[phenixbb] selection string for omit maps

Alexandra Deaconescu deacona at brandeis.edu
Fri Jan 28 17:33:55 PST 2011


Hi:

I am new to Phenix and I am currently using the GUI. I would like to compute a sa-omit map by leaving out residues 204-209 of my chain C.

In the GUI, what is the proper syntax for this selection string? I tried a few obvious formats but the jobs failed.

Thank you very much in advance,
Alexandra




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Subject: phenixbb Digest, Vol 62, Issue 25

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Today's Topics:

   1. Problem with loop fitting (Kendall Nettles)
   2. Re: Problem with loop fitting (Tom Terwilliger)
   3. Re: Problem with loop fitting (Kendall Nettles)
   4. Ligandfit bug report (Kendall Nettles)
   5. Re: Ligandfit bug report (Nigel Moriarty)
   6. ADP: fix_wxu and wxu_scale (fulvio saccoccia)
   7. Re: Problem with loop fitting (Tom Terwilliger)
   8. Re: ADP: fix_wxu and wxu_scale (Pavel Afonine)
   9. Re: adp values (Pavel Afonine)


----------------------------------------------------------------------

Message: 1
Date: Mon, 24 Jan 2011 15:47:02 -0500
From: Kendall Nettles <knettles at scripps.edu>
To: PHENIX user mailing list <phenixbb at phenix-online.org>
Subject: [phenixbb] Problem with loop fitting
Message-ID: <C9634F76.F559%knettles at scripps.edu>
Content-Type: text/plain; charset="iso-8859-1"

Dear PHENIX developers,
I am trying fit_loops for the first time and getting error message:
"No suitable gap found matching residues"

I'm not sure what the problem is.

Best regards,
Kendall Nettles

 knettles$ phenix.fit_loops pdb_in=Liganded_overall_best-coot-1.pdb mtz_in=cycle_best_refine_map_coeffs_1.mtz seq_file=seq.dat start=331 end=336 chain_id=A


#                       fit_loops
#
# Fit loops in a PDB file with gaps

# Type phenix.doc for help

Input sequence file is  seq.dat
Reading sequence from  seq.dat
Fit_loops: Fit a missing loop in a model.
Map from:  TEMP_cycle_best_refine_map_coeffs_1.mtz  using labin  FP=2FOFCWT PHIB=PH2FOFCWT
Model from:  Liganded_overall_best-coot-1.pdb
LABIN LINE:  FP=2FOFCWT PHIB=PH2FOFCWT


No suitable gap found matching residues  331 - 336  chain:  A
No final model obtained

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Message: 2
Date: Mon, 24 Jan 2011 14:31:46 -0700
From: Tom Terwilliger <terwilliger at lanl.gov>
To: PHENIX user mailing list <phenixbb at phenix-online.org>
Subject: Re: [phenixbb] Problem with loop fitting
Message-ID: <4AA17220-0930-4916-B521-614E750AA54A at lanl.gov>
Content-Type: text/plain; charset="windows-1252"

Hi Kendall,
Usually that would mean that there is no segment in your model that has a gap in chain A missing residues 331-336 (6-residue gap).  It could also mean that the sequence could not be aligned with your sequence file.  Is one of those possible?
-Tom T

On Jan 24, 2011, at 1:47 PM, Kendall Nettles wrote:

> Dear PHENIX developers, 
> I am trying fit_loops for the first time and getting error message: 
> ?No suitable gap found matching residues?
> 
> I?m not sure what the problem is. 
> 
> Best regards,
> Kendall Nettles
> 
>  knettles$ phenix.fit_loops pdb_in=Liganded_overall_best-coot-1.pdb mtz_in=cycle_best_refine_map_coeffs_1.mtz seq_file=seq.dat start=331 end=336 chain_id=A
> 
> 
> #                       fit_loops
> #
> # Fit loops in a PDB file with gaps
> 
> # Type phenix.doc for help
> 
> Input sequence file is  seq.dat
> Reading sequence from  seq.dat
> Fit_loops: Fit a missing loop in a model.
> Map from:  TEMP_cycle_best_refine_map_coeffs_1.mtz  using labin  FP=2FOFCWT PHIB=PH2FOFCWT 
> Model from:  Liganded_overall_best-coot-1.pdb
> LABIN LINE:  FP=2FOFCWT PHIB=PH2FOFCWT 
> 
> 
> No suitable gap found matching residues  331 - 336  chain:  A
> No final model obtained
> 
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://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: terwilliger at LANL.gov
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
CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss




