Re: [ccp4bb] ccp4i:buccaneer+refmac curiosity on Intel mac osx only
Dear Bryan, are there any differences when you look at the input scripts for the differing jobs? Tim On Wed, May 11, 2011 at 06:54:38PM -0400, Bryan Lepore wrote: it seems that shift-double-clicking on a buccaneer+refmac job in ccp4i and rerunning it with everything the same (except output name) will produce results (c-alphas built, Rfree, etc.) that are non-identical after a few cycles. apparently this is holds for Intel mac osx 10.5 or 10.6 only, not Linux. It would be interesting if any Intel mac osx users would be willing to confirm or refute this curiosity. Regards, -Bryan p.s: more details: ccp4 6.1.13 ccp4i 2.0.6 buccaneer 1.4.0 buccaneer-pipeline v1.4 refmac 5.5.0109 mac osx 10.5.8 or 10.6.7 -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A signature.asc Description: Digital signature
[ccp4bb] Macromolecular Crystallographer Post in the Industrial Liaison office at Diamond
Dear All, we have a permanent post available for a Macromolecular Crystallographer in the Industrial Liaison Group at Diamond. Full details and how to apply can be found at http://www.diamond.ac.uk/Home/Jobs/Current/DIA0619-TH.html. (Closing date for receipt of applications is the 17th June 2011) A brief summary of the post is given here: Industrial Liaison Scientist - MX Circa £32k Full-time Ref: DIA0619/TH Closing date: 17/6/2011 Diamond Light Source is the UK's national synchrotron science facility. Located at Harwell Science Innovation Campus in Oxfordshire, we enable world-leading research across a wide range of scientific disciplines and industrial applications We are seeking a Scientist to join our Industrial Liaison Group to develop and deliver the service offered to industrial users of Diamond in the field of macromolecular crystallography (MX). You will be involved in the optimisation, operation and marketing of the industrial aspects of the MX beamlines. As part of a multi disciplinary team you will be working closely with the MX Group and ideally you should have experience of working in a commercial environment. Please direct informal inquiries to Elizabeth Shotton (Elizabeth.shotton at diamond.ac.uk)
[ccp4bb] Technician Position available in Milan
Dear all, a technical position is available to work in the Crystallography Unit of the IFOM-IEO-Campus in Milan. (http://www.ifom-ieo-campus.it/joinus/detail_jobs.php?docuID=1566) The position is available immediately, and will be granted until March 2012. We are looking for a person who will be involved in the general management of the Unit's instrumentation, and who will take care of gathering samples from the Unit users, set up crystallization trials and perform biophysical experiments. Hence, we look for a person capable of independently organizing her/his work and with a great attitude to relate with people and work in a team. To apply, please send your CV, together with the name of at least one referee. Informal inquiries are welcome. cheers, Sebastiano PS: sorry for the double posting to those subscribed to both mailing lists. -- Sebastiano Pasqualato, PhD Crystallography Unit IFOM-IEO Campus Cogentech - Consortium for Genomic Technologies via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5172 fax +39 02 9437 5990
[ccp4bb] Bug in Pointless version 1.5.19
If anyone has picked up a very recent version of Pointless from our web site here, they should note that version 1.5.19 was seriously broken [1]. Versions 1.5.17 and earlier are OK, as is the very latest 1.5.21 which I've just put there [2] I don't think the broken versions have got into any widely distributed CCP4 versions, so with any luck this doesn't affect many people Phil [1] specifically, files written in a point group of lower symmetry than the apparent lattice group were not sorted, but were flagged as sorted in the file. This leads to apparent completeness in Scala 100% and failure to merge properly [2] ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless-1.5.21.tar.gz, .linux, .osx
[ccp4bb] mutation and minimization
Hey all, I would like to introduce point mutations in a structure and quickly (and dirtily) minimize the new residue. (Best rotamer dependent on local environment, or the like.) What are simple approaches that don't involve VMD/NAMD or some such overkill. Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
Re: [ccp4bb] mutation and minimization
Hi Andreas, I would like to introduce point mutations in a structure and quickly (and dirtily) minimize the new residue. (Best rotamer dependent on local environment, or the like.) What are simple approaches that don't involve VMD/NAMD or some such overkill. PyMOL has a Mutagenesis wizard but you have to pick the best rotamer yourself. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen
Re: [ccp4bb] mutation and minimization
You can try Swiss-PDB viewer.. 2011/5/12 Thomas Holder thomas.hol...@tuebingen.mpg.de Hi Andreas, I would like to introduce point mutations in a structure and quickly (and dirtily) minimize the new residue. (Best rotamer dependent on local environment, or the like.) What are simple approaches that don't involve VMD/NAMD or some such overkill. PyMOL has a Mutagenesis wizard but you have to pick the best rotamer yourself. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen
Re: [ccp4bb] mutation and minimization
Hi Andreas Without the x-ray data, phenix.pdbtools might do this (http://www.phenix-online.org/version_docs/dev-712/pdbtools.htm) From the website: [phenix.pdbtools can] Perform model geometry regularization. Minimize geometry target to idealize bond lenghths, bond angles, planarities, chiralities, dihedrals, and non-bonded interactions. Try to specify to only optimize/minimize a selected part of the model (i.e. your point mutation and the residues around it). An alternative could be to re-refine the point-mutant model using the original x-ray data if you have access to it. Since you are making only a minor change it should work just fine (quickly and dirtily as asked for :)). hth -Bjørn -- Bjørn Panyella Pedersen Macromolecular Structure Group Dept. of Biochemistry and Biophysics University of California, San Francisco On 2011-05-12 08:35, Andreas Förster wrote: Hey all, I would like to introduce point mutations in a structure and quickly (and dirtily) minimize the new residue. (Best rotamer dependent on local environment, or the like.) What are simple approaches that don't involve VMD/NAMD or some such overkill. Thanks. Andreas
Re: [ccp4bb] mutation and minimization
Or try SCWRL from Dunbrack's lab... --- On Thu, 5/12/11, gauri misra kamga...@gmail.com wrote: From: gauri misra kamga...@gmail.com Subject: Re: [ccp4bb] mutation and minimization To: CCP4BB@JISCMAIL.AC.UK Date: Thursday, May 12, 2011, 12:52 PM You can try Swiss-PDB viewer.. 2011/5/12 Thomas Holder thomas.hol...@tuebingen.mpg.de Hi Andreas, I would like to introduce point mutations in a structure and quickly (and dirtily) minimize the new residue. (Best rotamer dependent on local environment, or the like.) What are simple approaches that don't involve VMD/NAMD or some such overkill. PyMOL has a Mutagenesis wizard but you have to pick the best rotamer yourself. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen
[ccp4bb] Graduate Teaching Assistants- Birkbeck University of London
There are two graduate teaching assistant available for October 2011 in the Dept of Biological Sciences, Birkbeck University of London. These positions require you to teach and support teaching for up to 50% (17.5 hours a week) of your time during term and to undertake a Ph.D with a member of the academic staff. Much of the teaching will be between 6 and 9pm as Birkbeck teaches mainly part-time students in the evening. The post is not limited to UK or EU nationals,although you will be expected to teach in English. The Dept of Biological Sciences at Birkbeck includes the well known Crystallography grouping which has a history of protein crystallography going back to JD Bernal in the 1930s. For a list of current dept members linking through to their research interests see http://www.bbk.ac.uk/biology/our-staff/academic For applications and job details see https://www15.i-grasp.com/fe/tpl_birkbeckcollege01.asp?newms=jjid=40545; -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.k...@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G57 Office) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door
Re: [ccp4bb] mutation and minimization
Hi If you are familiar with turbo-frodo, you can use it for mutagenesis and refinement . Just go inside the editing menu, replace the residue, save the file and REFINE the residue. You can also select the stretch of residues by picking the first and last residues so you will get the refinement (best rotamer) based on local environment. Amit Luthra, Ph.D. Post-Doctoral Fellow The Radolf Laboratory Department of Medicine University of Connecticut Health Center [w] http://spirocheteresearch.uchc.edu From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Andreas Förster [docandr...@gmail.com] Sent: Thursday, May 12, 2011 11:35 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] mutation and minimization Hey all, I would like to introduce point mutations in a structure and quickly (and dirtily) minimize the new residue. (Best rotamer dependent on local environment, or the like.) What are simple approaches that don't involve VMD/NAMD or some such overkill. Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
[ccp4bb] B factor
Hey all, I would like to make one ribbon diagram of the structure showing the B factor in different colors (contour levels). I am using pymol but it is not representing the perfect contour level of B factor. Is any other program where I can change the color according to B factor? Thanks Amit Luthra, Ph.D. Post-Doctoral Fellow The Radolf Laboratory Department of Medicine University of Connecticut Health Center [w] http://spirocheteresearch.uchc.edu
[ccp4bb] how convert SF to intensities
Dear ccp4 users, I need to generate intensities from a model (.pdb). That is, I think that a correct procedure could be to convert model to structure factor and then obtain intensities squaring the SF.Does anyone know how can I do?Thanks in advanceFulvio Saccoccia
Re: [ccp4bb] how convert SF to intensities
Hi Fulvio, a possible option that will do what you want (almost - you will get SF that you will have to square): http://phenix-online.org/documentation/fmodel.htm Pavel. On Thu, May 12, 2011 at 12:13 PM, Fulvio Saccoccia fulvio.saccoc...@uniroma1.it wrote: Dear ccp4 users, I need to generate intensities from a model (.pdb). That is, I think that a correct procedure could be to convert model to structure factor and then obtain intensities squaring the SF. Does anyone know how can I do? Thanks in advance Fulvio Saccoccia
