[ccp4bb] Error running CCP4i on CCP4 6.1
Dear All : I have installed CCP4 6.1 on a linux box. Everything seems to be OK. When I try to run CCP4i I got the following error : /usr/local/ccp4_6.1/tcltk++/bin/bltwish: error while loading shared libraries: libtk8.4.so: cannot open shared object file: No such file or directory It looks that the program cannot open the library object, but the file is there (within tcltk++/lib directory). What I am doing wrong ??? Thanks for the help. All the best Francisco -- - Francisco J. Enguita, Ph.D. Host-pathogen Interactions Group Macromolecular Crystallography Laboratory ITQB EAN, Av. da República 2781-901 Oeiras Portugal Phone : +351-21-4469663 Fax : +351-21-4433644 E-mail : fengu...@itqb.unl.pt -
Re: [ccp4bb] Error running CCP4i on CCP4 6.1
Dear Francisco, Is this directory in your load library path? I assume not, given your error, which suggests you need to source the ccp4-others.setup from setup-scripts file appropriate for your shell - this sets up the paths etc. for everthing which is not actually ccp4. Best wishes, Graeme -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Francisco J. Enguita Sent: 06 January 2009 10:05 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Error running CCP4i on CCP4 6.1 Dear All : I have installed CCP4 6.1 on a linux box. Everything seems to be OK. When I try to run CCP4i I got the following error : /usr/local/ccp4_6.1/tcltk++/bin/bltwish: error while loading shared libraries: libtk8.4.so: cannot open shared object file: No such file or directory It looks that the program cannot open the library object, but the file is there (within tcltk++/lib directory). What I am doing wrong ??? Thanks for the help. All the best Francisco -- - Francisco J. Enguita, Ph.D. Host-pathogen Interactions Group Macromolecular Crystallography Laboratory ITQB EAN, Av. da República 2781-901 Oeiras Portugal Phone : +351-21-4469663 Fax : +351-21-4433644 E-mail : fengu...@itqb.unl.pt -
Re: [ccp4bb] Coot save file error under Mac OSX
Albert Guskov wrote: Dear all, I've installed coot with fink, everything works fine, except the fact I can not solve results of my work (that makes it totally senseless ;-)) The error I get is Gtk-WARNING **: Unable to find default local directory monitor type Could someone point me out what is wrong? I don't know about this error, but in the meantime here is a workaround - (unless you have done something to turn it off) your work is being saved in the coot-backup directory. You can dig out your files from there (all but the last modification is saved). Paul.
[ccp4bb] Mac pro
Dear all, I am thinking of getting a apple Mac pro desktop computer. I was wondering does all crystallography programs run on it? I think there are Mac OSX version of CCP4, CNS, SHELX etc. But how about programs in the Uppsala software factory etc?. Also is it difficult to install these programs - are there problems? Is linux still a safer choice? sheemei
[ccp4bb] Coot save file error under Mac OSX
Dear all, I've installed coot with fink, everything works fine, except the fact I can not solve results of my work (that makes it totally senseless ;-)) The error I get is Gtk-WARNING **: Unable to find default local directory monitor type Could someone point me out what is wrong? Kind regards, Albert Guskov, Freie Universitaet Berlin Fachbereich Biologie, Chemie, Pharmazie Institut fur Chemie/Kristallographie
Re: [ccp4bb] Mac pro
Hi Sheemei. The majority of crystallography programs run under osx, including the Uppsala software factory stuff. Installation has always been very straight forward for me. Bill Scott's webpages will have everything you need to get started. http://sage.ucsc.edu/xtal/ Cheers, David 2009/1/6 Sheemei s...@purdue.edu: Dear all, I am thinking of getting a apple Mac pro desktop computer. I was wondering does all crystallography programs run on it? I think there are Mac OSX version of CCP4, CNS, SHELX etc. But how about programs in the Uppsala software factory etc?. Also is it difficult to install these programs - are there problems? Is linux still a safer choice? sheemei -- David C. Briggs PhD Father Crystallographer http://drdavidcbriggs.googlepages.com/home Skype: DocDCB
