Found it!
It is under the "Calculate" menu!
Thank you Paul for answering!
Best,
A
El mar, 9 feb 2021 a las 14:44, Paul Emsley ()
escribió:
> On 09/02/2021 13:33, Almudena Ponce Salvatierra wrote:
> >
> > I have Coot 0.8.9.2 installed on macOS Catalina. I would like
Hello everybody,
I have Coot 0.8.9.2 installed on macOS Catalina. I would like to launch
RCrane, but I can't find it under "Extensions".
Does anybody know whether there is a way I can make it work on the version
of Coot, or should I rather uninstall it and look for another one?
Any help will be
Hello everyone,
I am using autoPROC in a series of datasets I referred to in an email a few
days ago.
I would like to merge them and see if the resulting dataset has enough
anomalous signal as to phase.
The thing is that, out of the massive output from autoPROC, I fail to find
which files to
; Dear Almudena,
>
> SPOT_MAXIMUM-CENTROID is probably the keyword in XDS.INP that you want to
> increase in your situation. The default is 3. Try e.g. 5, and increase
> slowly
> to make sure that the suggested solution makes sense
>
> Best regards,
> Tim
>
> On Frida
(e.g. instead of 50
> start from 52).
>
> In XDS.INP you can enable distance refinement (as well as beam center
> refinement) throughout all steps. Just remove the "!" in "Refine"
>
> Hope this helps,
>
> Best wishes,
>
> Raphael
>
>
> On 29.11.19 1
s add data in "block by block".
> I have successfully processed some pretty awful looking data with XDS, but
> it needs a bit of determination and quite a lot of time (hours, not
> minutes), so only invest if the data set is just unique
> Good luck
> Andy
>
> _
sing the refined
> parameters of the successful run.
>
>
>
> Good luck!
>
> Herman
>
>
>
> *Von:* CCP4 bulletin board *Im Auftrag von *Almudena
> Ponce Salvatierra
> *Gesendet:* Freitag, 29. November 2019 12:48
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betre
ena,
>
> SPOT_MAXIMUM-CENTROID is probably the keyword in XDS.INP that you want to
> increase in your situation. The default is 3. Try e.g. 5, and increase
> slowly
> to make sure that the suggested solution makes sense
>
> Best regards,
> Tim
>
> On Friday, November 29, 20
. Try e.g. 5, and increase
> slowly
> to make sure that the suggested solution makes sense
>
> Best regards,
> Tim
>
> On Friday, November 29, 2019 12:48:11 PM CET Almudena Ponce Salvatierra
> wrote:
> > Dear all,
> >
> > I have some data sets that don't want
Dear all,
I have some data sets that don't want to be processed :p
In one of them, when I look at IDXREF.LP I see virtually none of the found
spots were indexed and the reason is that they are "too far from the
expected position". The spots are smeary and elongated, so not the
prettiest.
I have
.AC.UK"
> Objet : Re: [ccp4bb] crysalis pro from rigaku
>
> The current version of CrysalisPro will directly import several image
> formats, or you can convert images to Esperanto format to import. The
> latter is a bit clumsy but does work.
>
> ______
>
Dear all,
does any of you have experience with using Crysalis Pro software from
Rigaku with data that were not collected on a Rigaku instrument?
Any help will be much appreciated.
All the best,
Almudena
To unsubscribe
Dear all,
We have an open position for a Research technician in biochemistry and
structural biology of RNAs and macromolecular complexes at the Laboratory
of Bioinformatics and Protein Engineering, International Institute of
Molecular and Cell Biology in Warsaw.
As a Research Technician, you
be I-centered. In
> XDS.INP, you just enter
> SPACE_GROUP_NUMBER=23 ! or 24 but for indexing that does not make a
> difference
> UNIT_CELL_CONSTANTS= all 90>
>
> hope this helps,
> Kay
>
> On Fri, 19 Apr 2019 20:11:18 +0200, Almudena Ponce Salvatierra <
> maps.fa..
nter
> 5323 Harry Hines Blvd.
