[ccp4bb] Ligand discrimination
Dear all, Could somebody point me to a good tool that providing a pdb id, could analyze its ligand(s) and distinguish between crystallographic agents and putative drugs. Many thanks in advance, Nicolas To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
Re: [ccp4bb] buying a cluster
Hi Veronica, Fragment-based molecular replacement programs such as ARCIMBOLDO are based on PHASER /SHELXE jobs parallelization over multiple CPUs in a single machine or in a cluster. All the best, Nicolas On 11/23/2018 11:30 AM, V F wrote: Dear all, Which programs benefit from multi-cpu cluster? Since the physics department is getting rid of a old 32 compute node cluster, I was hoping to find some benefit using for crystallographic work. Looking a ccp4wiki or google-fu did not help Many thanks Veronica To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac
Hi Randy, although learning Latex as a whole can for sure be time-consuming, an alternative solution is to use a Latex equation editor like Latexit. You just have to learn the (easy) equation syntax and then you can drag and drop the formatted result into Word or Page, it's rock solid : http://www.macupdate.com/app/mac/17889/latexit Hope that helps, Nicolas Le 18/05/15 09:10, Randy Read a écrit : Rather off-topic, but maybe someone on the list has found a way to work around this! There’s a problem with the Equation Editor in Office 2011 for Mac (i.e. the one that is based on a stripped-down version of MathType, which you get with Insert->Object->Microsoft Equation). You can insert an equation, re-open it and edit it several times, and then suddenly (and seemingly randomly) the equation object will be replaced by a picture showing the equation, which can no longer be edited. I’m writing a rather equation-heavy paper at the moment, and this is driving me crazy. This seems to be a known bug, which has existed from the release of Office 2011. Apparently it happens, unpredictably, when an AutoSave copy of the document is saved, so you can avoid it by turning off the AutoSave feature. The last time this drove me crazy, several years ago, I did try turning off AutoSave. For a while, I was very good about manually saving frequently, but I got into bad habits and eventually Word crashed after I had worked for several hours on a grant proposal without manually saving. So I turned AutoSave back on. At the moment, the least-bad solution seems to be to turn off AutoSave while I’m working on a document with lots of equations and then (hopefully) remember to turn it back on after that document is finished. But it would be great if someone has come up with a better cure for this problem. No doubt someone will suggest switching from Word to LaTeX, but I need to be able to collaborate on paper-writing, and even though I might be willing to invest the effort in learning LaTeX, I can’t really expect that of my collaborators. Most people in our field do use Microsoft Word, regardless of its failings. I’ve also tried using the professional version of MathType, but that requires your collaborators to install it as well — and I don’t think that cured the equation to picture problem anyway. Thanks! - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk -- Nicolas Soler Roger Williams group, PNAC MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH United Kingdom phone : +44(0) 1223 26 76 20 mail : nso...@mrc-lmb.cam.ac.uk
[ccp4bb] Sharp: Solomon density modification step
Dear all, A quick question regarding the density modification interface via the Sharp interface. Which resolution range / radius of the solvent sphere/ ncycles should be used for optimal result? The documentation seems to suggest to restrict yourself up to the resolution where good phasing information is available (6.5A in my case) and I get excellent indicators only if I do that (they become horrible if I use the full resolution range). How about phase extension ? Which parameters would you then use? Thanks, Nicolas -- Nicolas Soler Roger Williams group MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH United Kingdom phone : +44(0) 1223 26 76 20 mail : nso...@mrc-lmb.cam.ac.uk
[ccp4bb] Density modification tips
Dear all, There are many tutorials out there about how to use the different density modification programs but less about people's preferred strategy. I have a MIRAS solvent-flattened map from Sharp+Solomon. Alternatively running RESOLVE density modification on the phases obtained after my last Sharp run looks interesting. Do people usually try to combine the 2 approaches (traditional + statistical density modification?). What is your favourite approach? Thanks, Nicolas -- Nicolas Soler Roger Williams group MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH United Kingdom phone : +44(0) 1223 26 76 20 mail : nso...@mrc-lmb.cam.ac.uk
