Thanks for the reply. I think I didn't explain myself properly, of course I want to do bss, but we have noticed that previous versions of phenix (1.24 I think) did bss once per macro cycle and now with the newer versions, we get the same plus a final bbs cycle at the end of the whole process -shown in red- Is that final cycle introduced by default in the newer versions?
Thanks again.

Cesar.



REMARK��� 3_bss:�� 1.222� 0.008� 0.075 19.562� 0.005� 4.107�� 1.2876e-01
REMARK��� 3_xyz:�� 1.021� 0.005� 0.063 19.049� 0.004� 4.111�� 1.0306e-01
REMARK��� 3_adp:�� 1.021� 0.005� 0.063 19.049� 0.004� 4.111�� 1.0306e-01
REMARK��� 3_bss:�� 1.021� 0.005� 0.063 19.049� 0.004� 4.111�� 1.0306e-01�

On Dec 3, 2008, at 9:00 PM, [email protected] wrote:

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Today's Topics:

�� 1. Bulk solvent ([email protected])
�� 2. Re: Bulk solvent (junfeng liu)
�� 3. Re: Bulk solvent (Pavel Afonine)
�� 4. Re: Bulk solvent (Pavel Afonine)
�� 5. Re: Question regarding phenix.elbow (Nigel W Moriarty)


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

Message: 1
Date: Wed, 3 Dec 2008 10:15:30 +0100 (CET)
From: [email protected]
Subject: [phenixbb] Bulk solvent
To: [email protected]
Message-ID:
<[email protected]>
Content-Type: text/plain;charset=iso-8859-1

Hi all,
I'm refining a protein and after running phenix.refine I always get a bulk
solvent refinement cycle at the end of the process. Is there any way to
get rid of the last step?

------------------------------------------------------------------------
REMARK� stage � � � angl � bond � chir � dihe � plan � repu� geom_target
REMARK� � 0� � : � 1.007� 0.027� 0.237 18.975� 0.004� 4.107 � 2.7953e-01
REMARK� � 1_bss: � 1.007� 0.027� 0.237 18.975� 0.004� 4.107 � 2.7953e-01
REMARK� � 1_xyz: � 1.844� 0.015� 0.087 19.502� 0.005� 4.106 � 1.9824e-01
REMARK� � 1_adp: � 1.844� 0.015� 0.087 19.502� 0.005� 4.106 � 1.9824e-01
REMARK� � 2_bss: � 1.844� 0.015� 0.087 19.502� 0.005� 4.106 � 1.9824e-01
REMARK� � 2_xyz: � 1.222� 0.008� 0.075 19.562� 0.005� 4.107 � 1.2876e-01
REMARK� � 2_adp: � 1.222� 0.008� 0.075 19.562� 0.005� 4.107 � 1.2876e-01
REMARK� � 3_bss: � 1.222� 0.008� 0.075 19.562� 0.005� 4.107 � 1.2876e-01
REMARK� � 3_xyz: � 1.021� 0.005� 0.063 19.049� 0.004� 4.111 � 1.0306e-01
REMARK� � 3_adp: � 1.021� 0.005� 0.063 19.049� 0.004� 4.111 � 1.0306e-01
REMARK� � 3_bss: � 1.021� 0.005� 0.063 19.049� 0.004� 4.111 � 1.0306e-01
REMARK
------------------------------------------------------------------------


C?sar Santiago
Dept of Macromolecules Structure
Centro Nacional de Biotecnolog?a, CSIC
Campus Cantoblanco
28049 Madrid
Spain

[email protected]




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

Message: 2
Date: Wed, 03 Dec 2008 09:36:30 +0000
From: junfeng liu <[email protected]>
Subject: Re: [phenixbb] Bulk solvent
To: PHENIX user mailing list <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Add

bulk_solvent_and_scale=False�
when you run it again.



[email protected] wrote:
Hi all,
I'm refining a protein and after running phenix.refine I always get a bulk
solvent refinement cycle at the end of the process. Is there any way to
get rid of the last step?