[ccp4bb] POSTDOCTORAL POSITION IN X-RAY CRYSTALLOGRAPHY AT CEA SACLAY
POSTDOCTORAL POSITION IN X-RAY CRYSTALLOGRAPHY AT CEA SACLAY Position Description: The department of molecular engineering of proteins (SIMOPRO) CEA Saclay, near Paris, France (Head of the Department: Vincent DIVE) has an immediate career opportunity for a highly motivated and experienced crystallographer to work towards the identification of inhibitors of clostridial toxins under the direction of Enrico STURA. The laboratory focuses on the use of X-ray crystallography for macromolecular structure determination in support of research groups in the depertment, associated with drug development and antigen recognition. The department is a highly collegial and collaborative research environment and supports a diverse range of investigators and research projects. Dr. STURA will oversee the operation of the laboratory; provide expertise, training, and/or service in crystallization, diffraction and structure determination as required. For further information please contact est...@cea.fr. Position requirements: Ph.D. or equivalent degree in physics, chemistry, biochemistry or a closely related field. At least one year of experience in macromolecular X-ray structure refinement is required. This would preferably include experience working in collaborative and/or team-based projects and least two publications in leading peer-reviewed journals, related to macromolecular X-ray structure determination. Salary: Competitive commensurate with experience. This post is available immediately and is funded by the CEA under the program NRBC for an initial period of 9 months renewable once and it could potentially lead to a permanent position. The likely starting date is March 16, 2009 and applications will be reviewed as a a continuous process as applications are received continuous process until the position is filled. Letters of application including a CV and names and addresses of 2 referees should be sent to Vincent DIVE vincent.d...@cea.fr or Enrico STURA est...@cea.fr -- Enrico A. Stura D.Phil. (Oxon) ,Tel: 33 (0)1 69 08 4302 Office Room 19, Bat.152,Tel: 33 (0)1 69 08 9449 Lab LTMB, SIMOPRO, IBiTec-S, CEA Saclay, 91191 Gif-sur-Yvette Cedex FRANCE http://www-dsv.cea.fr/en/ibitecs/82 http://www.chem.gla.ac.uk/protein/mirror/stura/index2.html e-mail: est...@cea.frFax: 33 (0)1 69 08 90 71 -- Enrico A. Stura D.Phil. (Oxon) ,Tel: 33 (0)1 69 08 4302 Office Room 19, Bat.152,Tel: 33 (0)1 69 08 9449 Lab LTMB, SIMOPRO, IBiTec-S, CEA Saclay, 91191 Gif-sur-Yvette Cedex FRANCE http://www-dsv.cea.fr/en/ibitecs/82 http://www.chem.gla.ac.uk/protein/mirror/stura/index2.html e-mail: est...@cea.frFax: 33 (0)1 69 08 90 71
Re: [ccp4bb] Mac pro
Hi Sheemel, I assume you are waiting for today's announcements of the i7 core MacPro's ? If not wait another 6 hours before deciding to buy something. Jürgen On 6 Jan 2009, at 06:27, Sheemei wrote: Dear all, I am thinking of getting a apple Mac pro desktop computer. I was wondering does all crystallography programs run on it? I think there are Mac OSX version of CCP4, CNS, SHELX etc. But how about programs in the Uppsala software factory etc?. Also is it difficult to install these programs - are there problems? Is linux still a safer choice? sheemei - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Biochemistry and Molecular Biology, W8708 615 North Wolfe Street Baltimore, MD 21205 Phone: +1-410-614-4742
Re: [ccp4bb] problem about BALBES
