Hi, Got some questions in using phenix.refine. 1) Can phenix.refine use the ligand library generated by refmac5? 2) How do I use elbow to generate the ligand library when I have more than one kind of ligands? When I used --residue=xxx more than once, elbow will only generated library for the last ligand. If I use elbow multiple times to generate multiple libraries, how do I read the libraries in? Should I combine them to one file? 3) When I ran phenix.refine, I found the following message in the log. Number of residues, atoms: 32, 418 Unusual residues: {'NAG': 22, 'MAN': 10} Classifications: {'undetermined': 32} Link IDs: {None: 31} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 32 Number of residues, atoms: 18, 28 Unusual residues: {'GOL': 2, ' MG': 2, ' CA': 14} Classifications: {'undetermined': 18} Link IDs: {None: 17} I already gave the cif library for NAG. Looks like nothing happened. How come phenix.refine doesn't recognize Glycerol, Mg, and Ca? 4) The refinement (TLS + ML + B individual) went through, I got reasonable R, Rfree, rmsdBOND, rmsdANGLE. But the B factors are pretty low. The B factor of the backbone is much lower than the side chain, some have numbers like 4. Some metal atoms also have B factors around 4. What did I do wrong? Thanks. Jianghai
Jianghi I can answer some of your questions. See below. Jianghai Zhu wrote:
Hi,
Got some questions in using phenix.refine.
1) Can phenix.refine use the ligand library generated by refmac5?
Yes, it should.
2) How do I use elbow to generate the ligand library when I have more than one kind of ligands? When I used --residue=xxx more than once, elbow will only generated library for the last ligand. If I use elbow multiple times to generate multiple libraries, how do I read the libraries in? Should I combine them to one file?
If you have a more recent version of eLBOW you can create a single restraints file for a single PDB file thus elbow.builder protein_and_ligands.pdb --do-all --opt In older versions, you should be able to elbow.builder protein_and_ligands.pdb --residue=LG1,LG2,LG3 --opt to generate the residues you desire. Use elbow.join_cif_files to combine single CIF files into one file. To read more than one CIF file into phenix.refine simply add the file names to the command line phenix.refine filename.pdb filename.mtz ligand1.cif ligand2.cif
3) When I ran phenix.refine, I found the following message in the log.
Number of residues, atoms: 32, 418 Unusual residues: {'NAG': 22, 'MAN': 10} Classifications: {'undetermined': 32} Link IDs: {None: 31} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 32 Number of residues, atoms: 18, 28 Unusual residues: {'GOL': 2, ' MG': 2, ' CA': 14} Classifications: {'undetermined': 18} Link IDs: {None: 17}
I already gave the cif library for NAG. Looks like nothing happened. How come phenix.refine doesn't recognize Glycerol, Mg, and Ca?
The most recent version of phenix.refine will recognise the single metal atoms but currently you need to generate the CIF for glycerol with eLBOW. I have attached a CIF file for GOL using the standard atomic naming from the PDB MSDChem database.
4) The refinement (TLS + ML + B individual) went through, I got reasonable R, Rfree, rmsdBOND, rmsdANGLE. But the B factors are pretty low. The B factor of the backbone is much lower than the side chain, some have numbers like 4. Some metal atoms also have B factors around 4. What did I do wrong?
Thanks.
