You might have better luck running pdb2pqr directly, instead of having pymol
run it for you. I'd try downloading the recent version (I think it's on
sourceforge), and possibly trying different forcefield parameters. You can
then load the pqr file into pymol using apbs tools, or use it directly
coefficients
Yup, refmac too.
Pavel Afonine wrote:
> Not sure for other software, but in phenix.refine you can request to
> output I*mFo-J*DFc map, where I and J are any user specified values.
>
> Pavel.
>
>
> On 7/7/2008 6:00 PM, Meyer, Peter wrote:
>> It i
It is redundant, but it adds an additional step if someone wanted to calculate
something like a 3mFO-2DFc map.
Thanks,
Pete
-Original Message-
From: Kevin Cowtan [mailto:[EMAIL PROTECTED]
Sent: Mon 7/7/2008 10:18 AM
To: Meyer, Peter
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb
Slightly off-topic from the original question, but is there a reason that most
programs don't output D for sigma_a coefficients?
Pete
-Original Message-
From: CCP4 bulletin board on behalf of Mayer, Mark (NIH/NICHD) [E]
Sent: Sat 7/5/2008 2:39 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4
It looks like you need to install python2.4 (and python2.4-dev if using the
package manager) and use that as the default during the build (remove
/usr/bin/python and symlink it to python2.4 instead of /usr/bin/python2.5 ;
after compiling phaser you can change it back).
Pete
-Original Mess
Doesn't this just change the question to "what observation:parameter ratio is
needed for my structure to be over-determined?"?
As near as I'm aware, the answer to that one seems to be "as many observations
as you get".
Pete
-Original Message-
From: CCP4 bulletin board on behalf of [EMA
Regarding reason 1, you can configure sshd to block root from logging in
remotely ("PermitRootLogin no" in /etc/ssh/sshd_config). I was surprised to
see that this wasn't the default in some systems, but made sure to turn it on
after I saw my first dictionary attack (and since).
Not that I disa
Well, nobody's let me in on any anti-validation conspiracy (which make sense,
seeing as I don't write validation software). But Molprobity runs fine on a
local system, and is very easy to configure. PDB-ADIT (which you didn't
mention) can also be configured to run locally, but it takes more wo
Hi.
Based on your explanation it looks like you want to remove your "RUN 1
REFERENCE" and "EXCLUDE BATCH 400 TO 500" lines from your script. You might
also want to try without the NAME lines on the off chance that the harvesting
stuff is causing the problems.
My best guess is that the "RUN 1
Hi,
A few things you might try (or that you may have tried, but didn't mention):
1. Run the search models through chainsaw with their sequence alignments before
searching (or just use poly-alanine versions of the search models), and reset
the B-factor of the search models to the B-factor of the
Hi,
The recent discussion on Rwork/Rfree ratio reminded me of something I was
wondering about (*). When counting constraints as observations for determining
the observation to parameter ratio, is each unique constraint counted, or each
time a given constraint is used. For example, if there ar
Doubtlessly I'm confused, but my understanding was that alternative origins
would only be an issue once a dataset was phased (so that wouldn't cause
problem during integrating/scaling). I'd thought that using a consistent unit
cell during indexing and scaling was a separate issue.
Any chance y
Hi Rafael,
Phase combination is when you add the probability distributions from two
different sources of phase information (in your case, your SAD phases and model
phases; but this occurs in lots of other places as well...). The idea is that
combining two or more poor quality phase distributio
Hi Li,
setpaths.sh (and variants for other shells) are generated during the cctbx
build process (with ccp4-6.0.2, this might happen only if you're installing
phaser).
If you're doing a source install from both ccp4-6.0.2.tar.gz and
phaser-1.3.3-cctbx-src.tar.gz, and have extracted both of th
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