I just see the mail, I'd try my best to solve this problem. Maybe I'll try the web server later. Thanks for Dr.Long, Dr Zwart and all the people here. Xiang Liu the fourth year Ph.D candidate lab of structural biology, college of life science Peking University, Beijing, P.R.China 100871 Tel:86-10-62755714 ___ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/
[ccp4bb] Partially ordered side-chains and electrostatics
Dear all, When you calculate the electrostatic potential surface for a protein, what is the best way to treat charged residues with disordered or partially ordered side-chains, e.g. surface lysines? Do you just treat them as alanines? Thanks, Joe
Re: [ccp4bb] Mac pro
I was much more enticed by the proposition of the MacBook Wheel: http://www.theonion.com/content/video/apple_introduces_revolutionary Get your orders in now - there's reportedly a 3-15 month waiting time... Derek ;-) On Jan 6, 2009, week2, at 13:14, JBosch wrote: Hi Sheemel, I assume you are waiting for today's announcements of the i7 core MacPro's ? If not wait another 6 hours before deciding to buy something. Jürgen On 6 Jan 2009, at 06:27, Sheemei wrote: Dear all, I am thinking of getting a apple Mac pro desktop computer. I was wondering does all crystallography programs run on it? I think there are Mac OSX version of CCP4, CNS, SHELX etc. But how about programs in the Uppsala software factory etc?. Also is it difficult to install these programs - are there problems? Is linux still a safer choice? sheemei - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Biochemistry and Molecular Biology, W8708 615 North Wolfe Street Baltimore, MD 21205 Phone: +1-410-614-4742
[ccp4bb] Fwd: Twinning
Dear All, We are currently working on a structure of apparent P21 symmetry which has been solved by molecular replacement. The data are to 2.7Å but the Rfree will not drop below 30%. The density is clear for the model we have, however there is extra density that suggests a shift of the structure by 16Å in either direction - resulting in three possible overlapping positions for the structure. We assume this is the result of twinning. The unit cell dimensions are 102.7Å, 83.0Å, 115.3Å, 90°, 101.8°, 90°. Examining the data with phenix.xtriage also suggests pseudo translational symmetry with a separation of 16Å. A Patterson peak at 0.097, 0.000, -0.096 is approximately 30% of the origin peak, while a second peak of double the translation at 0.192, 0.000, 0.195 is 7% of the origin peak. The structure contains a dimer of dimers with an NCS 2 fold axis almost perpendicular to the crystallographic 2 fold. This NCS axis almost coincides with the diagonal between the A and C axes. A twin axis along the A C diagonal (l,-k,h) could explain the observed extra density, however this is not possible because A and C are different lengths. As a result of the NCS axis running almost perpendicular to the observed P21 axis, it is possible to merge the reflections in a larger orthorhombic unit cell - dimensions 137.1Å, 83.3Å, 169.8Å although here the Rmerge is higher and it is not possible to get a molecular replacement solution. Is it possible to define the (l,-k,h) twinning operator in our original unit cell? or have we missed the actual unit cell? Orsomething else? Steve Stephen Hare PhD Post doctoral research associate Jefferiss Research Laboratories Wright-Fleming Institute Division of Medicine Imperial College London Norfolk Place London W2 1PG UK Phone: +44 (0) 20 7594 3908 Fax: +44 (0) 20 7594 3906
[ccp4bb] Reminder: Please apply to the BNL-Biology and NSLS Course on Synchrotron Data Collection
