[ccp4bb] Reminder : GTBIO 2007 Lille Announcement
GTBIO 2007 Lille Announcement We are glad to welcome the french-speaking community of biocrystallographers to Lille (France) for the GTBIO 2007 Meeting (8-11 October 2007). This meeting will be organised by the Laboratoire de Cristallographie Macromoléculaire and will be hosted by the Institut de Biologie de Lille, on the campus of the Institut Pasteur de Lille. For further details and applications, please visit : http://www.ibl.fr/gtbio/Start.html Best wishes! The GTBIO 2007 organizing committee. Laboratoire de Cristallographie Macromoléculaire Institut de Biologie de Lille - UMR 8161 CNRS 1 Rue du Pr Calmette 59021 Lille Cedex France begin:vcard fn:Prakash Rucktooa n:Rucktooa;Prakash org:UMR 8161 CNRS;Groupe de Cristallographie adr:1 Rue du Pr. Calmette;;Institut de Biologie de Lille;Lille;;59021;France email;internet:[EMAIL PROTECTED] title:PhD Student tel;work:+ 33 3 20 87 10 63 tel;cell:+ 33 6 74 74 22 65 url:http://www.ibl.fr/rubrique.php3?id_rubrique=20 version:2.1 end:vcard
[ccp4bb] ERROR: can't read array(ef2ccp4): no such element in array
Dear all,
I got this error message in three circumstances:
1) when creating/modifying the project directory in DirectoriesProjDirets and
clicking APPLY or APPLYEXIT
2) when changing to another project
3) when running ccp4mg, and ccp4mg even refused to start.
I can't remember clearly, but the event triggering this error seems to be that
I deleted a specific task while another task was running.
Here is the error message:
can't read array(ef2ccp4): no such element in array
can't read array(ef2ccp4): no such element in array
while executing
set value $array($var)
(default arm line 2)
invoked from within
switch -regexp -- $type menu {
set value [GetMenuValue $arrayname $var ]
} default {
set value $array($var)
}
(procedure SaveArray line 104)
invoked from within
SaveArray $taskname $filename $arrayname -save_types
(procedure SavePreferences line 29)
invoked from within
SavePreferences directories directories -lock
(procedure SwitchProject line 16)
invoked from within
SwitchProject fabz .module.mesbar.switchProj.m
(menu invoke)
Could anyone tell me how to fix it?
Thanks in advance!
Tiancen Hu
Shanghai Institute of Materia Medica
Re: [ccp4bb] Conservation of momentum - was Is anomalous signal a different wavelength?
Apologies for the late posting (been away). Interesting question from James and an interesting answer from Ian! There should be a radiation pressure effect here resulting in a transfer of energy and momentum to the sample. The effect is very small (the term includes flux density divided by speed of light). Although this will not make your crystal fly away, the effect is proposed for space travel (using large solar sails). A very small change in energy of the photon results. This can be explained by quantum or more classical theory. The question referred to elastically scattered photons. In fact the Compton effect could also be considered an elastic scattering phenomena as the total energy and momentum of the particles (photon plus electron) is conserved. There is confusion about the terminology here between different disciplines. The difference is that a significant amount of the photons energy is transferred to the electron. Colin -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Behalf Of Ian Tickle Sent: 31 May 2007 10:53 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Is anomalous signal a different wavelength? I think it's to do with the Uncertainty Principle. You can't say for sure that a particular X-ray photon has gone off in that direction (if you could you would know both its position and momentum accurately which is not allowed). If you integrated the momentum over all possible outcomes I'm sure you would find that it's conserved (it has to be in an elastic collision). -- Ian -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Murray, James W Sent: 31 May 2007 10:30 To: CCP4BB@JISCMAIL.AC.UK Subject: RE: [ccp4bb] Is anomalous signal a different wavelength? Dear All, While we are talking about X-ray scattering, I have another question. If an X-ray is elastically scattered from an electron at an angle theta, its energy is the same is the incoming X-ray. However, the momentum is not the same, as it now has a component in a perpendicular direction (see fig below). As I don't believe that the conservation of momentum really is violated, what is the source of the discrepancy? Contrast this with most textbook descriptions of Compton scattering, where the X-ray loses energy and the electron gains kinetic energy. best wishes James X-ray e- \ \ \ Dr. James Murray Biochemistry Building Department of Biological Sciences Imperial College London London, SW7 2AZ Tel: +44 (0)20 7594 5276 Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
[ccp4bb] B-factor Space gr questions!
