Re: [ccp4bb] 3D fitting
One option would be molrep molrep -m -mx Of course it assumes that your two structures have overall similar structures and no substantial conformational changes. As the question posed, I think, it does not have solution (only approximations). Almost all programs assume either atom labeling or shape similarity (molrep assumes shape similarity). If you have connectivity and the number of atoms is small then graph matching would work fine (at least it would give correspondence between atoms and then it is just matter of calculating rotation matrix and applying it) Garib On 26 Feb 2010, at 15:11, Kevin Cowtan wrote: SSM is also available in Coot and CCP4MG of course... Eleanor Dodson wrote: would ssm serve your purpose? eleanor ebi or ccp4i Miri Hirshberg wrote: Sun., Jan. 17th 2010 EBI Greetings, I am looking for a 3D structure superposition program which takes two structures and superpose them based only on the coordinates X,Y,Z regardless of of residue/atoms name. (both files are in PDB format) Thanks Miri Dr Miri Hirshberg European Bioinformatics Institute UK PDBe - EBI -EMBL http://www.ebi.ac.uk/pdbe Phone: +44 (0) 1223 492647 FAX: +44 (0) 1223 494468
Re: [ccp4bb] 3D fitting
So it's really a non-CCP4 non-solution...
--G
On Fri, 26 Feb 2010, Pavel Afonine wrote:
On 2/26/10 8:35 AM, Gerard DVD Kleywegt wrote:
Nope - LSQMAN would still be looking for stretches of sequentially ordered
residues and would only match atoms with identical names (" CB " with " CB
", for instance).
--G
PS: Brownie points for the non-phenix solution, though!
A non-CCP4 (PHENIX) solution is:
phenix.superpose_pdbs fixed.pdb moving.pdb selection_fixed="chain A and name
XY" selection_moving="chain B and name ZX"
which is not as automated as desired since you need to define (manually,
sorry) atoms in moving and fixed structures that will be used in
superposition.
Pavel.
Best wishes,
--Gerard
**
Gerard J. Kleywegt
Dept. of Cell & Molecular Biology University of Uppsala
Biomedical Centre Box 596
SE-751 24 Uppsala SWEDEN
http://xray.bmc.uu.se/gerard/ mailto:ger...@xray.bmc.uu.se
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Re: [ccp4bb] 3D fitting
On 2/26/10 8:35 AM, Gerard DVD Kleywegt wrote:
Nope - LSQMAN would still be looking for stretches of sequentially
ordered residues and would only match atoms with identical names (" CB
" with " CB ", for instance).
--G
PS: Brownie points for the non-phenix solution, though!
A non-CCP4 (PHENIX) solution is:
phenix.superpose_pdbs fixed.pdb moving.pdb selection_fixed="chain A and
name XY" selection_moving="chain B and name ZX"
which is not as automated as desired since you need to define (manually,
sorry) atoms in moving and fixed structures that will be used in
superposition.
Pavel.
Re: [ccp4bb] 3D fitting
Nope - LSQMAN would still be looking for stretches of sequentially ordered
residues and would only match atoms with identical names (" CB " with " CB ",
for instance).
--G
PS: Brownie points for the non-phenix solution, though!
On Fri, 26 Feb 2010, J?rgen Bosch wrote:
How about LSQMAN ?
with ATOM_types Side_chain ?
That should do the trick.
J?rgen
P.S. sorry it's not really a CCP4 related program, but I use it very
frequently in conjunction with the CCP4 suite :-)
On Feb 26, 2010, at 11:22 AM, Ed Pozharski wrote:
On Fri, 2010-02-26 at 16:50 +0100, Gerard DVD Kleywegt wrote:
But it still won't solve Miri's problem. I think what she is asking
for is a
program that detects which atoms should be matched to which,
irrespective of
their names (i.e., not assuming they are called " CA ") and order
(i.e., not
nicely sequential such as amino-acid residues), and then applies the
operator
that follows from that.
How about FM option in molrep?
http://www.msg.ucsf.edu/local/programs/ccp4-6.0.2/html/molrep.html#FM
Other MR programs can be used as well, just generate FC from one model
in a suitable cell and run search with another.
HTH,
Ed.
