Re: [ccp4bb] Problem during refinement
One possibility is this: By default, REFMAC decided something is a cis-peptide if the omega angle is < 90.0 . It also reads and believes any CISPEP records you have in your input pdb. (You can turn this feature off by requesting REFMAC to only restrain to a cis peptide if you have a CISPEP record in your input pdb.) Once the cis restraints are imposed the output PDB file will have CISPEP records for all restrained residues. Many of these are unlikely, and you may well correct them when rebuilding. However the pdb file output by COOT will retain the CISPEP records.. You need to check and edit these yourself.. Eleanor anil kumar wrote: Dear All, I am refining a structure (resolution 2.4A) using Refmac and am getting a lot of cis-peptides (about 16 for prolines as well as other amino acids). There are some side chain swaps as well leading to high differences Rfactor: 20.6 and Rfree: 27.6. Although I tried to convert them to trans form and then tried to refine but it shows them again as cis peptides only. In order to rectify the second problem of side chain swaps I have tried to mutate back the residues followed by refinements but it is also of no use. I need to know if anyone of you have ever encountered these kind of problems. I will be greatly helped by your suggestions in this regard. Best regards, Anil Kumar (Graduate Student) - School of Biological Sciences Division of Structural & Computational Biology Nanyang Technological University, 60 Nanyang Drive Singapore 639798. anil0...@ntu.edu.sg Tel: +65-6316-2926 - Check out the all-new Messenger 9.0! Click here.
Re: [ccp4bb] more on lattice translocation defects
Dear Laurie, For copyright reasons, I would suggest that you ask the authors for a reprint or pdf. They can legally do it. Concerning lattice translocation defects, as I see it, it means that neighboring layers in a crystal are sometimes translated in one direction, sometimes in another direction. These maybe an integral part of the unit cell (1/2 or 1/3 etc.) as Zhu et al. seem to have, or random values (e.g. 0.32, 0.49). This can lead to several bizarre effects in the diffraction pattern: -if the defects occur frequently, this leads to small coherent domains, which leads to smeared spots. However, spots for which these domains cancel out, stay sharp. As a result, the diffraction pattern shows a mixture of sharp and smeared spots. -The self patterson shows strong peaks for both translations. However, since the translations occur in different unit cells, there are no corresponding cross peaks. -If the translation is almost an integral part of the unit cell, one sees a modulation. E.g. if the translation is 0.45, one sees extinctions for odd h, k or l indexes if the index is around 0, extinctions for even indexes if the index is around 10, extinctions for odd indexes if the index around 20 etc. Best regards, Herman -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Laurie Betts Sent: Sunday, January 25, 2009 4:57 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] more on lattice translocation defects May I inquire if someone has a copy of Zhu et. al. (Acta Cryst. D. 2008 D64, 843-850) that might be posted somewhere free? I don't have subscription to Acta Cryst D and this one is possibly a problem I have in a structure and I don't understand what it means exactly. Or if someone can give a definition in terms that is simple (for my simple mind). Thanks -- Laurie Betts X-ray Crystallography Facility Manager Department of Structural Biology University of Pittsburgh 1050 BST3 3501 Fifth Ave Pittsburgh, PA 15260 412-383-5839
[ccp4bb] Job Announcement - FACULTY POSITION IN X-RAY CRYSTALLOGRAPHY
FACULTY POSITION IN X-RAY CRYSTALLOGRAPHY Department of Biochemistry and Molecular Biology Thomas Jefferson University in Philadelphia USA Job Description: The Department of Biochemistry and Molecular Biology at Thomas Jefferson University in Philadelphia invites applications for tenure-track or tenured faculty positions in the areas of X-ray crystallography of proteins or nucleic acids. We seek established investigators who are currently supported by extramural funding and who have demonstrated research excellence and productivity. The Department offers a highly collaborative culture and provides state-of-the-art facilities for advanced structural biology and biophysical work. The successful candidate is expected to establish a dynamic and independently funded research program and participate in graduate training at the interface between biology, biochemistry, and biophysics. How to respond: Applicants should submit a curriculum vitae, a brief statement of research interests and future plans, and names of at least three references to: Professor Ya-Ming Hou Thomas Jefferson University Department of Biochemistry and Molecular Biology 233 South 10th Street, BLSB 220, Philadelphia, PA 19107 Email: ya-ming@jefferson.edu Thomas Jefferson University is located in center city Philadelphia, adjacent to a variety of cultural, entertainment and historical attractions. Affirmative Action/Equal Opportunity Employer.
