Nat, 1.4-160 works just fine. Thank you. Katya Ekaterina Heldwein, Ph.D. Assistant Professor Department of Molecular Biology and Microbiology Tufts University School of Medicine 136 Harrison Ave Boston, MA 02111 phone: 617-636-0858 fax: 617-636-0337 e-mail: [email protected] [email protected] wrote:

Send phenixbb mailing list submissions to [email protected]

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 [email protected]

You can reach the person managing the list at [email protected]

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

Today's Topics:

1. Phenix crashes (Katya Heldwein) 2. Re: Phenix crashes ([email protected]) 3. Re: Phenix crashes (Nathaniel Echols) 4. Re: Phenix crashes (Nathaniel Echols) 5. specifying column labels for input MTZ file (Tirumala Kumar Chowdary) 6. Re: specifying column labels for input MTZ file (Schubert, Carsten [PRDUS]) 7. Re: specifying column labels for input MTZ file (Pavel Afonine)

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

Message: 1 Date: Wed, 09 Sep 2009 12:02:36 -0400 From: Katya Heldwein Subject: [phenixbb] Phenix crashes To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset=ISO-8859-1; format="flowed"

Hi,

I am running phenix-1.4-159 on an Intel Mac. I get the following error:

Bus error (Python call stack above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical.

If I fix it by

setenv BOOST_ADAPTBX_FPE_DEFAULT 1

I still get the same error.

If I also do

setenv BOOST_ADAPTBX_SIGNALS_DEFAULT 1

I don't get the error but phenix crashes nonetheless.

How do I get around this problem?

Thanks,

Katya

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

Message: 2 Date: Wed, 9 Sep 2009 12:17:36 -0400 (EDT) From: [email protected] Subject: Re: [phenixbb] Phenix crashes To: "PHENIX user mailing list" Message-ID: <[email protected]> Content-Type: text/plain;charset=iso-8859-1

Hi, This looks like a version problem, try installing the latest nightly builds. Shya

...

Hi,

I am running phenix-1.4-159 on an Intel Mac. I get the following error:

Bus error (Python call stack above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical.

If I fix it by

setenv BOOST_ADAPTBX_FPE_DEFAULT 1

I still get the same error.

If I also do

setenv BOOST_ADAPTBX_SIGNALS_DEFAULT 1

I don't get the error but phenix crashes nonetheless.

How do I get around this problem?

Thanks,

Katya

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

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

Message: 3 Date: Wed, 9 Sep 2009 09:37:50 -0700 From: Nathaniel Echols Subject: Re: [phenixbb] Phenix crashes To: PHENIX user mailing list Message-ID: <[email protected]> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes

On Sep 9, 2009, at 9:02 AM, Katya Heldwein wrote:

...

I am running phenix-1.4-159 on an Intel Mac. I get the following error: Bus error (Python call stack above)

If I fix it by setenv BOOST_ADAPTBX_FPE_DEFAULT 1 I still get the same error. If I also do

setenv BOOST_ADAPTBX_SIGNALS_DEFAULT 1

I don't get the error but phenix crashes nonetheless.

How do I get around this problem?

Which programs are you running, and did you see a stack trace before the error message? I just noticed the same thing running phenix.refine from the same installer on my Mac, so it is probably an undiagnosed bug.

------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]

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

Message: 4 Date: Wed, 9 Sep 2009 09:46:24 -0700 From: Nathaniel Echols Subject: Re: [phenixbb] Phenix crashes To: PHENIX user mailing list Message-ID: <[email protected]> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes

On Sep 9, 2009, at 9:17 AM, [email protected] wrote:

...

Hi, This looks like a version problem, try installing the latest nightly builds. Shya

Actually, 1.4-159 was the latest build until ten minutes ago, but I just checked 1.4-160 and it does not appear to have this problem, so it's now ready to download. Sorry for the trouble.