Jianghai _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Fax : 510-486-5909 Email : [email protected] Web : CCI.LBL.gov # electronic Ligand Builder and Optimisation Workbench (eLBOW) # - a module of PHENIX version 1.25b (Mon Sep 17 16:26:00 2006) # - file written: Thu Dec 14 08:55:16 2006 # # Quantum optimisation: True # Method: AM1 # SMILES string: OCC(O)CO # Template file: /net/cci/filer1/share/rdb_resources/hicup/g/gol_clean.pdb # data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level LIG LIG 'Unknown ' ligand 14 6 . # data_comp_LIG # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z LIG O1 O OH1 . 0.0208 0.0709 0.0355 LIG C1 C CH2 . 1.4325 -0.0011 0.0109 LIG C2 C CH1 . 1.9132 0.0138 1.4647 LIG O2 O OH1 . 1.3682 -1.1074 2.1354 LIG C3 C CH2 . 3.4402 -0.1109 1.4474 LIG O3 O OH1 . 3.8600 -0.1930 2.7956 LIG 1H01 H HOH1 . -0.2646 0.0606 -0.8845 LIG 1H02 H HCH2 . 1.8594 0.8904 -0.5225 LIG 2H02 H HCH2 . 1.7739 -0.9421 -0.4960 LIG 1H03 H HCH1 . 1.6018 0.9730 1.9593 LIG 1H04 H HOH1 . 0.9761 -0.7765 2.9506 LIG 1H05 H HCH2 . 3.8935 0.7878 0.9507 LIG 2H05 H HCH2 . 3.7316 -1.0360 0.8822 LIG 1H06 H HOH1 . 4.8200 -0.2706 2.7757 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd LIG C1 O1 single 1.41370 0.02 LIG C2 C1 single 1.53131 0.02 LIG O2 C2 single 1.41559 0.02 LIG C3 C2 single 1.53210 0.02 LIG O3 C3 single 1.41441 0.02 LIG 1H01 O1 single 0.96335 0.02 LIG 1H02 C1 single 1.12320 0.02 LIG 2H02 C1 single 1.12196 0.02 LIG 1H03 C2 single 1.12330 0.02 LIG 1H04 O2 single 0.96319 0.02 LIG 1H05 C3 single 1.12248 0.02 LIG 2H05 C3 single 1.12263 0.02 LIG 1H06 O3 single 0.96326 0.02 # loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd LIG C2 C1 O1 107.24269 3.0 LIG 1H02 C1 O1 110.32761 3.0 LIG 2H02 C1 O1 110.75942 3.0 LIG 1H01 O1 C1 106.18066 3.0 LIG O2 C2 C1 108.73907 3.0 LIG C3 C2 C1 107.54137 3.0 LIG 1H03 C2 C1 109.83557 3.0 LIG 1H02 C1 C2 108.89201 3.0 LIG 2H02 C1 C2 109.97070 3.0 LIG 1H04 O2 C2 106.59896 3.0 LIG O3 C3 C2 106.84813 3.0 LIG 1H05 C3 C2 110.01935 3.0 LIG 2H05 C3 C2 109.35677 3.0 LIG C3 C2 O2 108.94178 3.0 LIG 1H03 C2 O2 111.15686 3.0 LIG 1H03 C2 C3 110.53511 3.0 LIG 1H06 O3 C3 106.30838 3.0 LIG 1H05 C3 O3 110.39062 3.0 LIG 2H05 C3 O3 110.79298 3.0 LIG 2H02 C1 1H02 109.60233 3.0 LIG 2H05 C3 1H05 109.39863 3.0 # loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period LIG Var_01 O2 C2 C1 O1 60.33884 10.0 1 LIG Var_02 C3 C2 C1 O1 178.16082 10.0 1 LIG Var_03 O3 C3 C2 C1 -175.86192 10.0 1 LIG Var_04 O3 C3 C2 O2 -58.17137 10.0 1
4) The refinement (TLS + ML + B individual) went through, I got reasonable R, Rfree, rmsdBOND, rmsdANGLE. But the B factors are pretty low. The B factor of the backbone is much lower than the side chain, some have numbers like 4. Some metal atoms also have B factors around 4. What did I do wrong?
What is the resolution of your data? Backbone B-s usually are lower than the main chain. What is the Wilson B value reported by phenix.refine? You could re-refine and randomize all B-values and see what happens (I have to get back to you to to get the exact command for this). Maybe it is useful to obtain a copy of the latest verison of phenix.refine by downloading cci_apps from our server http://www.phenix-online.org. If your B-values still come out lowish, try growing crystals that do not diffract very well, that usually does the trick. HTH Peter
The resolution is 2.5 A. The wilson B is about 50. I know B factor of the backbone is lower than that of the sidechian. But a B factor like 4 is definitely wrong. Jianghai On Dec 14, 2006, at 12:11 PM, Peter Zwart wrote:
4) The refinement (TLS + ML + B individual) went through, I got reasonable R, Rfree, rmsdBOND, rmsdANGLE. But the B factors are pretty low. The B factor of the backbone is much lower than the side chain, some have numbers like 4. Some metal atoms also have B factors around 4. What did I do wrong?
