[ccp4bb] protein sequence database with conservation score annotation
Hi,everyone, Does anyone here could recommend such a database for me? I've searched the web and only find tools like 'consurf'. Databases like 'consurf' are important for the analysis of the current known structures. However, for the original discoveries of new domains, sequence databases with such conservation score annotation could be as important as the secondary structure prediction. Although the 'conservation score' maynot be as accurate as that from the 'consurf database' which is based on the 3-D alignment. The information of such database could be much more helpful, especially for some new proteins, or proteins regions without any structure available. Best regards, Yuan SHANG HKUST
[ccp4bb] rosetta fragment viewer
Dear all, Is there any program that can view the fragment files generated from Rosetta Fragment library? For example, I want to build a model myself, and I know the secondary structure of the target protein, so I will dock the 9-fragment myself. But, at the first step, I have to choose one fragment from the Rosetta fragment library generated. So, I wish if I can find any program that integrate the 200 9ers at specific position together, and then choose a good model by the shape I wanted. Did anyone here know such a program? Best Regards, Yuan SHANG
[ccp4bb] Structure Determination combining X-ray Data and NMR
Dear All, I have a set of 3.2A data containing only 3000 reflections. From the SAD phasing and iterative modeling and density modification, I get a preliminary structure with bad geometric conformations(~8/160 ramachandran outliers in Coot). After Phenix MLHL refinement, the geometry is still bad with (10% ramachandran outliers and 25% Rotamer outliers), and the B-factors are all too high(all between 80 to 170, average ~120), and R-factor/R-free have a value of 0.328/0.326. The poor geometry of my model and the unusual B-factors indicates there are still a lot improvement in my model. The question is, as I only have ~3000 reflections, and the atoms in the sequence is around 1000, and each atom there are 4 parameters to be refined(X,Y,Z,B-factor, assuming occupancy is 1), so how to refine my model to avoid over-refinement? Should I trust the electron-density map of the refined mtz data, or should I adjust the local geometries using Coot rotamers tools? How to set a reasonable B-factor values in the refinement? Best Regards, Yuan
Re: [ccp4bb] Structure Determination combining X-ray Data and NMR
Also, there is one more information I forgot to mention---I also have the NMR assignment(HNCACB spectrum) of the protein, is it possible to combine the NMR data in my refinement? Regards, On Fri, Jan 6, 2012 at 4:14 PM, 商元 shangyuan5...@gmail.com wrote: Dear All, I have a set of 3.2A data containing only 3000 reflections. From the SAD phasing and iterative modeling and density modification, I get a preliminary structure with bad geometric conformations(~8/160 ramachandran outliers in Coot). After Phenix MLHL refinement, the geometry is still bad with (10% ramachandran outliers and 25% Rotamer outliers), and the B-factors are all too high(all between 80 to 170, average ~120), and R-factor/R-free have a value of 0.328/0.326. The poor geometry of my model and the unusual B-factors indicates there are still a lot improvement in my model. The question is, as I only have ~3000 reflections, and the atoms in the sequence is around 1000, and each atom there are 4 parameters to be refined(X,Y,Z,B-factor, assuming occupancy is 1), so how to refine my model to avoid over-refinement? Should I trust the electron-density map of the refined mtz data, or should I adjust the local geometries using Coot rotamers tools? How to set a reasonable B-factor values in the refinement? Best Regards, Yuan
[ccp4bb] Fwd: [ccp4bb] Did anyone here know how to config a local protein secondary structure prediction server?
-- Forwarded message -- From: 商元 shangyuan5...@gmail.com Date: Wed, Dec 7, 2011 at 6:41 PM Subject: Re: [ccp4bb] Did anyone here know how to config a local protein secondary structure prediction server? To: Jose Duarte jose.dua...@psi.ch Dear Jose, Thanks for you kind replies and they are very helpful. Both HSSP and consurf are based on known structures on PDB database. However, I want to scan for a certain motif, and use the conservation information as a filter to narrow down my searched results. In this case, most of these motifs exists in the linker region between domains and may not appears in the pdb database. Do you have any suggestions? Best regards, Yuan SHANG On Wed, Dec 7, 2011 at 4:31 PM, Jose Duarte jose.dua...@psi.ch wrote: HSSP has it. Have a look: http://swift.cmbi.kun.nl/swift/hssp/ also the consurf server will give you conservation values mapped to structure positions Cheers Jose On 12/07/2011 09:24 AM, 商元 wrote: By the way, do you know any available protein database with the sequence conservation annotation information included? Regards, Yuan On Sun, Dec 4, 2011 at 11:32 PM, Jose Duarte jose.dua...@psi.ch wrote: You can run psipred yourself locally by downloading the software available here: http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/ You will also require blast and a local sequence database (usually uniref90). Have a look at the README http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/README This gives you a local command line application to run psipred, not a graphical web interface. Anyway if you really want to run a lot of secondary structure prediction jobs that's really what you want. Hope this helps Jose Jose Duarte Laboratory of Biomolecular Research Paul Scherrer Institute 5232 Villigen PSI Switzerland On 12/04/2011 04:22 PM, Boaz Shaanan wrote: Hi, I would just submit your sequence to Phyre ( http://www.sbg.bio.ic.ac.uk/~phyre/). You'll get, among other good things, the secondary structure predictions, perhaps even a 3-D structure prediction, depending on the similarity of your sequence to that of known structures. Cheers, Boaz *Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710* ** ** * * -- *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of 商元 [ shangyuan5...@gmail.com] *Sent:* Sunday, December 04, 2011 2:00 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] Did anyone here know how to config a local protein secondary structure prediction server? Hi, everyone, I want to run plenty secondary structure prediction works and online prediction costs a lot of time. So I expect local software for secondary structure prediction will greatly help to my work. Has anyone ever configed such local secondary structure prediction server? Any suggestion will be welcome. Thanksregards, Yuan SHANG
[ccp4bb] Did anyone here know how to config a local protein secondary structure prediction server?
