;
> I would use the function new_molecule_by_symop
>
> e.g.
>
> # python
> imol = new_molecule_by_symop(0, "Y,-X+Y,Z+1/6", 0,0,0)
>
> then do this 5 more times selecting the other symmetry operators that
> generate the helix around the z axis..
>
> or the attached script
Yes I would do it that way by clicking on the ones I want to see -
then saving them and then reading them back in. You can change the
chainids so Coot makes them different colours which might help.
Things might be easier in PyMol if you want interactive control over
the colours for a picture say.
c
udos to Paul Emsley for this tool).
all the best
Martyn
Martyn Symmons
Cambridge
On Fri, Dec 9, 2016 at 10:12 AM, Smith Lee
<0459ef8548d5-dmarc-requ...@jiscmail.ac.uk> wrote:
> Dear All,
>
> There is a pdb, once opended in coot, it was a monomer (space group P 65 2
> 2
and can be output to a file.
https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html
(You have to read your structures into Chimera before launching
Multi-align viewer).
hope that helps.
Martyn
Martyn Symmons
Cambridge
On Sun, Oct 30, 2016 at 10:54 AM, Anastassi
found,
> I believe the depositor's code will be used if it is available,
> at least one of mine was last year, so there is some use for Nigel's
> utility if you want to stamp your new compound with a rememberable name.
>
> eab
>
>
> On 06/21/2015 06:33 PM, Marty
ot;), that looks to me an oversight by PDB. It is hard to believe that
>> > PDB intended to use the 3D coordinates from one entry for the other,
>> > ligand or not. In fact, the restraints as described by the ligand
>> > dictionary should also be kept separate as that
By oversimplifying the situation here the PDB does not answer my
related point about competing crystallographers:
My scenario:
Group A deposits structure with new drug - gets their three-letter
code for example ZA3
they then get to check the coordinates and chemical definition of this ligand.
Bu
t the PDB
do a switch at the last minute?
Best wishes,
Martyn
Martyn Symmons
Cambridge
On Mon, Jun 8, 2015 at 3:12 AM, Lau Sze Yi (SIgN) <
lau_sze...@immunol.a-star.edu.sg> wrote:
> Thanks Eleanor for relaying my question from COOT and everyone that
> follows up with the thread
As this is a ccp4 bb we should mention the jsPISA server which is at
http://www.ccp4.ac.uk/pisa/
This is a very nice implementation of the PISA approach.
Another approach is to use the Chimera clash finding approach
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html
these anomalies.
I was only making a figure - but for sure someone will be trying to use the
data for something more useful and quantitative. This sort of stuff will make
their analysis difficult.
All the best
Martyn
Martyn Symmons
Cambridge
Mentioned recently but worth mentioning again?
I have used Chimera rmsd from its own command line (find the command line under
the 'favorites' tab) - it is scriptable.
https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html
Must have equal number of atoms matched - use selection to make t
I usually add a fiducial waters to the pdb file (chain Z - remember those?) -
or otherwise heavy atoms which will come up in a distinctive colour usually...
Then 'go to atom' under draw menu?
Martyn
Cambridge
Original message
>From : alejandro.virru...@yale.edu
Date : 09/09/2014 - 21:17 (
program authors.
all the best
Martyn
Martyn Symmons
Cambridge
Original message
>From : f...@bernstein-plus-sons.com
Date : 23/07/2014 - 16:20 (GMTDT)
To : CCP4BB@JISCMAIL.AC.UK
Subject : Re: [ccp4bb] correlated alternate confs - validation?
I agree that it would be excellent to be a
ptable.
I think there are cases where water alternate positions make sense so they
should be allowed I would argue.
All the best
Martyn
Martyn Symmons
Cambridge
Original message
>From : robbie_joos...@hotmail.com
Date : 23/07/2014 - 10:05 (GMTDT)
To : CCP4BB@JISCMAIL.AC.UK
Subject
Is n't the danger here that you are just fitting to noise generated by the rest
of the Unit Cell that you are ignoring. So it is easy to do a 'good bit' of
modelling in a specific region. Just like some tennis players have very good
serves but do not win matches.
_
differences to work with.
