Re: [ccp4bb] How to align electron density maps?
Coot does this seamlessly.. Eleanor SSM superpose A to B NCS Maps will generate the map around A over B - or vice versa.. Eleanor On 01/28/2011 06:15 PM, RONG hui Rong wrote: Dear All, I have the problem as follows, but I can not find the corresponding solution. Can somebody give me some suggestions? Many Thanks, Hui Rong * [PyMOL] aligning electron density maps Eksterowicz, John Wed, 03 Mar 2004 15:03:43 -0800 I have a pdb and xplor file which contain two units of the same protein/inhibitor complex. What I am trying to do is align the two proteins to each other so I can compare the subunits. I can accomplish this by reading in the pdb file twice and aligning the b unit from the second pdb file to the a unit of the first pdb file. I then split everything into objects then delete what i don't want. In the end I have subunits a and b aligned to each other. I would like to be able to do the same thing for the electron denisty map. Is there a way to align maps? If I read in a protein and a map, then align the protein to another protein, the protein moves, but the map remains in it's original location. Can the map coordinates be transformed somehow? Is it possible to create some association with the protein and the map such that when the protein is aligned, the map will follow? Thanks, John * On 1/28/11, RONG hui Rongdaiwangs...@gmail.com wrote:
[ccp4bb] Counting of geometrical restraints?
Dear Ian other CCP4ers, I want to get a riddle about counting geometrical restraints solved, which emerged in my head after a recent discussion http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg17534.html on this board about the effect of NCS on the data:parameter ratio. This discussion quickly centered around the 1998 Acta Cryst paper about R-factor ratios [1]. So, here is my riddle: On one hand, geometrical restraints can be counted as observations. Refinement programs use differences between model geometry and ideal geometry restraints as least-squares targets, in a similar way to differences between model structure factor amplitudes and observed structure factor amplitudes. Model refinement is possible using geometrical restraints only, in the complete absence of observed structure factor amplitudes (idealization; whether this makes sense, is a different question). Geometrical restraints are also counted as observations in [1], both in Table 1 and in the text (for example in formula 2). On the other hand, it is shown in that paper, summarized in Table 2, that for the Rfree/Rwork ratios, geometrical restraints effectively reduce the number of refinement parameters, with a smooth transition from restraints to constraints via the residual term Drest. This implies that geometrical restraints can be counted as reducing the numbers of parameters, not as increasing the number of observations, which was also brought up as an argument in the aforementioned discussion. Thus, on one hand, geometrical restraints can be counted as observations, on the other hand they can be counted as reducing the number of parameters. The riddle for me is, that these two ways of counting are mutually exclusive alternatives - so, which one is the right one? I would be grateful, if you, Ian, or any other crystallographer on this board could help me (and maybe others) to solve this riddle. Best regards, Dirk. [1] Tickle, Laskowski, Moss. Rfree and the rfree ratio. I. Derivation of expected values of cross-validation residuals used in macromolecular least-squares refinement, Acta Cryst., D54, 547-557 (1998) -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Counting of geometrical restraints?
Hi Dirk I think cross-validation changed our ideas! Pre-Rfree the statistics of refinement was concerned with the 'number of degrees of freedom': Ndof = Nobs - N'par since this is the expectation of the properly weighted least-squares residual (chi-square or Dinc in the paper). If we substitute the effective no of parameters N'par: N'par = Npar - Ncon where Ncon is the actual number of constraints plus the effective number of restraints, we get: Ndof = Nobs - (Npar - Ncon) = Nobs + Ncon - Npar Thus if you are unconcerned with overfitting it _appears_ that constraints/restraints have the effect of increasing Nobs. However in fact what's happening is that Ncon reduces Npar. Post-Rfree things look different because now the expected free residual (Dfree in the paper) is proportional to: Dfree ~ Nobs + (Npar - Ncon) Now it's still true that Ncon reduces Npar but it's no longer true that Ncon increases Nobs. Cheers -- Ian On Mon, Jan 31, 2011 at 11:18 AM, Dirk Kostrewa kostr...