What is the resolution of your data?
Backbone B-s usually are lower than the main chain.
What is the Wilson B value reported by phenix.refine? You could re-refine and randomize all B-values and see what happens (I have to get back to you to to get the exact command for this). Maybe it is useful to obtain a copy of the latest verison of phenix.refine by downloading cci_apps from our server http://www.phenix-online.org.
If your B-values still come out lowish, try growing crystals that do not diffract very well, that usually does the trick.
HTH
Peter
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Hi Jianghai, could you please send us .log file from your refinement run, so we can analyze what's going on. In general, "bad" B-factors can be: - misplaced model; - inadequate TLS model (= domains chosen for TLS do not correspond to the reality). If you are using like 2 months old or older version of phenix.refine, you may want to get the latest CCI APPS since we made lots of improvements. Just goto http://www.phenix-online.org/download/cci_apps/ Pavel. Jianghai Zhu wrote:
The resolution is 2.5 A. The wilson B is about 50. I know B factor of the backbone is lower than that of the sidechian. But a B factor like 4 is definitely wrong.
Jianghai
On Dec 14, 2006, at 12:11 PM, Peter Zwart wrote:
4) The refinement (TLS + ML + B individual) went through, I got reasonable R, Rfree, rmsdBOND, rmsdANGLE. But the B factors are pretty low. The B factor of the backbone is much lower than the side chain, some have numbers like 4. Some metal atoms also have B factors around 4. What did I do wrong?
What is the resolution of your data?
Backbone B-s usually are lower than the main chain.
What is the Wilson B value reported by phenix.refine? You could re-refine and randomize all B-values and see what happens (I have to get back to you to to get the exact command for this). Maybe it is useful to obtain a copy of the latest verison of phenix.refine by downloading cci_apps from our server http://www.phenix-online.org.
If your B-values still come out lowish, try growing crystals that do not diffract very well, that usually does the trick.
HTH
Peter
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------------------------------------------------------------------------
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Hi, I am trying to use phenix.hyss to find 50 Se sites from my MAD data. Phenix.hyss has been running for more than 24 hrs now and is still going. I have 4 GB memories on my workstation. Phenix.hyss used more 95% of it and makes the machine basically unusable now. Is it normal for phenix.hyss to use so much memories? I am using Phenix 1.24.1b. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++
Hi Jianghai, Maybe Ralf will reply to you too, but this sounds way too long. Have a look at the output of hyss...and compare with the one below: A good output: f = peaklist index in two-site translation function cc = correlation coefficient after extrapolation scan r = number of dual-space recycling cycles cc = final correlation coefficient ... p=001 f=001 cc=0.088 r=010 cc=0.127 [ best cc: 0.144 ] p=001 f=002 cc=0.079 r=010 cc=0.138 [ best cc: 0.144 0.138 ] Number of matching sites of top 2 structures: 2 p=002 f=000 cc=0.074 r=010 cc=0.141 [ best cc: 0.144 0.141 ] Number of matching sites of top 2 structures: 2 ... p=010 f=001 cc=0.085 r=010 cc=0.119 [ best cc: 0.333 ] p=010 f=002 cc=0.110 r=010 cc=0.339 [ best cc: 0.339 0.333 ] Number of matching sites of top 2 structures: 45 A bad one would look just like this good one except there would be a long list of correlations, and none would be very high. An ok correlation is 0.3, good is 0.4 or more bad is 0.2 or less. The run above with 50 sites took 11 minutes... -Tom T At 08:48 AM 1/17/2007, you wrote:
Hi,
I am trying to use phenix.hyss to find 50 Se sites from my MAD data. Phenix.hyss has been running for more than 24 hrs now and is still going. I have 4 GB memories on my workstation. Phenix.hyss used more 95% of it and makes the machine basically unusable now. Is it normal for phenix.hyss to use so much memories? I am using Phenix 1.24.1b.
