"standard" monomer restraints - phenixbb - phenix-online.org

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"standard" monomer restraints

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wtempel

10 Jan 2018 10 Jan '18

8:34 p.m.

Hello, how/where (in the PHENIX installation tree?) can one look up target values (effective during restrained refinement in PHENIX) for specific bond lengths and angles of monomers like amino acids or nucleosides? Thanks. Wolfram Tempel

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Pavel Afonine

10 Jan 10 Jan

8:47 p.m.

Hi Wolfram,

how/where (in the PHENIX installation tree?) can one look up target values (effective during restrained refinement in PHENIX) for specific bond lengths and angles of monomers like amino acids or nucleosides?

If you know three-letter code: elbow.where_is_that_cif_file ATP or simply look at the file content directly in chem_data/mon_lib/ or in chem_data/geostd or inspect *.geo file (always created in refinemetn) that lists all restraints used in refinement. Pavel

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wtempel

10:36 p.m.

Thank you for the hints, Pavel. ideal O3'-C3' bond in *geo is 1.422, which interestingly matches C3*-O3* in `modules/chem_data/geostd/t/data_TD.cif`. `elbow.where_is_that_cif_file DT` pointed me to `${CLIB}/data/monomers/d/DT.cif`, where O3'-C3' is (now, but may be not at time of *geo generation) 1.431. How does phenix resolve which ideal values to use in the TD example? W. On Wed, Jan 10, 2018 at 3:47 PM, Pavel Afonine wrote:

Hi Wolfram,

how/where (in the PHENIX installation tree?) can one look up target values

...
(effective during restrained refinement in PHENIX) for specific bond lengths and angles of monomers like amino acids or nucleosides?

If you know three-letter code:

elbow.where_is_that_cif_file ATP

or simply look at the file content directly in

chem_data/mon_lib/ or in chem_data/geostd

or

inspect *.geo file (always created in refinemetn) that lists all restraints used in refinement.

Pavel

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Pavel Afonine

10:53 p.m.

ideal O3'-C3' bond in *geo is 1.422, which interestingly matches C3*-O3* in `modules/chem_data/geostd/t/data_TD.cif`.

This is expected. I would be worried if they didn't match. So, 1.422 is what actually used.

`elbow.where_is_that_cif_file DT` pointed me to `${CLIB}/data/monomers/d/DT.cif`, where O3'-C3' is (now, but may be not at time of *geo generation) 1.431.

What is ${CLIB} ? I'm wondering because Phenix distribution does not have "data/monomers" folders (if I remember correctly). Pavel

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wtempel

10:57 p.m.

$CCP4/lib On Wed, Jan 10, 2018 at 5:53 PM, Pavel Afonine wrote:

ideal O3'-C3' bond in *geo is 1.422, which interestingly matches C3*-O3*

...
in `modules/chem_data/geostd/t/data_TD.cif`.

This is expected. I would be worried if they didn't match. So, 1.422 is what actually used.

`elbow.where_is_that_cif_file DT` pointed me to

...
`${CLIB}/data/monomers/d/DT.cif`, where O3'-C3' is (now, but may be not at time of *geo generation) 1.431.

What is ${CLIB} ? I'm wondering because Phenix distribution does not have "data/monomers" folders (if I remember correctly).

Pavel

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Pavel Afonine

11:59 p.m.

Which is not Phenix.. So that explains the difference. Question for Nigel is: why elbow.where_is_that_cif_file pulls cif from CCP4 distribution? Pavel On 1/10/18 14:57, wtempel wrote:

$CCP4/lib

On Wed, Jan 10, 2018 at 5:53 PM, Pavel Afonine mailto:[email protected]> wrote:

ideal O3'-C3' bond in *geo is 1.422, which interestingly matches C3*-O3* in `modules/chem_data/geostd/t/data_TD.cif`.

This is expected. I would be worried if they didn't match. So, 1.422 is what actually used.

`elbow.where_is_that_cif_file DT` pointed me to `${CLIB}/data/monomers/d/DT.cif`, where O3'-C3' is (now, but may be not at time of *geo generation) 1.431.

What is ${CLIB} ? I'm wondering because Phenix distribution does not have "data/monomers" folders (if I remember correctly).

Pavel

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Nigel Moriarty

11 Jan 11 Jan

1:03 a.m.

It's possible that the code using using the CCP4 environmental variable to look for monomers. Phenix (cctbx really) does have a mechanism for looking into a user defined CCP4 library. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Wed, Jan 10, 2018 at 3:59 PM, Pavel Afonine wrote:

Which is not Phenix.. So that explains the difference.

Question for Nigel is: why elbow.where_is_that_cif_file pulls cif from CCP4 distribution?

Pavel

On 1/10/18 14:57, wtempel wrote:

$CCP4/lib

On Wed, Jan 10, 2018 at 5:53 PM, Pavel Afonine wrote:

...
ideal O3'-C3' bond in *geo is 1.422, which interestingly matches C3*-O3*

...
in `modules/chem_data/geostd/t/data_TD.cif`.

This is expected. I would be worried if they didn't match. So, 1.422 is what actually used.

`elbow.where_is_that_cif_file DT` pointed me to

...
`${CLIB}/data/monomers/d/DT.cif`, where O3'-C3' is (now, but may be not at time of *geo generation) 1.431.

What is ${CLIB} ? I'm wondering because Phenix distribution does not have "data/monomers" folders (if I remember correctly).

Pavel

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Paul Adams

1:11 a.m.

Is this intended though? I had assumed that elbow.where_is_that_cif_file command would return the cif file that Phenix would use.

On Jan 10, 2018, at 5:03 PM, Nigel Moriarty wrote:

It's possible that the code using using the CCP4 environmental variable to look for monomers. Phenix (cctbx really) does have a mechanism for looking into a user defined CCP4 library.

Cheers

Nigel

--- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

On Wed, Jan 10, 2018 at 3:59 PM, Pavel Afonine wrote: Which is not Phenix.. So that explains the difference.

Question for Nigel is: why elbow.where_is_that_cif_file pulls cif from CCP4 distribution?

Pavel

On 1/10/18 14:57, wtempel wrote:

...
$CCP4/lib

On Wed, Jan 10, 2018 at 5:53 PM, Pavel Afonine wrote:

ideal O3'-C3' bond in *geo is 1.422, which interestingly matches C3*-O3* in `modules/chem_data/geostd/t/data_TD.cif`.

This is expected. I would be worried if they didn't match. So, 1.422 is what actually used.

`elbow.where_is_that_cif_file DT` pointed me to `${CLIB}/data/monomers/d/DT.cif`, where O3'-C3' is (now, but may be not at time of *geo generation) 1.431.

What is ${CLIB} ? I'm wondering because Phenix distribution does not have "data/monomers" folders (if I remember correctly).

Pavel

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-- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 33, Room 347 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ [email protected] ][ 1-510-495-2506 ] --

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Nigel Moriarty
Paul Adams
Pavel Afonine
wtempel