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
On 15/05/2024 18:45, Filipe Maia wrote:
CAUTION: This email originated from outside of the LMB:
*.-owner-ccp...@jiscmail.ac.uk-.*
Do not click links or open attachments unless you recognize the sender
and know the content is safe.
If you think this is a phishing email, please forward it to
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
On 13/05/2024 13:03, Otsile Mojanaga wrote:
Dear All
I have been using coot as part of my normal workflow but since last
week I have been having issues with Coot after I built my own PC which
contains the following Hardware:
CPU - AMD Ryzen 9 5950X 16-Core Processor - 16 Cores, 32 Threads
On 13/05/2024 11:23, Laurent Maveyraud wrote:
Hello,
I like the function "update NCS ghosts with local match" found in the
calculate/NCT tools menu. It's really helpful when NCS is not really
strict. However, I find it clumsy that you have to go in a submenu to
get it, so I would like to
On 26/04/2024 02:44, Paul Emsley wrote:
On 25/04/2024 16:07, Simon Vecchioni wrote:
Paul,
Many thanks for fixing the [simple mutate] button for DNA in
v1.1.08--works like a charm!
I would ask about two other DNA features--
1) The [add terminal residue] button seems unresponsive for DNA
On 25/04/2024 13:01, FREITAG-POHL, STEFANIE wrote:
I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement:
I put in a smilesstring and the ligand is written ok, but since I can
only chose already 'taken' 3-letter-codes the refinement always
crashes as there is a clash with
On 25/04/2024 16:07, Simon Vecchioni wrote:
--
Paul,
Many thanks for fixing the [simple mutate] button for DNA in
v1.1.08--works like a charm!
I would ask about two other DNA features--
1) The [add terminal residue] button seems unresponsive for DNA,
I see what you mean. From the
On 04/04/2024 02:27, Simon Vecchioni wrote:
Dear CCP4 Wizards,
Hello Simon.
I've upgraded to COOT v1.1.07 from 0.9.6, and am working on DNA model
refinement.
exciting.
The current setup does not seem to let me sequence mutate (simple
mutate or mutate residue range), as it's hard coded
On 18/03/2024 10:26, Petr Pachl wrote:
--
Does anybody know if there is a function (or procedure) how to get info
about closest symmetry atom? For picking coot is performing something
like "Model atom pick (if failed) -> Symmetry atom pick", then it
returns to console and atom info at the
On 08/03/2024 10:47, Dean Derbyshire wrote:
Hi, I’m almost certain this has been addressed before so apologies…
but is there a trick to import EM map files into COOT, it keeps
crashing when I’ve tried.
My guess is that your computer is running out of memory. A pint into a
quart port?
On 16/02/2024 01:45, zx2...@connect.hku.hk wrote:
Dear all,
Hello Xin,
I encountered an issue while attempting to calculate the RMSD between
two PDB files (each containing 4 ASUs)
do they really though?
using the SSM Superpose tool in Coot. Unfortunately, the tool was
unable to
I agree with James and for the record, the function that it seem to me
that you want is
set_residue_to_rotamer_name(imol, chain_id, res_no, ins_code, alt_conf,
rotamer_name)
Paul.
To unsubscribe from the CCP4BB list,
On 21/11/2023 12:02, Yahui Liu wrote:
Dear all,
I got a protein crystal dataset of 4.3 A and would like to some the
structure with MR.
Now I am suffering with the refinement.
Just for the record, then intention of refinement is not to make you suffer.
Paul.