Jianghai
+++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
Hi Tom, Thanks for the response. It doesn't look like hyss has found anything. So far what I got is as following. p=016 f=000 cc=0.050 r=010 cc=0.094 [ best cc: 0.107 0.106 ] p=016 f=001 cc=0.056 r=010 cc=0.090 [ best cc: 0.107 0.106 ] ... I didn't get any good CC. How to get hyss to find a heavy atom cluster, i.e. tantalum bromide clusters? Jianghai On Jan 17, 2007, at 11:33 AM, Tom Terwilliger wrote:
Hi Jianghai, Maybe Ralf will reply to you too, but this sounds way too long. Have a look at the output of hyss...and compare with the one below:
A good output:
f = peaklist index in two-site translation function cc = correlation coefficient after extrapolation scan r = number of dual-space recycling cycles cc = final correlation coefficient ... p=001 f=001 cc=0.088 r=010 cc=0.127 [ best cc: 0.144 ] p=001 f=002 cc=0.079 r=010 cc=0.138 [ best cc: 0.144 0.138 ] Number of matching sites of top 2 structures: 2 p=002 f=000 cc=0.074 r=010 cc=0.141 [ best cc: 0.144 0.141 ] Number of matching sites of top 2 structures: 2 ... p=010 f=001 cc=0.085 r=010 cc=0.119 [ best cc: 0.333 ] p=010 f=002 cc=0.110 r=010 cc=0.339 [ best cc: 0.339 0.333 ] Number of matching sites of top 2 structures: 45
A bad one would look just like this good one except there would be a long list of correlations, and none would be very high. An ok correlation is 0.3, good is 0.4 or more bad is 0.2 or less.
The run above with 50 sites took 11 minutes... -Tom T
At 08:48 AM 1/17/2007, you wrote:
Hi,
I am trying to use phenix.hyss to find 50 Se sites from my MAD data. Phenix.hyss has been running for more than 24 hrs now and is still going. I have 4 GB memories on my workstation. Phenix.hyss used more 95% of it and makes the machine basically unusable now. Is it normal for phenix.hyss to use so much memories? I am using Phenix 1.24.1b.
Jianghai
+++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545
Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http:// solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe- mbi.ucla.edu/TB
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Hi Jianghai, Yes, looks bad. For a cluster, run at low resolution. Try 4 A, then 5, then 6... -Tom T At 10:51 AM 1/17/2007, you wrote:
Hi Tom,
Thanks for the response. It doesn't look like hyss has found anything. So far what I got is as following.
p=016 f=000 cc=0.050 r=010 cc=0.094 [ best cc: 0.107 0.106 ] p=016 f=001 cc=0.056 r=010 cc=0.090 [ best cc: 0.107 0.106 ] ...
I didn't get any good CC.
How to get hyss to find a heavy atom cluster, i.e. tantalum bromide clusters?
Jianghai
On Jan 17, 2007, at 11:33 AM, Tom Terwilliger wrote:
Hi Jianghai, Maybe Ralf will reply to you too, but this sounds way too long. Have a look at the output of hyss...and compare with the one below:
A good output:
f = peaklist index in two-site translation function cc = correlation coefficient after extrapolation scan r = number of dual-space recycling cycles cc = final correlation coefficient ... p=001 f=001 cc=0.088 r=010 cc=0.127 [ best cc: 0.144 ] p=001 f=002 cc=0.079 r=010 cc=0.138 [ best cc: 0.144 0.138 ] Number of matching sites of top 2 structures: 2 p=002 f=000 cc=0.074 r=010 cc=0.141 [ best cc: 0.144 0.141 ] Number of matching sites of top 2 structures: 2 ... p=010 f=001 cc=0.085 r=010 cc=0.119 [ best cc: 0.333 ] p=010 f=002 cc=0.110 r=010 cc=0.339 [ best cc: 0.339 0.333 ] Number of matching sites of top 2 structures: 45
A bad one would look just like this good one except there would be a long list of correlations, and none would be very high. An ok correlation is 0.3, good is 0.4 or more bad is 0.2 or less.
The run above with 50 sites took 11 minutes... -Tom T
At 08:48 AM 1/17/2007, you wrote:
Hi,
I am trying to use phenix.hyss to find 50 Se sites from my MAD data. Phenix.hyss has been running for more than 24 hrs now and is still going. I have 4 GB memories on my workstation. Phenix.hyss used more 95% of it and makes the machine basically unusable now. Is it normal for phenix.hyss to use so much memories? I am using Phenix 1.24.1b.