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Message: 3
Date: Mon, 24 Jan 2011 16:41:18 -0500
From: Kendall Nettles <knettles at scripps.edu>
To: PHENIX user mailing list <phenixbb at phenix-online.org>
Subject: Re: [phenixbb] Problem with loop fitting
Message-ID: <C9635C2E.F56C%knettles at scripps.edu>
Content-Type: text/plain; charset="iso-8859-1"

Tom,
The gap is there, but I'm not sure if I have generated the sequence file correctly. I used a fasta format of all the amino acids in the protein construct. The first three are from the tag, and then the sequence starts at amino acid number 299. The amino acid that is first visible varies from structure to structure and between chains in the same structure, and is between 299 and 307. For the structure I tried the loop fitting it starts at 305. Should I trim the beginning of the seq file? Do I need to tailor this file for each structure I run it on?

Kendall

On 1/24/11 4:31 PM, "Tom Terwilliger" <terwilliger at lanl.gov> wrote:

Hi Kendall,
Usually that would mean that there is no segment in your model that has a gap in chain A missing residues 331-336 (6-residue gap).  It could also mean that the sequence could not be aligned with your sequence file.  Is one of those possible?
-Tom T

On Jan 24, 2011, at 1:47 PM, Kendall Nettles wrote:

Dear PHENIX developers,
I am trying fit_loops for the first time and getting error message:
"No suitable gap found matching residues"

I'm not sure what the problem is.

Best regards,
Kendall Nettles

 knettles$ phenix.fit_loops pdb_in=Liganded_overall_best-coot-1.pdb mtz_in=cycle_best_refine_map_coeffs_1.mtz seq_file=seq.dat start=331 end=336 chain_id=A


#                       fit_loops
#
# Fit loops in a PDB file with gaps

# Type phenix.doc for help

Input sequence file is  seq.dat
Reading sequence from  seq.dat
Fit_loops: Fit a missing loop in a model.
Map from:  TEMP_cycle_best_refine_map_coeffs_1.mtz  using labin  FP=2FOFCWT PHIB=PH2FOFCWT
Model from:  Liganded_overall_best-coot-1.pdb
LABIN LINE:  FP=2FOFCWT PHIB=PH2FOFCWT


No suitable gap found matching residues  331 - 336  chain:  A
No final model obtained

_______________________________________________
phenixbb mailing list
phenixbb at phenix-online.org
http://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: terwilliger at LANL.gov
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
CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss





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Message: 4
Date: Mon, 24 Jan 2011 16:46:54 -0500
From: Kendall Nettles <knettles at scripps.edu>
To: PHENIX user mailing list <phenixbb at phenix-online.org>
Subject: [phenixbb] Ligandfit bug report
Message-ID: <C9635D7E.F56D%knettles at scripps.edu>
Content-Type: text/plain; charset="iso-8859-1"

We are generating pdb files with chemdraw3D, which turn out to not be "real" pdb files. PHENIX.ELBOW fixes them, but leaves some of the atom ID numbers blank, such as Oxygen #2, and Carbon #18:
HETATM   17  C16 LIG     1     -83.510  -0.856   0.582  1.00 20.00           C
HETATM   18  O01 LIG     1     -86.640  -2.401  -0.357  1.00 20.00           O
HETATM   19  O   LIG     1     -75.199   2.925   2.145  1.00 20.00           O
HETATM   20  C17 LIG     1     -83.058  -0.188   1.872  1.00 20.00           C
HETATM   21  C   LIG     1     -76.676   0.780  -1.835  1.00 20.00           C

After editing it to add in the missing numbers, I re-ran elbow, and found that the resulting optimized ligand had imploded, producing altered atom connectivity. If I ran it with --final_geometry it came out OK. If you would like files to reproduce the error, I am happy to send them.

Best,
Kendall Nettles
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Message: 5
Date: Mon, 24 Jan 2011 16:03:43 -0800
From: Nigel Moriarty <nwmoriarty at lbl.gov>
To: PHENIX user mailing list <phenixbb at phenix-online.org>
Subject: Re: [phenixbb] Ligandfit bug report
Message-ID:
	<AANLkTin--bR90NCYPqg8V+7Z5oZdaK5bAiLAMnrGQvtC at mail.gmail.com>
Content-Type: text/plain; charset=windows-1252

Kendall

Please send all the files directly (not the list). I believe your
first problem has been fixed recently but the second is strange.