> Rm. ND10.214A
> Dallas, TX 75390-8816
> diana.tomch...@utsouthwestern.edu
> (214) 645-6383 (phone)
> (214) 645-6353 (fax)
>
> On Apr 19, 2019, at 1:11 PM, Almudena Ponce Salvatierra <
> maps.fa...@gmail.com> wrote:
>
> Dear all,
&g
Dear all,
I'm processing my data with XDS and with DIALS and at first sight it
would seem reasonable to assume that the Laue group is
either orthorrombic or monoclinic. Autoprocessing brings me always to
P212121, but I have tried also to solve the
structure in space groups 1, 3, 4, 16, 17 and
igma = 0.02
>
> slack = None
>
> }
>
> angle {
>
> action = *add
>
> atom_selection_1 = chain B and resname GTP and name C3'
>
> atom_selection_2 = chain B and resname GTP and name O3'
>
> atom_selection_3 = chain B and res
Dear all,
I would like to add a GTP residue to a nucleic acid chain. For so I
followed the following steps in coot: add monomer from library, GTP,
changed chain ID and residue number accordingly, and then Extensions -->
Modelling --> link 2 atoms. I got a dashed line between the 3'O of the GTP
m.ac.uk
> Cambridge CB2 0XY, U.K.
> www-structmed.cimr.cam.ac.uk
>
> > On 14 Mar 2019, at 05:07, Almudena Ponce Salvatierra <
> maps.fa...@gmail.com> wrote:
> >
> > Dear all,
> >
> > I have a dataset with strong TNCS and I would like to know if there
Dear all,
I have a dataset with strong TNCS and I would like to know if there are a
"series of steps" that I could follow in order to find out whether I can
solve my structure or not.
I see on the Phaser wiki that structure determination in the presence of
TNCS is not fully automated. which
Just run mtzdump or do it here http://services.mbi.ucla.edu/SAVES/MTZ/
Best,
Almu
El jue., 7 mar. 2019 a las 13:52, Sanaz Asadollahpour (<
sanaz.asadollahp...@ocbc.uni-freiburg.de>) escribió:
> Dears,
> with which program in CCP4 I can read MTZ file?
>
> regards,
> S.A.
>
>
Dear colleagues,
At the moment we have several positions available. This e-mail is to bring
to your attention an opening for a Research Assistant position in our lab.
Please send applications by March 15th to employm...@genesilico.pl. See
details below.
Cheers,
Almudena
Research Assistant –
Dear colleagues,
this e-mail is to bring to your attention an opening for a PhD student
position in our lab. Please send applications by March 15th to
employm...@genesilico.pl. See details below.
Cheers,
Almudena
Ph.D. Student Position: development of software for modeling and design of
RNA
Dear colleagues,
this e-mail is to bring to your attention an opening for a PhD student
position in our lab. Please send applications by March 15th to
employm...@genesilico.pl. See details below.
Cheers,
Almudena
Ph.D. Student Position
Biochemistry and structural biology of RNA-ligand
Dear Pavel,
thanks for the quick reply. Indeed, when I place the ligand where I suspect
it could be, the program says: The polder map is likely to show the ligand.
Indeed I see a blob ...
I watched the video tutorial some time ago. It's very easy to use, indeed.
Concerning the Fobs-Fobs maps,
Dear all,
I have recently determined the structure of a protein for which useful data
extends to 4.2 angstroms (as assessed by paired refinement after pdb redo),
with some dazzling 80% solvent content and... I am expecting to find a
26-atom ligand bound to it. However the "blobbyness" of the maps
Dear all,
I have looked into the archive and I've tried to collect suggestions for
cryo protecting crystals that grew in 1.8 M Lithium sulphate containing
mother liquor or 2M.
What would make more sense? Transferring it into a cryo solution that
consists of mother liquor and a higher
temperature.
I can just get a result of two single strand DNA/RNA. PAGE analysis.
No double helix was founded.
Does anyone have the same problem or know how to fix it.
Thank you for your answering.
