Re: [ccp4bb] mapping sequence conservation metrics on the B factor column ...
Hi Tassos, I very much like Homolmapper: http://www.mcb.ucdavis.edu/faculty-labs/lagarias/homolmapper_home/homolmapper%20web%20page.htm You can map several conserved properties onto your structures, not just plain sequence. Best, Miguel Le 29 janv. 09 à 22:25, Anastassis Perrakis a écrit : Dear all, I was wondering what is the state of the art for this old dark art ... are there any good servers / programs that allow to easily upload your own sequence alignments or create a 'transparent' alignment (I want to see the alignment first and not a total black box) and then allow you to write out sequence conservation based either on identity or in e.g a Dayhoff matrix on the B factor column for displaying it later in eg Pymol? To be clear I do not want a structural alignment, but mapping sequence alignment of eg a family to a single structure of a family member. Thanks in advance, Tassos -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- Miguel Ortiz Lombardía Architecture et Fonction des Macromolécules Biologiques UMR6098 ( CNRS, U. de Provence, U. de la Méditerranée ) Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel : +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
Re: [ccp4bb] mapping sequence conservation metrics on the B factor column ...
I like the consurf coloring scheme the best. I forget things so I had to write down the instructions which I copied off of some website which I can't seem to find at the moment. The other program is ESPript which I've also included my cheat sheet. Mapping conservation onto your structure (ConSurf): Here we will map sequence conservation among species onto a structure so that you can visualize areas of conservation Create alignment file 1. Open your preferred internet browser and go to Clustalw (www.ebi.ac.uk/clustalw) 2. copy sequences into the "sequence box" in Clustalw The following format (FASTA) MUST be used as an input: >yeast (name followed by any text and carriage return) acgtacgtagc (sequence with or without carriage returns.) >human (next sequence name - must have unique first words) ataagtac . . . . 3. submit (you can choose to get results emailed back to you or you will be allowed to open a window containing you results) 4. Save the aln file in a place you wont forget Generating pdb file with conservation values replacing B-values Go to http://consurf.tau.ac.il/index.html How to load in pymol explanation http://consurf.tau.ac.il/gallery/1217929900/pyMOL_instructions.html this is from the web site, the key is that you have to download a consurf strip # Download the PDB_FILE updated with ConSurf's colors. (a) PDB_FILE showing Insufficient Data (b) PDB_FILE hiding Insufficient Data # Download the file consurf_new.py. # Start PyMOL. # Load the pdb file; In the PyMOL viewer window type: PyMOL>"load PDB_FILE" (no quotes) and hit return. # Run the script to define ConSurf's color; Type: PyMOL>"run consurf_new.py" (no quotes) and hit return. # Run the coloring scheme; Type this command: PyMOL>"colour_consurf" The other one I've used is ESPript Mapping conservation onto your structure (ESPript): Here we will map sequence conservation among species onto a structure so that you can visualize areas of conservation Create alignment file 1. Open your preferred internet browser and go to Clustalw (www.ebi.ac.uk/clustalw) 2. copy sequences into the "sequence box" in Clustalw (make sure your pdb sequence is the top sequence) The following format (FASTA) MUST be used as an input: >yeast (name followed by any text and carriage return) acgtacgtagc (sequence with or without carriage returns.) >human (next sequence name - must have unique first words) ataagtac . . . . 3. submit (you can choose to get results emailed back to you or you will be allowed to open a window containing you results) 4. Save the aln file in a place you wont forget Generating pdb file with conservation values replacing B-values 7. open ESPrint 2.2 http://espript.ibcp.fr/ESPript/ESPript/ i. Click on execute ii. Select expert (top EXP) iii. Browse to your aln sequence file (see figure below) iv. Two boxes will be available for you to input a pdb file (see the next page for the second pdb input) v. Browse to your pdb file in the first "Aligned Sequences" window vi. In addition you need to input the same pdb file into the bottom of the two boxes. This box maps secondary structure onto the aa sequence. If you do not input a pdb, it will map a structure prediction which can be quite useful when analyzing a sequence f an unsolved structure. There are different algorithms for calculations, choose which you think is applicable. For more information click on the question mark to get a small discussion To submit the job, return to the top of the page and click on Submit (MAKE SURE THAT THE POP-UP BLOCKER IS OFF) After a short time a new window will pop up. The BCOL [xx Kb] will have the pdb file now with conservation values in the B-value column (the other files are just your starting files The pdf [xx Kb] file will have the structure alignment in pretty colors with secondary structure predictions 8. save output pdb file (if you look at the text file, it will have conservation mapped in the B-factor column) 9. open output pdb in pymol (again-must be most recent version- 0.97) 10. show surface 11. color by B-factor fore even more fun type in cartoon putty show cartoon On 1/29/09 3:37 PM, "Nathaniel Echols" wrote: On Thu, Jan 29, 2009 at 1:25 PM, Anastassis Perrakis wrote: Dear all, I was wondering what is the state of the art for this old dark art ... are there any good servers / programs that allow to easily upload your own sequence alignments or create a 'transparent' alignment (I want to see the alignment first and not a total black box) and then allow you to write out sequence conservation based either on identity or in e.g a Dayhoff matrix on the B factor column for displaying it later in eg Pymol? To be clear I do not want a structural alignment, but mapping sequence alignment of eg a family to a single structure of a family member. ConSurf! You can submit your own Clustal alignment (the MSA program MUSCLE will also generate this file format). However, I
Re: [ccp4bb] mapping sequence conservation metrics on the B factor column ...
