2O and see just the magnetite. While the same concerns apply for single crystal neutron diffraction, you see more clearly regions of higher average density inside the protein shell. And lastly, have you tried crystallizing your ferritin/nanoparticle complexes in the presence of a magnetic field? It would be a neat trick, and people have tried such things in the past, such as for orienting biomolecules. Some even used old NMR magnets. Would be wild, if it worked. Good luck, Michael R. Michael Garavito, Ph.D. Professor of Biochemistry Molecular Biology 603 Wilson Rd., Rm. 513 Michigan State University East Lansing, MI 48824-1319 Office: (517) 355-9724 Lab: (517) 353-9125 FAX: (517) 353-9334Email: rmgarav...@gmail.com On May 7, 2012, at 12:30 PM, anna anna wrote: Dear all, I'd like some suggestions/opinions about the sense of an experiment proposed by a collaborator expert in saxs. In few words, he wants to collect SAXS data on a suspension of protein xtals to investigate low resolution periodicity of the xtal (more details below). The experiment requires a very huge number of xtals to obtain the circles typical of saxs and it is very time-consuming to me (I know nothing about saxs, I have only to prepare the sample). I proposed to measure a single rotating xtal (like in XRD) but he told they don't have a goniometer on saxs beamline. Here is my concern: does it make sense to measure many xtals together? Don't we lose information with respect to single xtal? And, most of all, what can I see by saxs that I can't see by waxs?? Sorry for the almost off-topic question but I think that only someone who knows both the techniques can help me!! Some detail for who is intrigued by my story: we prepared doped magnetite nanoparticles using ferritin as bioreactor. I crystallized this spheres filled with metal and solved the structure at 3.7A but I can see only the protein shell while there is no density inside, even if I know that the nanoparticles are there. A simple explanation is that the particles are free to move in the cavity(note that the diameter of the nanoparticle is shorter then the inner diameter of the protein shell), ie are disordered, and do not contribute to diffraction, in fact, to my knowledge, nobody have ever seen the metal core inside ferritin or dps proteins. However, since they are magnetic particles they must see each other through the protein wall, ie they can't be completely free to move in the cavity. Maybe, but this is just my opinion, I don't see the particle because the period of the particle in the xtal is different/longer than the period of the protein shell. Anyway, we are interested in the relative distance between the magnetic particles in the xtal to study the effects of magnetostatic interactions in nanoparticles 3D arrays. We are going to do this by saxs since, they told me, lower resolution is useful in studying this long range periodicity (the diameter of ferritin is about 120A) but it seems fool to me using a suspension of so many xtals to obtain a scattering curve while I could collect diffraction images from a single xtal!!! I know that saxs is used when you don't have xtals but if you have xtals, ie your system is ordered, xtallography is much more powerful!! Another question: how can I handle my diffraction data at 3.7A resolution to look for nanoparticles? Should I try a lower symmetry? Maybe the anomalous signal? Have you any reference for a similar case? Thank you very much!! anna
Re: [ccp4bb] saxs on xtals
Dear Colin, the table you gave seems to have been from Fe2+Fe3+2O4 or from Fe3-xTixO4. I am curious what the nature of the Fe inside the ferritin is (I don't think it has Ti in it, though...). Is it elemental iron? Also, to Anna: can you send a picture of that diffraction pattern with spot predictions superimposed? There seem to be some really bright spots which are outliers, and maybe multiple lattices. JPK On Tue, May 8, 2012 at 12:21 PM, Colin Nave colin.n...