Cheers

Nigel

On Mon, Jan 24, 2011 at 1:46 PM, Kendall Nettles <knettles at scripps.edu> wrote:
> We are generating pdb files with chemdraw3D, which turn out to not be ?real?
> pdb files. PHENIX.ELBOW fixes them, but leaves some of the atom ID numbers
> blank, such as Oxygen #2, and Carbon #18:
> HETATM ??17 ?C16 LIG ????1 ????-83.510 ?-0.856 ??0.582 ?1.00 20.00
> ??????????C
> HETATM ??18 ?O01 LIG ????1 ????-86.640 ?-2.401 ?-0.357 ?1.00 20.00
> ??????????O
> HETATM ??19 ?O ??LIG ????1 ????-75.199 ??2.925 ??2.145 ?1.00 20.00
> ??????????O
> HETATM ??20 ?C17 LIG ????1 ????-83.058 ?-0.188 ??1.872 ?1.00 20.00
> ??????????C
> HETATM ??21 ?C ??LIG ????1 ????-76.676 ??0.780 ?-1.835 ?1.00 20.00
> ??????????C
>
> After editing it to add in the missing numbers, I re-ran elbow, and found
> that the resulting optimized ligand had imploded, producing altered atom
> connectivity. If I ran it with --final_geometry it came out OK. If you would
> like files to reproduce the error, I am happy to send them.
>
> Best,
> Kendall Nettles
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://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? ?? Email : NWMoriarty at LBL.gov
Fax?? : 510-486-5909? ? ?? Web? : CCI.LBL.gov


------------------------------

Message: 6
Date: Tue, 25 Jan 2011 12:36:22 +0100
From: fulvio saccoccia <fulvio.saccoccia at uniroma1.it>
To: PHENIX user mailing list <phenixbb at phenix-online.org>
Subject: [phenixbb] ADP: fix_wxu and wxu_scale
Message-ID: <1295955382.14790.10.camel at fulvio-desktop>
Content-Type: text/plain; charset="UTF-8"

Dear Phenix users and developers,
	I'm trying to refine a 3 A resolution structure. In order to better
understand how can I use wxu_scale and fix_wxu options in phenix.refine,
may you explain me their use, since I have a lot of problems with ADPs?
In fact, I have big variations between atoms of the same residue.
So, is it better to use wxu_scale or to impose fix_wxu to refine the
ADPs?

Thanks to all

Fulvio Saccoccia




------------------------------

Message: 7
Date: Tue, 25 Jan 2011 08:56:25 -0700
From: Tom Terwilliger <terwilliger at lanl.gov>
To: PHENIX user mailing list <phenixbb at phenix-online.org>
Subject: Re: [phenixbb] Problem with loop fitting
Message-ID: <ED51257C-7E66-4639-9440-BB2AE015B462 at lanl.gov>
Content-Type: text/plain; charset="windows-1252"

Hi Kendall,

Oh I see. No, you should be able to use the same sequence file for any model that has any (reasonable) set of fragments from that sequence.  Might it be possible to send me directly (terwilliger at lanl.gov) the input files and I'll give it a try here?
All the best,
Tom T

On Jan 24, 2011, at 2:41 PM, Kendall Nettles wrote:

> Tom, 
> The gap is there, but I?m not sure if I have generated the sequence file correctly. I used a fasta format of all the amino acids in the protein construct. The first three are from the tag, and then the sequence starts at amino acid number 299. The amino acid that is first visible varies from structure to structure and between chains in the same structure, and is between 299 and 307. For the structure I tried the loop fitting it starts at 305. Should I trim the beginning of the seq file? Do I need to tailor this file for each structure I run it on? 
> 
> Kendall
> 
> On 1/24/11 4:31 PM, "Tom Terwilliger" <terwilliger at lanl.gov> wrote:
> 
> Hi Kendall,
> Usually that would mean that there is no segment in your model that has a gap in chain A missing residues 331-336 (6-residue gap).  It could also mean that the sequence could not be aligned with your sequence file.  Is one of those possible?
> -Tom T
> 
> On Jan 24, 2011, at 1:47 PM, Kendall Nettles wrote:
> 
> Dear PHENIX developers, 
> I am trying fit_loops for the first time and getting error message: 
> ?No suitable gap found matching residues?
> 
> I?m not sure what the problem is. 
> 
> Best regards,
> Kendall Nettles
> 
>  knettles$ phenix.fit_loops pdb_in=Liganded_overall_best-coot-1.pdb mtz_in=cycle_best_refine_map_coeffs_1.mtz seq_file=seq.dat start=331 end=336 chain_id=A
> 
> 
> #                       fit_loops
> #
> # Fit loops in a PDB file with gaps
> 
> # Type phenix.doc for help
> 
> Input sequence file is  seq.dat
> Reading sequence from  seq.dat
> Fit_loops: Fit a missing loop in a model.
> Map from:  TEMP_cycle_best_refine_map_coeffs_1.mtz  using labin  FP=2FOFCWT PHIB=PH2FOFCWT 
> Model from:  Liganded_overall_best-coot-1.pdb
> LABIN LINE:  FP=2FOFCWT PHIB=PH2FOFCWT 
> 
> 
> No suitable gap found matching residues  331 - 336  chain:  A
> No final model obtained
> 
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://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: terwilliger at LANL.gov
> 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
> CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
> 
> 
> 
> 
> 
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://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: terwilliger at LANL.gov
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
CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss




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Message: 8
Date: Tue, 25 Jan 2011 10:08:54 -0800
From: Pavel Afonine <pafonine at lbl.gov>
To: PHENIX user mailing list <phenixbb at phenix-online.org>
Subject: Re: [phenixbb] ADP: fix_wxu and wxu_scale
Message-ID: <4D3F11B6.40802 at lbl.gov>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

  Hi Fulvio,

to better understand this I recommend you to have a look at this article 
"On atomic displacement parameters (ADP) and their parametrization in 
PHENIX" here:

http://www.phenix-online.org/newsletter/

A quick reply:

the target function for ADP refinement is:

T = T_xray * wxu_scale * wxu + T_restraints * wu

Obviously, by making wxu_smaller you will put more emphasis on 
restraints. wxu is determined by the program, and wxu_scale is to allow 
the user to do adjustments (if needed or desired).

If you use fix_wxu then the target is

T = T_xray * fix_wxu + T_restraints

I would play with wxu_scale either manually or let phenix.refine to find 
a good value automatically (optimize_wxu=True, or whatever is the 
equivalent in the GUI). There is some information in the manual:
http://www.phenix-online.org/documentation/refinement.htm

Let me know should you have any questions.

Pavel.

On 1/25/11 3:36 AM, fulvio saccoccia wrote:
> Dear Phenix users and developers,
> 	I'm trying to refine a 3 A resolution structure. In order to better
> understand how can I use wxu_scale and fix_wxu options in phenix.refine,
> may you explain me their use, since I have a lot of problems with ADPs?
> In fact, I have big variations between atoms of the same residue.
> So, is it better to use wxu_scale or to impose fix_wxu to refine the
> ADPs?
>
> Thanks to all
>
> Fulvio Saccoccia



------------------------------

Message: 9
Date: Tue, 25 Jan 2011 10:21:35 -0800
From: Pavel Afonine <pafonine at lbl.gov>
To: PHENIX user mailing list <phenixbb at phenix-online.org>
Subject: Re: [phenixbb] adp values
Message-ID: <4D3F14AF.5060107 at lbl.gov>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

  Hi Agnieszka,

I just replied to similar questions (see Re: [phenixbb] ADP: fix_wxu and 
wxu_scale): all applies here too.

There can be lots of reasons for what you observe, and I think it will 
be inefficient if I start writing pages of text guessing. Alternatively, 
if you send me the data and model then I will have a look and may be 
find out what's happening in your specific case (if you decide to send 
the files please do so to my email address - not to the whole list).

Pavel.

On 1/24/11 8:30 AM, Agnieszka wrote:
> Hello,
>
> I have 1.96 resolution structure (RNA) which I refine with individual 
> adp factors. I found that in some cases the differences of apd between 
> the covalently bonded atoms is quite large, for example: phosphate 24 
> and one of the oxygen 33; O4' - 26 and C1'-18. In extreme case for the 
> so4 anion is: sulphate atom 63 and one of the oxygen 31. Why is it 
> happened? I was trying refmac and the b-factors are totally different 
> (they are much bigger). Is it because of scaling and resolution?
>
>
> thank you in advance,
>
> Agnieszka Kiliszek



------------------------------

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End of phenixbb Digest, Vol 62, Issue 25
****************************************

-- 
Alexandra M. Deaconescu, Ph.D.
Damon Runyon Cancer Research Foundation Postdoctoral Fellow
Grigorieff Laboratory
Brandeis University
Rosenstiel Center
415 South St. MS-029
Waltham, MA 02454

For deliveries:

c/o Grigorieff Laboratory
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415 South St.
Kalman Receiving Dock
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