Specification of chain of output atom files.

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Modeller error message

Richard Friedman

13 Mar 2003 13 Mar '03

9:07 a.m.

Dear Modellers,

How can I write a pdb file containing a chain specification?

My top file is

# Homology modelling by the MODELLER TOP routine 'model'.

INCLUDE # Include the predefined TOP routines

SET OUTPUT_CONTROL = 1 1 1 1 2 # uncomment to produce a large log file SET ALNFILE = 'monomer3.ali' # alignment filename SET KNOWNS = '1g2i' # codes of the templates SET SEQUENCE = 'prk7' # code of the target SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate)

CALL ROUTINE = 'model' # do homology modelling

My ali file is:

C; alignment >P1;1g2i structureX:1g2i:1 :A:166 :A:Protease:Pyrococcus Horikosh: 2.00:-1.00 M---KVLFLTANEFEDVELIYPYHRLKEEGHEVYIASFE-RGTITGKHGYSVKVDLTFDKVNPEE-FDALVLPGG RAPERVRLNEKAVS-IARKMFSEGKPVASICHGPQILISAGVLRGRKGTSYPGIKDDMINAG-VEWVDAEVVVDG NWVSSRVPADLYAWMREFVKLLK----------------* >P1;prk7 sequence:prk7:1 :A:189 :A:park7:human: 2.00:-1.00 MASKRALVILAKGAEEMETVIPVDVMRRAGIKVTVAGLAGKDPVQCSRDVVICPDASLEDAKKEGPYDVVVLPGG NLGAQNLSESAAVKEILKEQENRKGLIAAICAGPTALLAHEIGCGSKVTTHPLAKDKMMNGGHYTYSENRVEKDG LILTSRGPGTSFEFALAIVEALNGKEVAAQVKAPLVLKD*

I was hoping that inclusion of the chain designators in the prk7 sequence file, would produce a pdb file with the chain designators included, but that is not what had happened. How can I be sure that the output file includes the chain designation 'A' on every atom line?

Thanks and best wishes, Rich

-------------------------------------------------------------- Richard A. Friedman, PhD Associate Research Scientist Herbert Irving Comprehensive Cancer Center Oncoinformatics Core Lecturer Department of Medical Informatics Box 95, Room 130BB or P&S 1-420C Columbia University 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman@cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/

"You don't have ot do any more work to write a book. You already wrote a book. Your course notes are a book. I've seen them lying on the floor of your office. I've seen course notes used for books on everything from Math to Origami. Just hand your course notes in. Make sure you hand in the ones with the apple juice spilled on it." -Isaac Friedman, age 13

Upon Isaac's attainment of his majority I am discontinuing the quotes from him.

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Peter C. Lai

13 Mar 13 Mar

10:57 a.m.

Don't specify chain IDs in the alignments for PDBs that don't have chain IDs. Similarly, to return to a system with no chain IDs at all, strip the chain IDs out of any PDB that have chain IDs (by looking for <space>CHAINID<space>). Note that this will only work with monomeric PDBs, which is apparently what you are working with so it should work. (It worked for me).

Adding the chain ID to a pdb is tricky, but can be done with some clever perl tricks (read a line, explode the line into an array using whitespace as the delimiter, insert <space>A<space> into the appropriate element, serialize the array and write the resulting line into your new file, read next line, etc).