We are offering RapiData 2009, the eleventh offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 19-24 April 2009. Students could be at any level from advanced undergraduate to full professor. 48 students will be accepted; 24 will bring their own specimens for data collection. Please read the course description at http://www.px.nsls.bnl.gov/RapiData2009/. You'll see that many experts in the field will be available for lectures and tutorials, and you'll find the application materials at this site. For the seventh time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 19 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty. Please apply for the course, and then contact R. Sweet (sw...@bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Alex Soares, Sal Sclafani, and Bob Sweet = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
Re: [ccp4bb] Mac pro
The Mac Pro is what I use for all my crystallography calculations. The vast majority of programs run, the one major sticking point being the older version of HKL but I believe that HKL2000 may well run on OSX now. I use XDS and/or MOSFLM if I want to reprocess on this machine. With most packages the bad old days of actually having to edit the Makefile to install programs is past - you can either install via Fink (especially with all the fine work from Bill Scott) or via .dmg files and failing that most packages will compile with not too much pain. Coot did make the CPU almost glow on my MacBook when I installed all the dependencies via Fink back in early 2008, however. The principal problem with the Mac Pro is that it is difficult to get it to run stereo - the one supported configuration last time I checked was absurdly expensive. If you need stereo (and can actually find a CRT monitor) Linux supports a wider array of options, but I enjoy the relatively seamless integration of a conventional desktop environment with Unix on the Mac. There are also options for virtualization of Windoze and Linux via the software Parallels although I have yet to test this out. OSX has minor quirks, like the patch to make OSX treat e.g. the filenames MyJunkData.sca and myjunkdata.sca as the same file rather than the expected Unix behavior. But in practice I rarely find this to be an issue. Phil Jeffrey Princeton Sheemei wrote: Dear all, I am thinking of getting a apple Mac pro desktop computer. I was wondering does all crystallography programs run on it? I think there are Mac OSX version of CCP4, CNS, SHELX etc. But how about programs in the Uppsala software factory etc?. Also is it difficult to install these programs - are there problems? Is linux still a safer choice? sheemei
[ccp4bb] A senior research scientist position at the Marine Biological Laboratory in Woods Hole, MA, USA
A senior research scientist position is available at the Marine Biological Laboratory in Woods Hole MA to continue our study on the crystal structures of blood coagulation proteins, particularly Factor VIII (Structure. 2008;16:597-606). This is the protein missing in hemophilia. The candidate should have a sound knowledge and experience in protein X-ray crystallography and protein biochemistry. The work will include preparation of protein-protein complexes, biological assay, crystallization, and structure determination. This laboratory is a satellite of the Center for Hemostasis and Thrombosis located at the Beth Israel Deaconess Medical Center and Harvard Medical School in Boston. A joint appointment at the Marine Biological Laboratory and Harvard Medical School is anticipated. Funds are available to support this position for up to three years. The successful candidate must have a PhD degree in a relevant field and previous research experience in protein X-ray crystallography. Protein chemistry skills will be important for this position, as will be the importance of working independently. The position would suit a highly motivated and energetic individual who is keen to work in a multidisciplinary environment involved in structural biology research. Independence and ability to solve experimental problems are critical. Interested persons should send a detailed CV, covering letter and contact details of three referees to Dr. Bruce Furie at bfu...@mbl.edu.