On 04/11/2023 14:04, Sam Tang wrote:
Dear community,
I am solving the structure of a complex between proteins A and B,
where A is a protein with known homologs and B is a novel protein
isolated from plant. The diffraction data was at 1.9 Ang collected
in-house, indexed to P321. Using A as
On 19/09/2023 09:34, Deborah Harrus wrote:
Dear all,
Dear Deborah,
wwPDB asks users and software developers to review code to remove any
current limitations on CCD ID lengths, and to enable use of PDBx/mmCIF
format files. Example files with extended CCD IDs are available via
GitHub
On 17/08/2023 11:18, Palm, Gottfried wrote:
>
> I copied the EDO.cif from the library and changed the C1-C2 torsion
> angle definition to
> EDO sp3_sp3_4 O1 C1 C2
> O2 180.000 10.0 1
>
> After loading EDO in coot via "import cif
M. Lawson
Department of Biochemistry and Metabolism,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Web: https://www.jic.ac.uk/people/david-lawson
Email: david.law...@jic.ac.uk
-Original Message-
From: CCP4 bulletin board On Behalf Of Paul Emsley
Sent: Tuesday, July 18, 20
On 08/08/2023 09:57, Schaefer, Martina wrote:
>
> Hello,
>
>
>
> I have a problem running pandda.inspect after successful running
> pandda.analyse with the newest ccp4 version of pandda.
>
>
>
> What do we have:
>
> * We use Ubuntu as our Linux system
> * We installed CCP4-8.0.012
> *
On 02/08/2023 13:53, Andrea Smith wrote:
Dear all,
I used refmac in CCP4Cloud and then I opened the generated .pdb and
.mtz from the CCP4Cloud job both in Linux Coot 0.9.6. and WinCoot
0.9.6. I can see different anomalous maps in Coot and Wincoot - see
attached printscreen where on the left
On 18/07/2023 03:55, Mark Saper wrote:
I reported this problem to Paul and to the group at least 2-3 months ago.
Your email didn't arrive.
Just to be clear, Coot's real space refinement is not (was not) broken,
the problem is that the version of Coot distributed by CCP4 and the
version of
seems fine. Maybe this is a bug in
Coot 0.9.8.8 EL?
I doubt that it's a bug in Coot. A bug in Ventura though... that does
seem possible.
Paul.
Zhen
*From: *Paul Emsley
*Date: *Saturday, July 15, 2023 at 11:04
*To: *Gong, Zhen , CCP4BB@JISCMAIL.AC.UK
*Subject: *Re: [EXTERNAL] Re
thing. Do you have any clue what could be the problem?
Well, Shift G does a Reverse JED Flip (as does Ctrl Shift G) - that
sounds similar to what you are seeing. Perhaps you have the Caps Lock
key pressed?
Paul.
Zhen
*From: *Paul Emsley
*Date: *Saturday, July 15, 2023 at 02:40
On 15/07/2023 03:22, Gong, Zhen wrote:
Dear all,
Can anyone kindly tell me how to change the keyboard shortcuts
settings in Coot? My “control + g” did not go to the specified atoms
anymore. I might have changed the shortcut settings by accident. Thank
you very much for your help!
Ctrl-G
On 15/07/2023 03:49, Subramanian, Ramaswamy wrote:
I have over 50 pdb files that I have downloaded from PDB that all have
the same ligand bound.
I wamt to superpose the ligands (and move the protein coordinates
using that matrix). The goal is for me to see how difference in
ligand
On 14/07/2023 08:52, Jonas Emsley wrote:
Dear All
We have a crystal structure with O-glycans for the first time attached
to a Ser and a Thr sidechain
If anyone can recommend the procedure for adding these in coot and
refining them in phenix /refmac that would be greatly appreciated
Hi
On 06/07/2023 08:51, Tom Peat wrote:
Hello All,
I just had a very strange experience- I rebooted my linux machine
(Ubuntu jammy 7.81.0) and tried to start up Coot and received the
following error message:
It is my understanding that jammy jellyfish, by default, uses Wayland as
the
On 27/06/2023 15:01, Afshan Begum wrote:
Dear expert,
I am currently working on building my cryo-EM data using COOT.
However, I have encountered an issue when trying to add monomers such
as Glycerol or BCT using their letter code from the "Get monomer"
option in COOT. Whenever I attempt to
The Coot API is quite useful for this sort of thing
imol = 0 # replace as needed
residues = residues_matching_criteria(imol, lambda chain_id, res_no,
ins_code, serial: residue_name(imol, chain_id, res_no, ins_code) == "HOH")
refine_residues(0, residues)
Regards,
Paul.