@genzentrum.lmu.de wrote: Dear Ian other CCP4ers, I want to get a riddle about counting geometrical restraints solved, which emerged in my head after a recent discussion on this board about the effect of NCS on the data:parameter ratio. This discussion quickly centered around the 1998 Acta Cryst paper about R-factor ratios [1]. So, here is my riddle: On one hand, geometrical restraints can be counted as observations. Refinement programs use differences between model geometry and ideal geometry restraints as least-squares targets, in a similar way to differences between model structure factor amplitudes and observed structure factor amplitudes. Model refinement is possible using geometrical restraints only, in the complete absence of observed structure factor amplitudes (idealization; whether this makes sense, is a different question). Geometrical restraints are also counted as observations in [1], both in Table 1 and in the text (for example in formula 2). On the other hand, it is shown in that paper, summarized in Table 2, that for the Rfree/Rwork ratios, geometrical restraints effectively reduce the number of refinement parameters, with a smooth transition from restraints to constraints via the residual term Drest. This implies that geometrical restraints can be counted as reducing the numbers of parameters, not as increasing the number of observations, which was also brought up as an argument in the aforementioned discussion. Thus, on one hand, geometrical restraints can be counted as observations, on the other hand they can be counted as reducing the number of parameters. The riddle for me is, that these two ways of counting are mutually exclusive alternatives - so, which one is the right one? I would be grateful, if you, Ian, or any other crystallographer on this board could help me (and maybe others) to solve this riddle. Best regards, Dirk. [1] Tickle, Laskowski, Moss. Rfree and the rfree ratio. I. Derivation of expected values of cross-validation residuals used in macromolecular least-squares refinement, Acta Cryst., D54, 547-557 (1998) -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone:+49-89-2180-76845 Fax: +49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW: www.genzentrum.lmu.de ***
[ccp4bb] ID mapping
Hi all, (apologies if sounds off-topic) I have a list of pdb id's of the form 1XXX:Y (that is code:chain id). Is there a way to map this format to get uniprot id's for the entire list. I can use ID mapping in Uniprot but it takes only the code and not the above format. Although it gives the Uniprot id's for all the chains of pdb's containing multiple chain id's/different proteins I'm trying to avoid going back to the original list and manually delete hundreds id's I'm not interested in! (for eg. If I give a code 1XXX which has two chains A and B, I'm interested in getting the uniprot id of only A) Any help is much appreciated. Thanks. Kind regards, Sid. -- Sudharsan Sridharan, Ph.D. Scientist I Structural Bioinformatics, Protein Sciences, Lead Generation Department of Antibody Discovery and Protein Engineering MedImmune* Aaron Klug Building, Granta Park, Cambridge, CB21 6GH, UK. Direct line: +44 (0) 1223 898195 Facsimile: +44 (0) 1223 471472 Email: sridhar...@medimmune.com mailto:sridhar...@medimmune.com Web: www.medimmune.com http://www.medimmune.com/ *MedImmune Limited (formerly Cambridge Antibody Technology Limited) Registered Office: Milstein Building, Granta Park, Cambridge, CB21 6GH, UK. Registered in England and Wales number 2451177 Confidentiality Note: This information and any attachments is confidential and only for use by the individual or entity to whom it has been sent. Any unauthorised dissemination, distribution or copying of this message is strictly prohibited. If you are not the intended recipient please inform the sender immediately by reply e-mail and delete this message from your system. Thank you for your co-operation. We may monitor or record emails to or from MedImmune. E-mails may contain viruses or other harmful software that may damage your system. Whilst we have tried to eliminate such viruses and other harmful software we cannot accept liability for any damage caused to your system by any that remain. It is your responsibility to protect your system and you are advised to carry out your own checks on e-mails from us. To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.
Re: [ccp4bb] iMosflm execution error - solved?