Hi all, While reading a crystallographic paper describing the structure of an apo-protein and its complex I noticed that the authors described the space goup as P6122 for the unit cell: a=141.9, b=143.9, c=380.4 ! Could this be considered as a typo or I'm missing something here! the requirement for the hexagonal is a = b # Cright? Another observation in that paper too: the B-factors for the 2.4 A and 3.2 A structures are 39 and 40?? Does this make sense to anyone?? The last question: In the same paper, for the complex structure R and Rfree are equal (30%) is that an indication for improper refinement in these published structure? I'd love to hear your comments on that too. thanks, Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., Uinversity Park Pennsylvania State University, PA16802 Tel. (814)863-8703 Fax. (814)865-7927 --
[ccp4bb] error using NCS in dm
Hi. I'm having a problem with running dm with ncs averaging. I have a trimer and am inputting in 3 domains using euler angles calculated using the profess: Domain 1 should be the identity matrix, if I'm understanding things correctly, so I put 0.0 0.0 0.0 for the three angles and 0.0 0.0 0.0 for the x,y,z translations For Domain 2 + 3 I put in the appropriate euler angles. However, when I run dm, it gives me an error message: dm: (RCARDS) AVER: enter indentity matrix first I would have guessed that putting in all zeros for Domain 1 would be the identity matrix?? Am I doing something wrong here? I can't seem to figure out what is going wrong? Has anyone seen this problem before? Any advice or suggestions would be greatly appreciated. Thanks Jay
Re: [ccp4bb] B-factor Space gr questions!
Ibrahim M. Moustafa wrote: The last question: In the same paper, for the complex structure R and Rfree are equal (30%) is that an indication for improper refinement in these published structure? I'd love to hear your comments on that too. Several times I solved low resolution structures using high resolution models, and noticed that R-free increased during atomic positional refinement. This could be expected from the assertion that after refinement to convergence, the final values should not depend on the starting point: If I had started with a crude model and refined against low resolution data, Rfree would not have gone as low as the high-resolution model, so if I start with the high resolution model and refine, Rfree should worsen to the same value as the structure converges to the same point. Thinking about the main purpose of the Rfree statistic, in a very real way this tells me that the model was better before this step of refinement, and it would be better to omit the minimization step. Perhaps this is what the authors did. On the other hand it does not seem quite right submit a model that has simply been rigid-body-refined against the data- I would prefer to refine to convergence and submit the best model that can be supported by the data alone, rather than a better model which is really the model from a better dataset repositioned in the new crystal. Ed
[ccp4bb] Error/Bug in Pirate?
Hi All, I've having some problems running the program Pirate and was wondering if any wonderful ccp4er could help. I'm trying to run Pirate v 0.4.9 using the ccp4 6.0.2 GUI. However, whenever I run Pirate with NCS symmetry, I get an error message stating: The program run with command: cpirate -stdin has failed with error message child killed: segmentation violation Unfortunately, the error message is quite vague. It looks from the log file that the mtz didn't even load. But if I run the exact same job but without NCS symmetry the job runs fine. So it seems that my mtz file is fine. I checked the heavy atom pdb used to determine the NCS symmetry and the pdb looks okay in terms of formats. I'm puzzled as to why I'm having trouble with the NCS feature in Pirate. Has anyone also seen this problem with Pirate? Thanks Jeff