Re: [ccp4bb] Mac pro
with Unix on the Mac. There are also options for virtualization of Windoze and Linux via the software Parallels although I have yet to test this out. If you're trying to purchase a Mac so that you can run MS Office or other Windows only products without dual booting this is no longer necessary if you've got a Windows installation CD and a Linux system. I run Windows in Linux using Virtualbox (http://www.virtualbox.org) which is pretty much like a free version of VMWare Workstation. Do all of your research/graphics/modeling work on Linux and put it together using Adobe/MS publishing software in Windows running in VirtualBox. You can even share folders between the host Linux system and the guest Windows system without manually setting up a Samba server in Linux. VirtualBox doesn't support Direct3D so most Windows games won't work. I haven't tried OpenGL apps, but what's the point when you can just run these in Linux. HTH, Sabuj Pattanayek
Re: [ccp4bb] Mac pro
Hi I use Parallels on my Mac at home for both Windows XP and Ubuntu - it works fine for me when running the more number-crunching parts of CCP4 - haven't really looked at graphics programs like Coot MG. At work I'm running VMWare (Workstation 6.0.0) on a Linux box for Vista, and that, too, is fine. If anyone from Redmond is reading this, both my Windows licenses are legit. On 6 Jan 2009, at 17:55, Nathaniel Echols wrote: There are also options for virtualization of Windoze and Linux via the software Parallels although I have yet to test this out. Parallels is okay; I only use it for testing GUI code on Linux. It doesn't support multiple processors, which probably isn't necessary for most people. The graphics support was somewhat flaky in the past, but it now emulates 3D acceleration well enough to run Coot or PyMOL. I've heard anecdotal evidence that VMWare Fusion is better, but I've only used the Linux version. Unrelated advice: try iWork before spending a massive amount of money on MS Office. It's only about $40-$50 with the academic discount, and much less bloated. It'll still read and export Office documents, although I don't know how robust this is. -Nat Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] Mac pro
I've heard anecdotal evidence that VMWare Fusion is better, but I've only used the Linux version. As a heavy user of both products under Mac OS X on an eight-core Mac Pro, I find VMWare to be far more robust and feature rich than Parallels. Regardless, only Parallels supports 3D OpenGL acceleration (Windows only). Accordingly, I use Parallels on the desktop (only) and VMWare everywhere else. Cheers, Warren -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Harry Powell Sent: Tuesday, January 06, 2009 10:08 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Mac pro Hi I use Parallels on my Mac at home for both Windows XP and Ubuntu - it works fine for me when running the more number-crunching parts of CCP4 - haven't really looked at graphics programs like Coot MG. At work I'm running VMWare (Workstation 6.0.0) on a Linux box for Vista, and that, too, is fine. If anyone from Redmond is reading this, both my Windows licenses are legit. On 6 Jan 2009, at 17:55, Nathaniel Echols wrote: There are also options for virtualization of Windoze and Linux via the software Parallels although I have yet to test this out. Parallels is okay; I only use it for testing GUI code on Linux. It doesn't support multiple processors, which probably isn't necessary for most people. The graphics support was somewhat flaky in the past, but it now emulates 3D acceleration well enough to run Coot or PyMOL. I've heard anecdotal evidence that VMWare Fusion is better, but I've only used the Linux version. Unrelated advice: try iWork before spending a massive amount of money on MS Office. It's only about $40-$50 with the academic discount, and much less bloated. It'll still read and export Office documents, although I don't know how robust this is. -Nat Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] Mac pro
There are also options for virtualization of Windoze and Linux via the software Parallels although I have yet to test this out. Parallels is okay; I only use it for testing GUI code on Linux. It doesn't support multiple processors, which probably isn't necessary for most people. The graphics support was somewhat flaky in the past, but it now emulates 3D acceleration well enough to run Coot or PyMOL. I've heard anecdotal evidence that VMWare Fusion is better, but I've only used the Linux version. Unrelated advice: try iWork before spending a massive amount of money on MS Office. It's only about $40-$50 with the academic discount, and much less bloated. It'll still read and export Office documents, although I don't know how robust this is. -Nat