On Thu, Mar 13, 2003 at 12:07:53PM -0500, Richard Friedman wrote: > Dear Modellers, > > How can I write a pdb file containing a chain specification? > > My top file is > > # Homology modelling by the MODELLER TOP routine 'model'. > > INCLUDE # Include the predefined TOP routines > > SET OUTPUT_CONTROL = 1 1 1 1 2 # uncomment to produce a large log > file > SET ALNFILE = 'monomer3.ali' # alignment filename > SET KNOWNS = '1g2i' # codes of the templates > SET SEQUENCE = 'prk7' # code of the target > SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom > files > SET STARTING_MODEL= 1 # index of the first model > SET ENDING_MODEL = 1 # index of the last model > # (determines how many models to > calculate) > > CALL ROUTINE = 'model' # do homology modelling > > My ali file is: > > C; alignment > >P1;1g2i > structureX:1g2i:1 :A:166 :A:Protease:Pyrococcus Horikosh: 2.00:-1.00 > M---KVLFLTANEFEDVELIYPYHRLKEEGHEVYIASFE-RGTITGKHGYSVKVDLTFDKVNPEE-FDALVLPGG > RAPERVRLNEKAVS-IARKMFSEGKPVASICHGPQILISAGVLRGRKGTSYPGIKDDMINAG-VEWVDAEVVVDG > NWVSSRVPADLYAWMREFVKLLK----------------* > >P1;prk7 > sequence:prk7:1 :A:189 :A:park7:human: 2.00:-1.00 > MASKRALVILAKGAEEMETVIPVDVMRRAGIKVTVAGLAGKDPVQCSRDVVICPDASLEDAKKEGPYDVVVLPGG > NLGAQNLSESAAVKEILKEQENRKGLIAAICAGPTALLAHEIGCGSKVTTHPLAKDKMMNGGHYTYSENRVEKDG > LILTSRGPGTSFEFALAIVEALNGKEVAAQVKAPLVLKD* > > I was hoping that inclusion of the chain designators in the prk7 > sequence file, would produce a pdb file with the chain designators > included, but that is not what had happened. How can I be sure that the > output file includes the chain designation 'A' on every atom line? > > Thanks and best wishes, > Rich > > > > > -------------------------------------------------------------- > Richard A. Friedman, PhD > Associate Research Scientist > Herbert Irving Comprehensive Cancer Center > Oncoinformatics Core > Lecturer > Department of Medical Informatics > Box 95, Room 130BB or P&S 1-420C > Columbia University > 630 W. 168th St. > New York, NY 10032 > (212)305-6901 (5-6901) (voice) > friedman@cancercenter.columbia.edu > http://cancercenter.columbia.edu/~friedman/ > > "You don't have ot do any more work to write a book. You > already wrote a book. Your course notes are a book. I've > seen them lying on the floor of your office. I've seen > course notes used for books on everything from Math to > Origami. Just hand your course notes in. Make sure you > hand in the ones with the apple juice spilled on it." > -Isaac Friedman, age 13 > > Upon Isaac's attainment of his majority I am discontinuing > the quotes from him. > >

-- Peter C. Lai University of Connecticut Dept. of Molecular and Cell Biology Yale University School of Medicine SenseLab | Research Assistant http://cowbert.2y.net/

Richard Friedman

11:06 a.m.

Dear Peter,

My template is a homotrimer, not a monomer. I am modelling a sequence against each of the monomers in the template. I would then like to merge the 3 target monomers into a homotrimer of the target. I want to be able to write chain designations in the monomer pdb files.

I have done this with vi global change commands but hope that there is a faster way with Modeller.

Thanks and best wishes, Rich

On Thu, 13 Mar 2003, Peter C. Lai wrote:

