[ccp4bb] MoRDa update

[Alexey Vagin]

Dear MoRDa users

A new update to the package is now available. The structure solution program is 
improved and database is extended .
Both update and installation instructions are available from Morda homepage 
.

The update is also available for existing local Morda installations and can be 
installed from command line: change to installation directory (by default 
MoRDa_DB) and type ./update_morda.

MoRDa can be used online through ccp4cloud  and 
ccp4online .

Best regards
Alexey


To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] MoRDa update

[Alexey Vagin]

Dear MoRDa users

A new update to the package is now available. The structure solution program is 
improved and database is extended .
Both update and installation instructions are available from Morda homepage 
.

The update is also available for existing local Morda installations and can be 
installed from command line: change to installation directory (by default 
MoRDa_DB) and type ./update_morda.

MoRDa can be used online through ccp4cloud  and 
ccp4online .

Best regards
Alexey


To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] MoRDa update

[Alexey Vagin]

Dear MoRDa users 

A new update to the package is released. This is currently available for 
standalone MoRDa installations.

In addition to regular extension of the database, the following new features 
are added to the structure solution pipeline.

1. Multimeric search models reduced to interacting domains.

This type of models is generated if MoRDa database contains a homologous homo- 
or hetero-oligomeric structure. The domains belonging to different subunits of 
that structure but making close contacts with each other, are assembled into a 
single search model. Based on this, an ensemble model is generated if selected 
domains have other homologues in the database. Such search models are relevant 
for e.g. solution of immunoglobulin structures. (Previous MoRDa versions were 
only generating non-ensemble multimeric search models composed of complete 
chains).

2. A command line option to use a search model missing from Morda database 
(e.g. a model that has not yet been deposited in the PDB).

morda  -f file_sf -s file_seq -p my_model.pdb

morda_prep  -f file_sf -s file_seq -p my_model.pdb

If my_model.pdb contains a single polypeptide chain, an attempt will be made to 
generate ensemble models adding structures from the database. If the model 
contains DNA or RNA or more than one polypeptide chain, or is an NMR model, it 
will be used as is in MR trials.

3. A few more command line options for tweaking MR trials with a particular 
model, generated or provided by the user.

Run morda_solve  -h for details.

Both update and installation instructions are available from MoRDa homepage 
.

MoRDa can be used online through ccp4cloud  and 
ccp4online .

Best wishes

Alexey


To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] MoRDa update

[Alexey Vagin]

Dear MoRDa users 

A new update to the package is released. This is currently available for 
standalone MoRDa installations.

In addition to regular extension of the database, the following new features 
are added to the structure solution pipeline.

1. Multimeric search models reduced to interacting domains.

This type of models is generated if MoRDa database contains a homologous homo- 
or hetero-oligomeric structure. The domains belonging to different subunits of 
that structure but making close contacts with each other, are assembled into a 
single search model. Based on this, an ensemble model is generated if selected 
domains have other homologues in the database. Such search models are relevant 
for e.g. solution of immunoglobulin structures. (Previous MoRDa versions were 
only generating non-ensemble multimeric search models composed of complete 
chains).

2. A command line option to use a search model missing from Morda database 
(e.g. a model that has not yet been deposited in the PDB).

morda  -f file_sf -s file_seq -p my_model.pdb

morda_prep  -f file_sf -s file_seq -p my_model.pdb

If my_model.pdb contains a single polypeptide chain, an attempt will be made to 
generate ensemble models adding structures from the database. If the model 
contains DNA or RNA or more than one polypeptide chain, or is an NMR model, it 
will be used as is in MR trials.

3. A few more command line options for tweaking MR trials with a particular 
model, generated or provided by the user.

Run morda_solve  -h for details.

Both update and installation instructions are available from MoRDa homepage 
.

MoRDa can be used online through ccp4cloud  and 
ccp4online .

Best wishes

Alexey





To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] MoRDa update

[Alexey Vagin]

Dear MoRDa users 

A new update to the package is released. This is currently available for 
standalone MoRDa installations.

In addition to regular extension of the database, the following new features 
are added to the structure solution pipeline.

1. Multimeric search models reduced to interacting domains.

This type of models is generated if MoRDa database contains a homologous homo- 
or hetero-oligomeric structure. The domains belonging to different subunits of 
that structure but making close contacts with each other, are assembled into a 
single search model. Based on this, an ensemble model is generated if selected 
domains have other homologues in the database. Such search models are relevant 
for e.g. solution of immunoglobulin structures. (Previous MoRDa versions were 
only generating non-ensemble multimeric search models composed of complete 
chains).