------------------------------------------------------------------------
REMARK� stage � � � angl � bond � chir � dihe � plan � repu� geom_target
REMARK� � 0� � : � 1.007� 0.027� 0.237 18.975� 0.004� 4.107 � 2.7953e-01
REMARK� � 1_bss: � 1.007� 0.027� 0.237 18.975� 0.004� 4.107 � 2.7953e-01
REMARK� � 1_xyz: � 1.844� 0.015� 0.087 19.502� 0.005� 4.106 � 1.9824e-01
REMARK� � 1_adp: � 1.844� 0.015� 0.087 19.502� 0.005� 4.106 � 1.9824e-01
REMARK� � 2_bss: � 1.844� 0.015� 0.087 19.502� 0.005� 4.106 � 1.9824e-01
REMARK� � 2_xyz: � 1.222� 0.008� 0.075 19.562� 0.005� 4.107 � 1.2876e-01
REMARK� � 2_adp: � 1.222� 0.008� 0.075 19.562� 0.005� 4.107 � 1.2876e-01
REMARK� � 3_bss: � 1.222� 0.008� 0.075 19.562� 0.005� 4.107 � 1.2876e-01
REMARK� � 3_xyz: � 1.021� 0.005� 0.063 19.049� 0.004� 4.111 � 1.0306e-01
REMARK� � 3_adp: � 1.021� 0.005� 0.063 19.049� 0.004� 4.111 � 1.0306e-01
REMARK� � 3_bss: � 1.021� 0.005� 0.063 19.049� 0.004� 4.111 � 1.0306e-01
REMARK
------------------------------------------------------------------------


C?sar Santiago
Dept of Macromolecules Structure
Centro Nacional de Biotecnolog?a, CSIC
Campus Cantoblanco
28049 Madrid
Spain

[email protected]


_______________________________________________
phenixbb mailing list
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http://www.phenix-online.org/mailman/listinfo/phenixbb





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

Message: 3
Date: Wed, 03 Dec 2008 08:09:57 -0800
From: Pavel Afonine <[email protected]>
Subject: Re: [phenixbb] Bulk solvent
To: PHENIX user mailing list <[email protected]>
Cc: [email protected]
Message-ID: <[email protected]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi C?sar,

this step is important. Bulk solvent modeling is based on mask�
calculation and since during refinement of coordinates the atoms shift�
the mask gets invalidated. This is why we do a final bulk solvent�
correction step at the very last step of refinement just before the�
final statistics is reported. So I'm puzzled about why you want to turn�
it off. If it causes any problem, it's much better to find out the�
primary reason for it rather than turn bulk solvent correction. Could�
you please give more details?

If you do "main.bulk_solvent_and_scale=false" phenix.refine will not do�
bulk solvent correction and anisotropic scaling at all which is bad.

Pavel.

On 12/3/2008 1:15 AM, [email protected] wrote:
Hi all,
I'm refining a protein and after running phenix.refine I always get a bulk
solvent refinement cycle at the end of the process. Is there any way to
get rid of the last step?

------------------------------------------------------------------------
REMARK� stage � � � angl � bond � chir � dihe � plan � repu� geom_target
REMARK� � 0� � : � 1.007� 0.027� 0.237 18.975� 0.004� 4.107 � 2.7953e-01
REMARK� � 1_bss: � 1.007� 0.027� 0.237 18.975� 0.004� 4.107 � 2.7953e-01
REMARK� � 1_xyz: � 1.844� 0.015� 0.087 19.502� 0.005� 4.106 � 1.9824e-01
REMARK� � 1_adp: � 1.844� 0.015� 0.087 19.502� 0.005� 4.106 � 1.9824e-01
REMARK� � 2_bss: � 1.844� 0.015� 0.087 19.502� 0.005� 4.106 � 1.9824e-01
REMARK� � 2_xyz: � 1.222� 0.008� 0.075 19.562� 0.005� 4.107 � 1.2876e-01
REMARK� � 2_adp: � 1.222� 0.008� 0.075 19.562� 0.005� 4.107 � 1.2876e-01
REMARK� � 3_bss: � 1.222� 0.008� 0.075 19.562� 0.005� 4.107 � 1.2876e-01
REMARK� � 3_xyz: � 1.021� 0.005� 0.063 19.049� 0.004� 4.111 � 1.0306e-01
REMARK� � 3_adp: � 1.021� 0.005� 0.063 19.049� 0.004� 4.111 � 1.0306e-01
REMARK� � 3_bss: � 1.021� 0.005� 0.063 19.049� 0.004� 4.111 � 1.0306e-01
REMARK
------------------------------------------------------------------------


C?sar Santiago
Dept of Macromolecules Structure
Centro Nacional de Biotecnolog?a, CSIC
Campus Cantoblanco
28049 Madrid
Spain

[email protected]


_______________________________________________
phenixbb mailing list
[email protected]
http://www.phenix-online.org/mailman/listinfo/phenixbb



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

Message: 4
Date: Wed, 03 Dec 2008 08:13:21 -0800
From: Pavel Afonine <[email protected]>
Subject: Re: [phenixbb] Bulk solvent
To: PHENIX user mailing list <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset="iso-8859-1"

Yes, this will turn bulk solvent correction and anisotropic scaling off�
completely. In some cases it may result in R-factors increase by ~5% or�
similar. So it may only make sense in exotic cases or if you do�
numerical experiments (simulated data etc..).