> Don't specify chain IDs in the alignments for PDBs that don't have chain IDs. > Similarly, to return to a system with no chain IDs at all, strip > the chain IDs out of any PDB that have chain IDs (by looking for > <space>CHAINID<space>). Note that this will only work with monomeric PDBs, > which is apparently what you are working with so it should work. (It worked > for me). > > Adding the chain ID to a pdb is tricky, but can be done with some clever > perl tricks (read a line, explode the line into an array using whitespace > as the delimiter, insert <space>A<space> into the appropriate element, > serialize the array and write the resulting line into your new file, > read next line, etc). > > On Thu, Mar 13, 2003 at 12:07:53PM -0500, Richard Friedman wrote: > > Dear Modellers, > > > > How can I write a pdb file containing a chain specification? > > > > My top file is > > > > # Homology modelling by the MODELLER TOP routine 'model'. > > > > INCLUDE # Include the predefined TOP routines > > > > SET OUTPUT_CONTROL = 1 1 1 1 2 # uncomment to produce a large log > > file > > SET ALNFILE = 'monomer3.ali' # alignment filename > > SET KNOWNS = '1g2i' # codes of the templates > > SET SEQUENCE = 'prk7' # code of the target > > SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom > > files > > SET STARTING_MODEL= 1 # index of the first model > > SET ENDING_MODEL = 1 # index of the last model > > # (determines how many models to > > calculate) > > > > CALL ROUTINE = 'model' # do homology modelling > > > > My ali file is: > > > > C; alignment > > >P1;1g2i > > structureX:1g2i:1 :A:166 :A:Protease:Pyrococcus Horikosh: 2.00:-1.00 > > M---KVLFLTANEFEDVELIYPYHRLKEEGHEVYIASFE-RGTITGKHGYSVKVDLTFDKVNPEE-FDALVLPGG > > RAPERVRLNEKAVS-IARKMFSEGKPVASICHGPQILISAGVLRGRKGTSYPGIKDDMINAG-VEWVDAEVVVDG > > NWVSSRVPADLYAWMREFVKLLK----------------* > > >P1;prk7 > > sequence:prk7:1 :A:189 :A:park7:human: 2.00:-1.00 > > MASKRALVILAKGAEEMETVIPVDVMRRAGIKVTVAGLAGKDPVQCSRDVVICPDASLEDAKKEGPYDVVVLPGG > > NLGAQNLSESAAVKEILKEQENRKGLIAAICAGPTALLAHEIGCGSKVTTHPLAKDKMMNGGHYTYSENRVEKDG > > LILTSRGPGTSFEFALAIVEALNGKEVAAQVKAPLVLKD* > > > > I was hoping that inclusion of the chain designators in the prk7 > > sequence file, would produce a pdb file with the chain designators > > included, but that is not what had happened. How can I be sure that the > > output file includes the chain designation 'A' on every atom line? > > > > Thanks and best wishes, > > Rich > > > > > > > > > > -------------------------------------------------------------- > > Richard A. Friedman, PhD > > Associate Research Scientist > > Herbert Irving Comprehensive Cancer Center > > Oncoinformatics Core > > Lecturer > > Department of Medical Informatics > > Box 95, Room 130BB or P&S 1-420C > > Columbia University > > 630 W. 168th St. > > New York, NY 10032 > > (212)305-6901 (5-6901) (voice) > > friedman@cancercenter.columbia.edu > > http://cancercenter.columbia.edu/~friedman/ > > > > "You don't have ot do any more work to write a book. You > > already wrote a book. Your course notes are a book. I've > > seen them lying on the floor of your office. I've seen > > course notes used for books on everything from Math to > > Origami. Just hand your course notes in. Make sure you > > hand in the ones with the apple juice spilled on it." > > -Isaac Friedman, age 13 > > > > Upon Isaac's attainment of his majority I am discontinuing > > the quotes from him. > > > > > > -- > Peter C. Lai > University of Connecticut > Dept. of Molecular and Cell Biology > Yale University School of Medicine > SenseLab | Research Assistant > http://cowbert.2y.net/ > >

Upon Isaac's attainment of his majority I am discontinuing the quotes from him.

Tom Duncan

11:47 a.m.

Richard & Modellers -

A simple post-MODELLER solution is to use ACCELRYS's free Discovery viewer to edit the chain ID for each chain. It has a simple way to change each chain's ID; then, when you save the PDB file, a chain ID is added to each ATOM line as needed. If you're not familiar with this viewer, email me directly and I'll give you details.

Best to all,

Tom -- Thomas M Duncan Research Associate Professor Dept Biochemistry & Molecular Biology Institute for Human Performance, Rm 4311 SUNY Upstate Medical University 750 E Adams St Syracuse, NY 13210

Andrej Sali

1:14 p.m.

There are two MODELLER commands that allow some manipulkation of chain ids: RENAME_SEGMENTS and TRANSFER_RES_NUMB.

Andrej

-- Andrej Sali, Professor Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research Mission Bay Genentech Hall 600 16th Street, Suite N472D University of California, San Francisco San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier) Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4239 Email sali@salilab.org; Web http://salilab.org