On 26/06/2023
On 06/06/2023 08:19, Goldman, Adrian wrote:
I’m hoping for a coot implementation that allows immersive stereo…
Well, (a) you're in luck - Coot is Free Software and can develop it
however you like. I am happy to collaborate and handle the technical
details of integration and distribution. If
t; to
"peptide" and press enter in the entry, then "Apply"
Now you can refine your CSO in Coot.
Paul.
Best,
Nick Clark
On Fri, May 26, 2023 at 10:37 PM Paul Emsley
wrote:
On 27/05/2023 03:23, Nicholas Clark wrote:
Hey Paul,
I found the dictionary entry
On 27/05/2023 03:23, Nicholas Clark wrote:
Hey Paul,
I found the dictionary entry for CSO, it appears to be in the
"peptide" group (under CCP4-8.0->lib->data->monomers->c->CSO.cif):
"loop_
_chem_comp_alias.comp_id
_chem_comp_alias.group
_chem_comp_alias.atom_id
On 27/05/2023 00:43, Nicholas Clark wrote:
I have a cysteine residue that is oxidized and needs to be modeled as
CSO. In the past, when "replace residue" was used to substitute for
CSO, the CSO would "behave" during real-space refinement and
essentially take the place of the Cys. However,
On 19/05/2023 10:28, Frank von Delft wrote:
Hello - as in the subject line, does anybody know of, or have, code
that will parse (1) a PDB (or mmCIF?) file with a ligand, and (2) the
restraints CIF file used in refinement, and generate a .mol (or .sdf)
file?
Isn't this a bit of strange
On 28/04/2023 08:41, StrBio wrote:
CAUTION: This email originated from outside of the LMB.
Do not click links or open attachments unless you recognize the sender
and know the content is safe.
*.-owner-ccp...@jiscmail.ac.uk-.*
Hello,
Can you suggest how to make isopeptide bond in coot and
Last week I was using 13.2 and could reproduce the snap iconification on
delete item.
This morning I updated to 13.3 and the iconification problem is no more
- so the update fixed it. Apple didn't mention XQuartz or Coot in the
release notes (fwiw).
Paul.
On 06/03/2023 07:35, Armando Albert wrote:
I want to align several structures we obtained from a fragment screening
campaign and cluster them according to RMSD.
To what end, may I ask?
I would use LSQKAB, parse the log files for the RMSD and create an input
file for R.
(One cannot just do
Hello Elsa,
On 30/12/2022 17:13, Elsa Garcin wrote:
Is it possible to run coot on MacOS Ventura and xquartz version 2.8.4?
I believe so, but people have reported minimizing window when they try
to do so.
I tried installing coot with homebrew (instructions from Scottlab webpage),
This is a
On 17/11/2022 19:03, Alessandro S. Nascimento wrote:
Dear all,
We are refining a 24-mer complex composed of 12 copies of protein A
and 12 copies of protein B. Since the resolution is not very high
(~3.0 Ang), we will probably want to copy the modifications made in
Coot for one chain to the
On 09/11/2022 13:59, Deepak Deepak wrote:
Dear CCP4 users,
I am working towards solving a protein-ligand complex structure. The
ligand is 5.2 kDa (495 atoms) and made of 3 distinctive repetitive
monomers. [...]
I will happily provide more information if I am missing something here.
On 20/10/2022 02:06, Jiang Xu wrote:
Hi Garib,
I deleted the Met residue and imported the nle.cif file
Import the dictionary for NLE, make sure that the group is L-peptide,
then centre on your Met and Calculate -> Modelling -> Replace Residue -> NLE
Paul.
Coot is not (yet) an official part of brewsci, so the goocanvas update
bonked coot.
This morning I uninstalled my coot and rebuilt it with YoshitakaMo's
coot.rb. The second time it worked (i.e. build and installed just fine).
You can see from the patch
On 17/09/2022 15:48, Marion Schuller wrote:
>
>
>
> Dear CCP4bb community,
>
>
>
> I am writing regarding a problem with the refinement of an isomer
> ligand. I try to refine a structure which has the ligand “Carba-NAD”
> (as beta isomer) bound. This ligand is already in the pdb database as
>
Hopefully 0.9.8.4 should fix that.
