[ccp4bb] Available Xray diffraction system
Dear CCP4 Community, our laboratory is going to dismantle an in-house X-ray diffraction instrumentation. It consists of a Rigaku RU-200 rotating anode, an Osmic Blue confocal system, a RaxisIV++ detector, and an Oxford cryostream cooling device. All instruments have been properly maintained and are in good working conditions. If you are interested in this system, please contact me at the address below. Best regards, Andrea Mattevi -- Andrea Mattevi Dept. Genetics and Microbiology University of Pavia Via Ferrata 1, 27100 Pavia Italy Tel. +39-0382-985525/985534 Fax +39-0382-528496 Web www.unipv.it/biocry Email: andrea.matt...@unipv.it
Re: [ccp4bb] Alternatives to ChemDraw 3D? Yes, Chemdoodle!
Alternatives to ChemDraw 3D? Yes, ChemDoodle! I installed XDrawChem on Mac OSX 10.4.11 but it crashes all the time which is somewhat annoying. Then I finally stumbled upon ChemDoodle *which is not for free* but the trial version solved my problem at that time. Having worked with it, I really liked it so much that I finally purchased it for 60 US$. You only pay this amount once, software updates are for free. Hope this helps. - Jeroen - Wataru Kagawa wrote: Hi all, I would like to create a pdb file for a chemical compound (FW ~600) that was created in our chemistry department. ChemDraw 3D appears capable of doing this, but I would like to know if there are free alternatives that work great on Macs. Any info would be greatly appreciated. Thanks. Wataru ~ Wataru Kagawa, Ph. D. Waseda University Graduate School of Advanced Science & Engineering 2-2 Wakamatsu-cho, Shinjuku-ku Tokyo, Japan 162-8480 tel. 03-5369-7369 (ext. 3241) fax. 03-5367-2820 ~ -- Dr. Jeroen R. Mesters Gruppenleiter Strukturelle Neurobiologie und Kristallogenese Institut für Biochemie, Universität zu Lübeck Zentrum für Medizinische Struktur- und Zellbiologie Ratzeburger Allee 160, D-23538 Lübeck Tel: +49-451-5004065, Fax: +49-451-5004068 Http://www.biochem.uni-luebeck.de Http://www.iobcr.org Http://www.selfish-brain.org Http://www.opticryst.org -- If you can look into the seeds of time and say which grain will grow and which will not - speak then to me (Macbeth) --
[ccp4bb] transformation of cell
Dear All, Is there a way to transform a cell in Pymol? I want to superimpose cells of my two crystal forms, when I use the align command, molecule from one unit cell transforms on to other, but the cell stays the same. I just want to look if by any chance my cells of two different crystal forms are related!! Thanks Siva
[ccp4bb] Job advertisment: Head of Junior Research Group (tenure track)
Job Advertisement The Division of Structural Biology at the Helmholtz Centre for Infection Research in Braunschweig/Germany invites applications for the position of a Head of Junior Research Group (tenure track) Area of research: Structural biology Application: The applicants should provide a letter of intent, CV, list of publications, list of certificates as well as a short research proposal (max. 3 pages). Prerequisites: This call aims for top level postdoctoral fellows, 2 - 5 years after they have been conferred their doctorate (child-rearing periods will be taken into consideration) who would like to participate in the Helmholtz young investigator program (www.helmholtz.de). The candidates must have completed a continuous 6-month research period abroad during a doctorate or a post-doctorate phase. The most important selection criterion is the outstanding quality of the applicants. Funding: Position of group leader, scientific/technical staff plus expenses of materials, supplies and investments for 5 years. For further information please contact Prof. Dr. Dirk Heinz, Division of Structural Biology, Helmholtz Centre for Infection Research, Braunschweig/Germany, dirk.he...@helmholtz-hzi.de, phone: +49-(0)531-6181-7000 and visit our homepage www.helmholtz-hzi.de/en/research/research_groups/ structural_biology/ Please contact us if you have any questions! Christine Bentz Assistant to Prof. Dr. Dirk Heinz Division of Structural Biology Helmholtz Centre for Infection Research Inhoffenstrasse 7 38124 Braunschweig / Germany Fon 0049 (0)531.6181.7002 Fax 0049 (0)531.6181.7099 Protect the environment - please don't print this e-mail unless you really need to