Re: [ccp4bb] Fwd: Twinning
On Tuesday 06 January 2009 08:35:19 Stephen Hare wrote: Dear All, We are currently working on a structure of apparent P21 symmetry which has been solved by molecular replacement. The data are to 2.7Å but the Rfree will not drop below 30%. The density is clear for the model we have, however there is extra density that suggests a shift of the structure by 16Å in either direction - resulting in three possible overlapping positions for the structure. We assume this is the result of twinning. It sounds like an interesting case. You might want to go back and closely inspect your diffraction images after reading this paper: J. Appl. Cryst. (2008). 41, 600-605 Protein crystals can be incommensurately modulated JJ Lovelace, CR Murphy, L Daniels, K Narayan, CE Schutt, U Lindberg, C Svensson and GEO Borgstahl I am not certain that your description matches this case, but it might. Ethan The unit cell dimensions are 102.7Å, 83.0Å, 115.3Å, 90°, 101.8°, 90°. Examining the data with phenix.xtriage also suggests pseudo translational symmetry with a separation of 16Å. A Patterson peak at 0.097, 0.000, -0.096 is approximately 30% of the origin peak, while a second peak of double the translation at 0.192, 0.000, 0.195 is 7% of the origin peak. The structure contains a dimer of dimers with an NCS 2 fold axis almost perpendicular to the crystallographic 2 fold. This NCS axis almost coincides with the diagonal between the A and C axes. A twin axis along the A C diagonal (l,-k,h) could explain the observed extra density, however this is not possible because A and C are different lengths. As a result of the NCS axis running almost perpendicular to the observed P21 axis, it is possible to merge the reflections in a larger orthorhombic unit cell - dimensions 137.1Å, 83.3Å, 169.8Å although here the Rmerge is higher and it is not possible to get a molecular replacement solution. Is it possible to define the (l,-k,h) twinning operator in our original unit cell? or have we missed the actual unit cell? Orsomething else? Steve Stephen Hare PhD Post doctoral research associate Jefferiss Research Laboratories Wright-Fleming Institute Division of Medicine Imperial College London Norfolk Place London W2 1PG UK Phone: +44 (0) 20 7594 3908 Fax: +44 (0) 20 7594 3906 -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742
Re: [ccp4bb] Mac pro
I assume you are waiting for today's announcements of the i7 core MacPro's ? If not wait another 6 hours before deciding to buy something. hrmm, I was hoping store.apple.com was down due to modifications for this new item, it's back up but no new i7 mac pro ..
[ccp4bb] imosflm in ccp4 6.1.0 in linux problems
Hi everyone I've been trying to run the new imosflm version from ccp4i 6.1.0 gui on ubuntu 8.0.4, but keep having problems. After struggling with it to search for the correct MOSDIR directory path, it then complained it was missing several packages from wish8.4. I did manage to find some of them, but after searching the web I still can't find: treectrl 2.1 img::png 1.3 img::gif 1.3 img::jpeg 1.3 can anyone tell me where I can download them or what other solutions to get imosflm to run properly? Thanks a lot Paula
Re: [ccp4bb] imosflm in ccp4 6.1.0 in linux problems
The ActiveTcl distribution can be installed anywhere, eg /opt Then point imosflm to the wish binary in that. William G. Scott (via iPod and gmail -- forgive the typos and brevity) Please reply to wgsc...@chemistry.ucsc.edu On Jan 6, 2009, at 3:03 PM, Salgado, Paula p.salg...@imperial.ac.uk wrote: Hi everyone I've been trying to run the new imosflm version from ccp4i 6.1.0 gui on ubuntu 8.0.4, but keep having problems. After struggling with it to search for the correct MOSDIR directory path, it then complained it was missing several packages from wish8.4. I did manage to find some of them, but after searching the web I still can't find: treectrl 2.1 img::png 1.3 img::gif 1.3 img::jpeg 1.3 can anyone tell me where I can download them or what other solutions to get imosflm to run properly? Thanks a lot Paula
Re: [ccp4bb] imosflm in ccp4 6.1.0 in linux problems
Hi Paula:
Here is more info:
http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/CCP4-6.1.0_on_Ubuntu_Ibex
(There is no reason why you would have to do step 1.)
Sorry, but I couldn't figure out how to append the link using my iPod
while undergoing mind-numbing boredom in an interminable faculty
meeting.
As for the MOSDIR, I found this alias helpful:
alias imosflm='MOSDIR=${PWD} imosflm'
The single quotes are crucial. This makes whatever directory from
whence you issue the command the $MOSDIR.
HTH,
Bill
On Jan 6, 2009, at 3:18 PM, William G. Scott wrote:
The ActiveTcl distribution can be installed anywhere, eg /opt
Then point imosflm to the wish binary in that.