2. A command line option to use a search model missing from Morda database 
(e.g. a model that has not yet been deposited in the PDB).

morda  -f file_sf -s file_seq -p my_model.pdb

morda_prep  -f file_sf -s file_seq -p my_model.pdb

If my_model.pdb contains a single polypeptide chain, an attempt will be made to 
generate ensemble models adding structures from the database. If the model 
contains DNA or RNA or more than one polypeptide chain, or is an NMR model, it 
will be used as is in MR trials.

3. A few more command line options for tweaking MR trials with a particular 
model, generated or provided by the user.

Run morda_solve  -h for details.

Both update and installation instructions are available from MoRDa homepage 
.

MoRDa can be used online through ccp4cloud  and 
ccp4online .

Best wishes

Alexey





To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] MoRDa update

[Alexey Vagin]

Dear All

MoRDa is a pipeline for molecular replacement structure solution.

A new update to the package is now available. The structure solution program is 
improved and database is extended .

Both update and installation instructions are available from Morda homepage 
.

The update is also available for existing local Morda installations and can be 
installed from command line: change to installation directory (by default 
MoRDa_DB) and type ./update_morda.

MoRDa can be used online through ccp4cloud  and 
ccp4online .

Best regards
Alexey


To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] MoRDa update

[Alexey Vagin]

Dear All

MoRDa is a pipeline for molecular replacement structure solution.

A new update to the package is now available. The structure solution program is 
improved and database is extended .

Both update and installation instructions are available from Morda homepage 
.

The update is also available for existing local Morda installations and can be 
installed from command line: change to installation directory (by default 
MoRDa_DB) and type ./update_morda.

MoRDa can be used online through ccp4cloud  and 
ccp4online .

Best regards
Alexey




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] MoRDa update

[Alexey Vagin]

Dear All

MoRDa is a pipeline for molecular replacement structure solution.

A new update to the package is now available. The structure solution program is 
improved and database is extended .

Both update and installation instructions are available from Morda homepage 
.

The update is also available for existing local Morda installations and can be 
installed from command line: change to installation directory (by default 
MoRDa_DB) and type ./update_morda.

Also Morda at ccp4online  has been updated. 

Best regards
Alexey




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] MoRDa update

[Alexey Vagin]

Dear All

MoRDa is a pipeline for molecular replacement structure solution.

A new update to the package is now available. The structure solution program is 
improved and database is extended .

Both update and installation instructions are available from Morda homepage 
.

The update is also available for existing local Morda installations and can be 
installed from command line: change to installation directory (by default 
MoRDa_DB) and type ./update_morda.

Also Morda at ccp4online  has been updated. 

Best regards
Alexey




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] MoRDa update

[Alexey Vagin]

Dear All

MoRDa is a pipeline for molecular replacement structure solution.

A new update to the package is now available. The structure solution program is 
improved and database is extended .

Both update and installation instructions are available from Morda homepage 
.

The update is also available for existing local Morda installations and can be 
installed from command line: change to installation directory (by default 
MoRDa_DB) and type ./update_morda.

Also Morda at ccp4online  has been updated. 

Best regards
Alexey




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] MoRDa update

[Alexey Vagin]

Dear All

MoRDa is a pipeline for molecular replacement structure solution.

A new update to the package is now available. The structure solution program is 
improved and database is extended .

Both update and installation instructions are available from Morda homepage 
.

The update is also available for existing local Morda installations and can be 
installed from command line: change to installation directory (by default 
MoRDa_DB) and type ./update_morda.

Also Morda at ccp4online  has been updated. 

Best regards
Alexey




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] MoRDa update

[Alexey Vagin]

Dear All

MoRDa is a pipeline for molecular replacement structure solution.

A new update to the package is now available. The structure solution program is 
improved and database is extended .

Both update and installation instructions are available from Morda homepage 
.

The update is also available for existing local Morda installations and can be 
installed from command line: change to installation directory (by default 
MoRDa_DB) and type ./update_morda.

Also Morda at ccp4online  has been updated. 

Best regards
Alexey




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] MoRDa update

[Alexey Vagin]

Dear All

MoRDa is a pipeline for molecular replacement structure solution.