Jianghai
+++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++
_______________________________________________ phenixbb mailing list mailto:[email protected][email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545
Tel: 505-667-0072 email: mailto:[email protected][email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.govhttp://solve.lanl.gov PHENIX web site: http:www.phenix-online.orghttp:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.eduhttp://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TBhttp://www.doe-mbi.ucla.edu/TB
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_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
Hi Tom, What element_symbol should I use for tantalum bromide cluster? just "Ta"? How does hyss know it is a cluster, not a single atom? Jianghai On Jan 17, 2007, at 1:13 PM, Tom Terwilliger wrote:
Hi Jianghai, Yes, looks bad. For a cluster, run at low resolution. Try 4 A, then 5, then 6... -Tom T
At 10:51 AM 1/17/2007, you wrote:
Hi Tom,
Thanks for the response. It doesn't look like hyss has found anything. So far what I got is as following.
p=016 f=000 cc=0.050 r=010 cc=0.094 [ best cc: 0.107 0.106 ] p=016 f=001 cc=0.056 r=010 cc=0.090 [ best cc: 0.107 0.106 ] ...
I didn't get any good CC.
How to get hyss to find a heavy atom cluster, i.e. tantalum bromide clusters?
Jianghai
On Jan 17, 2007, at 11:33 AM, Tom Terwilliger wrote:
Hi Jianghai, Maybe Ralf will reply to you too, but this sounds way too long. Have a look at the output of hyss...and compare with the one below:
A good output:
f = peaklist index in two-site translation function cc = correlation coefficient after extrapolation scan r = number of dual-space recycling cycles cc = final correlation coefficient ... p=001 f=001 cc=0.088 r=010 cc=0.127 [ best cc: 0.144 ] p=001 f=002 cc=0.079 r=010 cc=0.138 [ best cc: 0.144 0.138 ] Number of matching sites of top 2 structures: 2 p=002 f=000 cc=0.074 r=010 cc=0.141 [ best cc: 0.144 0.141 ] Number of matching sites of top 2 structures: 2 ... p=010 f=001 cc=0.085 r=010 cc=0.119 [ best cc: 0.333 ] p=010 f=002 cc=0.110 r=010 cc=0.339 [ best cc: 0.339 0.333 ] Number of matching sites of top 2 structures: 45
A bad one would look just like this good one except there would be a long list of correlations, and none would be very high. An ok correlation is 0.3, good is 0.4 or more bad is 0.2 or less.
The run above with 50 sites took 11 minutes... -Tom T
At 08:48 AM 1/17/2007, you wrote:
Hi,
I am trying to use phenix.hyss to find 50 Se sites from my MAD data. Phenix.hyss has been running for more than 24 hrs now and is still going. I have 4 GB memories on my workstation. Phenix.hyss used more 95% of it and makes the machine basically unusable now. Is it normal for phenix.hyss to use so much memories? I am using Phenix 1.24.1b.
Jianghai
+++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++
_______________________________________________ phenixbb mailing list mailto:[email protected][email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545
Tel: 505-667-0072 email: mailto:[email protected][email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.govhttp://solve.lanl.gov PHENIX web site: http:www.phenix-online.orghttp:www.phenix- online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.eduhttp://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TBhttp://www.doe-mbi.ucla.edu/TB
_______________________________________________ phenixbb mailing list mailto:[email protected][email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545
Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http:// solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe- mbi.ucla.edu/TB
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Hi Jianghai, I think the element doesn't make much difference here at low resolution... -Tom T
Hi Tom,
What element_symbol should I use for tantalum bromide cluster? just "Ta"? How does hyss know it is a cluster, not a single atom?
Jianghai
On Jan 17, 2007, at 1:13 PM, Tom Terwilliger wrote:
Hi Jianghai, Yes, looks bad. For a cluster, run at low resolution. Try 4 A, then 5, then 6... -Tom T
At 10:51 AM 1/17/2007, you wrote:
Hi Tom,
Thanks for the response. It doesn't look like hyss has found anything. So far what I got is as following.
p=016 f=000 cc=0.050 r=010 cc=0.094 [ best cc: 0.107 0.106 ] p=016 f=001 cc=0.056 r=010 cc=0.090 [ best cc: 0.107 0.106 ] ...