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
-- / Lao Tse /
-
J?rgen 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/
Best wishes,
--Gerard
**
Gerard J. Kleywegt
Dept. of Cell & Molecular Biology University of Uppsala
Biomedical Centre Box 596
SE-751 24 Uppsala SWEDEN
http://xray.bmc.uu.se/gerard/ mailto:ger...@xray.bmc.uu.se
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Re: [ccp4bb] 3D fitting
No, there would still be an order involved. I think she wants to superimpose two small molecules with arbitrary atom names. So she needs a subgraph isomorphism detector without constraints on the labels and ordering of the vertices (atoms), but which is not scale-free (as we want low RMSDs as opposed to mere topological equivalence). But I'm just guessing. --Gerard On Fri, 26 Feb 2010, Soisson, Stephen M wrote: Would a simple hack, like renaming all of the atoms in each file to be 'CA' and then using a conventional alignment program work? Maybe I am caffeine deficient at the moment, but that seems worth trying. Steve -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Gerard DVD Kleywegt Sent: Friday, February 26, 2010 10:50 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] 3D fitting But it still won't solve Miri's problem. I think what she is asking for is a program that detects which atoms should be matched to which, irrespective of their names (i.e., not assuming they are called " CA ") and order (i.e., not nicely sequential such as amino-acid residues), and then applies the operator that follows from that. --dvd On Fri, 26 Feb 2010, Kevin Cowtan wrote: SSM is also available in Coot and CCP4MG of course... Eleanor Dodson wrote: would ssm serve your purpose? eleanor ebi or ccp4i Miri Hirshberg wrote: Sun., Jan. 17th 2010 EBI Greetings, I am looking for a 3D structure superposition program which takes two structures and superpose them based only on the coordinates X,Y,Z regardless of of residue/atoms name. (both files are in PDB format) Thanks Miri Dr Miri Hirshberg European Bioinformatics Institute UK PDBe - EBI -EMBL http://www.ebi.ac.uk/pdbe Phone: +44 (0) 1223 492647 FAX: +44 (0) 1223 494468 Best wishes, --Gerard ** Gerard J. Kleywegt Dept. of Cell & Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN 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. ** 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. Best wishes, --Gerard ** Gerard J. Kleywegt Dept. of Cell & Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN 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. **
Re: [ccp4bb] 3D fitting
How about LSQMAN ? with ATOM_types Side_chain ? That should do the trick. Jürgen P.S. sorry it's not really a CCP4 related program, but I use it very frequently in conjunction with the CCP4 suite :-) On Feb 26, 2010, at 11:22 AM, Ed Pozharski wrote: On Fri, 2010-02-26 at 16:50 +0100, Gerard DVD Kleywegt wrote: But it still won't solve Miri's problem. I think what she is asking for is a program that detects which atoms should be matched to which, irrespective of their names (i.e., not assuming they are called " CA ") and order (i.e., not nicely sequential such as amino-acid residues), and then applies the operator that follows from that. How about FM option in molrep? http://www.msg.ucsf.edu/local/programs/ccp4-6.0.2/html/molrep.html#FM Other MR programs can be used as well, just generate FC from one model in a suitable cell and run search with another. HTH, Ed. -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse / - 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/
Re: [ccp4bb] 3D fitting
On Fri, 2010-02-26 at 16:50 +0100, Gerard DVD Kleywegt wrote: > But it still won't solve Miri's problem. I think what she is asking > for is a > program that detects which atoms should be matched to which, > irrespective of > their names (i.e., not assuming they are called " CA ") and order > (i.e., not > nicely sequential such as amino-acid residues), and then applies the > operator > that follows from that. > > How about FM option in molrep? http://www.msg.ucsf.edu/local/programs/ccp4-6.0.2/html/molrep.html#FM Other MR programs can be used as well, just generate FC from one model in a suitable cell and run search with another. HTH, Ed. -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse /
Re: [ccp4bb] 3D fitting
Would a simple hack, like renaming all of the atoms in each file to be 'CA' and then using a conventional alignment program work? Maybe I am caffeine deficient at the moment, but that seems worth trying. Steve -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Gerard DVD Kleywegt Sent: Friday, February 26, 2010 10:50 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] 3D fitting But it still won't solve Miri's problem. I think what she is asking for is a program that detects which atoms should be matched to which, irrespective of their names (i.e., not assuming they are called " CA ") and order (i.e., not nicely sequential such as amino-acid residues), and then applies the operator that follows from that. --dvd On Fri, 26 Feb 2010, Kevin Cowtan wrote: > SSM is also available in Coot and CCP4MG of course... > > > Eleanor Dodson wrote: >> would ssm serve your purpose? >> >> eleanor >> >> ebi or ccp4i >> >> >> >> Miri Hirshberg wrote: >>> Sun., Jan. 17th 2010 >>> EBI >>> >>> Greetings, >>> >>> I am looking for a 3D structure superposition program which takes >>> two structures and superpose them based only on the coordinates X,Y,Z >>> regardless of of residue/atoms name. >>> >>> (both files are in PDB format) >>> >>> Thanks >>> Miri >>> >>> >>> Dr Miri Hirshberg >>> European Bioinformatics Institute UK >>> PDBe - EBI -EMBL >>> http://www.ebi.ac.uk/pdbe >>> >>> Phone: +44 (0) 1223 492647 >>> FAX: +44 (0) 1223 494468 >>> > Best wishes, --Gerard ** Gerard J. Kleywegt Dept. of Cell & Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN 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. ** 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] 3D fitting
Perhaps supcomb could do this: http://www.embl-hamburg.de/ExternalInfo/Research/Sax/supcomb.html Quoting Gerard DVD Kleywegt : But it still won't solve Miri's problem. I think what she is asking for is a program that detects which atoms should be matched to which, irrespective of their names (i.e., not assuming they are called " CA ") and order (i.e., not nicely sequential such as amino-acid residues), and then applies the operator that follows from that. --dvd On Fri, 26 Feb 2010, Kevin Cowtan wrote: SSM is also available in Coot and CCP4MG of course... Eleanor Dodson wrote: would ssm serve your purpose? eleanor ebi or ccp4i Miri Hirshberg wrote: Sun., Jan. 17th 2010 EBI Greetings, I am looking for a 3D structure superposition program which takes two structures and superpose them based only on the coordinates X,Y,Z regardless of of residue/atoms name. (both files are in PDB format) Thanks Miri Dr Miri Hirshberg European Bioinformatics Institute UK PDBe - EBI -EMBL http://www.ebi.ac.uk/pdbe Phone: +44 (0) 1223 492647 FAX: +44 (0) 1223 494468 Best wishes, --Gerard ** Gerard J. Kleywegt Dept. of Cell & Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN 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. ** __ S.M. Prince Phone: +44 (0)161 306 8919 Faculty of Life SciencesFAX: +44 (0)161 306 5201 Manchester Interdisciplinary Biocentre University of Manchester 131 Princess Street e-mail: steve.pri...@manchester.ac.uk Manchester M1 7DN U.K. __
Re: [ccp4bb] 3D fitting
But it still won't solve Miri's problem. I think what she is asking for is a program that detects which atoms should be matched to which, irrespective of their names (i.e., not assuming they are called " CA ") and order (i.e., not nicely sequential such as amino-acid residues), and then applies the operator that follows from that. --dvd On Fri, 26 Feb 2010, Kevin Cowtan wrote: SSM is also available in Coot and CCP4MG of course... Eleanor Dodson wrote: would ssm serve your purpose? eleanor ebi or ccp4i Miri Hirshberg wrote: Sun., Jan. 17th 2010 EBI Greetings, I am looking for a 3D structure superposition program which takes two structures and superpose them based only on the coordinates X,Y,Z regardless of of residue/atoms name. (both files are in PDB format) Thanks Miri Dr Miri Hirshberg European Bioinformatics Institute UK PDBe - EBI -EMBL http://www.ebi.ac.uk/pdbe Phone: +44 (0) 1223 492647 FAX: +44 (0) 1223 494468 Best wishes, --Gerard ** Gerard J. Kleywegt Dept. of Cell & Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN 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. **