A new update to the package is now available. The structure solution program is 
improved and database is extended .

Both update and installation instructions are available from Morda homepage 
.

The update is also available for existing local Morda installations and can be 
installed from command line: change to installation directory (by default 
MoRDa_DB) and type ./update_morda.

Also Morda at ccp4online  has been updated. 

Best regards
Alexey


To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] MoRDa update

[Alexey Vagin]

Dear All

MoRDa is a pipeline for molecular replacement structure solution.

A new update to the package is now available. The structure solution program is 
improved and database is extended .

Both update and installation instructions are available from Morda homepage 
.

The update is also available for existing local Morda installations and can be 
installed from command line: change to installation directory (by default 
MoRDa_DB) and type ./update_morda.

Also Morda at ccp4online  has been updated. 

Best regards
Alexey

[ccp4bb] MoRDa update

[Alexey Vagin]

Dear All

Morda at ccp4online has been updated. 
The structure solution program is improved and database is extended .

The update is also available for existing local Morda installations and can be 
installed from command line: change to installation directory (by default 
MoRDa_DB) and type ./update_morda.

Both update and installation instructions are available from Morda homepage.

Best regards
Alexey

[ccp4bb] MoRDa update

[Alexey Vagin]

Dear All

Morda at ccp4online has been updated. 
The structure solution program is improved and database is extended .

The update is also available for existing local Morda installations and can be 
installed from command line: change to installation directory (by default 
MoRDa_DB) and type ./update_morda.

Both update and installation instructions are available from Morda homepage.

Best regards
Alexey

[ccp4bb] MoRDa update

[Alexey Vagin]

Dear All

Morda at ccp4online has been updated. 
The structure solution program is improved and database is extended .

The update is also available for existing local Morda installations and can be 
installed from command line: change to installation directory (by default 
MoRDa_DB) and type ./update_morda.

Both update and installation instructions are available from Morda homepage.

Best regards
Alexey

[ccp4bb] MoRDa update

[Alexey Vagin]

Dear All

Morda at ccp4online has been updated. 
The structure solution program is improved and database is extended .

The update is also available for existing local Morda installations and can be 
installed from command line: change to installation directory (by default 
MoRDa_DB) and type ./update_morda.

Both update and installation instructions are available from Morda homepage.

Best regards
Alexey

[ccp4bb] MoRDa update

[Alexey Vagin]

Dear All

Morda at ccp4online has been updated. 
The structure solution program is improved and database is extended .

The update is also available for existing local Morda installations and can be 
installed from command line: change to installation directory (by default 
MoRDa_DB) and type ./update_morda.

Both update and installation instructions are available from Morda homepage.

Best regards
Alexey

[ccp4bb] MoRDa update

[Alexey Vagin]

Dear All

Morda at ccp4online has been updated. 
The structure solution program is improved and database is extended .

The update is also available for existing local Morda installations and can be 
installed from command line: change to installation directory (by default 
MoRDa_DB) and type ./update_morda.

Both update and installation instructions are available from Morda homepage.

Best regards
Alexey

[ccp4bb] MoRDa update

[Alexey Vagin]

Dear All

Morda at ccp4online has been updated. 
The structure solution program is improved and database is extended by about 
900 entries.

The update is also available for existing local Morda installations and can be 
installed from command line: change to installation directory (by default 
MoRDa_DB) and type ./update_morda.

Both update and installation instructions are available from Morda homepage.

Best regards
Alexey

[ccp4bb] MoRDa update

[Alexey Vagin]

Dear All

Morda at ccp4online has been updated to include 480 new  entries.

The update is also available for existing local Morda installations and can be 
installed from command line: change to installation directory (by default 
MoRDa_DB) and type ./update_morda.

Both update and installation instructions are available from Morda homepage.

Best regards
Alexey

[ccp4bb] MoRDa update

[Alexey Vagin]

Dear All

Morda at ccp4online has been updated to include 1229 new domain and 454 
multimer entries.

The update is also available for existing local Morda installations and can be 
installed from command line: change to installation directory (by default 
MoRDa_DB) and type ./update_morda.

Both update and installation instructions are available from Morda homepage.

Note: Morda update bundles have been moved to a new location on October 5 2016. 
To continue using updates for Morda installed on or before that data, please 
replace the script MoRDa_DB/update_morda with its new version from here and 
change permissions to executable. Ignore this note if you have already replaced 
the script.

Best regards
Alexey