Re: [ccp4bb] reforigin on 2FKA
Yes, thanks! I wish I had spotted that before! As you say Tables 2.2.3.2 (pp 212-213 in my ed.) & 2.2.3.4 (pp 214-215), for non-centrosymmetric primitive & centred space groups respectively, contain all the authoritative information you need to define the allowed origin shifts (as well as info on semi-invariants etc). I think it would be useful if all documentation/scripts/programs which claim to specify alternate origins etc referenced (and of course were consistent with!) these tables. Cheers -- Ian > -Original Message- > From: George M. Sheldrick [mailto:gshe...@shelx.uni-ac.gwdg.de] > Sent: 05 February 2010 23:08 > To: Ian Tickle > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] reforigin on 2FKA > > > I have just noticed that there is a definitive table of equivalent > origins for all 230 space groups in volume B of International > Tables (in Chapter 2.2 by Carmelo Giacovazzo). This appears to > agree with Ian's last email in this thread for the space groups > discussed there. It gives the origins directly rather than the > Cheshire groups so may be slightly easier to use. > > George > > Prof. George M. Sheldrick FRS > Dept. Structural Chemistry, > University of Goettingen, > Tammannstr. 4, > D37077 Goettingen, Germany > Tel. +49-551-39-3021 or -3068 > Fax. +49-551-39-22582 > > > On Wed, 27 Jan 2010, Ian Tickle wrote: > > > Correction: my apologies, I see now that the table of Cheshire groups > > that I referred to originally came from: Hirshfeld (1968), Acta Cryst. > > A24, 301-311. I got it from Jorge: it's still good to know that it has > > Jorge's seal of approval! > > > > Cheers > > > > -- Ian > > > > > -Original Message- > > > From: owner-ccp...@jiscmail.ac.uk > > > [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Ian Tickle > > > Sent: 27 January 2010 22:25 > > > To: James Holton; Francois Berenger > > > Cc: CCP4BB@jiscmail.ac.uk > > > Subject: RE: [ccp4bb] reforigin on 2FKA > > > > > > ... and I was assuming that since it was clear that there are > > > omissions > > > for F222 and F23 on the CCP4 'alternate origins' page, that > > > James' page > > > was 100% correct! But I think we have both made the same mistake of > > > assuming that F222, F23 and F432 all behave identically as > > > far as origin > > > shifts are concerned. > > > > > > According to this document: > > > http://www.ccp4.ac.uk/dist/html/cheshirecell.html which I > > > have no reason > > > to question since it comes from an excellent authority (Jorge Navaza), > > > the Cheshire space group and cell for both F222 and F23 is I centred > > > (Immm & Im3m resp) with cell lengths a/2, b/2, c/2. This implies the > > > origin shift (1/4,1/4,1/4), and therefore by unit translations in the > > > Cheshire lattice (3/4,3/4,3/4) also, is a non-equivalent origin. For > > > F432 the Cheshire cell is the same as for F222 & F23 but the Cheshire > > > space group is primitive (Pm3m), which implies that (1/4,1/4,1/4) is > > > *not* an allowed origin shift, i.e. 'disallowed' in the sense that you > > > can't use the same SF calculation formula and still expect to get the > > > right answer: if you're willing to use a different formula > > > then anything > > > (including completely arbitrary origin shifts, i.e. as in P1) is > > > allowed! > > > > > > So the one redeeming factor from all this is that reforigin at least > > > appears to give the right answer. > > > > > > Cheers > > > > > > -- Ian > > > > > > > -Original Message- > > > > From: owner-ccp...