You could then work in the anomalous as a sort of SIRAS solution.
SeMet as isomorphous has been used previously in many structure solutions.
All the best
Martyn
Martyn Symmons
Cambridge
From: vijay srivastava
To: CCP4BB@JISCMAIL.
Dear V.
are you sure these are crystalline? - I have had similar growth from
'spherulites' that I thought was promising. But then when I went in with a
needle to break them for seeding, it turned out they were fibrous not
crystalline. This made me think they were a product of denatured protein
** Zachary A. Wood,
>>Ph.D. Associate Professor Department of Biochemistry & Molecular
>>Biology University of Georgia Life Sciences Building, Rm A426B 120
>>Green Street Athens, GA 30602-7229 Office: 706-583-0304 Lab:
>>706-583-0303 FAX: 706-542-1738
>>**
I agree some forum for community annotation and commenting would be a good
thing for users of structural data.
There was an attempt to do that with the pdbwiki project which was a community
resource for the bioinformatics community. Unfortunately pdbwiki has now folded
(see http://pdbwiki.org/)
I had thought that after discussion on this bulletin board we could find no
rational scientific reason why the PDB renumbers waters from the N to the C
term of the polypeptides (and 5' to 3' of nucleic chains?).
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1311&L=CCP4BB&D=0&P=12314
I think
at the PDB will clarify - when I ask them specific questions as
an individual then they don't bother replying - but if the bulletin board shows
sufficient interest then we usually get at 'Public Service Announcement' of
some kind ;)
All the best
Martyn
Martyn Symmons
Cambridge
Hi Dilip
the numbering can be given for the top and the bottom sequence only in
ESPRIPT
you enter the command to produce these in the SPECIAL COMMANDS AND
CHARACTERS BOX. You only get this box on the server input page if you select
the ADV version in the header - this is the ADVANCED ver
Yes, thanks Robbie
That is just my point - a structure submitted and then validated for paper
reviewers by the PDB can be changed almost completely after the paper is
accepted.
The data can be changed too and only stipulation seems to be that it cannot be
new data i.e. it has to have a date of c
I have recently had the same problem. But generally, the PDB will usually allow
a further 6 months hold for review or modifications to an already submitted
paper.
But what I wanted to say was that the correct term is 'withdrawal' if the entry
is removed pre-release - 'retraction' carries a pej
Not a pymol approach but I've noticed this dual mode display with transparency
is the default in Molsoft ICM browser if you toggle on ball and sticks
together with spacefill for the same atoms.
Molsoft ball-and-stick also shows the bond order or aromaticity of ligand atoms
- which I guess is a
s not obsoleted.
Sincerely,
Rachel Green
Rachel Kramer Green, Ph.D.
RCSB PDB
kra...@rcsb.rutgers.edu
Twitter: https://twitter.com/#!/buildmodels
Facebook: http://www.facebook.com/RCSBPDB
On 10/21/2013 6:28 AM, MARTYN SYMMONS wrote:
As a post
id at least that issue?
Thx, BR
From:CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of MARTYN
SYMMONS
Sent: Montag, 4. November 2013 15:17
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Comparison of Water Positions across PDBs
Thank you for that, Rachel
Even though the to
chains in the structure?
- appending all waters to chain A? Thanks. Andreas On 30/10/2013 11:57, MARTYN
SYMMONS wrote:
>>At deposition the PDB runs a script that renumbers authors' waters
according to a scheme based on the residue they are nearest from N to C
terminus along each ch
At deposition the PDB runs a script that renumbers authors' waters according
to a scheme based on the residue they are nearest from N to C terminus along
each chain. This renumbering started when waters were assigned to
macromolecular chains rather than getting a chain id of their own. I have
As a postscript it might be worth mentioning one problematic ligand that
suggested to me a way to correct some of the errors mentioned in this thread
R12 is indicated as 9-(4-HYDROXY-2,6-DIMETHYL-PHENYL)-3 in the most recent
Coot monomer library. But in the PDB ligand description it is
9-
Hi Oliver
a few years ago I used the ccp4 FFFEAR program from Kevin Cowtan for
this sort of domain search. It was very good but also quite
labour-intensive. I have not followed up since to see if it was updated
or the functionality was included in Buccaneer.
cheers
Martyn
Sorry to contradict,
But the mmCIF data model certainly does not seem to require hkl unique
within the reflection data.