Pavel.


On 12/3/2008 1:36 AM, junfeng liu wrote:
Add

bulk_solvent_and_scale=False�
when you run it again.



[email protected] wrote:

Hi all,
I'm refining a protein and after running phenix.refine I always get a bulk
solvent refinement cycle at the end of the process. Is there any way to
get rid of the last step?

------------------------------------------------------------------------
REMARK� stage � � � angl � bond � chir � dihe � plan � repu� geom_target
REMARK� � 0� � : � 1.007� 0.027� 0.237 18.975� 0.004� 4.107 � 2.7953e-01
REMARK� � 1_bss: � 1.007� 0.027� 0.237 18.975� 0.004� 4.107 � 2.7953e-01
REMARK� � 1_xyz: � 1.844� 0.015� 0.087 19.502� 0.005� 4.106 � 1.9824e-01
REMARK� � 1_adp: � 1.844� 0.015� 0.087 19.502� 0.005� 4.106 � 1.9824e-01
REMARK� � 2_bss: � 1.844� 0.015� 0.087 19.502� 0.005� 4.106 � 1.9824e-01
REMARK� � 2_xyz: � 1.222� 0.008� 0.075 19.562� 0.005� 4.107 � 1.2876e-01
REMARK� � 2_adp: � 1.222� 0.008� 0.075 19.562� 0.005� 4.107 � 1.2876e-01
REMARK� � 3_bss: � 1.222� 0.008� 0.075 19.562� 0.005� 4.107 � 1.2876e-01
REMARK� � 3_xyz: � 1.021� 0.005� 0.063 19.049� 0.004� 4.111 � 1.0306e-01
REMARK� � 3_adp: � 1.021� 0.005� 0.063 19.049� 0.004� 4.111 � 1.0306e-01
REMARK� � 3_bss: � 1.021� 0.005� 0.063 19.049� 0.004� 4.111 � 1.0306e-01
REMARK
------------------------------------------------------------------------


C?sar Santiago
Dept of Macromolecules Structure
Centro Nacional de Biotecnolog?a, CSIC
Campus Cantoblanco
28049 Madrid
Spain



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

Message: 5
Date: Wed, 03 Dec 2008 11:32:05 -0800
From: Nigel W Moriarty <[email protected]>
Subject: Re: [phenixbb] Question regarding phenix.elbow
To: PHENIX user mailing list <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

YoungJin

I have fixed this error and its will be in the next release.� Did you�
try ReadySet! as Pavel suggested?� I can provide a restraints so you can�
continue your refinement if you desire.

Thanks

Nigel

On 12/1/08 6:53 AM, Young-Jin Cho wrote:
Hi
I would like to know how I can add H atoms to my ligand, ADP in the protein complex.
I was trying to add H atoms to one of my ligand, ADP.
When I types "phenix.elbow --final-geometry=test10bcoot_h_refine_001.pdb --residue=ADP --output=model_h",
it went on but failed with the following error message:
Traceback (most recent call last):
� File "/home2/yjcho/phenix-1.3-final/elbow/elbow/command_line/builder.py", line 1201, in <module>
� � run()
� File "/home2/yjcho/phenix-1.3-final/elbow/elbow/command_line/builder.py", line 1108, in run
� � molecule = post_process(molecule, options)
� File "/home2/yjcho/phenix-1.3-final/elbow/elbow/command_line/builder.py", line 577, in post_process
� � options,
� File "/home2/yjcho/phenix-1.3-final/elbow/elbow/utilities/optimisation_manager.py", line 331, in optimisation_manager
� � pre_opt))
� File "/home2/yjcho/phenix-1.3-final/elbow/elbow/chemistry/IOMixins.py", line 857, in WritePDB
� � original_order=original_order,
� File "/home2/yjcho/phenix-1.3-final/elbow/elbow/chemistry/IOMixins.py", line 965, in WritePDB2String
� � self.AdjustHydrogenNames()
� File "/home2/yjcho/phenix-1.3-final/elbow/elbow/chemistry/IOMixins.py", line 940, in AdjustHydrogenNames
� � if test_name[3]==" ": test_name[3]="0"
TypeError: 'str' object does not support item assignment

FYI. ADP is names as ADP as a residue name in the pdb file but has different chain names.

By the way, I should mention that I used phenix.reduce first for adding H atoms but it was not able to add sugar H's in ADP molecule albeit other residues were fine.

Thanks in advance for your help.

Best,
YoungJin
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--�
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



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

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End of phenixbb Digest, Vol 37, Issue 3
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