Problem refining structure, error message
Hello, I’m building a structure at the moment, and I have since removed lithium ions from structure. However, when I go to refine using phenix, I get the error message: “No atom selected: name LI and Chain F and rename LI resseq 8” I’ve tried using earlier files, prior to my addition of lithium ions and I still get the same error message. I’m using Phenix version 1.10.1-2155-000 Could anyone help me overcome this error message? Cheers, Nat _____________________________ Natalia E. Ketaren, PhD Research Associate Rout Laboratory Box 213 The Rockefeller University 1230 York Avenue New York, NY 10065 Tel: (212) 327-8136 Fax: (212) 327-7193 [email protected]mailto:[email protected] website: http://lab.rockefeller.edu/rout/ NCDIR: http://www.ncdir.org/
Hi Nat, Open your PDB file in text, remove information of Li in 'remark', save the pdb file and use it for refinement. This should work. Best, Bishal Bishal Singh, PhD student German Cancer Research Center (DKFZ) University of Heidelberg Germany From: [email protected] [[email protected]] On Behalf Of Natalia Ketaren [[email protected]] Sent: Friday, February 19, 2016 2:00 AM To: [email protected] Subject: [phenixbb] Problem refining structure, error message Hello, I’m building a structure at the moment, and I have since removed lithium ions from structure. However, when I go to refine using phenix, I get the error message: “No atom selected: name LI and Chain F and rename LI resseq 8” I’ve tried using earlier files, prior to my addition of lithium ions and I still get the same error message. I’m using Phenix version 1.10.1-2155-000 Could anyone help me overcome this error message? Cheers, Nat _____________________________ Natalia E. Ketaren, PhD Research Associate Rout Laboratory Box 213 The Rockefeller University 1230 York Avenue New York, NY 10065 Tel: (212) 327-8136 Fax: (212) 327-7193 [email protected]mailto:[email protected] website: http://lab.rockefeller.edu/rout/ NCDIR: http://www.ncdir.org/
Hi Natalia, Are you using old settings to refine your new structure? If you're using the GUI, try starting with a new job (e.g. clicking on phenix.refine instead of restoring an old job). If you're using the CLI, you can send me your parameter file (ends with .eff) and I can take a look. There could be a selection for Li that is floating around if you're using the same parameter file from and earlier job. Let me know if that doesn't work for you. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org On Thu, Feb 18, 2016 at 5:00 PM, Natalia Ketaren < [email protected]> wrote:
Hello,
I’m building a structure at the moment, and I have since removed lithium ions from structure. However, when I go to refine using phenix, I get the error message: “No atom selected: name LI and Chain F and rename LI resseq 8”
I’ve tried using earlier files, prior to my addition of lithium ions and I still get the same error message. I’m using Phenix version 1.10.1-2155-000 Could anyone help me overcome this error message?
Cheers,
Nat
_____________________________ Natalia E. Ketaren, PhD Research Associate Rout Laboratory Box 213 The Rockefeller University 1230 York Avenue New York, NY 10065
Tel: (212) 327-8136 Fax: (212) 327-7193 [email protected] website: http://lab.rockefeller.edu/rout/ NCDIR: http://www.ncdir.org/
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Something still remembers about Li.. may be a parameter file from previous run or something else... I'm actually curious to know what is that, so please post your solution once you have it. Is it really remark records?.. Pavel On 2/18/16 17:00, Natalia Ketaren wrote:
Hello,
I’m building a structure at the moment, and I have since removed lithium ions from structure. However, when I go to refine using phenix, I get the error message: “No atom selected: name LI and Chain F and rename LI resseq 8”
I’ve tried using earlier files, prior to my addition of lithium ions and I still get the same error message. I’m using Phenix version 1.10.1-2155-000 Could anyone help me overcome this error message?
Cheers,
Nat
_____________________________ Natalia E. Ketaren, PhD Research Associate Rout Laboratory Box 213 The Rockefeller University 1230 York Avenue New York, NY 10065
Tel: (212) 327-8136 Fax: (212) 327-7193 [email protected] mailto:[email protected] website: http://lab.rockefeller.edu/rout/ NCDIR: http://www.ncdir.org/
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phenix.refine does not use REMARKS. you must have somewhere the selection line.
You probably use the automatically generated metal restrains and the atom name there does not match the one in PDB.
Can you share your phenix.refine command line?
Oleg Borbulevych
-----Original Message-----
From: "Pavel Afonine"
Hello,
I’m building a structure at the moment, and I have since removed lithium ions from structure. However, when I go to refine using phenix, I get the error message: “No atom selected: name LI and Chain F and rename LI resseq 8”
I’ve tried using earlier files, prior to my addition of lithium ions and I still get the same error message. I’m using Phenix version 1.10.1-2155-000 Could anyone help me overcome this error message?
Cheers,
Nat
_____________________________ Natalia E. Ketaren, PhD Research Associate Rout Laboratory Box 213 The Rockefeller University 1230 York Avenue New York, NY 10065
Tel: (212) 327-8136 Fax: (212) 327-7193 [email protected] mailto:[email protected] website: http://lab.rockefeller.edu/rout/ NCDIR: http://www.ncdir.org/
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]
phenix.refine does not use REMARKS.
Actually it uses some information from REMARK records (if it finds it and validates it is good, otherwise continues), such as TLS selections, twin operator, perhaps something else which I forgot. Recently it started outputting LINK records for internally generated extra restraints, such as metal coordination or ligand linking. I can't remember if we read them back and if we do what happens if LINK defines nonexistent (obsolete) atoms. Pavel
Thank you everyone for all your helpful suggestion! Easily my favorite message board!
What solved the error was Georg’s suggestion, being to got to the ‘Utilities’ menu and selecting ‘clear custom selections’.
Happy weekend!
Nat
_____________________________
Natalia E. Ketaren, PhD
Research Associate
Rout Laboratory
Box 213
The Rockefeller University
1230 York Avenue
New York, NY 10065
Tel: (212) 327-8136
Fax: (212) 327-7193
[email protected]mailto:[email protected]
website: http://lab.rockefeller.edu/rout/
NCDIR: http://www.ncdir.org/
On Feb 18, 2016, at 9:26 PM, Pavel Afonine
Just to answer Pavel, the only reading of LINK records is done by an
obsolete script for converting them to .edits.
Cheers
Nigel
---
Nigel W. Moriarty
Building 33R0349, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : [email protected]
Fax : 510-486-5909 Web : CCI.LBL.gov
On Thu, Feb 18, 2016 at 6:26 PM, Pavel Afonine
phenix.refine does not use REMARKS.
Actually it uses some information from REMARK records (if it finds it and validates it is good, otherwise continues), such as TLS selections, twin operator, perhaps something else which I forgot.
Recently it started outputting LINK records for internally generated extra restraints, such as metal coordination or ligand linking. I can't remember if we read them back and if we do what happens if LINK defines nonexistent (obsolete) atoms.
Pavel
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participants (6)
-
Billy Poon -
Natalia Ketaren -
Nigel Moriarty -
oleg＠quantumbioinc.com -
Pavel Afonine -
Singh, Bishal