@diamond.ac.ukwrote: Anna Yes, you have understood the suggestion. Could be the 220 and 311 reflections. See for example http://rruff.info/magnetite/R080025 and http://rruff.info/repository/sample_child_record_powder/by_minerals/Magnetite__R080025-1__Powder__DIF_File__9448.txt Trying to index powder patterns from 2 rings is risky and the intensities don't seem to agree. I guess you don't have higher angle data. Should be able to evaluate a particle size from the breadth of the rings though. For example a 57A crystal examined with 1A radiation would give broadening of about a degree. There do seem to be other spots - I guess these are ice rings but you should check. Also be nice to know if apoferritin crystallised under the same conditions (if it can be) shows these rings Regards Colin From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of anna anna Sent: 08 May 2012 16:55 To: ccp4bb Subject: Re: [ccp4bb] saxs on xtals Dear all, first of all I want to thank you for your attention and all your brilliant suggestions that really cleared my head!!! Thanks to you (or because of you!!) now I have many ideas and very much to do. Colin, I was just re-considering my diffraction images. Who knows if they are single xtals indeed! Let's see if I understood your point. Assuming that they are single xtals, if they are located at independent positions in the protein-cage it would be like powder diffraction, with rings at diffraction angles corresponding to magnetite lattice. If they are ordered they should give a diffraction pattern. The corresponding lattice can differ from the protein lattice, do you agree? If this is true, what would I see? Two superimposed diffraction patterns? Actually, I am not able to evaluate it... I attached one of the diffraction images. It seems to me that there are two diffused rings at about 2.5 and 2.9 A. Michael, I just read your reply. I think that the eventual periodicity of the partcles can't be completely independent of the protein periodicity (I attached a hypotethical scheme), as you suggest I will try P1. Once I tryed a naive version of what you suggest: I put a magnet over the xtallization plate. All my collegues made fun of me... :) !! I will check the literature that you all quoted (hard work!) Thank you again, new suggestions will be really appreciated. Cheers, anna 2012/5/8 R. M. Garavito rmgarav...@gmail.commailto:rmgarav...@gmail.com Dear Anna, I know that you already have gotten replies from some top experts, but your intriguing problem brought up some issues I have run across in the past. First, from you experience with single crystal diffraction, your results are not that much different from those seen in virus structures where the nucleic acid structure is averaged out. As the nucleic acid doesn't (and mostly can't) adopt the symmetry of the protein shell, the crystallization process alone does the averaging. Just because that ferritin and magnetite have cubic symmetry elements, if they don't line up, the magnetite structure can be averaged out upon crystallization. So, working at lower symmetry may not help, unless there is some directional correlation of the magnetite symmetry and position with the crystal axes. But try P1 and see what happens. A second comment is why not try neutron scattering (SANS or single crystal neutron diffraction), particularly as you can match out the protein with D2O and see just the magnetite. While the same concerns apply for single crystal neutron diffraction, you see more clearly regions of higher average density inside the protein shell. And lastly, have you tried crystallizing your ferritin/nanoparticle complexes in the presence of a magnetic field? It would be a neat trick, and people have tried such things in the past, such as for orienting biomolecules. Some even used old NMR magnets. Would be wild, if it worked. Good luck, Michael R. Michael Garavito, Ph.D. Professor of Biochemistry Molecular Biology 603 Wilson Rd., Rm. 513 Michigan State University East Lansing, MI 48824-1319 Office: (517) 355-9724tel:%28517%29%20355-9724 Lab: (517) 353-9125 tel:%28517%29%20353-9125 FAX: (517) 353-9334tel:%28517%29%20353-9334Email: rmgarav...@gmail.commailto:garav...@gmail.com On May 7, 2012, at 12:30 PM,
Re: [ccp4bb] saxs on xtals
Jacob, Anna There are 5 magnetite examples in http://rruff.info/magnetite/ with different elemental compositions. All similar cells but the data for some is very noisy. R06 is the least noisy - contains nickel. Isn't iron stored as ferrihydrite in normal ferritin? Would be interesting to see whether this gives any similar diffuse rings in ferritin single crystal diffraction patterns. People must have checked after all these years. There is even the powder diffraction pattern in Wikipedia (http://en.wikipedia.org/wiki/Ferrihydrite) The bright spots you refer might be the ones I was fretting about. All diffraction features (rings or spots) should be indexed otherwise the job is incomplete! Colin From: Jacob Keller [mailto:j-kell...