Paul.
On 16/09/2022 13:54, Jan Dohnalek wrote:
This has been quite variable in (several?) last versions of Coot.
I have some three latest versions available and when one does not work
I start another one. Sad but true.
Jan
On Thu, Sep 15, 2022 at 11:39
A spectre is haunting structural biology - it is the spectre of the PDBx
format.
We at CCP4 are interested in providing tools that are equivalents of
those that one might have trivially made with utilities such as grep or sed.
For example:
delete the hydrogen atoms
extract the
On 07/08/2022 07:00, Cryo EM wrote:
Hi everyone,
I am using Coot 0.9.8.3 EL (ccp4) on my iMac M1 with MacOS Monterey.
The phenix version I am using is 1.20.1-4487.
At the end of validation run or real space refinement for my cryo-EM
map, I want to fix the problems in the model interactively
On 06/08/2022 09:08, Cryo EM wrote:
Hi everyone,
I am trying to mutate modified RNA nucleotide to standard nucleotide
by coot using "Simple Mutate" button. But it is not working despite
selecting the correct residue from the standard base list that pop up
on clicking "simple mutate button".
I wonder if others are curious about (or know how to solve) the
following problem:
I am looking at a PDB file that I've downloaded from a wwPDB site and I
would like to see the AlphaFold model(s) overlaid. What the best (or
easiest) way of doing that? (let's imagine that I can do a bit of
On 27/07/2022 01:44, Dale C wrote:
Hi all,
I recently updated my ccp4 package to Program suite v8.0.002 and i have now run
into a few issues with other programs. The issues are highlighted below...
- When i click 'Open in Coot' on any output through Phenix (so far only tested
phenix.refine
On 18/07/2022 07:59, Cryo EM wrote:
Hi all,
I am working on a pdb of RNA where I intend to change the modified
nucleotides to their parent unmodified original residues. For example,
PSU to U, 1MG to G and so on.
I was wondering if there is a better way to do that by either manually
editing
On 13/07/2022 19:18, Ravikumar wrote:
I would like to calculate One-dimension electron density profiles of
the different number of ions bound to an ion channel. Are there any
programs in CCP4/ Phenix which can do the same job as the MAPMAN
(UPPSALA electron density server) program to
On 11/07/2022 12:36, Colin Levy wrote:
Hi All,
Is there an equivalent functionality to Phenix.refine Sequence check
in CCP4? A quick alignment tool of model sequence from pdb to the
provided sequence?
It seems to me there are a number of ways that one can check a model
(and map)
On 09/07/2022 12:36, Goldman, Adrian wrote:
On a related theme, Paul, I often find that the undo button doesn’t
work, but I can’t figure out why it sometimes does and sometimes
doesn’t. Is this something to do with how I open .pdb files - that
somehow Coot can’t find the backup files, even
Is there an option to save the session automatically every 10-15
minutes or so?
And now to actually answer your question:
yes: Edit -> Settings ->Enable Quick-Save Check-pointing... (the default
is 30 seconds)
On 08/07/2022 16:30, Oganesyan, Vaheh wrote:
Hi All,
Sorry for posting on CCP4BB.
This is an appropriate venue for such a message.
Coot installed together with latest CCP4 on Win10 crashes time to time
with no messages/warnings. Is there an option to save the session
automatically
The ligand is acetamido-thiadiazole-2-sulfonamide and has code AZM - do
your PDB atom names match the CCD?
To unsubscribe from the CCP4BB list, click the following link:
On 01/07/2022 04:50, Joel Tyndall wrote:
Hi folks,
I frustratingly cant find “maltose” as a ligand in the pdb or ccp4
database. Does any one have the code for the ligand? Surely its been
used before.
In Coot:
File -> Search Monomer Library -> "maltose" -> Search
-> MAL
Although it may not be apparent, there has been a lot of work going on
in Acedrg development regarding Boron.
One cannot say the same for Coot though and I can reproduce the
behaviour reported by Rafa Dolot. If/when I can fix it, it will be
available in 0.9.8.4.
Paul.