@jiscmail.ac.uk > > > > [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of James Holton > > > > Sent: 27 January 2010 21:35 > > > > To: Francois Berenger > > > > Cc: CCP4BB@jiscmail.ac.uk > > > > Subject: Re: [ccp4bb] reforigin on 2FKA > > > > > > > > Francois Berenger wrote: > > > > > It correspond to what is found at the end of James Holton's > > > > > origins.com script > > > > > http://bl831.als.lbl.gov/~jamesh/pickup/origins.com > > > > > so I guess it should be correct. > > > > Uhhh... > > > > > > > > > > He also says how he found them: > > > > > > > > > > # TABLE OF ALLOWED ORIGIN SHIFTS > > > > > These origin shifts were determined emprirically using 100 > > > > > randomly-placed atoms > > > > > that were shifted around with pdbset and checked with SFALL > > > > for identical > > > > > amplitudes to the 0 0 0 origin. They should be correct for > > > > the CCP4 > > > > > convention > > > > > of symmetry. (I.E. R3 and R32 have hexagonal indexing) > > > > > > > > > Okay, I just went back to my notes on this. I should admit > > > > that in my > > > > completely brain-dead allowed-origin-shift search described above I > > > > originally found no "allowed" shifts for F432 (not sure why, > > > > but maybe > > > > because it was last on my list). Years later, I think it was > > > > Peter Zwart > > > > who pointed out to me that I was missing a few of what ought to be > > > > allowed origins. As I recall, at least one of them passed my > > > > pdbset/s
[ccp4bb] refmac5 and spericity restraints
Hi there, I am refining a 1.3AA structure for SSGCID using -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com
[ccp4bb] Map transformation
Hi all, I am trying to use the transform map command in coot but i am getting the following error 6:19: In expression (0.9956 -0.08709 -0.03537 ...)::6:19: Wrong type to apply: 0.9956 the command that i used was: (transform-map 13 (0.9956 -0.08709 -0.03537 -0.08702 -0.9962 0.003531 -0.03554 -0.0004371 -0.9994) (1.235 1.005 0.1625) (11.6806 -8.6401 -14.960) 10) i have also added the word list before each group of numbers, (transform-map 13 (list 0.9956 -0.08709 -0.03537 -0.08702 -0.9962 0.003531 -0.03554 -0.0004371 -0.9994) (list 1.235 1.005 0.1625) (list 11.6806 -8.6401 -14.960) 10) and i got the following error, arguments to transform-map incomprehensible: args: (13 (0.9956 -0.08709 -0.03537 -0.08702 -0.9962 0.003531 -0.03554 -4.371e-4 -0.9994) (1.235 1.005 0.1625) (11.6806 -8.6401 -14.96) 10) I am not sure what i am doing wrong, could you please point me in the right direction ? Many thanks Regards, Rana
Re: [ccp4bb] Map transformation
I think the space-group and cell are missing: It should be something like: (transform-map imol rotation-matrix trans point radius space-group cell) i.e. in your example, say: (transform-map 13 (list 0.9956 -0.08709 -0.03537 -0.08702 -0.9962 0.003531 -0.03554 -0.0004371 -0.9994) (list 1.235 1.005 0.1625) (list 11.6806 -8.6401 -14.960) 10 "P 21 21 21" (list 45 100 39 90 90 90)) or some such. But are you sure you actually need this? -- Extensions->Maps->Transform map by LSQ does something similar... JED. (Oh, the coot documentation is misleading... shock horror!) -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 15 Stanhope Gate, London W1K 1LN. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies. -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Rana Refaey Sent: 08 February 2010 14:42 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Map transformation Hi all, I am trying to use the transform map command in coot but i am getting the following error 6:19: In expression (0.9956 -0.08709 -0.03537 ...)::6:19: Wrong type to apply: 0.9956 the command that i used was: (transform-map 13 (0.9956 -0.08709 -0.03537 -0.08702 -0.9962 0.003531 -0.03554 -0.0004371 -0.9994) (1.235 1.005 0.1625) (11.6806 -8.6401 -14.960) 10) i have also added the word list before each group of numbers, (transform-map 13 (list 0.9956 -0.08709 -0.03537 -0.08702 -0.9962 0.003531 -0.03554 -0.0004371 -0.9994) (list 1.235 1.005 0.1625) (list 11.6806 -8.6401 -14.960) 10) and i got the following error, arguments to transform-map incomprehensible: args: (13 (0.9956 -0.08709 -0.03537 -0.08702 -0.9962 0.003531 -0.03554 -4.371e-4 -0.9994) (1.235 1.005 0.1625) (11.6806 -8.6401 -14.96) 10) I am not sure what i am doing wrong, could you please point me in the right direction ? Many thanks Regards, Rana
[ccp4bb] refmac5 and sphericity restraints, 2nd attempt
Hi there, apologies for the previous email, hit the send button too early. Hope everyone could stand the suspense for the continuation of the story ;-) Here we go: I am refining a 1.3AA structure for SSGCID using refmac5.5.102 or 109, OSX. A typical grey zone case for anisotropic refinement, yet it improves Rfactors by some 2%. A few B factors go a bit wild though: "MAKE_U_POSITIVE". Therefore, I try to restrain the sphericity using the SPHER keyword. Even though the logfile acknowledges the keyword, the refinements with spher=2 and spher=5 are identical. Is this keyword still active? Cheers Jan On Mon, Feb 8, 2010 at 6:29 AM, Jan Abendroth wrote: > Hi there, > I am refining a 1.3AA structure for SSGCID using > -- > Jan Abendroth > Emerald BioStructures > Seattle / Bainbridge Island WA, USA > home: Jan.Abendroth_at_gmail.com > work: JAbendroth_at_embios.com > http://www.emeraldbiostructures.com > > > > > > > -- Jan Abendroth Emerald Biostructures Seattle / Bainbridge Island, WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com
Re: [ccp4bb] Map transformation
Rana Refaey wrote: Hi all, I am trying to use the transform map command in coot but i am getting the following error 6:19: In expression (0.9956 -0.08709 -0.03537 ...)::6:19: Wrong type to apply: 0.9956 the command that i used was: (transform-map 13 (0.9956 -0.08709 -0.03537 -0.08702 -0.9962 0.003531 -0.03554 -0.0004371 -0.9994) (1.235 1.005 0.1625) (11.6806 -8.6401 -14.960) 10) i have also added the word list before each group of numbers, (transform-map 13 (list 0.9956 -0.08709 -0.03537 -0.08702 -0.9962 0.003531 -0.03554 -0.0004371 -0.9994) (list 1.235 1.005 0.1625) (list 11.6806 -8.6401 -14.960) 10) and i got the following error, arguments to transform-map incomprehensible: args: (13 (0.9956 -0.08709 -0.03537 -0.08702 -0.9962 0.003531 -0.03554 -4.371e-4 -0.9994) (1.235 1.005 0.1625) (11.6806 -8.6401 -14.96) 10) I am not sure what i am doing wrong, could you please point me in the right direction ? Dear Rana Refaey, It seems that the documentation is inconsistent with the functionality (i.e. there is (was) either an error in the manual or the code, take your pick). Your courses of actions are: 1) Tomorrow morning pick up pre-release revision 2790 from here: http://www.biop.ox.ac.uk/coot/devel/build-info.html 2) right now you can drop in the replacement coot-utils.scm which you can get from here: http://coot.googlecode.com/svn/trunk/scheme/coot-utils.scm 3) Alternatively and right now (as JED says) provide the cell and space-group too: (transform-map 13 (list 0.9956 -0.08709 -0.03537 -0.08702 -0.9962 0.003531 -0.03554 -0.0004371 -0.9994) (list 1.235 1.005 0.1625) (list 11.6806 -8.6401 -14.960) 10 (show-spacegroup 13) (cell 13)) And as JED also said, you are doing something pretty jolly sophisticated if "Transform map by LSQ" won't do what you want. Thanks, Paul.