> -----Original Message----- > From: owner-modeller_usage@salilab.org > [mailto:owner-modeller_usage@salilab.org] On Behalf Of > Richard Friedman > Sent: Thursday, March 13, 2003 9:08 AM > To: modeller_usage@salilab.org > Subject: Specification of chain of output atom files. > > > Dear Modellers, > > How can I write a pdb file containing a chain specification? > > My top file is > > # Homology modelling by the MODELLER TOP routine 'model'. > > INCLUDE # Include the predefined > TOP routines > > SET OUTPUT_CONTROL = 1 1 1 1 2 # uncomment to produce a large log > file > SET ALNFILE = 'monomer3.ali' # alignment filename > SET KNOWNS = '1g2i' # codes of the templates > SET SEQUENCE = 'prk7' # code of the target > SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories > for input atom files > SET STARTING_MODEL= 1 # index of the first model > SET ENDING_MODEL = 1 # index of the last model > # (determines how many models to > calculate) > > CALL ROUTINE = 'model' # do homology modelling > > My ali file is: > > C; alignment > >P1;1g2i > structureX:1g2i:1 :A:166 :A:Protease:Pyrococcus Horikosh: > 2.00:-1.00 > M---KVLFLTANEFEDVELIYPYHRLKEEGHEVYIASFE-RGTITGKHGYSVKVDLTFDKVN > PEE-FDALVLPGG > RAPERVRLNEKAVS-IARKMFSEGKPVASICHGPQILISAGVLRGRKGTSYPGIKDDMINAG > -VEWVDAEVVVDG > NWVSSRVPADLYAWMREFVKLLK----------------* > >P1;prk7 > sequence:prk7:1 :A:189 :A:park7:human: 2.00:-1.00 > MASKRALVILAKGAEEMETVIPVDVMRRAGIKVTVAGLAGKDPVQCSRDVVICPDASLEDAK > KEGPYDVVVLPGG > NLGAQNLSESAAVKEILKEQENRKGLIAAICAGPTALLAHEIGCGSKVTTHPLAKDKMMNGG > HYTYSENRVEKDG > LILTSRGPGTSFEFALAIVEALNGKEVAAQVKAPLVLKD* > > I was hoping that inclusion of the chain designators in the > prk7 sequence file, would produce a pdb file with the chain > designators included, but that is not what had happened. How > can I be sure that the output file includes the chain > designation 'A' on every atom line? > > Thanks and best wishes, > Rich > > > > > -------------------------------------------------------------- > Richard A. Friedman, PhD > Associate Research Scientist > Herbert Irving Comprehensive Cancer Center > Oncoinformatics Core > Lecturer > Department of Medical Informatics > Box 95, Room 130BB or P&S 1-420C > Columbia University > 630 W. 168th St. > New York, NY 10032 > (212)305-6901 (5-6901) (voice) friedman@cancercenter.columbia.edu > http://cancercenter.columbia.edu/~friedman/ > > "You don't have ot do any more work to write a book. You > already wrote a book. Your course notes are a book. I've seen > them lying on the floor of your office. I've seen course > notes used for books on everything from Math to Origami. Just > hand your course notes in. Make sure you hand in the ones > with the apple juice spilled on it." -Isaac Friedman, age 13 > > Upon Isaac's attainment of his majority I am discontinuing > the quotes from him. > >

Richard Friedman

2:06 p.m.

Dear Andrej and Everybody,

The only place I was able to find RENAME_SEGMENTS in the Modeller manual, December 21, 2001, was on page 85, where it is used implictly. Is it documented elsewhere in detail?

The top program that I wrote based upon my best understanding of the command was

READ_MODEL FILE = 'park7a' RENAME_SEGMENTS SEGMENT_IDS = 'A' 'I', RENUMBER_RESIDUES = 1 1 WRITE_MODEL FILE = 'park7i.atm'

It wrote a file park7i.atm but did not change the chain ID. Any suggestions would be appreciated.

Thanks and best wishes, Rich

On Thu, 13 Mar 2003, Andrej Sali wrote:

