Re: [ccp4bb] Superpositions: Deviation by Residue
On 11/28/2011 10:22 PM, Jacob Keller wrote: Dear Crystallographers, is there a ccp4 program--or otherwise--which can compute ca-ca distances of corresponding residues between two superposed structures? Jacob Dont you get that from SSM and lsqkab (you have to turn on - list atom distances or some such in the GUI) Eleanor
Re: [ccp4bb] Superpositions: Deviation by Residue
Dear Crystallographers, is there a ccp4 program--or otherwise--which can compute ca-ca distances of corresponding residues between two superposed structures? You mean to produce something like this? http://xray.bmc.uu.se/usf/pics/distplot_1chr.gif That can be done with LSQMAN - http://xray.bmc.uu.se/usf/lsqman_man.html#S65 Of course, there are lots of other interesting metrics and plots to assess structural differences between two models - http://xray.bmc.uu.se/usf/lsqman_man.html#H17 One of my favourite ones is the CD plot, for comparing multiple models, which looks a bit like a gel: http://xray.bmc.uu.se/usf/pics/cdplot_1ldn.gif For other options, see http://xray.bmc.uu.se/usf/lsqman_man.html#H19 --DVD ** 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] Superpositions: Deviation by Residue
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Jacob, Coot prints this information to the terminal, so you can start coot and 'tee' its output into a file. Tim On 11/28/2011 11:53 PM, Jacob Keller wrote: Let me refine my question (sorry for my lack of clarity): is there a program that will output the distances between the corresponding ca's of a superposition on a residue-by-residue basis, and not just a global RMSD value (doubtless these numbers are part of the superposition algorithm itself)? I want to plot these values as a function of residue number to show which parts of the structures deviate more or less from each other. Jacob - -- - -- 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/ iD8DBQFO1KmAUxlJ7aRr7hoRAjy0AJ0WepnWXxMHVFfAE1oSX0rQ5BV4zQCggo/N OQ67cZNE7jMPZyXL4v1zOjE= =JXFJ -END PGP SIGNATURE-
Re: [ccp4bb] Superpositions: Deviation by Residue
Dear Crystallographers, Thanks very much for all who responded to my request. Below is a compiled list of the various ways to skin this crystallographic cat! Jacob -Moleman ca plot distance-CCP4's superpose-distance matrix analysis, e.g. http://www.csb.yale.edu/userguides/datamanip/ddmp/ddmp_descrip.html, or other programs-Lsqkab, with the deltas card-If you use the MatchMaker tool in UCSF Chimera to make the superposition, it has an option to show the corresponding sequence alignment. The sequence alignment will have an RMSD header running across the top, which is a bar graph of the RMSD values. You can the alignment's Headers-Save... menu item to save the numerical values to a file if you want. OR If you already have the structures superimposed on your own, you can use Chimera's Match-Align tool to create a superposition-based sequence alignment, and do the same thing with its RMSD header.-Coot prints this information to the terminal, so you can start coot and 'tee' its output into a file.-Various fortran/homebrew programs available from individuals-LGA server: http://proteinmodel.org/AS2TS/LGA/lga.html On Tue, Nov 29, 2011 at 3:44 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Jacob, Coot prints this information to the terminal, so you can start coot and 'tee' its output into a file. Tim On 11/28/2011 11:53 PM, Jacob Keller wrote: Let me refine my question (sorry for my lack of clarity): is there a program that will output the distances between the corresponding ca's of a superposition on a residue-by-residue basis, and not just a global RMSD value (doubtless these numbers are part of the superposition algorithm itself)? I want to plot these values as a function of residue number to show which parts of the structures deviate more or less from each other. Jacob - -- - -- 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/ iD8DBQFO1KmAUxlJ7aRr7hoRAjy0AJ0WepnWXxMHVFfAE1oSX0rQ5BV4zQCggo/N OQ67cZNE7jMPZyXL4v1zOjE= =JXFJ -END PGP SIGNATURE- -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Superpositions: Deviation by Residue
I'd say you have to look into the USF toolbox e.g. Moleman2 You want to calculate rmsd's there's an option for that. Jürgen On Nov 28, 2011, at 5:22 PM, Jacob Keller wrote: Dear Crystallographers, is there a ccp4 program--or otherwise--which can compute ca-ca distances of corresponding residues between two superposed structures? Jacob -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edumailto:j-kell...@northwestern.edu *** .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://web.mac.com/bosch_lab/
Re: [ccp4bb] Superpositions: Deviation by Residue
Hi Jacob, I used Moleman to do that once (http://xray.bmc.uu.se/usf/moleman2_man.html ) The Distance LIst command is probably what you are looking for. Mario Sanches On Mon, Nov 28, 2011 at 5:22 PM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Dear Crystallographers, is there a ccp4 program--or otherwise--which can compute ca-ca distances of corresponding residues between two superposed structures? Jacob -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** -- Mario Sanches Postdoctoral Researcher Samuel Lunenfeld Research Institute Mount Sinai Hospital 600 University Ave Toronto - Ontario Canada M5G 1X5 http://ca.linkedin.com/in/mariosanches