Re: [ccp4bb] reforigin on 2FKA
Dear Ian, Although these tables are indeed very useful, on closer perusal I have found a typo in my edition (which appears to be the same as yours but slightly different to the on-line edition) - in the 3rd column of table 2.2.3.2, "P6" should obviously have a bar over the "6", though this is unlikely to cause problems for most readers of CCP4bb. Less satisfactory from our point of view is that R3 and R32 are only given for the primitive rhombohedral setting, not for the hexagonal cell with three times the volume (H3 or H32) that protein crystallographers seem to prefer. Best wishes, George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Mon, 8 Feb 2010, Ian Tickle wrote: > > Yes, thanks! I wish I had spotted that before! > > As you say Tables 2.2.3.2 (pp 212-213 in my ed.) & 2.2.3.4 (pp 214-215), > for non-centrosymmetric primitive & centred space groups respectively, > contain all the authoritative information you need to define the allowed > origin shifts (as well as info on semi-invariants etc). I think it > would be useful if all documentation/scripts/programs which claim to > specify alternate origins etc referenced (and of course were consistent > with!) these tables. > > Cheers > > -- Ian > > > -Original Message- > > From: George M. Sheldrick [mailto:gshe...@shelx.uni-ac.gwdg.de] > > Sent: 05 February 2010 23:08 > > To: Ian Tickle > > Cc: CCP4BB@JISCMAIL.AC.UK > > Subject: Re: [ccp4bb] reforigin on 2FKA > > > > > > I have just noticed that there is a definitive table of equivalent > > origins for all 230 space groups in volume B of International > > Tables (in Chapter 2.2 by Carmelo Giacovazzo). This appears to > > agree with Ian's last email in this thread for the space groups > > discussed there. It gives the origins directly rather than the > > Cheshire groups so may be slightly easier to use. > > > > George > > > > Prof. George M. Sheldrick FRS > > Dept. Structural Chemistry, > > University of Goettingen, > > Tammannstr. 4, > > D37077 Goettingen, Germany > > Tel. +49-551-39-3021 or -3068 > > Fax. +49-551-39-22582 > > > > > > On Wed, 27 Jan 2010, Ian Tickle wrote: > > > > > Correction: my apologies, I see now that the table of Cheshire > groups > > > that I referred to originally came from: Hirshfeld (1968), Acta > Cryst. > > > A24, 301-311. I got it from Jorge: it's still good to know that it > has > > > Jorge's seal of approval! > > > > > > Cheers > > > > > > -- Ian > > > > > > > -Original Message- > > > > From: owner-ccp...@jiscmail.ac.uk > > > > [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Ian Tickle > > > > Sent: 27 January 2010 22:25 > > > > To: James Holton; Francois Berenger > > > > Cc: CCP4BB@jiscmail.ac.uk > > > > Subject: RE: [ccp4bb] reforigin on 2FKA > > > > > > > > ... and I was assuming that since it was clear that there are > > > > omissions > > > > for F222 and F23 on the CCP4 'alternate origins' page, that > > > > James' page > > > > was 100% correct! But I think we have both made the same mistake > of > > > > assuming that F222, F23 and F432 all behave identically as > > > > far as origin > > > > shifts are concerned. > > > > > > > > According to this document: > > > > http://www.ccp4.ac.uk/dist/html/cheshirecell.html which I > > > > have no reason > > > > to question since it comes from an excellent authority (Jorge > Navaza), > > > > the Cheshire space group and cell for both F222 and F23 is I > centred > > > > (Immm & Im3m resp) with cell lengths a/2, b/2, c/2. This implies > the > > > > origin shift (1/4,1/4,1/4), and therefore by unit translations in > the > > > > Cheshire lattice (3/4,3/4,3/4) also, is a non-equivalent origin. > For > > > > F432 the Cheshire cell is the same as for F222 & F23 but the > Cheshire > > > > space group is primitive (Pm3m), which implies that (1/4,1/4,1/4) > is > > > > *not* an allowed origin shift, i.e. 'disallowed' in the sense that > you > > > > can't use the same SF calculation formula and still expect to get > the > > > > right answer: if you're willing to use a different formula > > > > then anything > > > > (including completely arbitrary origin shifts, i.e. as in P1) is > > > > allowed! > > > > > > > > So the one redeeming factor from all this is that reforigin at > least > > > > appears to give the right answer. > > > > > > > > Cheers > > > > > > > > -- Ian > > > > > > > > > -Original Message- > > > > > From: owner-ccp...@jiscmail.ac.uk > > > > > [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of James Holton > > > > > Sent: 27 January 2010 21:35 > > > > > To: Francois Berenger > > > > > Cc: CCP4BB@jiscmail.ac.uk > > > > > Subject: Re: [ccp4bb] reforigin on 2FKA > > > > > > > > > > Francois Berenger wrote: > > > > > > It correspond to what is found at the end of James Holton's > > > > > > origins.com script > > > > > > http://bl831.als.lbl.gov/~j
[ccp4bb] Sixth International Workshop on X-ray Radiation Damage to Biological,Crystalline Samples, SSRL, 11th-13th March 2010. Registration now open.