@fsm.northwestern.edu] Sent: 08 May 2012 18:29 To: Nave, Colin (DLSLtd,RAL,DIA) Cc: ccp4bb Subject: Re: [ccp4bb] saxs on xtals Dear Colin, the table you gave seems to have been from Fe2+Fe3+2O4 or from Fe3-xTixO4. I am curious what the nature of the Fe inside the ferritin is (I don't think it has Ti in it, though...). Is it elemental iron? Also, to Anna: can you send a picture of that diffraction pattern with spot predictions superimposed? There seem to be some really bright spots which are outliers, and maybe multiple lattices. JPK On Tue, May 8, 2012 at 12:21 PM, Colin Nave colin.n...@diamond.ac.ukmailto:colin.n...@diamond.ac.uk wrote: Anna Yes, you have understood the suggestion. Could be the 220 and 311 reflections. See for example http://rruff.info/magnetite/R080025 and http://rruff.info/repository/sample_child_record_powder/by_minerals/Magnetite__R080025-1__Powder__DIF_File__9448.txt Trying to index powder patterns from 2 rings is risky and the intensities don't seem to agree. I guess you don't have higher angle data. Should be able to evaluate a particle size from the breadth of the rings though. For example a 57A crystal examined with 1A radiation would give broadening of about a degree. There do seem to be other spots - I guess these are ice rings but you should check. Also be nice to know if apoferritin crystallised under the same conditions (if it can be) shows these rings Regards Colin From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of anna anna Sent: 08 May 2012 16:55 To: ccp4bb Subject: Re: [ccp4bb] saxs on xtals Dear all, first of all I want to thank you for your attention and all your brilliant suggestions that really cleared my head!!! Thanks to you (or because of you!!) now I have many ideas and very much to do. Colin, I was just re-considering my diffraction images. Who knows if they are single xtals indeed! Let's see if I understood your point. Assuming that they are single xtals, if they are located at independent positions in the protein-cage it would be like powder diffraction, with rings at diffraction angles corresponding to magnetite lattice. If they are ordered they should give a diffraction pattern. The corresponding lattice can differ from the protein lattice, do you agree? If this is true, what would I see? Two superimposed diffraction patterns? Actually, I am not able to evaluate it... I attached one of the diffraction images. It seems to me that there are two diffused rings at about 2.5 and 2.9 A. Michael, I just read your reply. I think that the eventual periodicity of the partcles can't be completely independent of the protein periodicity (I attached a hypotethical scheme), as you suggest I will try P1. Once I tryed a naive version of what you suggest: I put a magnet over the xtallization plate. All my collegues made fun of me... :) !! I will check the literature that you all quoted (hard work!) Thank you again, new suggestions will be really appreciated. Cheers, anna 2012/5/8 R. M. Garavito rmgarav...@gmail.commailto:rmgarav...@gmail.commailto:rmgarav...@gmail.commailto:rmgarav...@gmail.com Dear Anna, I know that you already have gotten replies from some top experts, but your intriguing problem brought up some issues I have run across in the past. First, from you experience with single crystal diffraction, your results are not that much different from those seen in virus structures where the nucleic acid structure is averaged out. As the nucleic acid doesn't (and mostly can't) adopt the symmetry of the protein shell, the crystallization process alone does the averaging. Just because that ferritin and magnetite have cubic symmetry elements, if they don't line up, the magnetite structure can be averaged out upon crystallization. So, working at lower symmetry may not help, unless there is some directional correlation of the magnetite symmetry and position with the crystal axes. But try P1 and see what happens. A second comment is why not try neutron scattering (SANS or single crystal neutron diffraction), particularly as you can match out the protein with D2O and see just the magnetite. While the same concerns apply for
[ccp4bb] number of reflections
When I index data, high resolution for example, I can get over 100,000 reflections. However, when I refine using PHENIX, it says only around 40,000. I am wondering why the number of reflections don't match up. I notice that the resolution range in PHENIX does not match that in HKL2000. I assumed the resolution range could be altered, but if it is using data from the indexing (output.sca file) I figured it would match. Can anybody explain why this is? It confuses me figuring out which number of reflections to use when writing tables. I normally use the number from the indexing file. Is this something related to default parameters in PHENIX?
