Dear Patrick,
Apologies for a partly non-CCP4 answer! You can use the HHPRED alignments in
some of the software available in Phenix. One option is to provide the .hhr
file to MRage, which will fetch the PDB entries, run Sculptor to modify the
templates with one or more protocols, based on
Dear Pat
Yes, AMPLE does it's own, purely structure-based, alignment of the
homologs provided using GESAMT. You provide a directory of structures to
work with and, crucially, give AMPLE the
-homologs True
flag so that it knows the inputs have different sequences (unlike in
modelling mode),
I’m intrigued by the prospect of using AMPLE to test multiple distant homologs
in a MR problem. I’ve used HHPRED to identify about 20 high-probability
homologs of known structure, each of which has about 20-25% identity with the
unknown protein. However, it’s not clear to me from the
Hi Robert,
Thanks for your interest in AMPLE and reporting this bug. There is a
small bug that has come about as a result of the latest MRBUMP update
last week that causes this problem. We're preparing a fix for it which
should be in the next ccp4 update towards the end of this week or early
Hi,
I'm trying to run AMPLE from ccp4-6.4.0 on Linux Ubuntu. It looks like it
found all the program dependencies that it needs and Rosetta looks like it ran
okay and I think MRBUMP looks alright, but then the program stopped with the
following error message:
MR and shelx DONE
ALL DONE (in
.
Best wishes,
Jens
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Robert
Kirchdoerfer [rkirc...@scripps.edu]
Sent: 12 July 2014 18:58
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] AMPLE failure
Hi,
I'm trying to run AMPLE from ccp4-6.4.0
Dear all,
I'm trying to use Ample from CCP4 (6.4) to solve a structure of 2x197
residues from 2.0 A data.
After the generation of initial (120) models by Rosetta (3.3) Ample
stops with the error-message below.
Could anyone provide me information about the origin of this error and
possibly how to
[florian.sau...@virchow.uni-wuerzburg.de]
Sent: 11 July 2014 08:37
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Ample fails
Dear all,
I'm trying to use Ample from CCP4 (6.4) to solve a structure of 2x197 residues
from 2.0 A data.
After the generation of initial (120) models by Rosetta (3.3) Ample
Hi,
I've been running Ample and I'm a bit confused about the input for the
shelxe-beta auto-tracing. The input mtz for Ample has F, SIGF and FreeR and it
appears that Ample converts the structure factor amplitudes to intensities
using mtz2various with the FSQUARED keyword as the log file
Dear Huw,
It looks as though you have correctly diagnosed a problem with AMPLE.
For expansion from borderline partial structures, I recommend the latest
SHELXE (on my beta-test server since Jan. 20th) and experimenting with
the -O and -F switches, e.g.
-F0.9 -O100 -a30
However SHELXE is
Of Huw
Jenkins
Sent: 28 January 2013 10:14
To: ccp4bb
Subject: [ccp4bb] Ample, shelxe-beta and F to I conversion confusion
Hi,
I've been running Ample and I'm a bit confused about the input for the
shelxe-beta auto-tracing. The input mtz for Ample has F, SIGF and FreeR and it
appears that Ample
Correct, shelxe does not use the free -R flags, and works just
as well with the original unmerged unctruncated intensities.
George
Hi Ronan,
On 28 Jan 2013, at 12:18, ronan.kee...@stfc.ac.uk wrote:
Well spotted! We originally gave structure factors to SHELXE in our testing as for most
of
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