Sixth International Workshop on X-ray Radiation Damage to Biological Crystalline Samples To be held at the Stanford Synchrtron Radiation Laboratory from 13:00 March 11th to 13:00 March 13th 2010. Registration and Abstract submission is now open and can be found at: http://www-conf.slac.stanford.edu/xrayradiation2010/ Registration is $75 ($100 after March 1st). Abstract submission will close on the 1st March. This series of workshops was originally concerned with the effects of radiation damage during investigation of protein structures by X-ray crystallography. Other techniques of structural biology are now being included to ensure greater information exchange. The workshop will therefore be of interest to all those using ionising radiation to examine biological structures at the molecular and cellular level. It will consist of around 30 talks of 20-25 minutes each covering: * • Reducing and Mitigating Radiation Damage. * • Radiation chemistry and radiolysis of biological molecules. * • Progress in the understanding of radiation damage in MX. * • Correcting for the effects of radiation damage. * • Reduction of metalloproteins and study of protein function. * • Radiation Damage in Electron Microscopy and Electron Crystallography. * • Pulsed Sources: Radiation Damage issues. * • Complementary (or non-crystallographic) methods to study radiation damage. Some Abstracts will be selected for aural presentation - please indicate if you would like to be considered for this in the comments box on the registration form. The organizers are Ana Gonzales, Elspeth Garman, Colin Nave, Sean McSweeney, Raimond Ravelli, Gerd Rosenbaum, Soichi Wakatsuki and Martin Weik. -- Professor Elspeth F. Garman, President, British Crystallographic Association Postal address: Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Tel: (44)-1865-613297 South Parks Road, FAX: (44)-1865-613201 OXFORD, OX1 3QU, U.K. E-mail: elspeth.gar...@bioch.ox.ac.uk http://www.biop.ox.ac.uk/www/garman/gindex.html -
[ccp4bb] problem of imosflm in ccp4
Hi all, I use fink to install ccp4-6.1.2 on my Mac OS X 10.6. All programs in ccp4 works well except imosflm. when I run it, it gives me the following error message" Top level CCP4 directory is /sw64/share/xtal/ccp4-6.1.2 Using CCP4 programs from /sw64/share/xtal/ccp4-6.1.2/bin MOSDIR is /Users/yamei/mosdir Error in startup script: unknown namespace in import pattern "itcl::*" while executing "namespace import itcl::*" (file "/sw64/share/xtal/ccp4-6.1.2/ccp4i/imosflm/src/imosflm.tcl" line 91) invoked from within "source $env(IMOSFLM)" (file "/sw64/share/xtal/ccp4-6.1.2/ccp4i/imosflm/imosflm.tcl" line 117) " Dose any one know how to fix this problem? Thank you very much! yamei
Re: [ccp4bb] reforigin on 2FKA
Hi George, Ian, I have attached a script that computes the alternative origins for a given space group (or all of them) using procedures outlined by Ralf (Acta Cryst. 1999, A55, 383-395). Run it with phenix.python origins.py For R3 and R32 in both rhombohedral and hexagonal setting we get R32:H (0,0,1/2) R32:R (1/2,1/2,1/2) R3:H 0,0,z R3:R (x,x,x) Also, I2 is not listed in the IT tables ( or in the paper I quoted earlier (http://scripts.iucr.org/cgi-bin/paper?a10657)): I2: (1/2,0,0) and (0,y,0) HTH Peter 2010/2/8 George M. Sheldrick : > Dear Ian, > > Although these tables are indeed very useful, on closer perusal I have > found a typo in my edition (which appears to be the same as yours but > slightly different to the on-line edition) - in the 3rd column of table > 2.2.3.2, "P6" should obviously have a bar over the "6", though this is > unlikely to cause problems for most readers of CCP4bb. Less > satisfactory from our point of view is that R3 and R32 are only given > for the primitive rhombohedral setting, not for the hexagonal cell with > three times the volume (H3 or H32) that protein crystallographers seem > to prefer. > > Best wishes, George > > Prof. George M. Sheldrick FRS > Dept. Structural Chemistry, > University of Goettingen, > Tammannstr. 