Like CIF the mmCIF formalism has been developed to allow a complete
description of a diffraction experiment and the data arising from it.
There is a full description at
ht
Hi there,
To my knowledge the PDB does not include unmerged data in entries - you are
required to deposit the data that the coordinates were refined against.
I believe you can deposit other data which will be archived and can be
requested by other users - problem is that none of the distributio
n official
human-readable extended PDB format would really help.
Cheers,
Dirk.
Am 30.08.13 18:14, schrieb MARTYN SYMMONS:
Hold your horsemen!
Does not this option save us from 'formatagedon'?
We currently only have single letters or numbers for chains. But we could
easily agree to sw
the
case with most computing identifiers - however not many programs seem to pay
attention to the atom 'numbers' in any case.
Cheers
Martyn
Martyn Symmons (not Winn)
Cambridge
From: Dirk Kostrewa
To: CCP4BB@JISCMAIL.AC.UK
Sent: Friday, 3
have to make a call on which kind of backbone they will
>> feature in
>> within the pdb.
>> That is why there is 'D5M' for non-polymer deoxyAMP. Also known as ' DA'
>>when it
>> is 'DNA-linking' but so far not fessing up to life un
t is 'DNA-linking' but so far not fessing up to life under a third code
as 'RNA-linking'
Now is perhaps the time to ask for explanations of these nomenclature features
before they become hard-wired in the new pdb deposition system (however there
may be time - I refer you t
ages/wwpdbac-2010-report.pdf
or perhaps more pertinently:
'In early 2010, the annotation module will be put into service,'
(http://www.wwpdb.org/wwpdbac-pages/wwpdbac-2010-report.pdf)
Perhaps as in many things it is often better to travel hopefully than to
arrive...
Cheers
Mart
Dear Dave
I have found the Molsoft ICM browser useful for showing students
structures. There is a freely distributed version available for both ipad and
android. I have not used it for maps but I believe it can display them.
SGC Oxford originally showed me this software and have great exam
tarts with c axis reflections including 0,
0, l odd as well as even, which is sort of a hint here
From: MARTYN SYMMONS
To: CCP4BB@JISCMAIL.AC.UK
Sent: Tuesday, 16 April 2013, 14:30
Subject: Re: [ccp4bb] Puzzling Structure
Just as a postscript.
It has
Just as a postscript.
It has been pointed out to me that the space group was correct in the uploaded
PDB and in the mtz reflection file. And there was no editing of this data
pre-deposition.
I am sort of surprised how quickly people are to beat up on the authors in such
cases since we do not
Dear Robbie
A shame then that these 'helpful' annotators did not make use of Pavel's basic
sanity on the space group (*mentioned below) and check back to the one listed
in the uploaded PDB file.
I often wonder why the PDB does not make the deposited coordinate file publicly
available so that
acknowledgement too?
Yours perplexedly,
Martyn
Dr Martyn Symmons
Cambridge
From: Gary Battle
To: CCP4BB@JISCMAIL.AC.UK
Sent: Thursday, 14 March 2013, 10:27
Subject: [ccp4bb] PDBe website update: What's new
Dear all,
Twice a year, the Protein Data Ba
get an multiple fastA alignment of the
superimposed structures and explains the format.
Hope that helps.
Martyn
Martyn Symmons
EBI Cambridge
From: Eric Pettersen
To: CCP4BB@JISCMAIL.AC.UK
Sent: Monday, 16 July 2012, 2:17
Subject: Re: [cc
Posted on behalf of Dr Callaghan - please contact her directly.
4 year Ph.D. Studentship on RNase structure and metabolic control.
School of Biological Sciences.
University of Portsmouth.
Supervisor: Dr Anastasia Callaghan
Co-supervisor: Dr Sarah Newbury (Sussex Medical School)
Understanding
Attached is a picture of making the bookend setup - step b. shows the razor
levering up the flap from the plastic coverslip - be careful not to cut right
through (I have done that and the drop dries extra quick in such a case) also
be careful to apply the protein/well droplet as shown with to t
rtainly gave me some chunkier needles and gave them space to grow upwards.