On 06/06/2022
On 27/05/2022 19:22, Jan Abendroth wrote:
Hi all,
not sure if this appropriate for this BB, since right at the interface
between CCP4, Coot and Phenix.
I wonder if someone else also experiences these issues after upgrading
to CCP4 8.0 (or 8.001) and with that to Coot 0.9.8.1. This happens
On 11/04/2022 15:55, Martin Moche wrote:
Dear colleagues,
We are refining a structure where an acetate ion (ACT) binds a zinc
ion, Zn+2 (ZN), using an excellent quality 1.38Å dataset, [...]
When doing COOT sphere refinement, the acetate ion moves on top of the
ZN? like the ZN was not
On 07/04/2022 09:24, Munoz.Ines wrote:
Dear all,
Is there any program or server that automatically assign the secondary
structure elements into a pdb generated by alpha fold?
If you are using Coot, you can use
Calculate -> Scripting -> Python
add_header_secondary_structure_info(imol)
On 06/04/2022 07:05, Laurent wrote:
Good morning (French time…)
Two unrelated questions…
Using Coot, I would like to define some key binding… How can I find
the command that is actually issued from an option in the
« calculate » menu ? I would like to define a key binding for the
function «
That, for the record, is more or less what Ralf said 18 years ago.
On 01/04/2022 23:38, Pavel Afonine wrote:
It's April 1st today, isn't it? -;)
On Fri, Apr 1, 2022 at 3:15 AM Paul Emsley
wrote:
Coot 1
18 years after the release of Coot 0 it's time that I actually
released
Coot 1
18 years after the release of Coot 0 it's time that I actually released
Coot 1.
Coot 1 is a major change beyond Coot 0. It has required a lot of writing
and rewriting [1]
and has been the preponderance of my work since 2017. I have had to
learn how to program
graphics from scratch
On 27/03/2022 00:17, Jon Cooper wrote:
Hello, I have been trying to put together a thing for viewing small
blocks of CCP4 electron density maps with a mobile web browser. If
anyone is interested, the current state of it is here:
http://ic50.org/jbctest14.html
Have you seen/heard about
On 17/03/2022 17:37, Mohd Syed Ahangar wrote:
I have been doing some protein crystal soaking with some covalently
binding fragments and in one structure I have got an extra density on
Cysteine but that density doesn't match with the expected fragment.
The fragment was in the form of iodide
On 13/03/2022 14:05, Tomas Malinauskas wrote:
Dear All,
Is it possible to add hydrogens to a specific residue using Coot?
Something like Calculate -> Scripting -> Python -> coot_reduce(0) but
targeting one residue only.
sprout_hydrogens(0, "L", 101, "") # or some such: molecule-number
On 11/02/2022 21:53, Laurence Pearl wrote:
Does anyone know where I can download a pre-built Coot that will work
on OS X Monterey (12.2) on an iMac with an Intel i7 ?
The packages I can find all fail at the File finder which comes up
blank. X11 latest is installed.
Not an answer to your
.
Kindly let me know How I could fix this ligand.
Thank you
Regards
Yuvara
On Tue, Jan 25, 2022 at 12:03 AM Paul Emsley
mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:
On 24/01/2022 11:11, YUVARAJ I wrote:
Respected Prof. Paul,
Thank you for your kind reply, After refinement using
the output and refmac log file with this mail. kindly
let me know how I could fix this.
Many thanks in advance.
On Mon, Jan 24, 2022 at 12:39 PM Paul Emsley
mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:
On 23/01/2022 09:56, YUVARAJ I wrote:
Respected Prof. Paul,
Thank you s
nd another cif file for (HgI3-) as well and set of
instructions, It will be very much helpful.
Thank you in advance.
Regards
Yuvaraj
On Sun, Jan 23, 2022 at 5:07 AM Paul Emsley <mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:
On 22/01/2022 22:10, Georg Mlynek wrote:
Dear Paul,
, before I tried now.)
Many thanks, br Georg.
Am 22.01.2022 um 22:51 schrieb Paul Emsley:
On 22/01/2022 21:47, Paul Emsley wrote:
On 22/01/2022 17:34, YUVARAJ I wrote:
I have solved a protein structure using anomalous signal using
mercury(II)potassium Iodide(K2HgI4).
