Hi Paul,
On 10/24/2014 02:04 AM, Paul Emsley wrote:
> [remove context]
> It doesn't yet fit the map to the model.
> [/remove context]
> Paul.
This would make crystallographer's life so much easier ;-)
Cheers,
Tim
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goetting
On 23/10/14 16:39, Tim Gruene wrote:
Hello Jie,
doesn't Coot also read EM-maps?
It does.
In that case Coot should at least do it
right.
You can scale the cell using something like:
Calculate -> Scripting -> Python
scale_cell(1, 1.2, 1.2, 1.2)
the first argument is the model number.
I
Hello Jie,
doesn't Coot also read EM-maps? In that case Coot should at least do it
right.
Best,
Tim
On 10/23/2014 07:45 PM, jie liu wrote:
> Dear you all
>
> May I ask a question? I tried to dock my protein structure onto an
> cryo-EM density map. I loaded both the map file and my model coordin
I added zinc manually in the text version of the pdb file: have a look at other
crystal structures that contain zinc and copper, and see how they specify the
coordinates in the text file. Do the same in your one and hopefully it will
work!!
Good luck
Martina
Date: Thu, 23 Oct 2014 13:36:33 -
You could try situs colores, which does fitting of model into map
automatically.
Sent from Jack's iPhone
> On Oct 23, 2014, at 12:49 PM, "jie liu" wrote:
>
> Dear you all
>
> May I ask a question? I tried to dock my protein structure onto an cryo-EM
> density map. I loaded both the map file
Dear you all
May I ask a question? I tried to dock my protein structure onto an cryo-EM
density map. I loaded both the map file and my model coordinates into
Chimera. But it looks apparently that they are not in the same size scale.
My model is much bigger than the size of the EM map region wh
There is a bug in version 0.7.2 Coot that causes metal ions added via
the "place atom at pointer" to be a water. However, if you add the metal
ions through the "Get Monomer" dialog I think it will work OK.
___
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Dear ccp4bb Community ,i hope this email finds you well, i am trying to do add
Zink and Copper to my Superoxid dismuase Enzyme by Coot , i encountered two
problems.1- after adding Zink and copper by place atom at pointer << other <<<
writing ZN OR CU then running Refmac5 , both atom is turned
Thank all of you!
I have not " change the residue numbers so they do not overlap", so the
"change chain IDs" doesn't work when I try to change chain ID to an existed
chain ID.
Edit the PDB file is another good idea but when I have 20 SO4 in 20 chains,
things become boring.
Best wishes
One option is to change the chain IDs and residue numbers manually using a text
editor like nedit.
Sent from Jack's iPad
On Oct 23, 2014, at 6:03 AM, luzuok mailto:luzuo...@126.com>>
wrote:
Dear all,
Sorry to ask a simple question. There are many SO4 in my PDB file, one
belongs to a differ
This brings me a related issue with COOT: the spherical refinement does
not consider symeqs either or does it?
Xavier
Original Message
Subject:Re: [ccp4bb] molprobity clashscore, symmetry-related molecules?
Date: Thu, 23 Oct 2014 14:53:53 +0200
From: Jose Manuel Du
Hi Tim,
AFAIK MolProbity is not symmetry aware. If you want to detect cross-symmetry
clashes you can use WHAT_CHECK.
Cheers,
Robbie
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Tim
> Sent: Thursday, October 23, 2014 12:43
> To: CCP4BB@J
Molprobity does not look at contacts from symmetry partners, but only at
the asymmetric unit ones.
Unfortunately the clash scores in the PDB validation reports are based
on Molprobity and thus they won't count clashes outside the AU. See for
instance structures 4bmw or 1jkm. Both contain serio
Dear Lu,
You could do this in Coot as well if you are uncomfortable doing this in a text
editor. First change the residue numbers so they do not overlap, then change
the chainID.
Rather than putting all your sulfates in a separate chain, it is better to add
them to the correct protein chain. PD
Dear Lu,
- you could just edit the pdb-file by hand in a suitable texteditor (which is
what I usually do, in MacOSX TextEdit).
- smarter people may find a functionality in COOT, PDBSET or other existing
program that can do it.
- even smarter people would probably write a script or little program
Edit the ATOM records?
Sent on a Sprint Samsung Galaxy S® III
Original message From: luzuok
Date:10/23/2014 6:51 AM (GMT-05:00)
To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Merge PDB
chains
Dear all,
Sorry to ask a simple question. There are many SO4 in my PDB file, one
on 23/10/14 11:52 AM, Tim wrote:
> Hi everybody,
> Molprobity does not take into account contacts/clashes from
> symmetry-related molecules, or does it?
> Thanks in advance,
> Tim
>
Tim,
I am not sure. In my experience MolProbity reduce does not take crystal
contacts
into account (but reduce do
Dear all,
Sorry to ask a simple question. There are many SO4 in my PDB file, one
belongs to a different chain. I want to merge them into one chain, can anyone
tell me how to do this?
Best regards!
Lu Zuokun
--
卢作焜
南开大学新生物站A202
Hi everybody,
Molprobity does not take into account contacts/clashes from
symmetry-related molecules, or does it?
Thanks in advance,
Tim
PhD student position in structural studies on Plasmodium actin-based motility
We are looking for outstanding, highly motivated PhD student candidates to join
the group of Inari Kursula studying the structure and function of Plasmodium
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