Ah thanks, I've managed to get it sorted out.
In case anyone else has this issue, I downloaded the CCP4 source code,
increased MAX3D in fsearch.f, and recompiled. I first built CCP4 (./configure
&& make) and then fsearch explicitly (cd src && make fsearch).
Thanks,
Jason.
--
Jason Busby
PhD
Another option might be to reduce the resolution of the search. With
SAXS you don't have much resolution in your search model anyway.
On 06/13/12 16:33, Jason Busby wrote:
Hi,
I am trying to run fsearch to do molecular replacement from a SAXS envelope,
but it gives an error: FSEARCH: *out
Matthew Vetting
Enzyme Function Initiative
Structural Biology
Albert Einstein College of Medicine
- Reply message -
From: "Pavel Afonine"
To:
Subject: [ccp4bb] PHENIX: sequence files input problem
Date: Wed, Jun 13, 2012 4:51 pm
Hi Qixu Cai,
first off -- as a reminder, there is Phenix
Matthew Vetting
Enzyme Function Initiative
Structural Biology
Albert Einstein College of Medicine
- Reply message -
From: "Jahan Alikhajeh"
To:
Subject: [ccp4bb] Off-Topic
Date: Wed, Jun 13, 2012 5:05 pm
Dear Friends,
Does anyone know how to control the polymerization of G-actin to F
Jason,
It seems like you're on the right track - it's usually not a problem to
increase array sizes and rebuild.
How are you building (aka "cd $CCP4/src; make fsearch" or something
else)? If you're calling the fortran compiler (or ld) directly, it
looks like there's an a problem with the li
Dear Friends,
Does anyone know how to control the polymerization of G-actin to F-actin?
I need F-actin with <100 DP (degree of polymerization).
Any suggestion is highly appreciated.
Jahan
Hi Qixu Cai,
first off -- as a reminder, there is Phenix mailing list to post
Phenix-related questions:
http://www.phenix-online.org/
Your first question: yes, give it one sequence file containing all.
Your second question: see here
http://phenix-online.org/documentation/autobuild_gui.htm
Pavel
Hi,
I am trying to run fsearch to do molecular replacement from a SAXS envelope,
but it gives an error: FSEARCH: *out of allocated memory*
I assume this is because of my large unit cell: 133.9180 147.8250 274.7790
90. 90. 90.
Is it possible to increase the amount of memory
Lisa,
As others have said, using careful data collection and the modern program
suites available (SHARP, Phenix, etc.), a 300 KD complex with 111 Se-Met
residues should be quite solvable. But you didn't state is what is in the
asymmetric unit (the important figure): one complex with 111 Se-Me
Dear all,
Sorry for the non-CCP4 question.
My crystal is a complex of two proteins. I use Se-Met SAD method to
solve the structure, and only one of the proteins is Se-Met protein.
When I use phenix.autobuild to auto-build the model, how do I input the
sequences? in a file or two files?
And
We cordially invite you to participate in the 14th International
Conference on the Crystallization of Biological Macromolecules (ICCBM14)
on September 23-28, 2012. The conference will be held in Huntsville, the
"/Rocket City/," in the beautiful state of Alabama. The meeting site
will be at the
Just to be clear, the CCP4 data processing programs (SCALA and its replacement
AIMLESS) always give you I+ and I- in the output. The only difference between
"anomalous on & off" is in the outlier rejection, since if you have a large
anomalous signal you don't want to reject as "outliers" reflect
>I think there is a misconception floating around that processing your
>data with "anomalous turned on" will somehow degrade the quality of
>"normal" intensity data.
I can think of very few circumstances when I would NOT want anomalous data, yet
for many data processing pipelines, it is the defa
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