> There are two MODELLER commands that allow some manipulkation of chain ids: > RENAME_SEGMENTS and TRANSFER_RES_NUMB. > > Andrej > > -- > Andrej Sali, Professor > Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and > California Institute for Quantitative Biomedical Research > Mission Bay Genentech Hall > 600 16th Street, Suite N472D > University of California, San Francisco > San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier) > Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 > Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4239 > Email sali@salilab.org; Web http://salilab.org > > > > -----Original Message----- > > From: owner-modeller_usage@salilab.org > > [mailto:owner-modeller_usage@salilab.org] On Behalf Of > > Richard Friedman > > Sent: Thursday, March 13, 2003 9:08 AM > > To: modeller_usage@salilab.org > > Subject: Specification of chain of output atom files. > > > > > > Dear Modellers, > > > > How can I write a pdb file containing a chain specification? > > > > My top file is > > > > # Homology modelling by the MODELLER TOP routine 'model'. > > > > INCLUDE # Include the predefined > > TOP routines > > > > SET OUTPUT_CONTROL = 1 1 1 1 2 # uncomment to produce a large log > > file > > SET ALNFILE = 'monomer3.ali' # alignment filename > > SET KNOWNS = '1g2i' # codes of the templates > > SET SEQUENCE = 'prk7' # code of the target > > SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories > > for input atom files > > SET STARTING_MODEL= 1 # index of the first model > > SET ENDING_MODEL = 1 # index of the last model > > # (determines how many models to > > calculate) > > > > CALL ROUTINE = 'model' # do homology modelling > > > > My ali file is: > > > > C; alignment > > >P1;1g2i > > structureX:1g2i:1 :A:166 :A:Protease:Pyrococcus Horikosh: > > 2.00:-1.00 > > M---KVLFLTANEFEDVELIYPYHRLKEEGHEVYIASFE-RGTITGKHGYSVKVDLTFDKVN > > PEE-FDALVLPGG > > RAPERVRLNEKAVS-IARKMFSEGKPVASICHGPQILISAGVLRGRKGTSYPGIKDDMINAG > > -VEWVDAEVVVDG > > NWVSSRVPADLYAWMREFVKLLK----------------* > > >P1;prk7 > > sequence:prk7:1 :A:189 :A:park7:human: 2.00:-1.00 > > MASKRALVILAKGAEEMETVIPVDVMRRAGIKVTVAGLAGKDPVQCSRDVVICPDASLEDAK > > KEGPYDVVVLPGG > > NLGAQNLSESAAVKEILKEQENRKGLIAAICAGPTALLAHEIGCGSKVTTHPLAKDKMMNGG > > HYTYSENRVEKDG > > LILTSRGPGTSFEFALAIVEALNGKEVAAQVKAPLVLKD* > > > > I was hoping that inclusion of the chain designators in the > > prk7 sequence file, would produce a pdb file with the chain > > designators included, but that is not what had happened. How > > can I be sure that the output file includes the chain > > designation 'A' on every atom line? > > > > Thanks and best wishes, > > Rich > > > > > > > > > > -------------------------------------------------------------- > > Richard A. Friedman, PhD > > Associate Research Scientist > > Herbert Irving Comprehensive Cancer Center > > Oncoinformatics Core > > Lecturer > > Department of Medical Informatics > > Box 95, Room 130BB or P&S 1-420C > > Columbia University > > 630 W. 168th St. > > New York, NY 10032 > > (212)305-6901 (5-6901) (voice) friedman@cancercenter.columbia.edu > > http://cancercenter.columbia.edu/~friedman/ > > > > "You don't have ot do any more work to write a book. You > > already wrote a book. Your course notes are a book. I've seen > > them lying on the floor of your office. I've seen course > > notes used for books on everything from Math to Origami. Just > > hand your course notes in. Make sure you hand in the ones > > with the apple juice spilled on it." -Isaac Friedman, age 13 > > > > Upon Isaac's attainment of his majority I am discontinuing > > the quotes from him. > > > > > >

Upon Isaac's attainment of his majority I am discontinuing the quotes from him.

Andrej Sali

2:08 p.m.

Don't have the ps version of the manual handy right now, but this is the url to rename_segments

http://salilab.org/modeller/manual/node70.html

Maybe there is a problem with modeller? I'd be happy to try if you email me a tarball with all the input files.