I didn't get any good CC.
How to get hyss to find a heavy atom cluster, i.e. tantalum bromide clusters?
Jianghai
On Jan 17, 2007, at 11:33 AM, Tom Terwilliger wrote:
Hi Jianghai, Maybe Ralf will reply to you too, but this sounds way too long. Have a look at the output of hyss...and compare with the one below:
A good output:
f = peaklist index in two-site translation function cc = correlation coefficient after extrapolation scan r = number of dual-space recycling cycles cc = final correlation coefficient ... p=001 f=001 cc=0.088 r=010 cc=0.127 [ best cc: 0.144 ] p=001 f=002 cc=0.079 r=010 cc=0.138 [ best cc: 0.144 0.138 ] Number of matching sites of top 2 structures: 2 p=002 f=000 cc=0.074 r=010 cc=0.141 [ best cc: 0.144 0.141 ] Number of matching sites of top 2 structures: 2 ... p=010 f=001 cc=0.085 r=010 cc=0.119 [ best cc: 0.333 ] p=010 f=002 cc=0.110 r=010 cc=0.339 [ best cc: 0.339 0.333 ] Number of matching sites of top 2 structures: 45
A bad one would look just like this good one except there would be a long list of correlations, and none would be very high. An ok correlation is 0.3, good is 0.4 or more bad is 0.2 or less.
The run above with 50 sites took 11 minutes... -Tom T
At 08:48 AM 1/17/2007, you wrote:
Hi,
I am trying to use phenix.hyss to find 50 Se sites from my MAD data. Phenix.hyss has been running for more than 24 hrs now and is still going. I have 4 GB memories on my workstation. Phenix.hyss used more 95% of it and makes the machine basically unusable now. Is it normal for phenix.hyss to use so much memories? I am using Phenix 1.24.1b.
Jianghai
+++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++
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Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545
Tel: 505-667-0072 email: mailto:[email protected][email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.govhttp://solve.lanl.gov PHENIX web site: http:www.phenix-online.orghttp:www.phenix- online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.eduhttp://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TBhttp://www.doe-mbi.ucla.edu/TB
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Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545
Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http:// solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe- mbi.ucla.edu/TB
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p=016 f=000 cc=0.050 r=010 cc=0.094 [ best cc: 0.107 0.106 ] p=016 f=001 cc=0.056 r=010 cc=0.090 [ best cc: 0.107 0.106 ]
This indeed doesn't look very promising. Do you have any reasonable anomalous differences? Check the measurability table/graph from mmtbx.xtriage or look at the anomalous correlations with iotbx.reflection_statistics. If you are looking for clusters, you might want to lower the resolution to something like 4 A or so. Do you have any native data that might do you any good? Cheers Peter
How to get hyss to find a heavy atom cluster, i.e. tantalum bromide clusters?
Jianghai
On Jan 17, 2007, at 11:33 AM, Tom Terwilliger wrote:
Hi Jianghai, Maybe Ralf will reply to you too, but this sounds way too long. Have a look at the output of hyss...and compare with the one below:
A good output:
f = peaklist index in two-site translation function cc = correlation coefficient after extrapolation scan r = number of dual-space recycling cycles cc = final correlation coefficient ... p=001 f=001 cc=0.088 r=010 cc=0.127 [ best cc: 0.144 ] p=001 f=002 cc=0.079 r=010 cc=0.138 [ best cc: 0.144 0.138 ] Number of matching sites of top 2 structures: 2 p=002 f=000 cc=0.074 r=010 cc=0.141 [ best cc: 0.144 0.141 ] Number of matching sites of top 2 structures: 2 ... p=010 f=001 cc=0.085 r=010 cc=0.119 [ best cc: 0.333 ] p=010 f=002 cc=0.110 r=010 cc=0.339 [ best cc: 0.339 0.333 ] Number of matching sites of top 2 structures: 45
A bad one would look just like this good one except there would be a long list of correlations, and none would be very high. An ok correlation is 0.3, good is 0.4 or more bad is 0.2 or less.
