Does anyone has got some information about how to get a mac version (intel), of
the old unix program naccess?. It was meant to calculate the solvent
accessibility per residue from a pdb file.
Armando
On 06/17/2011 05:25 PM, Armando Albert wrote:
Does anyone has got some information about how to get a mac version (intel), of
the old unix program naccess?. It was meant to calculate the solvent
accessibility per residue from a pdb file.
Armando
Maybe this server can do the job:
http://cgal.
Hello everyone,
I got this error, attached below, while running a restrained refinement in
Refmac-5.5.0109. I tried to run the refinement by removing the SCALE entries in
pdb file but got the same error.
* Information from CCP4Interface script
**
On 16 Jun 2011, at 17:19, Pavel Afonine wrote:
> Hi,
>
> On Thu, Jun 16, 2011 at 7:49 AM, Jan Dohnalek wrote:
>
> Modeling more UNKNOWN atoms might be the future for these cases?
>
> one needs to specify chemical element type in 77-78 position, otherwise these
> records are useless.
But if
Thank you!! It's really encouraging & refreshing to begin a day with so many
advices! ccp4bb is always helpful~
Thanks to one of my committee member who suggested me to get out a paper
from the structure, and thanks to all the people at the mid-Atlantic
crystallography meeting who told me my struct
Dear Xun,
> > I have a 3.2A dataset for a protein-DNA complex. The protein is
> > a homodimer, and the DNA is almost palindromic (except one base pair
> > in the middle and two or three base pairs at both two ends). It is my
> > first time solving structures, and unfortunately the resolutio
For the record:-UNK is for unknown residues only. That means that you know that
you are looking at an amino acid you just don't know which. You should assign
element types. It used to be defined to CB (just like ALA), it now goes to CG.
I don't see the point of this update.-UNL is for unknown h
Another thing you should bookmark and check out is the Molprobity page (google
for it), upload your pdb file and let it evaluate what you have done. The chart
it generates will guide you through your structure and you will be able to do a
good job.
Jürgen
..
Jürgen Bosch
Jo
To add to this discussion:
Many of the comments to my question that started this thread do not
sufficiently differentiate between accuracy and precision.
While we all want an assay that is internally consistent (i.e., high
precision), we do care a lot about accuracy ("the degree of closeness of
Hi!
I am having a problem of visualizing the PLT files in CCP4 6.1.13 CCP1
interface 2.0.7 running on Windows 7/64.
I installed the GSscript and GSview but I am not sure how to change
parameters in the System administration.
Any help and advice will be highly appreciated!
Hi, the '.plt' files are in an internal CCP4 format & cannot be visualised
directly. You have to convert them first to PostScript (.ps) format using
the 'pltdev' program; then you can visualise them with ghostscript (or any
other PS viewer).
Cheers
-- Ian
On Fri, Jun 17, 2011 at 5:53 PM, Tatyan
Thanks!
How do I get the pltdev? I checked the program list in CCP4 and it is not
there, so I need to download it, I presume, and install.
cheers,
Tanya
On Fri, Jun 17, 2011 at 1:25 PM, Ian Tickle wrote:
>
> Hi, the '.plt' files are in an internal CCP4 format & cannot be visualised
> directly.
On Fri, Jun 17, 2011 at 06:25:14PM +0100, Ian Tickle wrote:
> Hi, the '.plt' files are in an internal CCP4 format & cannot be visualised
> directly. You have to convert them first to PostScript (.ps) format using
> the 'pltdev' program; then you can visualise them with ghostscript (or any
> other
Hi Tatyana,
It is funny that I just had that same problem a few days ago.
Here is the solution:
First of all, install Ghostgum and Ghostscript to your computer- which you have
done. I installed them to my C:\Program Files\ directory.
Then in CCP4i->system configuration->Config CCP4interface->
Forgot to mention: the trick is, CCP4i uses the Linux/UNIX '/' to specify the
subdirectories, not the Windows '\'. That is why if you copy the path from
windows explorer and paste it it won't work.
From: Tatyana Sysoeva
Sent: Friday, June 17, 2011 12:53 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject
Thank you! this works perfectly fine! (I was not smart enough to put the
path into both boxes)
Yes, had to change forward to backward slash (or how one calls them) and it
is saved now.
Thank you very much!!!
Cheers,
Tanya
On Fri, Jun 17, 2011 at 4:30 PM, Zhijie Li wrote:
> **
> Hi Tatyana,
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