Thank you,

Andrej

> -----Original Message----- > From: Richard Friedman [mailto:friedman@cancercenter.columbia.edu] > Sent: Thursday, March 13, 2003 2:06 PM > To: Andrej Sali > Cc: modeller_usage@salilab.org > Subject: RE: Specification of chain of output atom files. > > > Dear Andrej and Everybody, > > The only place I was able to find RENAME_SEGMENTS in > the Modeller manual, December 21, 2001, was on page 85, where > it is used implictly. Is it documented elsewhere in detail? > > The top program that I wrote based upon my best > understanding of the command was > > READ_MODEL FILE = 'park7a' > RENAME_SEGMENTS SEGMENT_IDS = 'A' 'I', RENUMBER_RESIDUES = 1 > 1 WRITE_MODEL FILE = 'park7i.atm' > > It wrote a file park7i.atm but did not change the chain ID. > Any suggestions would be appreciated. > > Thanks and best wishes, > Rich > > > > On Thu, 13 Mar 2003, Andrej Sali wrote: > > > There are two MODELLER commands that allow some > manipulkation of chain > > ids: RENAME_SEGMENTS and TRANSFER_RES_NUMB. > > > > Andrej > > > > -- > > Andrej Sali, Professor > > Departments of Biopharmaceutical Sciences and > Pharmaceutical Chemistry, and > > California Institute for Quantitative Biomedical > Research Mission > > Bay Genentech Hall 600 16th Street, Suite N472D > > University of California, San Francisco > > San Francisco, CA 94143-2240 (CA 94107 for direct delivery > by courier) > > Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 > > Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4239 > > Email sali@salilab.org; Web http://salilab.org > > > > > > > -----Original Message----- > > > From: owner-modeller_usage@salilab.org > > > [mailto:owner-modeller_usage@salilab.org] On Behalf Of Richard > > > Friedman > > > Sent: Thursday, March 13, 2003 9:08 AM > > > To: modeller_usage@salilab.org > > > Subject: Specification of chain of output atom files. > > > > > > > > > Dear Modellers, > > > > > > How can I write a pdb file containing a chain specification? > > > > > > My top file is > > > > > > # Homology modelling by the MODELLER TOP routine 'model'. > > > > > > INCLUDE # Include the predefined > > > TOP routines > > > > > > SET OUTPUT_CONTROL = 1 1 1 1 2 # uncomment to > produce a large log > > > file > > > SET ALNFILE = 'monomer3.ali' # alignment filename > > > SET KNOWNS = '1g2i' # codes of the templates > > > SET SEQUENCE = 'prk7' # code of the target > > > SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for > > > input atom files > > > SET STARTING_MODEL= 1 # index of the first model > > > SET ENDING_MODEL = 1 # index of the last model > > > # (determines how > many models to > > > calculate) > > > > > > CALL ROUTINE = 'model' # do homology modelling > > > > > > My ali file is: > > > > > > C; alignment > > > >P1;1g2i > > > structureX:1g2i:1 :A:166 :A:Protease:Pyrococcus Horikosh: > > > 2.00:-1.00 > > > M---KVLFLTANEFEDVELIYPYHRLKEEGHEVYIASFE-RGTITGKHGYSVKVDLTFDKVN > > > PEE-FDALVLPGG > > > RAPERVRLNEKAVS-IARKMFSEGKPVASICHGPQILISAGVLRGRKGTSYPGIKDDMINAG > > > -VEWVDAEVVVDG > > > NWVSSRVPADLYAWMREFVKLLK----------------* > > > >P1;prk7 > > > sequence:prk7:1 :A:189 :A:park7:human: 2.00:-1.00 > > > MASKRALVILAKGAEEMETVIPVDVMRRAGIKVTVAGLAGKDPVQCSRDVVICPDASLEDAK > > > KEGPYDVVVLPGG > > > NLGAQNLSESAAVKEILKEQENRKGLIAAICAGPTALLAHEIGCGSKVTTHPLAKDKMMNGG > > > HYTYSENRVEKDG > > > LILTSRGPGTSFEFALAIVEALNGKEVAAQVKAPLVLKD* > > > > > > I was hoping that inclusion of the chain designators in the prk7 > > > sequence file, would produce a pdb file with the chain > designators > > > included, but that is not what had happened. How can I be > sure that > > > the output file includes the chain designation 'A' on every atom > > > line? > > > > > > Thanks and best wishes, > > > Rich > > > > > > > > > > > > > > > -------------------------------------------------------------- > > > Richard A. Friedman, PhD > > > Associate Research Scientist > > > Herbert Irving Comprehensive Cancer Center > > > Oncoinformatics Core > > > Lecturer > > > Department of Medical Informatics > > > Box 95, Room 130BB or P&S 1-420C > > > Columbia University > > > 630 W. 168th St. > > > New York, NY 10032 > > > (212)305-6901 (5-6901) (voice) friedman@cancercenter.columbia.edu > > > http://cancercenter.columbia.edu/~friedman/ > > > > > > "You don't have ot do any more work to write a book. You already > > > wrote a book. Your course notes are a book. I've seen > them lying on > > > the floor of your office. I've seen course notes used for > books on > > > everything from Math to Origami. Just hand your course notes in. > > > Make sure you hand in the ones with the apple juice > spilled on it." > > > -Isaac Friedman, age 13 > > > > > > Upon Isaac's attainment of his majority I am discontinuing the > > > quotes from him. > > > > > > > > > > > > -------------------------------------------------------------- > Richard A. Friedman, PhD > Associate Research Scientist > Herbert Irving Comprehensive Cancer Center > Oncoinformatics Core > Lecturer > Department of Medical Informatics > Box 95, Room 130BB or P&S 1-420C > Columbia University > 630 W. 168th St. > New York, NY 10032 > (212)305-6901 (5-6901) (voice) friedman@cancercenter.columbia.edu > http://cancercenter.columbia.edu/~friedman/ > > "You don't have ot do any more work to write a book. You > already wrote a book. Your course notes are a book. I've seen > them lying on the floor of your office. I've seen course > notes used for books on everything from Math to Origami. Just > hand your course notes in. Make sure you hand in the ones > with the apple juice spilled on it." -Isaac Friedman, age 13 > > Upon Isaac's attainment of his majority I am discontinuing > the quotes from him. > >