I wanted
On 22/01/2022 21:47, Paul Emsley wrote:
On 22/01/2022 17:34, YUVARAJ I wrote:
I have solved a protein structure using anomalous signal using
mercury(II)potassium Iodide(K2HgI4).
I wanted to submit the structure of the protein with mercury(II)
potassium iodide to PDB.
I am facing
On 22/01/2022 17:34, YUVARAJ I wrote:
I have solved a protein structure using anomalous signal using
mercury(II)potassium Iodide(K2HgI4).
I wanted to submit the structure of the protein with mercury(II)
potassium iodide to PDB.
I am facing problems while making the ligand (HGI4) . HGI4
What's the difference between a dummy water and a real one?
Paul
On 22/11/2021 14:34, Schreuder, Herman /DE wrote:
Dear Paul,
I agree with Oliver and Norbert, in the early phases of refinement,
when a lot of rebuilding has to be done, the coot RSR is not very
helpful and in general I
ere extensive rebuilding is required.
Best regards
Oliver
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Paul Emsley
[pems...@mrc-lmb.cam.ac.uk]
Sent: 20 November 2021 11:37
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] COOT RSR
On 20/11/2021 09
On 20/11/2021 09:42, Matthew Snee wrote:
I had a bit of trouble getting used to the new COOT real space
refine... it took me an embarrassingly long time to work out that
there is nothing wrong with the fitting/restraints..
You are not alone in finding Coot's RSR unintuitive (at least
On 08/11/2021 08:55, Guenter Fritz wrote:
Dear all,
with ccp4 update 7.1.016 pyrogen was updated from pyrogen-0.0-pre revision 10365 to pyrogen-0.0-pre revision
10625. I saw that the --MMFF (usage of Merck forcefield) option is now missing.
Yes, it's the default now (i.e. without mogul).
I
On 29/09/2021 12:03, Sam Tang wrote:
This may appear to be a silly question -- I am trying to add hydrogens
to the structure in PDB 1CDW. My initial thought is to run a single
run of refinement with a refinement program.[...] So... is there an
easy way to do what I want in this case?
On 16/09/2021 08:40, WENHE ZHONG wrote:
Dear CCP4 community,
The COOT is not running smoothly on my M1 chip Macbook. For example,
when both model and the electron density map are displayed, the moving
from one residue to the next (pressing SPACE bar) is lagging/slow
(>2s). This only happened
On Sun, 2021-08-01 at 00:54 +, Prasun Kumar wrote:
> Hi All:
>
> I am trying to solve a structure that has got D-amino acids. The sequence has
> also got few achiral residues but is
> mentioned as a part of L-peptide in the monomer library. For example GLY or
> AIB. Since my sequence has
On Fri, 2021-07-09 at 13:49 -0400, Ashok Nayak wrote:
>
> Is it possible to increase the radius of real space refinement
Yes. Use sphere_refine with an argument, e.g. sphere_refine(8.5)
You can add your own button to do this using Right Mouse on the Tool bar and
selecting "Add a User-defined
On 22/06/2021 06:47, Jiang Xu wrote:
I have a problem building and refining an xtal structure. My protein has a N-glycosylation site and I
want to add N-acetylglucosamine and manose to my protein structure. I used Coot's carbohydrate module and
let Coot automatically build the sugar chain
On Mon, 2021-06-14 at 10:42 -0400, Cheng Zhang wrote:
> I had this issue before and tried several ways to fix it. The best way that
> works for me is to edit the PDB and cif
> files of this unnatural amino acid for Coot or Phenix.
I am already furrowing my brow...
> The goal is to allow COOT
On 10/06/2021 12:14, Gambelli, Lavinia wrote:
I'm looking for a software to make topology diagrams of proteins. Ideally, I'd like to submit a pdb file and
obtain the topology model. Do you know what alternatives are out there? So far I'm only aware of PDBsum that
can do this, but I was
On Wed, 2021-06-09 at 20:44 +0100, Paul Emsley wrote:
> On Thu, 2021-06-10 at 00:20 +0530, Firdous Tarique wrote:
> > Hello everyone
> >
> > Can anybody tell me the Coot shortcut key for mutate or mutate and refine.