Re: [ccp4bb] Cryo
Hi Vitul, Having a final concentration of 2M for lithium sulphate worked for me (from a 2.5M stock solution). Nicolas On 09/10/2014 10:27, vitul jain wrote: Hello everybody, can anyone please suggest a good Cryo for condition having 0.8 M Lithium sulphate and 0.1 M Sodium acetate 4.6. Thanks in advance Vitul -- Vitul Jain PhD student C/O Dr. Amit Sharma Structural and Computational Biology lab International Center for Genetic Engineering and Biotechnology Aruna Asaf Ali road, New Delhi 110067. Mb. no: +91-9818004350, 8860942543 E-mail: vituljain...@gmail.com <mailto:vituljain...@gmail.com> / vi...@icgeb.res.in <mailto:vi...@icgeb.res.in> -- Nicolas Soler Roger Williams group MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH United Kingdom phone : +44(0) 1223 26 76 20 mail : nso...@mrc-lmb.cam.ac.uk
Re: [ccp4bb] tNCS: indexing and EP problems
Thanks for your answers, I realized too late that my question number 2 was misleading. I wondered in fact whether shelxd or another program could handle tNCS fine. Otherwise for my indexing concerns, I have been trying to feed xds with the unit cell parameters found by mosflm via the UNIT_CELL_CONSTANTS keyword in XDS.INP but I didn't find them back in the solution list proposed by IDXREF.LP. Has anybody had similar issues? Cheers, Nicolas On 23/09/2013 15:22, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Nicolas, shelxd is one answer to question 2 (http://shelx.uni-ac.gwdg.de/SHELX/shelxd_mm_keywords.php: PATS). I am sure there are others. You can provide the cell from mosflm to XDS. If you want XDS to find the cell without this information, there are plenty of keywords to tweak, although in my experience it is often sufficient to find a decent set of images to collect spots from, play with the things you let XDS refine (REFINE(...)) and finding the correct ORGX and ORGY. In difficult cases I use adxv to get an estimate for the cell dimensions to judge whether or not XDS found the correct one. Best, Tim On 09/23/2013 04:04 PM, Nicolas Soler wrote: Dear experts, I am dealing at the moment with a case involving translated NCS copies of my asymmetric unit along one axis of the unit cell (3 clear non-origin peaks in the native Patterson). I could get Mosflm to find the corresponding big unit cell only after restricting the "max deviation from integral hkl" parameter to 0.1 and thus get the majority of the spots under prediction boxes (although the cell parameters don't look very accurate sometimes). I have 2 questions about it : 1) Do you know whether it would be possible to configure XDS the same way, to make it find this enlarged unit cell ? (no success so far...) 2) Are you aware of any experimental phasing program making use of the information provided by the Patterson for finding the substructure? Many thanks in advance, Nicolas - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14 (GNU/Linux) Comment: Using GnuPG with Mozilla -http://enigmail.mozdev.org/ iD8DBQFSQE6XUxlJ7aRr7hoRAnUEAJ9l0CNtIOuFytwWO1+MY7zYijcRKQCbBibF 0RJPhc5dGV0LJlzsRozjy6c= =7JHE -END PGP SIGNATURE-
Re: [ccp4bb] tNCS: indexing and EP problems
Hi Boaz, I'm looking for one or several XDS keyword(s) to configure, in order to find the same unit cell that Mosflm found. Thanks, Nicolas On 23/09/2013 15:04, Boaz Shaanan wrote: Hi, I'm not sure what you mean by 'configuring XDS the same way', do you mean that you tried to use the results from Mosflm as input to XDS? If not, it's worth trying. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Nicolas Soler [nso...@mrc-lmb.cam.ac.uk] Sent: Monday, September 23, 2013 5:04 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] tNCS: indexing and EP problems Dear experts, I am dealing at the moment with a case involving translated NCS copies of my asymmetric unit along one axis of the unit cell (3 clear non-origin peaks in the native Patterson). I could get Mosflm to find the corresponding big unit cell only after restricting the "max deviation from integral hkl" parameter to 0.1 and thus get the majority of the spots under prediction boxes (although the cell parameters don't look very accurate sometimes). I have 2 questions about it : 1) Do you know whether it would be possible to configure XDS the same way, to make it find this enlarged unit cell ? (no success so far...) 2) Are you aware of any experimental phasing program making use of the information provided by the Patterson for finding the substructure? Many thanks in advance, Nicolas -- Nicolas Soler Roger Williams group MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH United Kingdom phone : +44(0) 1223 26 76 20 mail : nso...@mrc-lmb.cam.ac.uk
