On 16/05/2024 01:51, Lucas Bleicher wrote:
--
Dear all,
I've been outside of the field for a few years (I have very fond
memories of the 2008 Crystallographic Computing School, but did a lot
of different stuff since then), but I'd love to come back and figured
this would be the best place to
Dear all,
I've been outside of the field for a few years (I have very fond memories
of the 2008 Crystallographic Computing School, but did a lot of different
stuff since then), but I'd love to come back and figured this would be the
best place to ask - what are the go-to resources today for those
Thank you to all who provided helpful suggestions so far.
A few things I'd recommend for this particular beamline (which I have
been running for 20+ years)
Do NOT collect one wavelength at a time. This was a good strategy on old
beamlines with noisy detectors and slow, drifty monochromators.
On 15/05/2024 19:03, Paul Emsley wrote:
On 13/05/2024 17:38, Otsile Mojanaga wrote:
*From:*Otsile Mojanaga
*Sent:* Monday, May 13, 2024 3:29 PM
*To:* Paul Emsley
*Subject:* RE: [ccp4bb] Request for help in optimizing Coot for AMD
5950x CPU and RX6600XT GPU hardware PC
Dear Paul/All
Thank
The old BNL PDB format documents are available at
https://www.wwpdb.org/documentation/file-format
I looked at the Feb 1992 document to be certain that my memory was
correct [I am 6 days shy of 82 and am reassured that my recollection
was,in fact, correct] for information about the representati
It says in aforementioned docs:
"Alignment of one-letter atom name such as C starts at column 14, while
two-letter atom name such as FE starts at column 13.
"
and no, hopefully they don't mean that, since their example shows plenty
of 2-letter and 3-letter atom names starting at column 14 in t
'CA' for carbon-alpha is a 2-letter atom name so applying the rule exactly
as stated it should start in column 13; it states that only 1-letter atom
names (C, N, O) go in column 14. This must be a case of poorly-written
documentation; it must mean 'element symbol' not 'atom name' in those cases
wh
On 15/05/2024 18:45, Filipe Maia wrote:
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phi
It is, I think you would agree, unconventional to put a CA label for a
main-chain carbon at positions 13 and 14 (I have never seen such a
thing). But is it wrong ("Incorrect" - as Harry labels it)? In this
case, putting "CHA" in positions 13-15 is unconventional (again, I have
never seen such a thi
Hi Robbie
I’m not actually using PDB files of proteins - I’m using the PDB format files
in PDBeChem, because at the moment I’m interested in doing stuff with
ligands/substrates/etc. The charges I’ve seen so far seem to be not quite what
I’d expect, but I’m prepared to work around that.
Harry
On 13/05/2024 17:38, Otsile Mojanaga wrote:
*From:*Otsile Mojanaga
*Sent:* Monday, May 13, 2024 3:29 PM
*To:* Paul Emsley
*Subject:* RE: [ccp4bb] Request for help in optimizing Coot for AMD
5950x CPU and RX6600XT GPU hardware PC
Dear Paul/All
Thank you for the response. I am on Windows 11
On 15/05/2024 11:28, Harry Powell wrote:
Hi folks
[...]
I noticed this because I was encouraged to try Moorhen and found that a HEM
(apparently written by this module) did not have the atoms connected with bonds
in the display.
Q: Is it necessary to check columns 77-78 if I really want to be
Dear all,
On behalf of the UK cellular structural biology community, with support from
Diamond and Instruct-ERI (UK centre), we would like to alert all UK based
groups using or intending to use CryoEM as part of their research, the
opportunity to attend a one-day community meeting together wi
Hi Harry,It might be better now, but there used to positively charged aspartates in the PDB. You have a better chance taking charges out of the CCD for your atoms of interest. I'm not saying all charges in the CCD are correct, but they are much more reliable. If you find errors, please report them
> It sounds as though you need the power of the script. You can (from memory)
> run pdbcur to drop the aniso lines and hydrogen atoms, which helps.
Or from command-line:
gemmi convert --anisou=no --remove-h in.pdb out.pdb
> You could probably get it to delete everything except CA's too.
this wo
Dear Jon,
If I understand your question right, I would use Gemmi for this purpose:
https://gemmi.readthedocs.io/en/latest/mol.html
https://gemmi.readthedocs.io/en/latest/analysis.html
It's not in GUI, it involves scripting in Python. It's a very powerful
tool and capable of working with both PD
For those wanting a text editor solution, there is the purpose built pdb-mode
plugin for (x)emacs which works under most operating systems.
The download location has moved around a bit, but a current version is
available from
https://github.com/mmagnus/emacs-pdb-mode/
with more details at
https
Hi
This is very, very useful and hits on the four-letter name problem that I am
encountering - thank you. Saves me trying to produce a new design for a
circular object with an axle…
For the files that I am trying to use, columns 77-78 are present (actually,
columns 79-80 are there so I can rea
You could probably get it to delete everything except CA's too.
Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
Sent from Proton Mail mobile
Original Message
On 15 May 2024, 13:22, Jon Cooper wrote:
> It sounds as though you need the power of the script. You can (from mem
It sounds as though you need the power of the script. You can (from memory) run
pdbcur to drop the aniso lines and hydrogen atoms, which helps.
Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
Sent from Proton Mail mobile
Original Message
On 15 May 2024, 13:11, Hughes, Jon
hello CCP4 people,
rather off-topic: is there a purpose-written windows editor for PDF files? with
interleaved anisotropy lines, missing column delimiters etc., simply extracting
the B-factors for Ca atoms is hard work using a standard character editor.
would anyone think of working with DNA wit
It would also be good to check the monomer library (expanded with any
user-supplied dictionaries). Cases where an element in columns 77-78 exists
and it does not agree with the component definition should probably be
flagged up.
Cheers,
Paul
On Wed, 15 May 2024 at 12:39, Marcin Wojdyr wrote:
>
>
> > • Alignment of one-letter atom name such as C starts at column 14, while
> > two-letter atom name such as FE starts at column 13.
>
> indicating a rule does exist.
There are programs that don't read/write the element from columns
77-78, so this rule still matters, but using it is less reli
Hi Harry,Deducing the element from the atom name has always been unreliable so since PDB version 3 you have to get it from columns 77-78. There is no implied element in the atom name anymore.HTH,RobbieOn 15 May 2024 12:28, Harry Powell <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:Hi folks
Sorry - just read that
> • Alignment of one-letter atom name such as C starts at column 14, while
> two-letter atom name such as FE starts at column 13.
indicating a rule does exist.
Harry
> On 15 May 2024, at 11:54, Harry Powell
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>
Hi Ezra
Thanks for this.
In other words, would it be true to say that there are no actual rules about
what appears in columns 13-16 because “it's a rose by any other name”?
Harry
> On 15 May 2024, at 11:38, Ezra Peisach wrote:
>
> If you take a look at
> https://www.wwpdb.org/documentation
If you take a look at
https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM
you will see the following:
77 - 78 LString(2) element Element symbol, right-justified.
Going by atom name will get you in trouble. As you stated calcium vs
Calpha. The elem
Hi folks
I’m sure that this has been answered many times before (I’m sure that when I
was young I even read it here…), and I *know* that we should all be using
mmCIF, but I’m using PDB format files generated by a popular Python module and
I wanted to check the output against a definitive format
Hi all,
I want to remind you about our next industry talk by Brannon Batson a hardware
design engineer at D. E. Shaw Research. The talk "Using specialized hardware
pipelines to massively accelerate molecular dynamics simulations in Anton 3" is
online Wednesday 29 May 2024, 15:00 UK time. Free re
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