-Nat

------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]

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

Message: 5 Date: Wed, 09 Sep 2009 14:10:27 -0400 From: Tirumala Kumar Chowdary Subject: [phenixbb] specifying column labels for input MTZ file To: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset=ISO-8859-1; format="flowed"

Hi,

I am trying to run phenix.refine with a sharp output MTZ file (column labels H K L NUMORB FB PHIB FOM HX HY FH PHIH FP SIGFP HLA HLB HLC HLD HL0 Fcent PHIcent FOMcent Fmap PHImap FHref PHIHref Fav SIGFav).

Phenix.refine stopped at

'Multiple equally suitable arrays of observed xray data found.

Possible choices: sharp_sad_se_eden.mtz:FP,SIGFP sharp_sad_se_eden.mtz:Fav,SIGFav

Please use refinement.input.xray_data.labels'

Can someone tell me on how to use this 'refinement.input.xray_data.labels' and how to specify which column labels to use. There is nothing written in the documentation about it.

Thanks Tirumal

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

Message: 6 Date: Wed, 9 Sep 2009 14:22:40 -0400 From: "Schubert, Carsten [PRDUS]" Subject: Re: [phenixbb] specifying column labels for input MTZ file To: "PHENIX user mailing list" Message-ID: <[email protected]> Content-Type: text/plain; charset="us-ascii"

Tirumal:

refinement.input.xray_data.labels="FP,SIGFP"

should do the trick.

Cheers,

Carsten

...

-----Original Message----- From: [email protected] [mailto:phenixbb- [email protected]] On Behalf Of Tirumala Kumar Chowdary Sent: Wednesday, September 09, 2009 2:10 PM To: [email protected] Subject: [phenixbb] specifying column labels for input MTZ file

Hi,

I am trying to run phenix.refine with a sharp output MTZ file (column labels H K L NUMORB FB PHIB FOM HX HY FH PHIH FP SIGFP HLA HLB HLC

HLD

...

HL0 Fcent PHIcent FOMcent Fmap PHImap FHref PHIHref Fav SIGFav).

Phenix.refine stopped at

'Multiple equally suitable arrays of observed xray data found.

Possible choices: sharp_sad_se_eden.mtz:FP,SIGFP sharp_sad_se_eden.mtz:Fav,SIGFav

Please use refinement.input.xray_data.labels'

Can someone tell me on how to use this 'refinement.input.xray_data.labels' and how to specify which column labels to use. There is nothing written in the documentation about it.

Thanks Tirumal

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

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

Message: 7 Date: Wed, 09 Sep 2009 11:24:46 -0700 From: Pavel Afonine Subject: Re: [phenixbb] specifying column labels for input MTZ file To: PHENIX user mailing list Cc: [email protected] Message-ID: <[email protected]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi Tirumala,

I agree, you are not the first who confused by this and an example right in the message would help.

First, your MTZ file contains the following data: (FP,SIGFP) and (Fav,SIGFav) and it is your choice to select the one that you want to use in refinement.

Second, once decided on the data - for example it is FP, then just add to your command line this:

refinement.input.xray_data.labels=FP

or, which is the same

xray_data.labels="FP,SIGFP"

Pavel.

On 9/9/09 11:10 AM, Tirumala Kumar Chowdary wrote:

...

Hi,

I am trying to run phenix.refine with a sharp output MTZ file (column labels H K L NUMORB FB PHIB FOM HX HY FH PHIH FP SIGFP HLA HLB HLC HLD HL0 Fcent PHIcent FOMcent Fmap PHImap FHref PHIHref Fav SIGFav).

Phenix.refine stopped at

'Multiple equally suitable arrays of observed xray data found.

Possible choices: sharp_sad_se_eden.mtz:FP,SIGFP sharp_sad_se_eden.mtz:Fav,SIGFav

Please use refinement.input.xray_data.labels'

Can someone tell me on how to use this 'refinement.input.xray_data.labels' and how to specify which column labels to use. There is nothing written in the documentation about it.

Thanks Tirumal

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

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

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

End of phenixbb Digest, Vol 46, Issue 14 ****************************************