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, phenixbb-request@phenix-online.org wrote:

Send phenixbb mailing list submissions to
phenixbb@phenix-online.org

To subscribe or unsubscribe via the World Wide Web, visit
http://www.phenix-online.org/mailman/listinfo/phenixbb
or, via email, send a message with subject or body 'help' to
phenixbb-request@phenix-online.org

You can reach the person managing the list at
phenixbb-owner@phenix-online.org

When replying, please edit your Subject line so it is more specific
than "Re: Contents of phenixbb digest..."


Today's Topics:

   1. Bulk solvent (csantiag@cnb.csic.es)
   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: csantiag@cnb.csic.es
Subject: [phenixbb] Bulk solvent
To: phenixbb@phenix-online.org
Message-ID:
<49732.150.244.83.180.1228295730.squirrel@webmail.cnb.csic.es>
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

csantiag@cnb.csic.es




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

Message: 2
Date: Wed, 03 Dec 2008 09:36:30 +0000
From: junfeng liu <jliu@nimr.mrc.ac.uk>
Subject: Re: [phenixbb] Bulk solvent
To: PHENIX user mailing list <phenixbb@phenix-online.org>
Message-ID: <4936531E.5030505@nimr.mrc.ac.uk>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Add

bulk_solvent_and_scale=False 
when you run it again.



csantiag@cnb.csic.es 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

csantiag@cnb.csic.es


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





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

Message: 3
Date: Wed, 03 Dec 2008 08:09:57 -0800
From: Pavel Afonine <pafonine@lbl.gov>
Subject: Re: [phenixbb] Bulk solvent
To: PHENIX user mailing list <phenixbb@phenix-online.org>
Cc: csantiag@cnb.csic.es
Message-ID: <4936AF55.8010508@lbl.gov>
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, csantiag@cnb.csic.es 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

csantiag@cnb.csic.es


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



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

Message: 4
Date: Wed, 03 Dec 2008 08:13:21 -0800
From: Pavel Afonine <pafonine@lbl.gov>
Subject: Re: [phenixbb] Bulk solvent
To: PHENIX user mailing list <phenixbb@phenix-online.org>
Message-ID: <4936B021.7010401@lbl.gov>
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.



csantiag@cnb.csic.es 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



_______________________________________________
phenixbb mailing list




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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://www.phenix-online.org/pipermail/phenixbb/attachments/20081203/46389290/attachment-0001.htm

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

Message: 5
Date: Wed, 03 Dec 2008 11:32:05 -0800
From: Nigel W Moriarty <NWMoriarty@lbl.gov>
Subject: Re: [phenixbb] Question regarding phenix.elbow
To: PHENIX user mailing list <phenixbb@phenix-online.org>
Message-ID: <4936DEB5.5030000@lbl.gov>
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
_______________________________________________
phenixbb mailing list
phenixbb@phenix-online.org
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 : NWMoriarty@LBL.gov
Web   : CCI.LBL.gov



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

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


End of phenixbb Digest, Vol 37, Issue 3
***************************************