Hi, everyone, I want to run plenty secondary structure prediction works and online prediction costs a lot of time. So I expect local software for secondary structure prediction will greatly help to my work. Has anyone ever configed such local secondary structure prediction server? Any suggestion will be welcome. Thanksregards, Yuan SHANG
[ccp4bb] How to labe the stereo-view figs?
Dear members, I use stereo-view to show my structure, and label the residue name on the figs. But after labeling, the label and the residues are not in the same place from the stereo angle. Anyone know how to fix this? Regards, Yuan
[ccp4bb] Detergents to eliminate non specific aggregations
Hi, everyone, I can get my protein complex but there are some non-specific aggregation from the NMR spectra, and chaps can improve it. So, besides chaps, is there any other detergents to be used during crystal screening? All suggestions are welcome. ThanksRegards, Yuan
Re: [ccp4bb] Method to calculate the axis of an alpha helix
Dear CCP4 members, I have finally used Eleanor's idea, and it works very well. After applying SSM, we can get a rotation matrix(M), and a displacement vector N: (Xnew,Ynew,Znew)'=M*(X,Y,Z)'+N Then, from the rotation matrix M, we can get its another representative format-*quaternion number. *The quaternion number has 4 elements, the first element(w) of which represents the cosine value of half of the rotation anger, and the next 3 elements(x0,y0,z0) represent the rotation vector. That means the molecule rotates an angle of acos(w)*2*180/pi degrees around the vector (x0,y0,z0). The attached file is the matlab program i wrote to translate M into a quaternion number. That should be very easy to be translated into other language formats. Best regards, Yuan SHANG On Thu, Aug 19, 2010 at 7:34 PM, Frances C. Bernstein f...@bernstein-plus-sons.com wrote: Pete Artymiuk wrote: --- I have an old badly-written Fortran program (I wrote it for a Vax, but it still compiles and runs in g95 - isn't Fortran wonderful?) that takes Arnott Dover's polar coordinates and converts them to a helix of any required length* in PDB (or Diamond!) format. --- Wow, that is an old program! For everyone under the ago of 60 reading this list, Diamond format was the very first PDB format, used for the first 100 or so entries that we had. It was based on the output format of the Diamond real-space refinement program and each line was 132 characters long. Long lines were awkward, in some ways, to handle on computers of that time so we designed what is now known as PDB format. If you want to know more, you can look at page 9 of the September 1974 PDB Newsletter (available on the RCSB web site if you start at http://www.rcsb.org/pdb/static.do?p=general_information/news_publications/newsletters/newsletter.html#pre1999) for the format of coordinate records in the original format. The reason that I know that there were about 100 entries released in the original format is that I was the one who had to convert them all into the new PDB format in 1976. Frances Bernstein = 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 = function V=Matrix2Quat(M) tq(1)=1+M(1,1)+M(2,2)+M(3,3); tq(2)=1+M(1,1)-M(2,2)-M(3,3); tq(3)=1-M(1,1)+M(2,2)-M(3,3); tq(4)=1-M(1,1)-M(2,2)+M(3,3); j=1; QW=0; QX=0; QY=0; QZ=0; for i=1:4 if(tq(i)tq(j)) j=i; end end % check the diagonal if (j==1) %/* perform instant calculation */ QW = tq(j); QX = M(2,3)-M(3,2); QY = M(3,1)-M(1,3); QZ = M(1,2)-M(2,1); elseif (j==2) QW = M(2,3)-M(3,2); QX = tq(j); QY = M(1,2)+M(2,1); QZ = M(1,3)+M(1,3); elseif (j==3) QW = M(3,1)-M(1,3); QX = M(1,2)+M(2,1); QY = tq(j); QZ = M(2,3)+M(3,2); else QW = M(1,2)-M(2,1); QX = M(3,1)+M(1,3); QY = M(2,3)+M(3,2); QZ = tq(j); end s = sqrt(0.25/tq(j)); QW = QW*s; QX = QX*s; QY = QY*s; QZ = QZ*s; V(1,1)=QX; V(2,1)=QY; V(3,1)=QZ; V(4,1)=QW; V(5,1)=acos(QW)*2*180/pi;
Re: [ccp4bb] Method to calculate the axis of an alpha helix
Thanks, lan. For quaternions, it needs w^2+x^2+y^2+z^2=1, thus reduces variables to 3. But fortunately,(x,y,z) here only represents a direction of the rotation angle, and the absolute value of them are not that important. I think a rotation vector and the rotation angle could be a very good representation of any rotation in 3D space, and that's more directviewing than the rotation Matrix which is a Matrix, or Euler Angles, which need three rotation angles. The Exponential Map, it's too complicated, so many mathematicsBut, from the definition of q = e^v, I think they are identical. and the direction of v is identical to (x,y,z) in the quaternion. Regards, Yuan SHANG On Tue, Sep 14, 2010 at 12:09 AM, Ian Tickle ianj...