The run above with 50 sites took 11 minutes... -Tom T
At 08:48 AM 1/17/2007, you wrote:
Hi,
I am trying to use phenix.hyss to find 50 Se sites from my MAD data. Phenix.hyss has been running for more than 24 hrs now and is still going. I have 4 GB memories on my workstation. Phenix.hyss used more 95% of it and makes the machine basically unusable now. Is it normal for phenix.hyss to use so much memories? I am using Phenix 1.24.1b.
Jianghai
+++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++
_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545
Tel: 505-667-0072 email: [email protected] mailto:[email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
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The MAD data only goes to 4 A. I tried SOLVE and based on the CC table output from SOLVE, the anomalous signal goes to 4.3 A. I believe the cut of CC in SOLVE is 0.3. Unfortunately, the native data is not isomorphous. Jianghai On Jan 17, 2007, at 1:17 PM, Peter Zwart wrote:
p=016 f=000 cc=0.050 r=010 cc=0.094 [ best cc: 0.107 0.106 ] p=016 f=001 cc=0.056 r=010 cc=0.090 [ best cc: 0.107 0.106 ]
This indeed doesn't look very promising. Do you have any reasonable anomalous differences? Check the measurability table/graph from mmtbx.xtriage or look at the anomalous correlations with iotbx.reflection_statistics.
If you are looking for clusters, you might want to lower the resolution to something like 4 A or so. Do you have any native data that might do you any good?
Cheers
Peter
How to get hyss to find a heavy atom cluster, i.e. tantalum bromide clusters?
Jianghai
On Jan 17, 2007, at 11:33 AM, Tom Terwilliger wrote:
Hi Jianghai, Maybe Ralf will reply to you too, but this sounds way too long. Have a look at the output of hyss...and compare with the one below:
A good output:
f = peaklist index in two-site translation function cc = correlation coefficient after extrapolation scan r = number of dual-space recycling cycles cc = final correlation coefficient ... p=001 f=001 cc=0.088 r=010 cc=0.127 [ best cc: 0.144 ] p=001 f=002 cc=0.079 r=010 cc=0.138 [ best cc: 0.144 0.138 ] Number of matching sites of top 2 structures: 2 p=002 f=000 cc=0.074 r=010 cc=0.141 [ best cc: 0.144 0.141 ] Number of matching sites of top 2 structures: 2 ... p=010 f=001 cc=0.085 r=010 cc=0.119 [ best cc: 0.333 ] p=010 f=002 cc=0.110 r=010 cc=0.339 [ best cc: 0.339 0.333 ] Number of matching sites of top 2 structures: 45
A bad one would look just like this good one except there would be a long list of correlations, and none would be very high. An ok correlation is 0.3, good is 0.4 or more bad is 0.2 or less.
The run above with 50 sites took 11 minutes... -Tom T
At 08:48 AM 1/17/2007, you wrote:
Hi,
I am trying to use phenix.hyss to find 50 Se sites from my MAD data. Phenix.hyss has been running for more than 24 hrs now and is still going. I have 4 GB memories on my workstation. Phenix.hyss used more 95% of it and makes the machine basically unusable now. Is it normal for phenix.hyss to use so much memories? I am using Phenix 1.24.1b.
Jianghai
+++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++
_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545
Tel: 505-667-0072 email: [email protected] mailto:[email protected] Fax: 505-665-3024 SOLVE web site: http:// solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe- mbi.ucla.edu/TB
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Hi Jianghi, > 4) The refinement (TLS + ML + B individual) went through, I got > reasonable R, Rfree, rmsdBOND, rmsdANGLE. But the B factors are > pretty low. The B factor of the backbone is much lower than the side > chain, some have numbers like 4. Some metal atoms also have B > factors around 4. What did I do wrong? - Low B-factors are common for high resolution models, like higher 1.0A. - Also, you can get low B-factors at very low resolution, since in this case they are mostly modeled by overall B-factor (ether though TLS or by overall exponential scaling). - In rare cases side chain atoms can have lower B than corresponding main chain atoms if they are involved in H-bonding. I need more details for further diagnostics. Cheers, Pavel.
participants (6)
-
Jianghai Zhu -
Nigel W. Moriarty -
Pavel Afonine -
Peter Zwart -
Thomas C. Terwilliger -
Tom Terwilliger