Best regards,
Weifei
--
Almudena Ponce-Salvatierra
Macromolecular crystallography
somehow to write down/save the
solutions for which the TFZ score will be higher than 7? Even though the
clashes
Thanks a lot in advance
All the best,
Almu
--
Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical Chemistry
Am
--
Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11 37077 Göttingen
Germany
in advance.
Best,
Almudena
--
Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11 37077 Göttingen
Germany
it generates,
edit MAXM to make space for more then run shelxc from the command line.
With kind regards,
Tobias
From: CCP4 bulletin board on behalf of Almudena Ponce Salvatierra
Reply-To: Almudena Ponce Salvatierra
Date: Monday 22 June 2015 09:58
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb
was
assigned properly or not from the electron density.
Any ideas?
Thanks a lot in advance.
Best wishes,
Almudena.
--
Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11 37077 Göttingen
Germany
, at 13:04, Almudena Ponce Salvatierra maps.fa...@gmail.com
wrote:
Hi everyone,
I would like to ask if any of you know how to measure the angle between
two nucleic acid helices? I am trying with pymol, but have not found a
solution to it yet.
Any ideas?
Thanks a lot.
Best
Hi everyone,
I would like to ask if any of you know how to measure the angle between two
nucleic acid helices? I am trying with pymol, but have not found a solution
to it yet.
Any ideas?
Thanks a lot.
Best,
Almudena.
A
C
Hope that helps,
Sam
--
*From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Almudena
Ponce Salvatierra [maps.fa...@gmail.com]
*Sent:* 04 February 2015 17:07
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] off topic pymol
Dear all
Dear all,
does anyone know why if I open a pdb in pymol (that appears normal and
fully connected in coot) it appears as if it was broken into pieces?
Thanks,
Almudena.
--
Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical
Hi,
this sounds weird but I am adding a Cobalt atom within Coot, with the
option place atom at pointer, then I select other and type in the
textbox CO. It adds an Atom that it calls A, why does this happen?
Any ideas?
Thanks in advance.
Best wishes,
Almudena
--
Almudena Ponce-Salvatierra
.
Regards from Stockholm,
Julia
On 02/02/15 15:40, Almudena Ponce Salvatierra wrote:
Hi,
this sounds weird but I am adding a Cobalt atom within Coot, with the
option place atom at pointer, then I select other and type in the
textbox CO. It adds an Atom that it calls A, why does
.
___
Roger S. Rowlett
Gordon Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346
tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu
On 2/2/2015 9:40 AM, Almudena Ponce Salvatierra
On 01/26/2015 10:01 AM, Almudena Ponce Salvatierra wrote:
Dear all,
is there a fast way of changing the chain type from RNA to DNA or from
DNA to RNA within coot? I have already quite a bit built into density,
but it is the wrong kind of nucleic acid.
Best,
Almudena
--
Almudena Ponce
Dear all,
is there a fast way of changing the chain type from RNA to DNA or from
DNA to RNA within coot? I have already quite a bit built into density, but
it is the wrong kind of nucleic acid.
Best,
Almudena
--
Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid
Zuokun
Nankai University
--
卢作焜
南开大学新生物站A202
--
Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11 37077 Göttingen
Germany
Karplus and Diederichs. Science 2012.
Hendrickson. Science. 2012
some references :-)
2015-01-16 16:01 GMT+01:00 Almudena Ponce Salvatierra maps.fa...@gmail.com
:
Dear Izuok,
1. There are different metrics you can look at in order to know on how
much anomalous signal you can rely: CCano
that got carried our to the next refinement run.. It's
difficult to guess without more information.
Pavel
P.S.: there is Phenix mailing list for Phenix-specific questions.
--
Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute
Thank you all for the suggestions.
What worked better for me was to run XDS with different batches of images
and to merge them later with XSCALE.
Best,
Almudena
2014-09-29 11:56 GMT+02:00 Almudena Ponce Salvatierra maps.fa...@gmail.com
:
Dear all,
I would like to ask something regarding
it?
Thank you very much in advance.