Richard Friedman

14 Mar 14 Mar

5:38 a.m.

Dear Andrej,

Based on the instructions on the web page, I was able to rename the chain.

Thanks and best wishes, Rich

On Thu, 13 Mar 2003, Andrej Sali wrote:

> Don't have the ps version of the manual handy right now, but this is the url > to rename_segments > > http://salilab.org/modeller/manual/node70.html > > Maybe there is a problem with modeller? I'd be happy to try if you email me > a tarball with all the input files. > > Thank you, > > Andrej > > -- > Andrej Sali, Professor > Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and > California Institute for Quantitative Biomedical Research > Mission Bay Genentech Hall > 600 16th Street, Suite N472D > University of California, San Francisco > San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier) > Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 > Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4239 > Email sali@salilab.org; Web http://salilab.org > > > > -----Original Message----- > > From: Richard Friedman [mailto:friedman@cancercenter.columbia.edu] > > Sent: Thursday, March 13, 2003 2:06 PM > > To: Andrej Sali > > Cc: modeller_usage@salilab.org > > Subject: RE: Specification of chain of output atom files. > > > > > > Dear Andrej and Everybody, > > > > The only place I was able to find RENAME_SEGMENTS in > > the Modeller manual, December 21, 2001, was on page 85, where > > it is used implictly. Is it documented elsewhere in detail? > > > > The top program that I wrote based upon my best > > understanding of the command was > > > > READ_MODEL FILE = 'park7a' > > RENAME_SEGMENTS SEGMENT_IDS = 'A' 'I', RENUMBER_RESIDUES = 1 > > 1 WRITE_MODEL FILE = 'park7i.atm' > > > > It wrote a file park7i.atm but did not change the chain ID. > > Any suggestions would be appreciated. > > > > Thanks and best wishes, > > Rich > > > > > > > > On Thu, 13 Mar 2003, Andrej Sali wrote: > > > > > There are two MODELLER commands that allow some > > manipulkation of chain > > > ids: RENAME_SEGMENTS and TRANSFER_RES_NUMB. > > > > > > Andrej > > > > > > -- > > > Andrej Sali, Professor > > > Departments of Biopharmaceutical Sciences and > > Pharmaceutical Chemistry, and > > > California Institute for Quantitative Biomedical > > Research Mission > > > Bay Genentech Hall 600 16th Street, Suite N472D > > > University of California, San Francisco > > > San Francisco, CA 94143-2240 (CA 94107 for direct delivery > > by courier) > > > Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 > > > Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4239 > > > Email sali@salilab.org; Web http://salilab.org > > > > > > > > > > -----Original Message----- > > > > From: owner-modeller_usage@salilab.org > > > > [mailto:owner-modeller_usage@salilab.org] On Behalf Of Richard > > > > Friedman > > > > Sent: Thursday, March 13, 2003 9:08 AM > > > > To: modeller_usage@salilab.org > > > > Subject: Specification of chain of output atom files. > > > > > > > > > > > > Dear Modellers, > > > > > > > > How can I write a pdb file containing a chain specification? > > > > > > > > My top file is > > > > > > > > # Homology modelling by the MODELLER TOP routine 'model'. > > > > > > > > INCLUDE # Include the predefined > > > > TOP routines > > > > > > > > SET OUTPUT_CONTROL = 1 1 1 1 2 # uncomment to > > produce a large log > > > > file > > > > SET ALNFILE = 'monomer3.ali' # alignment filename > > > > SET KNOWNS = '1g2i' # codes of the templates > > > > SET SEQUENCE = 'prk7' # code of the target > > > > SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for > > > > input atom files > > > > SET STARTING_MODEL= 1 # index of the first model > > > > SET ENDING_MODEL = 1 # index of the last model > > > > # (determines how > > many models to > > > > calculate) > > > > > > > > CALL ROUTINE = 'model' # do homology modelling > > > > > > > > My ali file is: > > > > > > > > C; alignment > > > > >P1;1g2i > > > > structureX:1g2i:1 :A:166 :A:Protease:Pyrococcus Horikosh: > > > > 2.00:-1.00 > > > > M---KVLFLTANEFEDVELIYPYHRLKEEGHEVYIASFE-RGTITGKHGYSVKVDLTFDKVN > > > > PEE-FDALVLPGG > > > > RAPERVRLNEKAVS-IARKMFSEGKPVASICHGPQILISAGVLRGRKGTSYPGIKDDMINAG > > > > -VEWVDAEVVVDG > > > > NWVSSRVPADLYAWMREFVKLLK----------------* > > > > >P1;prk7 > > > > sequence:prk7:1 :A:189 :A:park7:human: 2.00:-1.00 > > > > MASKRALVILAKGAEEMETVIPVDVMRRAGIKVTVAGLAGKDPVQCSRDVVICPDASLEDAK > > > > KEGPYDVVVLPGG > > > > NLGAQNLSESAAVKEILKEQENRKGLIAAICAGPTALLAHEIGCGSKVTTHPLAKDKMMNGG > > > > HYTYSENRVEKDG > > > > LILTSRGPGTSFEFALAIVEALNGKEVAAQVKAPLVLKD* > > > > > > > > I was hoping that inclusion of the chain designators in the prk7 > > > > sequence file, would produce a pdb file with the chain > > designators > > > > included, but that is not what had happened. How can I be > > sure that > > > > the output file includes the chain designation 'A' on every atom > > > > line? > > > > > > > > Thanks and best wishes, > > > > Rich > > > > > > > > > > > > > > > > > > > > -------------------------------------------------------------- > > > > Richard A. Friedman, PhD > > > > Associate Research Scientist > > > > Herbert Irving Comprehensive Cancer Center > > > > Oncoinformatics Core > > > > Lecturer > > > > Department of Medical Informatics > > > > Box 95, Room 130BB or P&S 1-420C > > > > Columbia University > > > > 630 W. 168th St. > > > > New York, NY 10032 > > > > (212)305-6901 (5-6901) (voice) friedman@cancercenter.columbia.edu > > > > http://cancercenter.columbia.edu/~friedman/ > > > > > > > > "You don't have ot do any more work to write a book. You already > > > > wrote a book. Your course notes are a book. I've seen > > them lying on > > > > the floor of your office. I've seen course notes used for > > books on > > > > everything from Math to Origami. Just hand your course notes in. > > > > Make sure you hand in the ones with the apple juice > > spilled on it." > > > > -Isaac Friedman, age 13 > > > > > > > > Upon Isaac's attainment of his majority I am discontinuing the > > > > quotes from him. > > > > > > > > > > > > > > > > > > -------------------------------------------------------------- > > Richard A. Friedman, PhD > > Associate Research Scientist > > Herbert Irving Comprehensive Cancer Center > > Oncoinformatics Core > > Lecturer > > Department of Medical Informatics > > Box 95, Room 130BB or P&S 1-420C > > Columbia University > > 630 W. 168th St. > > New York, NY 10032 > > (212)305-6901 (5-6901) (voice) friedman@cancercenter.columbia.edu > > http://cancercenter.columbia.edu/~friedman/ > > > > "You don't have ot do any more work to write a book. You > > already wrote a book. Your course notes are a book. I've seen > > them lying on the floor of your office. I've seen course > > notes used for books on everything from Math to Origami. Just > > hand your course notes in. Make sure you hand in the ones > > with the apple juice spilled on it." -Isaac Friedman, age 13 > > > > Upon Isaac's attainment of his majority I am discontinuing > > the quotes from him. > > > > > >

Upon Isaac's attainment of his majority I am discontinuing the quotes from him.

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Andrej Sali
Peter C. Lai
Richard Friedman
Tom Duncan