Re: [ccp4bb] RCrane in Coot 0.8.9.2 for Mac

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

[ccp4bb] RCrane in Coot 0.8.9.2 for Mac

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

[ccp4bb] autoPROC question

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 mer

Re: [ccp4bb] 8/ 2263 spots indexed XDS

Gruene () escribió: > 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, &g

Re: [ccp4bb] 8/ 2263 spots indexed XDS

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

Re: [ccp4bb] 8/ 2263 spots indexed XDS

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 > >

Re: [ccp4bb] [EXTERNAL] [ccp4bb] 8/ 2263 spots indexed XDS

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

Re: [ccp4bb] 8/ 2263 spots indexed XDS

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

Re: [ccp4bb] 8/ 2263 spots indexed XDS

. 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

[ccp4bb] 8/ 2263 spots indexed XDS

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

Re: [ccp4bb] crysalis pro from rigaku

CMAIL.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. > > ______

[ccp4bb] crysalis pro from rigaku

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 fr

[ccp4bb] Research technician position at IIMCB Warsaw

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 w

Re: [ccp4bb] pointless warning - space group ambiguity

may 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

Re: [ccp4bb] pointless warning - space group ambiguity

al Center > 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 al

[ccp4bb] pointless warning - space group ambiguity

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 18,

Re: [ccp4bb] naive question how to add GTP as a residue to a nucleic acid chain and refine!

.6 > > sigma = 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

[ccp4bb] naive question how to add GTP as a residue to a nucleic acid chain and refine!

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 and

Re: [ccp4bb] help with TNCS + MR

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 ar

[ccp4bb] help with TNCS + MR

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 steps

[ccp4bb]

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. > > ###

[ccp4bb] Research Assistant - Software Developer Position for the development of bioinformatics software and web servers

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 – Softw

[ccp4bb] Ph.D. Student Position development of software for modeling and design of RNA molecules

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 molecu

[ccp4bb] PhD Student Position in Structural Biology of RNA-ligand interactions

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 interaction

Re: [ccp4bb] high SOLVENT content low RESOLUTION and a LIGAND to be found

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, th

[ccp4bb] high SOLVENT content low RESOLUTION and a LIGAND to be found

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

[ccp4bb] cryo suggestions for lithium sulphate xt condition containing 1.8 - 2 M Li2SO4

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 concentratio

Re: [ccp4bb] DNA RNA annealing problem

o 95 for 5min, cooling down slowly for nearly 2h to room > 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. > >

[ccp4bb] accept MR solution even if the number of clashes is above the threshold

can I tell phaser 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 Biophy

[ccp4bb] anomalous phasing with HySS - phaser - Autobuild

-- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

Re: [ccp4bb] off topic: hkl2map message error

ates, > 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 &g

[ccp4bb] off topic: hkl2map message error

advance. Best, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

[ccp4bb] pukka puckers within coot

the pucker 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

Re: [ccp4bb] off topic: measuring angle between two nucleic acid helices

> > Cheers, > Thomas > > On 04 Mar 2015, at 13:04, Almudena Ponce Salvatierra > 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

[ccp4bb] off topic: measuring angle between two nucleic acid helices

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.

Re: [ccp4bb] off topic pymol

.33 A >C > ATOM381 CD ARG A 49 -14.933 -23.259 -30.207 1.00104.16 A >C > > Hope that helps, > > Sam > -- > *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Almudena > Ponce Salvatierra

[ccp4bb] off topic pymol

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

Re: [ccp4bb] adding a Cobalt atom within Coot

fixed in Coot 0.8.1. > > ___ > 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...@col

Re: [ccp4bb] adding a Cobalt atom within Coot

don't know the answer. > > 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 "

[ccp4bb] adding a Cobalt atom within Coot

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. Be

Re: [ccp4bb] changing chain type in coot from RNA to DNA and viceversa

the > residues, but that is really slow. > > HTH, > Robbie > > > 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

[ccp4bb] changing chain type in coot from RNA to DNA and viceversa

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 Nu

Re: [ccp4bb] Assess anomalous signal?

Karplus and Diederichs. Science 2012. Hendrickson. Science. 2012 some references :-) 2015-01-16 16:01 GMT+01:00 Almudena Ponce Salvatierra : > Dear Izuok, > > 1. There are different metrics you can look at in order to know on how > much anomalous signal you can rely: CCano, ΔF

Re: [ccp4bb] Assess anomalous signal?

> heavy atom derivatives. > > Best! > > Lu 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

Re: [ccp4bb] Phenix refinement

ion of this refinement will >> be more than welcome. >> > > I would do refinement run afresh. Perhaps you have some settings specific > to that atom that got carried our to the next refinement run.. It's > difficult to guess without more information. > > Pavel > &

[ccp4bb] Phenix refinement

inement will be more than welcome. 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

Re: [ccp4bb] XDS

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 : > Dear all, > > I would like to ask something regarding XDS. Is it

[ccp4bb] OASIS bug?

Task failed Any ideas how to solve 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

[ccp4bb] XDS

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

[ccp4bb] sharp error

, Almudena. -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

[ccp4bb] packing test PHASER

for a bit. How should I think about this? I would assume that the clashes are too many only by seeing those numbers, but maybe there is something else to take into account? Thanks a lot in advance. Best wishes, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic

[ccp4bb] solvent flattening with resolve - phenix

you very much in advance. 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

[ccp4bb] Fwd: [ccp4bb] phaser issue MR

ed to accomodate search components. Thank you very much for your time and consideration. Best wishes, Almudena. 2014-06-02 22:33 GMT+02:00 Airlie McCoy : Hi Almundena, Apologies, I had not had a chance to look at it... what was > your fix? Airlie > > > On Jun 2 2014, Almudena

[ccp4bb] phaser issue MR

nd/or data to cimr-pha...@lists.cam.ac.uk 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 Ponc

Re: [ccp4bb] data processing with XDS

t; > 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

Re: [ccp4bb] Sea Urchin like crystals

ues ranging from 6.0 -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. > > R

[ccp4bb] data processing with XDS

all? 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 I

Re: [ccp4bb] error xds

= BEAM_DIVERGENCE_E.S.D.= 2014-04-01 17:27 GMT+02:00 Almudena Ponce Salvatierra : > 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, fil

[ccp4bb] error xds

h 300 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 B

Re: [ccp4bb] generate Hendrickson Lattman coefficients

http://www.phenix-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 ch

[ccp4bb] generate Hendrickson Lattman coefficients

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

[ccp4bb] a couple of doubts: phaser and something else

. 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

[ccp4bb] autosol error// phaser error

Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

Re: [ccp4bb] refining nucleic acids with Coot

gt; > Ashley > > > > *From:* CCP4 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 > > > >

[ccp4bb] autosharp error message

ith this software so any suggestions are welcome! Best, Almudena. -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

[ccp4bb] refining nucleic acids with Coot

w to solve 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

[ccp4bb] convert orientation matrix format

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

[ccp4bb] Coot. Problems with bonds and angles regularization

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