Otherwise they flattened down as the droplet flattened with equilibration and
often they 'glued' themselves to the horizontal surface.
Hope it helps
Martyn
Martyn Symmons
Cambridge
___
Dear All
I may not have understood but if I run PDBe PISA
and go Interface>Details
then I get a table of the form eg for H-bonds
Hydrogen bonds
1 A:GLN 213[ NE2] 3.52A:SER 3[ O ]
2 A:ASN 112[ ND2] 2.77A:SER 3[ O ]
3 A:GLN 213[ NE2] 2.
-MPD
which wins out at 585 entries
http://www.ebi.ac.uk/pdbe-srv/view/search?Chemical_code=MPD
cheers,
Martyn
Martyn Symmons
Cambridge
--- On Thu, 25/11/10, Linda Schuldt wrote:
> From: Linda Schuldt
> Subject: Re: [ccp4bb] DTU vs DTT ?
> To: CCP4BB@JISCMAIL.AC.
I have had excellent service from Mike Weldon (m.a.wel...@bioc.cam.ac.uk) at
PNAC University of Cambridge Biochemistry. He will accept outside orders
subject to capacity being available.
http://www.bioc.cam.ac.uk/pnac/
Cheers
Martyn
Martyn Symmons
EBI - Cambridge
>
> On 24/09/
transfer bands
on binding to cys.
So make sure you include EDTA or similar chelator (after metal affinity
obviously). Oxidation is more likely if your protein unfolds - so try to keep
it happy with nicely buffered pH and any ligands that might stabilize it.
Good luck.
Martyn
Martyn
this point I guess the copies can
bump and so apply a force on each other but that is a local, and likely to be
perturbing, force.
best wishes
Martyn
Martyn Symmons
Cambridge
--- On Thu, 23/9/10, Ian Tickle wrote:
> From: Ian Tickle
> Subject: Re: [ccp4bb] Effect of NCS on estim
That's a good point, Ed
Based on the formula: HO CH2-(CH2-O-CH2)n-CH2OH, PEG MW = 44n+62, a table of n
to MW goes like below which gives an idea of what range is possible. Someone
maybe knows what polydispersity can be expected from the synthetic process. As
you say though, a specific range cou
Dear Klaus
depends how many missing residue you want advertised in the
header of your deposited file. The pdb will put in a special Remark 610 and
Remark 615 to indicate any missing residues from your heterogen list. However
the policy is not to list every missing (or zero occup
precipitate settles strongly into a circle at the
bottom of the droplet then I would say this is a bad sign :(
Hope this helps.
regards
Martyn Symmons
EBI, Hinxton, Cambs. UK
--- On Thu, 10/6/10, joybeiyang wrote:
From: joybeiyang
Subject: [ccp4bb] How to distinguish microcrystalline
Sounds like good advice - I suppose that since pure water un-freezes last, you
could have protein concentration inhomogeneities? So in areas where the protein
concentration is raised it could start to feel like crashing out.
All the best
Martyn
Martyn Symmons
Cambridge
- Original
periment(s) is useful to see - if only
for people to plan their own experiments building on past experience.
Best wishes and regards
Martyn
Martyn Symmons
Cambridge
- Original Message
From: Ian Tickle
To: CCP4BB@JISCMAIL.AC.UK
Sent: Wednesday, 14 April, 2010 15:42:51
S
final_ model in the _original_
map?
In the real world ;) I don't see that happening anytime soon
all the best
Martyn
Martyn Symmons
Cambridge
- Original Message
From: "Soisson, Stephen M"
To: CCP4BB@JISCMAIL.AC.UK
Sent: Tuesday, 13 April, 2010 19:09:12
Su
might be nice to see too. There used to be a heavy atom database for
such like things - not sure of the current status of that.
see you
all the best
Martyn
Martyn Symmons
Cambridge
From: Frank von Delft
To: CCP4BB@JISCMAIL.AC.UK
Sent: Monday, 12
). Just how brief
this is depends on your dexterity and also how well the crystal is engaged in
the loop. My crystals were not very happy about the cryo but I could make it
brief enough to get them out intact.