Best wishes,
Almudena
--
Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11 37077 Göttingen
Germany
out wedges like this? I have tried like
so, but I have the Impression it only takes then the last number of Frames,
in this example it would only take 1001 to 1200.
Thanks a lot.
Best wishes,
Almudena
--
Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max
,
Almudena.
--
Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11 37077 Göttingen
Germany
.
Best wishes, from sunny Göttingen!
Almudena
--
Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11 37077 Göttingen
Germany
.
Thank you very much for your time and consideration.
Best wishes,
Almudena.
2014-06-02 22:33 GMT+02:00 Airlie McCoy ajm...@cam.ac.uk:
Hi Almundena, Apologies, I had not had a chance to look at it... what was
your fix? Airlie
On Jun 2 2014, Almudena Ponce Salvatierra wrote:
Dear Airlie
Could anybody please tell me how to proceed? Maybe there is some option I
am not using or some addtional data I need to provide the program... I
don't know.
Any suggestions are welcome!
Thanks a lot in advance!
Best wishes,
Almu
--
Almudena Ponce-Salvatierra
Macromolecular crystallography
-9.0 with 0.5
units increment, PEG conc. from 10 -30% and NH4I conc. from 0.1 -0.5 M
independently in hanging drop method and ended up with NO Crystals. Can
somebody suggest strategy to improve crystals. Please find the crystal pic
with attachment.
Regards,
Venkat.
--
Almudena Ponce
.
best wishes,
Kay
On Mon, 19 May 2014 18:18:46 +0200, Almudena Ponce Salvatierra
maps.fa...@gmail.com wrote:
Dear all,
I am looking for some suggestions here. I have lately collected some
datasets but the spots are very very weak... it is very difficult to
process them. At times it looks
? or rather not?
I wonder if the problem is to find the spots, I have tried with HKL2000 and
it can't even find enough of them for indexing.
Any ideas are welcome.
Best wishes,
Almudena.
--
Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute
frames, but not with 600 or with 500. I get this message when I do so.
Any suggestions are welcome. I'm looking forward to hearing from you.
Best wishes,
Almudena
--
Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical
= BEAM_DIVERGENCE_E.S.D.=
2014-04-01 17:27 GMT+02:00 Almudena Ponce Salvatierra maps.fa...@gmail.com
:
Dear CCP4 users,
while I am running CORRECT within XDS, the program suddenly stops, and
gives the following message:
forrtl: severe (24): end-of-file during read, unit 2, file
/data
Dear all,
I would like to generate HL coefficients to an mtz file I get from Phaser
after Molecular replacement. Does anyone know how to? also, does anyone
know how to within Phenix?
Best
Almu
--
Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck
-online.org/documentation/reciprocal_space_arrays.htm
Note there is a corresponding utility in the GUI (if I recall correctly
under Reflection tools).
Pavel
--
Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical Chemistry
. Could you help me?
Thank you very much in advance.
Best wishes,
Almudena.
--
Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11 37077 Göttingen
Germany
.
Phaser gives the following error message:
ERROR setting up data inputs (FATAL RUNTIME) Can not find MTZ column
F_SAD_SAD(+)
Instead Autosol gives the following:
ERROR sorry can not read segment library
Could anyone help me out here?
Thank you very much in advance.
Best,
Almudena
--
Almudena Ponce
this?
Best wishes,
Almudena.
--
Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11 37077 Göttingen
Germany
bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of
*Almudena
Ponce Salvatierra
*Sent:* 14 January 2014 15:52
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] refining nucleic acids with Coot
Dear all,
I am trying to refine an oligonucleotide chain in Coot and I get the
following
Hi everyone,
I would like to know how to change matrix format from the one I get out of
XDS to the one that comes out of SAINTS. Or the other way around.
My question is: is the beam along the same axis in both matrices? as well
as the rotation axis and the third axis?
How can I convert one into
Dear all,
I would like to know if it is possible to use either the real space refine
zone or the regularize zone tools just between two atoms in a cofactor
molecule. It works perfectly between two atoms when I use it on the
protein, but it doesn't when I try to modellate the cofactor. Instead of
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