Dear All, Thanks to all that replied in private and in the bb! Answers are and will be 'permanently' summarized at: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/ http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Mapping_sequence_alignment_to_a_structure (a nice opportunity to create a missing chapter!) Tassos On 29 Jan 2009, at 22:39, Luca Jovine wrote: On 29 Jan 2009, at 22:25, Anastassis Perrakis wrote: Dear all, I was wondering what is the state of the art for this old dark art ... are there any good servers / programs that allow to easily upload your own sequence alignments or create a 'transparent' alignment (I want to see the alignment first and not a total black box) and then allow you to write out sequence conservation based either on identity or in e.g a Dayhoff matrix on the B factor column for displaying it later in eg Pymol? To be clear I do not want a structural alignment, but mapping sequence alignment of eg a family to a single structure of a family member. Thanks in advance, Tassos Hi Tassos, Consurf will do the job! Have a look at: http://consurf.tau.ac.il HTH, Luca Luca Jovine, Ph.D. Group Leader, Protein Crystallography Unit Karolinska Institutet Department of Biosciences and Nutrition Hälsovägen 7, SE-141 57 Huddinge, Sweden Voice: +46.(0)8.6083-301 FAX: +46.(0)8.6089-290 E-mail: luca.jov...@ki.se W3: http://jovinelab.org
Re: [ccp4bb] mapping sequence conservation metrics on the B factor column ...
AL2CO ( http://www.ncbi.nlm.nih.gov/pubmed/11524371 ) may be what you need. It takes the multiple alignment (made by user, so it isn't a black box) that must contain the sequence of your structure, and maps the positional conservation in the B-factor column of the structure. To see whether this is what you want, try: http://rnajournal.cshlp.org/content/10/11/1698/F1.expansion.html Although the image was created by Bobscript, this also works fine with Pymol. Hope this helps, Mensur At 02:25 PM 1/29/2009, Anastassis Perrakis wrote: Dear all, I was wondering what is the state of the art for this old dark art ... are there any good servers / programs that allow to easily upload your own sequence alignments or create a 'transparent' alignment (I want to see the alignment first and not a total black box) and then allow you to write out sequence conservation based either on identity or in e.g a Dayhoff matrix on the B factor column for displaying it later in eg Pymol? To be clear I do not want a structural alignment, but mapping sequence alignment of eg a family to a single structure of a family member. Thanks in advance, Tassos == | Mensur Dlakic, PhD| Tel: (406) 994-6576| | Department of Microbiology| Fax: (406) 994-4926| | Montana State University | Lab: (406) 994-6237| | 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur| | Bozeman, MT 59717-3520| E-mail: mdla...@montana.edu| ==
Re: [ccp4bb] mapping sequence conservation metrics on the B factor column ...
On Thu, Jan 29, 2009 at 1:25 PM, Anastassis Perrakis wrote: > Dear all, > I was wondering what is the state of the art for this old dark art ... are > there any good servers / programs that allow to easily upload your own > sequence alignments or create a 'transparent' alignment (I want to see the > alignment first and not a total black box) and then allow you to write out > sequence conservation based either on identity or in e.g a Dayhoff matrix on > the B factor column for displaying it later in eg Pymol? > > To be clear I do not want a structural alignment, but mapping sequence > alignment of eg a family to a single structure of a family member. > ConSurf! You can submit your own Clustal alignment (the MSA program MUSCLE will also generate this file format). However, I was never able to visualize the PDB files it generates very well in PyMOL; I ended up extracting a different, simpler type of score (integers 1-9) from the results and applying that to the B-factor column instead of the score ConSurf writes.