4, > D37077 Goettingen, Germany > Tel. +49-551-39-3021 or -3068 > Fax. +49-551-39-22582 > > > On Mon, 8 Feb 2010, Ian Tickle wrote: > >> >> Yes, thanks! I wish I had spotted that before! >> >> As you say Tables 2.2.3.2 (pp 212-213 in my ed.) & 2.2.3.4 (pp 214-215), >> for non-centrosymmetric primitive & centred space groups respectively, >> contain all the authoritative information you need to define the allowed >> origin shifts (as well as info on semi-invariants etc). I think it >> would be useful if all documentation/scripts/programs which claim to >> specify alternate origins etc referenced (and of course were consistent >> with!) these tables. >> >> Cheers >> >> -- Ian >> >> > -Original Message- >> > From: George M. Sheldrick [mailto:gshe...@shelx.uni-ac.gwdg.de] >> > Sent: 05 February 2010 23:08 >> > To: Ian Tickle >> > Cc: CCP4BB@JISCMAIL.AC.UK >> > Subject: Re: [ccp4bb] reforigin on 2FKA >> > >> > >> > I have just noticed that there is a definitive table of equivalent >> > origins for all 230 space groups in volume B of International >> > Tables (in Chapter 2.2 by Carmelo Giacovazzo). This appears to >> > agree with Ian's last email in this thread for the space groups >> > discussed there. It gives the origins directly rather than the >> > Cheshire groups so may be slightly easier to use. >> > >> > George >> > >> > Prof. George M. Sheldrick FRS >> > Dept. Structural Chemistry, >> > University of Goettingen, >> > Tammannstr. 4, >> > D37077 Goettingen, Germany >> > Tel. +49-551-39-3021 or -3068 >> > Fax. +49-551-39-22582 >> > >> > >> > On Wed, 27 Jan 2010, Ian Tickle wrote: >> > >> > > Correction: my apologies, I see now that the table of Cheshire >> groups >> > > that I referred to originally came from: Hirshfeld (1968), Acta >> Cryst. >> > > A24, 301-311. I got it from Jorge: it's still good to know that it >> has >> > > Jorge's seal of approval! >> > > >> > > Cheers >> > > >> > > -- Ian >> > > >> > > > -Original Message- >> > > > From: owner-ccp...@jiscmail.ac.uk >> > > > [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Ian Tickle >> > > > Sent: 27 January 2010 22:25 >> > > > To: James Holton; Francois Berenger >> > > > Cc: CCP4BB@jiscmail.ac.uk >> > > > Subject: RE: [ccp4bb] reforigin on 2FKA >> > > > >> > > > ... and I was assuming that since it was clear that there are >> > > > omissions >> > > > for F222 and F23 on the CCP4 'alternate origins' page, that >> > > > James' page >> > > > was 100% correct! But I think we have both made the same mistake >> of >> > > > assuming that F222, F23 and F432 all behave identically as >> > > > far as origin >> > > > shifts are concerned. >> > > > >> > > > According to this document: >> > > > http://www.ccp4.ac.uk/dist/html/cheshirecell.html which I >> > > > have no reason >> > > > to question since it comes from an excellent authority (Jorge >> Navaza), >> > > > the Cheshire space group and cell for both F222 and F23 is I >> centred >> > > > (Immm & Im3m resp) with cell lengths a/2, b/2, c/2. This implies >> the >> > > > origin shift (1/4,1/4,1/4), and therefore by unit translations in >> the >> > > > Cheshire lattice (3/4,3/4,3/4) also, is a non-equivalent origin. >> For >> > > > F432 the Cheshire cell is the same as for F222 & F23 but the >> Cheshire >> > > > space group is primitive (Pm3m), which implies that (1/4,1/4,1/4) >> is >> > > > *not* an allowed origin shift, i.e. 'disallowed' in the sense that >> you >> > > > can't use the same SF calculation formula and still expect to get >> the >> > > > right answer: if you're willing to use a different formula >> > > > then anything >> > > > (including completely arbitrary origin shifts, i.e. as in P1) is >> > > > allowe
[ccp4bb] coot and probe clash
Hi all, I have installed coot 0.6.1 in my Mac OS X 10.6. But the Prove chashes button in validate is grey. How to get 'Probe clashes" work in coot? Thank you very much! yamei
Re: [ccp4bb] problem of imosflm in ccp4
