Dear Yuan,
maybe you only have four - and a high solvent content.
Why don't you refine the four for a while with strict NCS, and then
use that improved model of one of them to do the original search again
(to satisfy yourself there are only four, or to find additional ones)?
On the other hand
Tim, Garib,
Sorry, maybe I'm missing something here but how does the user specify
that (s)he wants a TRANS link between standard amino-acids (ASN-GLY) in
this case? Isn't that the default? I always thought the answer was to
add a LINK record for those two residues in the PDB file using the
forma
Hi,
The drop in LLG for the 5th monomer could fit with your observation that it
didn't look good in the e.d. map.
There two things I can suggest (based on a similar experience with 6 mols. in
the a.u.)
1) I would definitely try other possible s.g.'s (very easy in Phaser).
2) You might want to
Ian,
Perhaps someone from one of the PDB deposition sites
could comment and verify my reading of this?
let me take the liberty. Your reading of PDB documentation is
absolutely correct. PDB format has got 3 types of links: SSBOND,
LINK and CISPEP. And indeed, residue numbers have no significanc
Yes. There is a confusion at the moment.
REFMAC LINK or LINKR record require link record that is absent in the
pdb.
If primary structure (sequence of amino acids/RNA/DNA and closeness in
3d of sugars) allow linking then links between residues used
automatically (TRANS/CIS/PTRANS/PCIS for pep
Hi,
"The LINK records specify connectivity between residues *that is not
implied
by the primary structure*." (my emphasis).
My reading of this is that it's the primary structure (i.e. the SEQRES
records) that specify that the residues are contiguous, *not* the
residue numbering. Perhaps someon
Hi Eugene & Jawahar
Thanks for responding!
> let me take the liberty. Your reading of PDB documentation is
> absolutely correct. PDB format has got 3 types of links: SSBOND,
> LINK and CISPEP. And indeed, residue numbers have no significance
> in the PDB whatsoever. The connectivity is given by S
Hi Ian,
I may be wrong here, in which case Jawahar will correct me.
I understand that to mean that it's the *order* of residues that must be
identical, not the residues themselves, i.e. it's valid for residues to
be omitted from the co-ordinate section (but not of course from the
SEQRES section
Hi Eugene
> If I were to deal with your example, I would look into distance
> profile between residues in coordinate section, which then
> gives answer to your question.
OK that's interesting, I hadn't realised that the interatomic distances
played an active role in determining connectivity: I ha
I am an imosflm novice and have a relatively simple question. I have a 360 deg
data set collected in two swathes of 180 deg (one with phi=0 and omega going
0-180 and the second with phi = 180 and omega going 0-180). What is the easiest
way to process the two datasets using a matching orientation
Dear Tom,
There is a straightforward way to do what you want.
It is probably simplest to start by reading in only the images from the
first segment (0-180). Then do the indexing, cell refinement and
integration in the usual way.
Then read in the second segment of data. You
If I were to deal with your example, I would look into distance
profile between residues in coordinate section, which then
gives answer to your question.
OK that's interesting, I hadn't realised that the interatomic distances
played an active role in determining connectivity: I had assumed the
w
I didnt realize the following:
You read in images from the two wedges collected with the same
crystal orientation.
mydata_1_###.img
mydata_101_###.img
Now when you index ,if you say use images from both "datasets"
mydata_1_###.img use image 1,90
mydata_101_###.img use image 30 , 120
The matri
Peter Zwart wrote:
Hi,
This can might well be due to wrong space group.
I suggest fixing the space groups by hand and running it in each
possible space group that is possible.
(P 31 2 1, P 32 2 1, P 3 2 1 are your options)
Did you run xtriage already?
P
2009/8/17 Yuan Cheng :
Hey,
I am try
Dear All,
Thanks to everyone who replied to my query about extracting an amino
acid sequence from a PDB file!
Here is a summary of responses of my query;
1. Use SwissPDBViewer
2. Use Pymol 1.2
load $TUT/1hpv.pdb
save 1hpv.fasta
# or by selection
save 1hpv_A.fasta, chain A
3. With Phen
Hi,
I have a question; recently I have encountered a few space groups which are
not supported by Refmac5. Examples include I2 and P21221. Both these space
groups have been identified as the best solutions for the two different
datasets I am working on using Pointless. However, I am faced with
diff
For the latter, P21221, you could reindex to get P21212, which is
supported.
-
===
You can't possibly be a scientist if you mind people
thinking that you're a fool. - Wonko the Sane
==
On Monday 17 August 2009 09:37:40 Arefeh Seyedarabi wrote:
> Hi,
>
> I have a question; recently I have encountered a few space groups which are
> not supported by Refmac5. Examples include I2 and P21221.
This is not correct. Refmac is perfectly happy with these settings,
although there are som
Hi,
Following mail (retrived from ccp4bb archieve) may help for intechanging the
cell axis.
HTH
S.Karthikeyan
==
I have a CCP4 script for this:
http://bl831.als.lbl.gov/~jamesh/elves/scripts/reindex.com
If you run the script like t
Yeah, I2 works indeed just fine (for me, right now).
Andreas
Ethan Merritt wrote:
On Monday 17 August 2009 09:37:40 Arefeh Seyedarabi wrote:
Hi,
I have a question; recently I have encountered a few space groups which are
not supported by Refmac5. Examples include I2 and P21221.
This is n
Hello All,
Can anyone tell me what are the programs used to find out the different
interactions in a protein.
I am talking about both intra and intermolecular interactions.
Thanks in advance.
Mariah
--
Mariah Jones
Department of Biochemistry
University of Florida
CCP4 has a program called "contact" where you can specify the chains, distances
and atoms you want to explore for contacts and it will give a list of all
contacts that fit that criteria, along with the distance. It works best if you
already have an idea for which chain interfaces you want to ex
Dear Crystallographers,
At the Canadian Light Source the Call for Proposals is currently open
AND accepting General User Proposals.
* Macromolecular Crystallography (08ID-1 beamline)
* Deadline: September 2, 2009
* Scheduling Period: October 27 - December 18,
Hello all,
I have incomplete data from two different crystals. Is there a
program in ccp4 that I can use to merge the two scaled datasets? I
used CAD and scaleit, but it does not give any scaling statistics like
completeness and Rmerge. Any help would be appreciated.
-Donald.
If you want to treat the end result as a single dataset, you're probably
better off combining unmerged datasets (two different batches in
scala, or two different scaling sets in scalepack).
As far as I understand it, the data model in the mtz files
(project/crystal/dataset/column) isn't reall
Hi all,
I am a novice working on protein structure. When I pick water using COOT, too
many waters picked, filling in the whole cell. My question is how can I
determine which water is needed, which is not needed?
Hi Antonio,
My question is how can I determine which water is needed, which is not
needed?
may be this will give you some clues - here are the approximate criteria
for water picking that are used in automatic water picking and
refinement in phenix.refine:
1) peak at mFo-DFc map is higher
Actually, drag-and-drop DOES work, and is *dead* handy!
(But a considerable annoyance: you HAVE to open the sector to be able
to click on the matrix line -- and then you have to drag that matrix
past all the 300 (or whatever) images to get to the next sector. For
many images, this really slo
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