Re: [ccp4bb] Superpositions: Deviation by Residue
Let me refine my question (sorry for my lack of clarity): is there a program that will output the distances between the corresponding ca's of a superposition on a residue-by-residue basis, and not just a global RMSD value (doubtless these numbers are part of the superposition algorithm itself)? I want to plot these values as a function of residue number to show which parts of the structures deviate more or less from each other. Jacob
Re: [ccp4bb] Superpositions: Deviation by Residue
CCP4's superpose does this. It produces a table like this, but only for residues that are used in the alignment. .-..-. |Query| Dist.(A) | Target| |-++-| | + A:ARG 10 ||H+ A:GLN 223 | | + A:ARG 11 ||H+ A:ASN 224 | |H+ A:LYS 12 | ..6.19.. |H+ A:PRO 225 | |H+ A:LYS 13 | --4.03-- |H+ A:ASN 226 | |H+ A:LYS 14 | --3.73-- |H+ A:GLN 227 | |H+ A:GLN 15 | ..4.05.. |H- A:LEU 228 | |H+ A:LYS 16 | ..3.41.. |H- A:ILE 229 | |H+ A:GLU 17 | ..1.75.. |H. A:SER 230 | |H- A:ILE 18 | ++1.97++ |H- A:LEU 231 | Thanks, Abhinav JCSG@SSRL, SLAC Phone: (650) 926-2992 Fax: (650) 926-3292 On 11/28/2011 02:53 PM, Jacob Keller wrote: Let me refine my question (sorry for my lack of clarity): is there a program that will output the distances between the corresponding ca's of a superposition on a residue-by-residue basis, and not just a global RMSD value (doubtless these numbers are part of the superposition algorithm itself)? I want to plot these values as a function of residue number to show which parts of the structures deviate more or less from each other. Jacob
Re: [ccp4bb] Superpositions: Deviation by Residue
Hi Jacob, This sounds like what you get from ddmp ( http://www.csb.yale.edu/userguides/datamanip/ddmp/ddmp_descrip.html ). Good Luck, -bob On Mon, Nov 28, 2011 at 5:22 PM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Dear Crystallographers, is there a ccp4 program--or otherwise--which can compute ca-ca distances of corresponding residues between two superposed structures? Jacob -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Superpositions: Deviation by Residue
On Nov 28, 2011, at 4:03 PM, Jacob Keller wrote: Let me refine my question (sorry for my lack of clarity): is there a program that will output the distances between the corresponding ca's of a superposition on a residue-by-residue basis, and not just a global RMSD value (doubtless these numbers are part of the superposition algorithm itself)? I want to plot these values as a function of residue number to show which parts of the structures deviate more or less from each other. If you use the MatchMaker tool in UCSF Chimera to make the superposition, it has an option to show the corresponding sequence alignment. The sequence alignment will have an RMSD header running across the top, which is a bar graph of the RMSD values. You can the alignment's Headers-Save... menu item to save the numerical values to a file if you want. If you already have the structures superimposed on your own, you can use Chimera's Match-Align tool to create a superposition-based sequence alignment, and do the same thing with its RMSD header. Some links: Chimera home page: http://www.cgl.ucsf.edu/chimera alignment tool's RMSD header: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/multalignviewer/multalignviewer.html#assessment --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Re: [ccp4bb] Superpositions: Deviation by Residue
The program: http://sb20.lbl.gov/berry/for/pdbdist2b.for does this. If you run it by the wrapper pdbd2b: echo 'Find distances greater than threshold between corresponding atoms in 2 PDB files' echo 'Usage: pdbd2b file1 file2 startres# [thresh]' pdbdist2b eof $1 $2 $3 1 $3 $4 3.0 eof then the format is: pdbd2b file1 file2 startresiduenumber threshold (set the threshold to -1 to print all distances) then it is easy to redirect the output table to a textfile which can be imported to scalc or excel for plotting. It is kind of stupid: ignores chain letters, and once it finds startresiduenumber in both files it proceeds without looking at numbers or chains, so the atoms have to be in the same order in both files. But if you have an insertion deletion you can just run twice, starting after the midmatch the second time. N GLU A 13 N GLU A 13 0.0105 CA GLU A 13 CA GLU A 13 0.0092 CB GLU A 13 CB GLU A 13 0.0186 CG GLU A 13 CG GLU A 13 0.0369 CD GLU A 13 CD GLU A 13 0.0490 OE1 GLU A 13 OE1 GLU A 13 0.0623 OE2 GLU A 13 OE2 GLU A 13 0.0494 C GLU A 13 C GLU A 13 0.0231 O GLU A 13 O GLU A 13 0.0648 N THR A 14 N THR A 14 0.0156 CA THR A 14 CA THR A 14 0.0112 CB THR A 14 CB THR A 14 0.0160 OG1 THR A 14 OG1 THR A 14 0.0164 CG2 THR A 14 CG2 THR A 14 0.0273 C THR A 14 C THR A 14 0.0157 - written for g77 but seems to compile with gfortran I need to look in Dave's calendar prog to remind me how to get command lines parameters in fortran - then can dispense with the wrapper. Jacob Keller wrote: Let me refine my question (sorry for my lack of clarity): is there a program that will output the distances between the corresponding ca's of a superposition on a residue-by-residue basis, and not just a global RMSD value (doubtless these numbers are part of the superposition algorithm itself)? I want to plot these values as a function of residue number to show which parts of the structures deviate more or less from each other. Jacob