William G. Scott
(via iPod and gmail -- forgive the typos and brevity)
Please reply to wgsc...@chemistry.ucsc.edu
On Jan 6, 2009, at 3:03 PM, Salgado, Paula
p.salg...@imperial.ac.uk wrote:
Hi everyone
I've been trying to run the new imosflm version from ccp4i 6.1.0
gui on ubuntu 8.0.4, but keep having problems. After struggling
with it to search for the correct MOSDIR directory path, it then
complained it was missing several packages from wish8.4. I did
manage to find some of them, but after searching the web I still
can't find:
treectrl 2.1
img::png 1.3
img::gif 1.3
img::jpeg 1.3
can anyone tell me where I can download them or what other
solutions to get imosflm to run properly?
Thanks a lot
Paula
Re: [ccp4bb] imosflm in ccp4 6.1.0 in linux problems
On Jan 6, 2009, at 7:10 PM, William Scott wrote: (There is no reason why you would have to do step 1.) Sorry, that should have been no reason ... to do step THREE.
Re: [ccp4bb] Fwd: Twinning
This is an interesting case but your description lacked the diffraction part. Assuming no Heavy Atom sites in the native structure. Based on your description, another possibility may be Lattice Translocation. - Ref: J. Wang, S. Kamtekar, A. J. Berman and T. A. Steitz. Correction of X-ray intensities from single crystals containing lattice-translocation defects. Acta Cryst. (2005). D61, 67-74. - By the way, indexing with orthorhombic cell (137.1Å, 83.3Å, 169.8Å) should gain a large penalty since the new beta angle has a 5 degree tolerance from right angle, derived from your P21 cell constants (a, c and beta angle) (if they were well determined), implying this may not be the case. Good luck! Lijun Liu, PhD Institute of Molecular Biology HHMI Department of Physics University of Oregon Eugene, OR 97403 541-346-5176 http://www.uoregon.edu/~liulj/ -- On Jan 6, 2009, at 8:35 AM, Stephen Hare wrote: Dear All, We are currently working on a structure of apparent P21 symmetry which has been solved by molecular replacement. The data are to 2.7Å but the Rfree will not drop below 30%. The density is clear for the model we have, however there is extra density that suggests a shift of the structure by 16Å in either direction - resulting in three possible overlapping positions for the structure. We assume this is the result of twinning. The unit cell dimensions are 102.7Å, 83.0Å, 115.3Å, 90°, 101.8°, 90°. Examining the data with phenix.xtriage also suggests pseudo translational symmetry with a separation of 16Å. A Patterson peak at 0.097, 0.000, -0.096 is approximately 30% of the origin peak, while a second peak of double the translation at 0.192, 0.000, 0.195 is 7% of the origin peak. The structure contains a dimer of dimers with an NCS 2 fold axis almost perpendicular to the crystallographic 2 fold. This NCS axis almost coincides with the diagonal between the A and C axes. A twin axis along the A C diagonal (l,-k,h) could explain the observed extra density, however this is not possible because A and C are different lengths. As a result of the NCS axis running almost perpendicular to the observed P21 axis, it is possible to merge the reflections in a larger orthorhombic unit cell - dimensions 137.1Å, 83.3Å, 169.8Å although here the Rmerge is higher and it is not possible to get a molecular replacement solution. Is it possible to define the (l,-k,h) twinning operator in our original unit cell? or have we missed the actual unit cell? Orsomething else? Steve Stephen Hare PhD Post doctoral research associate Jefferiss Research Laboratories Wright-Fleming Institute Division of Medicine Imperial College London Norfolk Place London W2 1PG UK Phone: +44 (0) 20 7594 3908 Fax: +44 (0) 20 7594 3906 Lijun Liu, PhD Institute of Molecular Biology HHMI Department of Physics University of Oregon Eugene, OR 97403 541-346-5176 http://www.uoregon.edu/~liulj/