Good luck,
Martyn
Martyn Symmons
MBU Cambridge
- Original Message
From
buffer, salt, reductant, detergent, metal ions,
etc will be concentrated up alongside the protein.
cheers
Martyn
Martyn Symmons, MBU Cambridge.
As an aside I heard that the 1:1 derives from the days when pipettes could not
be trusted with such small volumes. The 1:1 ratio is the best chance
e a boon
and a blessing
cheers,
Martyn
Martyn Symmons
MRC-MBU
- Original Message
From: Gerard DVD Kleywegt
To: CCP4BB@JISCMAIL.AC.UK
Sent: Tuesday, 23 February, 2010 14:57:02
Subject: Re: [ccp4bb] Per-residue RMSD for multiple structures?
Thanks Stephen!
I was going to sugg
hoose loops with care -
maybe go with litholoops?
Martyn
Martyn Symmons
MRC-MBU
Cambridge
- Original Message
From: Kelly Daughtry
To: CCP4BB@JISCMAIL.AC.UK
Sent: Thursday, 21 January, 2010 14:27:58
Subject: Re: [ccp4bb] smeared spot in diffraction
Fengxia,
To me the diffra
t crystals (I'd
like to stick with this cut-off as the physical and sealing properties of other
membranes might be different). Or if someone has a higher MW cheap alternative
protein/condition?
Best wishes - agus 'Bliadhna Mhath Ur Dhuibh Uile' as we say in gaelic.
Martyn
-
f 6ul..."
So perhaps sometimes I am just not respectful enough to deserve crystals ?
good wishes to all
regards,
Martyn
-------
Martyn Symmons
MRC-MBU Cambridge UK
'Chan fhiosrach mur feòraich.'
Gaelic proverb -
Nothing asked, nothing learned.
july 2008 pdb I
think (culled to 99% seq ident. is the best one). But could be something more
recent available?
Good luck
Martyn
Martyn Symmons - Cambridge
From: Patrick Loll
To: CCP4BB@JISCMAIL.AC.UK
Sent: Monday, 14 December, 2009 20:02:53
Subject: [ccp4bb] 3D
Discussing with Fred Vellieux offlist I suggested the following: would it be
useful to have a sort of 'simulated annealing' of the B-factor values? - in
refinement I often try resetting them to higher values (Moleman has a function
for this I think) and then see which ones refine back down nicel
IMHO this is a bad idea as the restraints can give undue weight to poorly
ordered residues in order to favour the tighter distribution that you are
specifying.
I have found bindividual.inp to perform at low resolution reasonably well, and
I think it is more realistic than group B-factors. The
Dear All
- I am looking for a multiple alignment program that will work
with upper and lower case letters in the sequences and preserve them through to
the output. I used to use PILEUP but that is no longer supported here.
Any suggestions much appreciated.
regards
%a)
cmd.select("s2","%s`%d"%b)
if cmd.select("(s1|s2) and not ?skip"):
if cmd.dist("tmp","s1","s2") < 20.0 :
print '',cmd.iterate("s1|s2",&
Dear Joe
one thing that has helped me a lot with similar problems is G.
Kleywegt's SPASM - you make your best guess of the mainchain then add a total
guess of the sidechains (say with mutate in COOT - choosing the top rotamer).
Then you cut out the loop and run this in SPASM as a s
rches with crosslinking
restraints. It works nicely interactively if you explore the receptor surface
by centring the search on different residues.
Best wishes
Martyn
Martyn Symmons
Department of Pathology
University of Cambridge
Martyn
Martyn Symmons
Department of Pathology
University of Cambridge
Message Received: Apr 13 2007, 01:37 PM
From: "John Walker" <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
Cc: [EMAIL PROTECTED]
Subject: Re: [ccp4bb] oxi
structures
cheers
Martyn
Martyn Symmons
Department of Pathology
University of Cambridge
Message Received: Apr 12 2007, 06:06 PM
From: "Flip Hoedemaeker" <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
Cc:
Subject: Re: [ccp4
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