Re: [ccp4bb] how convert SF to intensities
That is, I think that a correct procedure could be to convert model to structure factor and then obtain intensities squaring the SF. Does anyone know how can I do? Use sftools -- Hurry up before we all come back to our senses! Julian, King of Lemurs
[ccp4bb] Detecting and dealing with Pseudotranslation and/or twinning
I’ve been working on a troublesome protein structure. The native protein forms crystals that diffract to 2.75A and belong to P212121 (55.179 64.316 233.748 90.000 90.000 90.000) with 4 molecules in the ASU. I have 3 versions of the same protein where selenomethionine mutations are incorporated at different positions. Interestingly, these mutations cause the protein to form crystals belonging to C2221 (56.130 64.665 240.854 90.000 90.000 90.000). Looking back at the native datasets, Xtraige indicates the largest Patterson peak is (0.5, 0.486, 0), height is 11.8% of the origin peak, and p_value(height) is 0.08549, which is just outside of the threshold for being identified as containing pseudotranslation. Datasets from a couple of the selenomet incorporated crystals yield diffraction to ~3.5A and anomalous signal to ~6.7A. Some of the datasets give a solution with reasonable maps, but the best maps are achieved from combining MAD/SAD selenomet datasets and one from a mercury derivatized crystal using the ‘group’ command in Phenix. --- 5: STEP: finished Top solution: # 39 Dataset #0 BAYES-CC: 69.2 +/- 13.4 FOM: 0.6 Built: 219 Side-chains: 44 Chains: 9 CC: 0.74 Score type: SKEWCORR_RMSNCS_OVERLAP Raw scores:0.41 0.82 0.00 100x EST OF CC: 69.17 43.34 31.25 --- Maps from this solution show connected electron density that looks like helices, consistent with the predicted secondary structure. Strangely, there is absolutely no side-chain density, only c-beta at most. I can build a poly-ala model into the map and the distances between the heavy atom sites appear correct based upon the known positions of the selenomethionines and the single cysteine in the protein sequence. However the model does not refine. R-free starts and remains near 0.45. I’ve tried indexing in lower symmetry space groups (P2, C2, P1) and re-solving by molecular replacement, but the refinement still fails. Xtriage does not indicate twinning. Twinning and intensity statistics summary (acentric data): Statistics independent of twin laws I^2/I^2 : 2.305 F^2/F^2 : 0.758 |E^2-1| : 0.788 |L|, L^2: 0.501, 0.333 Multivariate Z score L-test: 1.643 The multivariate Z score is a quality measure of the given spread in intensities. Good to reasonable data are expected to have a Z score lower than 3.5. Large values can indicate twinning, but small values do not necessarily exclude it. One possible clue as to what is going on comes from analysis of SOLVE results. I was analyzing whether SOLVE/PHENIX solutions were related with one another by various origin shifts and came across one particular SOLVE run from a SeMet SAD dataset in C2221 that gave good statistics for a solution FOM=0.57, Z-score=20.26, peak height between 7.1 and 10.8 for 4 SeMet sites to 3.8A). The maps, however, looked poor. What was interesting, though, was that 2 of the Se sites matched well with where I was expecting the Se sites in one molecule in the asymmetric unit. The other two matched with where I would expect the sites in the other molecule when the model is shifted by one half the unit cell distance along the ‘a’ or ‘b’ axis. I’d appreciate any advice as to what might be happening, and how might I go about detecting the problem, and how to dealing with the data? Brent Hamaoka UC San Diego 9500 Gilman Drive 0375 La Jolla, CA 92093
Re: [ccp4bb] how convert SF to intensities
Hi, Use SFALL to convert coordinates to structure factors...and then use mtz2various to convert to intensities...use the scalepack format under mtz2various. On Thu, May 12, 2011 at 3:13 PM, Fulvio Saccoccia fulvio.saccoc...@uniroma1.it wrote: Dear ccp4 users, I need to generate intensities from a model (.pdb). That is, I think that a correct procedure could be to convert model to structure factor and then obtain intensities squaring the SF. Does anyone know how can I do? Thanks in advance Fulvio Saccoccia
Re: [ccp4bb] B factor
hello sir , in chimera its available in module Render by Attribute. go through this link http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html . regards On Fri, May 13, 2011 at 12:01 AM, Luthra,Amit alut...@uchc.edu wrote: Hey all, I would like to make one ribbon diagram of the structure showing the B factor in different colors (contour levels). I am using pymol but it is not representing the perfect contour level of B factor. Is any other program where I can change the color according to B factor? Thanks Amit Luthra, Ph.D. Post-Doctoral Fellow The Radolf Laboratory Department of Medicine University of Connecticut Health Center [w] http://spirocheteresearch.uchc.edu -- Vandana Kukshal Postdoc Fellow structure biology group international Center For Genetic Engineering and Biotechnolgy India