Hi folks Most of you won't want to know about this It seems that on Ubuntu, there is a difference between the Bourne shell (sh) and the Bourne-again shell (bash). On most Linuces, the two are synonymous, though the iMosflm launch script uses specifically sh syntax rather than using the bash extensions. This error is raised by the shell (sh) when testing the HOSTTYPE environment variable, which seems to be defined under bash but not sh. The test is actually to see if you're running on an Intel Mac, and is ignored because of the unexpected operator error - so it should be harmless, since Ubuntu isn't OSX. If it isn't harmless, please let us know! On 28 Jan 2011, at 19:44, Andrew T. Torelli wrote: To the CCP4bb, I am working on installing the latest version of iMosflm (version 1.0.5) on my computer (running Ubuntu 10.10 (Meerkat). I've followed the installation instructions at the following link. I also have CCP4 ver. 6.1 and ActiveTcl ver. 8.4.19.3 installed and working (as far as I know) as per the instructions: http://www.mrc-lmb.cam.ac.uk/harry/imosflm/ver105/installation.html The only problem I encountered is that I had to correct pointers set up by my CCP4 installation to the CCP4-packaged Tcl/Tk and iMosflm components. I believe I have corrected those problems and I am able to get iMosflm loaded with no errors *as reported by the program*. However, after running the iMosflm executable, the following text is produced before the iMosflm GUI is loaded: snip VM% /usr/local/imosflm1.0.5/src/imosflm MOSFLM_EXEC set to /usr/local/imosflm1.0.5/bin/mosflm [: 180: =: unexpected operator testing MOSFLM_WISH (/usr/local/ActiveTcl8.4.19.3/bin/wish8.4) /snip I can't figure out what is generating this 'unexpected operator' error or how to correct it. I haven't recognized anything on the internet or in the documentation to help me identify the source of the problem. Can anyone provide insight on how to trace its origin or what it means? I will also test/confirm the ability to actually process data with the program later tonight, but I'm just puzzled by this error. Thanks for your help and insight, -Andy = Andrew T. Torelli, Ph.D. Department of Chemistry Chemical Biology Baker Laboratory, Cornell University Ithaca, NY 14853-1301 = Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
[ccp4bb] heavy atom clusters
Dear All, I wonder whether it is possible to get some recommendations/suggestions for a new set of powerful heavy atom clusters used to phase macromolecular complexes. Additionally, is anybody familiar whether Pentamethylcyclopentadienyliridium (III) chloride dimer is soluble in water? Your suggestions in this regard will be very helpful and highly appreciated. Thanking you, Jan
Re: [ccp4bb] ID mapping
Hi, SIFTS provides mappings between PDB and UniProt (and a number of other resources) - see pdbe.org/sifts This file may contain the info you need: ftp://ftp.ebi.ac.uk/pub/databases/msd/sifts/text/pdb_chain_uniprot.lst --Gerard On Mon, 31 Jan 2011, Sridharan, Sudharsan wrote: Hi all, (apologies if sounds off-topic) I have a list of pdb id's of the form 1XXX:Y (that is code:chain id). Is there a way to map this format to get uniprot id's for the entire list. I can use ID mapping in Uniprot but it takes only the code and not the above format. Although it gives the Uniprot id's for all the chains of pdb's containing multiple chain id's/different proteins I'm trying to avoid going back to the original list and manually delete hundreds id's I'm not interested in! (for eg. If I give a code 1XXX which has two chains A and B, I'm interested in getting the uniprot id of only A) Any help is much appreciated. Thanks. Kind regards, Sid. -- Sudharsan Sridharan, Ph.D. Scientist I Structural Bioinformatics, Protein Sciences, Lead Generation Department of Antibody Discovery and Protein Engineering MedImmune* Aaron Klug Building, Granta Park, Cambridge, CB21 6GH, UK. Direct line: +44 (0) 1223 898195 Facsimile: +44 (0) 1223 471472 Email: sridhar...@medimmune.com mailto:sridhar...@medimmune.com Web: www.medimmune.com http://www.medimmune.com/ *MedImmune Limited (formerly Cambridge Antibody Technology Limited) Registered Office: Milstein Building, Granta Park, Cambridge, CB21 6GH, UK. Registered in England and Wales number 2451177 Confidentiality Note: This information and any attachments is confidential and only for use by the individual or entity to whom it has been sent. Any unauthorised dissemination, distribution or copying of this message is strictly prohibited. If you are not the intended recipient please inform the sender immediately by reply e-mail and delete this message from your system. Thank you for your co-operation. We may monitor or record emails to or from MedImmune. E-mails may contain viruses or other harmful software that may damage your system. Whilst we have tried to eliminate such viruses and other harmful software we cannot accept liability for any damage caused to your system by any that remain. It is your responsibility to protect your system and you are advised to carry out your own checks on e-mails from us. To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. Best wishes, --Gerard ** Gerard J. Kleywegt Dept. of Cell Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN http://xray.bmc.uu.se/gerard/ mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. **