@gmail.com wrote: Hi Yuan You might want to look at the 'exponential map' as an alternative to quaternions. This article evaluates all the various representations of rotations, including Eulerian angles, polar angles, rotation matrices, quaternions etc: http://webhome.cs.uvic.ca/~blob/courses/485c/notes/pdf/expmap.pdfhttp://webhome.cs.uvic.ca/%7Eblob/courses/485c/notes/pdf/expmap.pdf The advantage of the exponential map representation is that only 3 variables are used, which, as for the Eulerian polar angle representations, is exactly the number that are needed to represent an arbitrary rotation in 3-D so it's an optimally parsimonious representation. However it doesn't suffer from the well-known singularities as Eulerian polar angles (it suffers from different singularities but it's possible to sweep them under the carpet). Quaternions, as you say, require 4 variables but a constraint is needed (i.e. normalisation of the vector) to reduce it back to 3. Cheers -- Ian On Mon, Sep 13, 2010 at 4:21 PM, 商元 shangyuan5...@gmail.com wrote: Dear CCP4 members, I have finally used Eleanor's idea, and it works very well. After applying SSM, we can get a rotation matrix(M), and a displacement vector N: (Xnew,Ynew,Znew)'=M*(X,Y,Z)'+N Then, from the rotation matrix M, we can get its another representative format-quaternion number. The quaternion number has 4 elements, the first element(w) of which represents the cosine value of half of the rotation anger, and the next 3 elements(x0,y0,z0) represent the rotation vector. That means the molecule rotates an angle of acos(w)*2*180/pi degrees around the vector (x0,y0,z0). The attached file is the matlab program i wrote to translate M into a quaternion number. That should be very easy to be translated into other language formats. Best regards, Yuan SHANG On Thu, Aug 19, 2010 at 7:34 PM, Frances C. Bernstein f...@bernstein-plus-sons.com wrote: Pete Artymiuk wrote: --- I have an old badly-written Fortran program (I wrote it for a Vax, but it still compiles and runs in g95 - isn't Fortran wonderful?) that takes Arnott Dover's polar coordinates and converts them to a helix of any required length* in PDB (or Diamond!) format. --- Wow, that is an old program! For everyone under the ago of 60 reading this list, Diamond format was the very first PDB format, used for the first 100 or so entries that we had. It was based on the output format of the Diamond real-space refinement program and each line was 132 characters long. Long lines were awkward, in some ways, to handle on computers of that time so we designed what is now known as PDB format. If you want to know more, you can look at page 9 of the September 1974 PDB Newsletter (available on the RCSB web site if you start at http://www.rcsb.org/pdb/static.do?p=general_information/news_publications/newsletters/newsletter.html#pre1999 ) for the format of coordinate records in the original format. The reason that I know that there were about 100 entries released in the original format is that I was the one who had to convert them all into the new PDB format in 1976. Frances Bernstein = 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 =
[ccp4bb] Method to calculate the axis of an alpha helix
Dear all, I want to compare the conformational change of two similar structures, using one alpha helix as the reference. Then, how can I get a vector that can represent both the position and direction of the helix? Is there any well-known software can do this？ Or, should I build a cylinder model, with parameters [radius,bottom center(x1,y1,z1),top center(x1,y2,z2)], using the coordinates of C,C(alpha) and N to fit these parameters? Thanks for any suggestions Regards, Yuan SHANG
[ccp4bb] How to align a sequence to a know profile
Hello, everyone, I've a protein sequence of known domain. Based on structure alignment, I've got a alignment of those with known structures. Then how to add my sequence to the alignment?Any suggestions? Regards, Yuan SHANG
[ccp4bb] The effect of the absence of various diffraction data to the electronic density
I've seen a website where there are some dynamic pictures to show the effects of the absence of various diffraction data to the electronic density, such as the changing process of the electron density as the deletion of low-resolution data. But I can't find this website now, could anyone here also know this website? I first found that website from a CCP4BB email last winter. Thanks in advance, Yuan SHANG
[ccp4bb] A polar core
Hi all, A non-ccp4 question. I found a buried helix in my structure contains several highly conserved polar residues (as well as some hydrophobic residues) whose sidechains form extensively interhelical H-bonds with backbone atoms. I searched in pubmed try to find out some similar cases but failed. Do anyone know about this? Any suggestion or comments are also greatly welcome. Best, Yuan SHANG