The easiest thing to do is: export MOSFLM_WISH=/usr/bin/wish8.4 or fink install imosflm-aqua will make sure everything is set up ok for 10.6, where the supplied aqua TclTK plays well with imosflm. Yamei Yu wrote: > Hi all, > > I use fink to install ccp4-6.1.2 on my Mac OS X 10.6. All programs in > ccp4 > works well except imosflm. when I run it, it gives me the following error > message" > > Top level CCP4 directory is /sw64/share/xtal/ccp4-6.1.2 > Using CCP4 programs from /sw64/share/xtal/ccp4-6.1.2/bin > MOSDIR is /Users/yamei/mosdir > Error in startup script: unknown namespace in import pattern "itcl::*" > while executing > "namespace import itcl::*" > (file "/sw64/share/xtal/ccp4-6.1.2/ccp4i/imosflm/src/imosflm.tcl" line > 91) > invoked from within > "source $env(IMOSFLM)" > (file "/sw64/share/xtal/ccp4-6.1.2/ccp4i/imosflm/imosflm.tcl" line > 117) > > " > Dose any one know how to fix this problem? > > Thank you very much! > > yamei >
Re: [ccp4bb] coot and probe clash
This is available to install as a binary from here: http://molprobity.biochem.duke.edu/get_molprobity.php Although probe and MolProbity3 are said to be "free and open source software distributed under a BSD-style license", I can't find the source code, so I can't make coot depend on it within fink. On Feb 8, 2010, at 12:53 PM, Yamei Yu wrote: > Hi all, > > I have installed coot 0.6.1 in my Mac OS X 10.6. But the Prove chashes > button in validate is grey. > How to get 'Probe clashes" work in coot? > > Thank you very much! > > yamei
Re: [ccp4bb] coot and probe clash
On Mon, Feb 8, 2010 at 1:51 PM, William G. Scott wrote: > This is available to install as a binary from here: > > http://molprobity.biochem.duke.edu/get_molprobity.php > > > Although probe and MolProbity3 are said to be "free and open source > software distributed under a BSD-style license", I can't find the source > code, so I can't make coot depend on it within fink. http://kinemage.biochem.duke.edu/software/probe.php and Reduce (also required for Coot, I think) is here: http://kinemage.biochem.duke.edu/software/reduce.php -Nat
Re: [ccp4bb] Alternatives to ChemDraw 3D
This may be somewhat convoluted but for this exact purpose try ZINC. For other drawing things then yes use one of the other packages http://zinc.docking.org/ Draw the molecule using the widget, save the smiles file and let their server make the 3D version for you, properly protonated etc. And you get things like logP, and other descriptors as well. true you get it as .mol2.gz or .sdf.gz but babel is your friend -Martin
Re: [ccp4bb] coot and probe clash
On Feb 8, 2010, at 2:07 PM, Nathaniel Echols wrote: > On Mon, Feb 8, 2010 at 1:51 PM, William G. Scott > wrote: > >> This is available to install as a binary from here: >> >> http://molprobity.biochem.duke.edu/get_molprobity.php >> >> >> Although probe and MolProbity3 are said to be "free and open source >> software distributed under a BSD-style license", I can't find the source >> code, so I can't make coot depend on it within fink. > > > http://kinemage.biochem.duke.edu/software/probe.php > > and Reduce (also required for Coot, I think) is here: > http://kinemage.biochem.duke.edu/software/reduce.php > > -Nat OK, I have added both now to fink cvs (unstable branch). Feedback appreciated.
Re: [ccp4bb] Alternatives to ChemDraw 3D
There are several more options to create 3D coordinates from it's 2D drawing: You can build any 3D molecule easily in Discovery Studio Visualizer - It is free but not for Mac OS there is nice server called Frog, that convert 2D to 3D and can build set of conformers http://bioserv.rpbs.jussieu.fr/cgi-bin/Frog2 Corina is another server that do simple 2D to 3D conversion http:// www.molecular-networks.com/online_demos/corina_demo and you have the PRODRG server http://davapc1.bioch.dundee.ac.uk/ prodrg/ that can convert 2D to 3D and in addition can create topology file in many formats (e.g GROMACS, CNS...). PRODRG support only common atom types (N, C, O, S, P, Cl, I, Br, F) Rotem - Rotem Sertchook, Ph.D. Bioinformatics Unit, Biological Services Weizmann Institute of Science, Rehovot 76100, Israel. -