Re: [ccp4bb] heavy atom clusters
Hi, I suggest that you check out the lanthanide compounds investigated by a number of people including Richard Kahn. Papers can be found using the iucr web site (and its search function). Commercially available. Fred. Message du 31/01/11 17:02 De : Jan Rashid Umar A : CCP4BB@JISCMAIL.AC.UK Copie à : Objet : [ccp4bb] heavy atom clusters Dear All, I wonder whether it is possible to get some recommendations/suggestions for a new set of powerful heavy atom clusters used to phase macromolecular complexes. Additionally, is anybody familiar whether Pentamethylcyclopentadienyliridium (III) chloride dimer is soluble in water? Your suggestions in this regard will be very helpful and highly appreciated. Thanking you, Jan
[ccp4bb] Post Doc position in Structural Biology at the University of Warwick, UK
Dear CCP4 bb ??I have a Post doc position available for a biochemist/structural biologist with expertease in Protein crystallography at the University of Warwick in the UK. The project is on aspects of peptidoglycan biosynthesis in Mycobacterium tuberculosis in collaboration with Prof G.S. Besra at Birmingham University who also has a position to offer for in a complimentary research position. The closing date/time for applications is midnight (British time) at the end of Tuesday 15 February 2011. ??Further details on the project and how to apply can be found at http://www.jobs.ac.uk/job/ACD463/research-fellow/ Yours with thanks Dr David I Roper Associate Professor of Structural Biology School of Life Sciences University of Warwick Gibbet Hill Road Coventry CV4 7AL UK Tel +44 (0)24 7652 8369/2568 Fax +44 (0)24 7652 3701 email: david.ro...@warwick.ac.uk www.warwick.ac.uk/go/ropergroup
Re: [ccp4bb] contour map
Hi Leila, it was 10 years ago when I looked at the maps this way, and at that time I used the program called CAN to do this (see below). It worked really well. If you are lucky it might still be available by request from the authors. Pavel. 1. Vernoslova, E.A., Lunin, V.Yu. (1993) The FROG PC series : programs for electorn-density and model investigations for proteins. *J.Appl. Cryst.,* 26, 291-294 The program allow to visualise different 3D or 2D distributions (maps), periodic or not. The program allows also to superpose 2 distributions and superpose them with an atomic model. The second map can be translated relatively to the first one. An atomic model can be moved as a rigid body. The maps are represented by a set of equipotential levels. 3D maps can be represented either section by section or as a set of superposed sections. A number of options is available to visualise and to analyse the maps. A special black/which option is provided to produce better quality pictures. The program accept several input formats but specially tuned to the ones linked to the corresponding FFT program (Vernoslova and Lunin). The program is written in FORTRAN, runs under MS DOS and is available by request from the authors. On Mon, Jan 31, 2011 at 2:28 PM, Leila Foroughi lforo...@gmail.com wrote: I'm currently trying to compare single crystal X-ray data for a protein crystal with previously published electron miscroscopy data. I would really like to be able to take my electron density map (from X-ray) and view it as a 2D projection of 3D space (essentially a contour map). The attached is an example of the type of electron density map I'm trying to mimic. Does anyone have any suggestions on what software I could use to do this? Image Source: J Mol. Biol. (1975) 94, 425-440. Thanks, Leila
Re: [ccp4bb] contour map
mapview_x from PHASES shows maps (and masks) in 2D. Pete Leila Foroughi wrote: I'm currently trying to compare single crystal X-ray data for a protein crystal with previously published electron miscroscopy data. I would really like to be able to take my electron density map (from X-ray) and view it as a 2D projection of 3D space (essentially a contour map). The attached is an example of the type of electron density map I'm trying to mimic. Does anyone have any suggestions on what software I could use to do this? Image Source: J Mol. Biol. (1975) 94, 425-440. Thanks, Leila
Re: [ccp4bb] contour map
Leila Foroughi wrote: I'm currently trying to compare single crystal X-ray data for a protein crystal with previously published electron miscroscopy data. I would really like to be able to take my electron density map (from X-ray) and view it as a 2D projection of 3D space (essentially a contour map). The attached is an example of the type of electron density map I'm trying to mimic. Does anyone have any suggestions on what software I could use to do this? Image Source: J Mol. Biol. (1975) 94, 425-440. My, that looks familiar! First, you need to calculate the projection map- this was discussed recently. It is easy if you want a projection along a principal axis, but someone reported a program that will give the projection onto arbitrary planes. Then as for plotting the contours, the CCP4 program is NPO. The sections may have to be regular map sections though, not at arbitrary angles. eab PS- in general, projection maps of proteins are not interpretable. The bR just happens to have three or four helices nearly perpendicular to the membrane.