[ccp4bb] tNCS: indexing and EP problems
Dear experts, I am dealing at the moment with a case involving translated NCS copies of my asymmetric unit along one axis of the unit cell (3 clear non-origin peaks in the native Patterson). I could get Mosflm to find the corresponding big unit cell only after restricting the "max deviation from integral hkl" parameter to 0.1 and thus get the majority of the spots under prediction boxes (although the cell parameters don't look very accurate sometimes). I have 2 questions about it : 1) Do you know whether it would be possible to configure XDS the same way, to make it find this enlarged unit cell ? (no success so far...) 2) Are you aware of any experimental phasing program making use of the information provided by the Patterson for finding the substructure? Many thanks in advance, Nicolas
[ccp4bb] Coot question
Dear all, My question concerns the Extension-> modelling-> Rigid body fit residue ranges function in Coot. Although it works well through the interface, I cannot have it to work in a python script, does somebody know the correct syntax? Thanks in advance, Nicolas
[ccp4bb] NCS from electron density
Dear all, Is there a pipeline that will find NCS operators from a map, select the relevant ones and apply them all in NCS averaging density modification? Otherwise, what would be the best way to proceed ? (I have a P21 spacegroup so I wonder what happens with the origin when I pass the NCS operators from one program to another). Thanks for your help, Nicolas
[ccp4bb] translational NCS
Dear CCP4bbs, I am dealing with a case involving pseudo-translational symmetry. I wanted to know what was the simplest way to draw NCS copies of a molecule deduced from the positions I observed in native Patterson. Is there a "translate" option where on can give fractional coordinates in Coot or Pymol? Thanks for your help! Nicolas
Re: [ccp4bb] Making a Poly ala model
If you have perl installed, just use this script to convert as many
files as you want once by typing : perl mutala.pl myfile.pdb myfile2.pdb etc
Bottomley, Matthew wrote:
Dear All,
Can anyone recommend a windows/PC-friendly program (website?) to
convert a PDB file into a poly-Ala model?
Thanks a lot!
Matt
Matthew J. Bottomley, Ph.D.
Senior Research Biochemist
IRBM / MRL-Rome
Notice: This e-mail message, together with any attachments, contains information of
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#!/usr/bin/perl -w
# Mutala: script mutate each residue in alanine in a pdb
file#
# Written by Nicolas
Soler
#
FONCTIONS###
foreach $fichier (@ARGV) {
open (ENTREE,$fichier);
if (glob "polyala$fichier"){unlink "polyala$fichier"};
open SORTIE, ">>polyala$fichier";
select SORTIE;
while (){if (/^ATOM.{9}(N |C |O
|CA|CB)..(\w{3})/){s/$2/ALA/;print $_}};
print "END";
close ENTREE;
close SORTIE;}
Re: [ccp4bb] pdb format
Hi Raja You can use a command-line script like this one: #!/bin/tcsh sed -e "/ATOM/ s/'/*/g" -e "/ATOM/ s/O5T/O3T/" -e "/ATOM/ s/ADE/ DA/g" -e "/ATOM/ s/CYT/ DC/g" -e "/ATOM/ s/GUA/ DG/g" -e "/ATOM/ s/THY/ DT/g" <$1>refmacok_$1 cat refmacok_$1|grep ATOM|more>/dev/tty Save the script in a new file (ex:DNArefmac.sh) and make sure it is executable on your computer (in a terminal type chmod -x DNArefmac.sh). I used it for rna to convert from CNS format to refmac, and adapted it for dna. Just put it in the same directory with your pdb then run it (ie: sh DNArefmac.sh thing.pdb). It will normally produce a new pdb suitable for refmac.called refmacok_thing.pdb and also display it on the terminal. Hope this will help. Nicolas Raja Dey wrote: Hi, The out pdb file from 'CNS' or from 'O' is not readable in 'CCP4'. I have dna and protein in my pdb file. Do you the best way to convert the pdb file I got from 'CNS" or from 'O' into 'CCP4' format? Especially CCP4 follows 1 letter code for dna whereas CNS and O follow 3 letter code. Looking forward to hearing from you Thanks... Raja BMR - a key player in weight issues. Know more. <http://in.rd.yahoo.com/tagline_glue_4/*http://in.search.yahoo.com/search?&fr=na_onnetwork_mail_taglines&ei=UTF-8&rd=r1&p=basal+metabolic+rate> -- Nicolas Soler Institut de Chimie des Substances Naturelles 91190 Gif-sur-Yvette tel 33-1-69823764 fax 33-1-69823784 http://perso.nicodam.org/