Re: [ccp4bb] 3D fitting
SSM is also available in Coot and CCP4MG of course... Eleanor Dodson wrote: would ssm serve your purpose? eleanor ebi or ccp4i Miri Hirshberg wrote: Sun., Jan. 17th 2010 EBI Greetings, I am looking for a 3D structure superposition program which takes two structures and superpose them based only on the coordinates X,Y,Z regardless of of residue/atoms name. (both files are in PDB format) Thanks Miri Dr Miri Hirshberg European Bioinformatics Institute UK PDBe - EBI -EMBL http://www.ebi.ac.uk/pdbe Phone: +44 (0) 1223 492647 FAX: +44 (0) 1223 494468
Re: [ccp4bb] 3D fitting
would ssm serve your purpose? eleanor ebi or ccp4i Miri Hirshberg wrote: Sun., Jan. 17th 2010 EBI Greetings, I am looking for a 3D structure superposition program which takes two structures and superpose them based only on the coordinates X,Y,Z regardless of of residue/atoms name. (both files are in PDB format) Thanks Miri Dr Miri Hirshberg European Bioinformatics Institute UK PDBe - EBI -EMBL http://www.ebi.ac.uk/pdbe Phone: +44 (0) 1223 492647 FAX: +44 (0) 1223 494468
Re: [ccp4bb] 3D fitting
PISA will do that - an EBI service or available less prettily from ccp4i Eleanot Miri Hirshberg wrote: Sun., Jan. 17th 2010 EBI Greetings, I am looking for a 3D structure superposition program which takes two structures and superpose them based only on the coordinates X,Y,Z regardless of of residue/atoms name. (both files are in PDB format) Thanks Miri Dr Miri Hirshberg European Bioinformatics Institute UK PDBe - EBI -EMBL http://www.ebi.ac.uk/pdbe Phone: +44 (0) 1223 492647 FAX: +44 (0) 1223 494468
Re: [ccp4bb] 3D fitting
In ccp4i select "Coordinate utilities/Superpose" And then on the first menu select "Superpose using secondary structure matching". It will automatically superpose based on fold rather than atom alignment. (This is the same software as used at the EBI for what used to be called MSDfold). Miri Hirshberg wrote: Sun., Jan. 17th 2010 EBI Greetings, I am looking for a 3D structure superposition program which takes two structures and superpose them based only on the coordinates X,Y,Z regardless of of residue/atoms name. (both files are in PDB format) Thanks Miri Dr Miri Hirshberg European Bioinformatics Institute UK PDBe - EBI -EMBL http://www.ebi.ac.uk/pdbe Phone: +44 (0) 1223 492647 FAX: +44 (0) 1223 494468
Re: [ccp4bb] 3D fitting
The Matchmaker utility in Chimera is another good one: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html On Sun, Jan 17, 2010 at 12:54 PM, Miri Hirshberg wrote: > Sun., Jan. 17th 2010 > EBI > > Greetings, > > I am looking for a 3D structure superposition program which takes > two structures and superpose them based only on the coordinates X,Y,Z > regardless of of residue/atoms name. > > (both files are in PDB format) > > Thanks > Miri
Re: [ccp4bb] 3D fitting
Hi Miri, you can do this (and more) using a tool from PHENIX: phenix.superpose_pdbs [pdb_file_fixed] [pdb_file_moving] [parameter_file] A couple of examples: phenix.superpose_pdbs fixed.pdb moving.pdb selection_fixed="chain A and name CA" selection_moving="chain B and name CA" phenix.superpose_pdbs fixed.pdb moving.pdb More details you can find here: http://www.phenix-online.org/documentation/superpose_pdbs.htm Please let me know if you have any questions or problems using this tool. Pavel. On 1/17/10 10:54 AM, Miri Hirshberg wrote: Sun., Jan. 17th 2010 EBI Greetings, I am looking for a 3D structure superposition program which takes two structures and superpose them based only on the coordinates X,Y,Z regardless of of residue/atoms name. (both files are in PDB format) Thanks Miri Dr Miri Hirshberg European Bioinformatics Institute UK PDBe - EBI -EMBL http://www.ebi.ac.uk/pdbe Phone: +44 (0) 1223 492647 FAX: +44 (0) 1223 494468
[ccp4bb] 3D fitting
Sun., Jan. 17th 2010 EBI Greetings, I am looking for a 3D structure superposition program which takes two structures and superpose them based only on the coordinates X,Y,Z regardless of of residue/atoms name. (both files are in PDB format) Thanks Miri Dr Miri Hirshberg European Bioinformatics Institute UK PDBe - EBI -EMBL http://www.ebi.ac.uk/pdbe Phone: +44 (0) 1223 492647 FAX: +44 (0) 1223 494468