> > Is there any way to turn it on or to
>
On Thu, 2021-06-10 at 00:20 +0530, Firdous Tarique wrote:
> Hello everyone
>
> Can anybody tell me the Coot shortcut key for mutate or mutate and refine. Is
> there any way to turn it on or to assign
> a particular key if it is disabled ?
>
"Keyboard mutate" Curlew. You will have to remember
On Tue, 2021-06-08 at 19:34 +0200, Mohamed Ibrahim wrote:
>
> I am trying to get the peak values from omit maps. The peakmax from the GUI
> works fine. However, I tried to run
> peakmax from the terminal, and it stuck when returning P1. Same map file
> works fine, when I use the GUI. Any ideas,
On Mon, 2021-06-07 at 01:35 +0530, vivek sharma wrote:
>
> How does one validate if 2 atoms (non-hydrogen) which are close enough,
> actually participate in H-bonding?
> I have a recent data that i am currently working on, the NH2 of ARG is at
> 2.61A from ligand's oxygen atom (refer to
>
On Tue, 2021-05-25 at 20:04 +, Frank Von Delft wrote:
> Yes I thought so too, but discovered I am too stupid to decode the highly
> parsimonious manual on the ccp4 pages.
>
The first thing that I'd try (using Coot) is Calculate -> PISA -> Assemblies...
On 07/04/2021 07:46, Hari shankar wrote:
I have a ligand-protein complex and I wish to calculate different kinds of omit maps (say, composite omit
maps, simulated annealing maps, other unbiased fo-fc maps ). I wish to omit the ligand and 3.5 angstrom 3D
space around it. I have tried phenix
On Thu, 2021-04-01 at 15:02 +0200, Fred Vellieux wrote:
> Hello there,
>
> After running autodock vina on certain small molecules, the graphics
> software I am using (e.g. Pymol, Coot) draws far too many bonds on the
> docked small molecule. See enclosed screen capture.
>
> Is there any way to
On Wed, 2021-03-31 at 19:48 -0400, Jessica Besaw wrote:
>
> I once again am asking for your advice. ☺ I am trying to solve the
> structure of an RBD:Fab complex.
>
> After molecular replacement, the density fits the model very well.
> Looking at the overall crystal structure (by applying
On 31/03/2021 04:37, rohit kumar wrote:
I tried to remove H atoms in pdbcur in ccp4 but still there are lots of HD and HH atoms present in the pdb.
Could anyone please suggest how to fix this problem.
PDBCUR would want to use the element column in order to identify that the atom
is a Hydrogen
On 30/03/2021 02:52, Srivastava, Dhiraj wrote:
I am sorry about phenix related question. But since the question was
refinement related I thought it will be ok to ask on ccp4bb.
For the record, it's not wrong, it just that questions about Phenix are more likely to get accurate and
timely
The geometry targets for protein are well established (by which I mean
"agreed upon") and so the distribution
On 18/03/2021 07:19, Cyril Hamiaux wrote:
Dear Jasmine (and all),
Many thanks for the article. I have a question regarding the Z cutoffs
used to flag geometry outliers in the PDB
On 11/03/2021 01:12, Weston Lane wrote:
Does anyone know if there is a way of showing if a chiral compound is
R or S configuration in Coot? It would be nice to not resort to
thumbs while modelling!
Coot does not show you if your chiral compound is R or S. The closest it
gets is the
On 09/03/2021 17:04, Roversi, Pietro (Dr.) wrote:
Dear all,
sorry to bother you all with such mundane headaches - but all of a
sudden I cannot launch Coot nor ccp4i from the Terminal on my Mac
laptop (running MacOS Mojave):
[bioch3242-596:~] pietro% coot(coot-bin:15697):
(Coot does not
It might just be possible that background modelling of diffraction data
in the presence of ice rings is better done in more modern software.
Paul.
On 06/03/2021 00:10, Edward A. Berry wrote:
(Obviously this is for culling the bad data after data reduction is
complete- doesn't do anything to
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