[ccp4bb] refmac
I'm trying to run 2 refmac jobs at the same time (6.1.0, with updated refmac 5.5.0070) When I try to submit the second job I get the message There is already a job running which will create a file called tcN1_r15_iso_refmac1.cif You MUST give an alternative file name but I haven't specified this file & I don't know how to change it (this file has the same name as the PDB in file (xyzin), but with a .cif extension) what should I do? Phil
Re: [ccp4bb] brute force molecular replacement
Why is it called "queen of spades?" JPK *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** - Original Message - From: "Nicholas M Glykos" To: Sent: Sunday, January 25, 2009 9:14 AM Subject: Re: [ccp4bb] brute force molecular replacement Dear Xie, What are the other brute force programs for molecular replacement out there? Qs (available via http://www.mbg.duth.gr/~glykos/Qs.html) can be as brutal with your CPU(s) as they can take. Nicholas -- Dr Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, 68100 Alexandroupolis, Greece, Fax +302551030613 Tel ++302551030620 (77620), http://www.mbg.duth.gr/~glykos/
Re: [ccp4bb] brute force molecular replacement
Jacob I suspect it's derived from the card game "Queen of Spades", also called "Hearts", but is apparently originally from China where it is called "Gong Zhu". I (mis)spent a lot of time in my youth playing it! This site explains the rules: http://www.pagat.com/reverse/gongzhu.html . The game is fairly brutal, as indicated by this excerpt: "An approximate English translation of the name of the game is Chase the Pig: zhu means pig or boar and gong is to root out, or force out of hiding. In the game, the queen of spades is a penalty card, known as the pig - players may try to drive out the pig by leading spades; also the loser of the game is known as the pig, and may be required to grovel under the table as a penalty." Have fun! -- Ian > -Original Message- > From: owner-ccp...@jiscmail.ac.uk > [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Jacob Keller > Sent: 26 January 2009 17:30 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] brute force molecular replacement > > Why is it called "queen of spades?" > > JPK > > *** > Jacob Pearson Keller > Northwestern University > Medical Scientist Training Program > Dallos Laboratory > F. Searle 1-240 > 2240 Campus Drive > Evanston IL 60208 > lab: 847.491.2438 > cel: 773.608.9185 > email: j-kell...@northwestern.edu > *** > > - Original Message - > From: "Nicholas M Glykos" > To: > Sent: Sunday, January 25, 2009 9:14 AM > Subject: Re: [ccp4bb] brute force molecular replacement > > > > Dear Xie, > > > >> What are the other brute force programs for molecular > replacement out > >> there? > > > > Qs (available via http://www.mbg.duth.gr/~glykos/Qs.html) > can be as brutal > > with your CPU(s) as they can take. > > > > Nicholas > > > > -- > > > > > > Dr Nicholas M. Glykos, Department of Molecular > > Biology and Genetics, Democritus University of Thrace, > > University Campus, 68100 Alexandroupolis, Greece, Fax > +302551030613 > > Tel ++302551030620 (77620), http://www.mbg.duth.gr/~glykos/ > > > > 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 i.tic...@astex-therapeutics.com 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
Re: [ccp4bb] more on lattice translocation defects
There is also another paper on this that may be useful... Acta Cryst. (2005). D61, 67-74. Correction of X-ray intensities from single crystals containing lattice-translocation defects. J Wang et al. Regards -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of herman.schreu...@sanofi-aventis.com Sent: Monday, January 26, 2009 6:04 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] more on lattice translocation defects Dear Laurie, For copyright reasons, I would suggest that you ask the authors for a reprint or pdf. They can legally do it. Concerning lattice translocation defects, as I see it, it means that neighboring layers in a crystal are sometimes translated in one direction, sometimes in another direction. These maybe an integral part of the unit cell (1/2 or 1/3 etc.) as Zhu et al. seem to have, or random values (e.g. 0.32, 0.49). This can lead to several bizarre effects in the diffraction pattern: -if the defects occur frequently, this leads to small coherent domains, which leads to smeared spots. However, spots for which these domains cancel out, stay sharp. As a result, the diffraction pattern shows a mixture of sharp and smeared spots. -The self patterson shows strong peaks for both translations. However, since the translations occur in different unit cells, there are no corresponding cross peaks. -If the translation is almost an integral part of the unit cell, one sees a modulation. E.g. if the translation is 0.45, one sees extinctions for odd h, k or l indexes if the index is around 0, extinctions for even indexes if the index is around 10, extinctions for odd indexes if the index around 20 etc. Best regards, Herman -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Laurie Betts Sent: Sunday, January 25, 2009 4:57 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] more on lattice translocation defects May I inquire if someone has a copy of Zhu et. al. (Acta Cryst. D. 2008 D64, 843-850) that might be posted somewhere free? I don't have subscription to Acta Cryst D and this one is possibly a problem I have in a structure and I don't understand what it means exactly. Or if someone can give a definition in terms that is simple (for my simple mind). Thanks -- Laurie Betts X-ray Crystallography Facility Manager Department of Structural Biology University of Pittsburgh 1050 BST3 3501 Fifth Ave Pittsburgh, PA 15260 412-383-5839
[ccp4bb] ccp4-6.1, imosflm, phaser
Hey all,
I have a questions regarding imosflm in ccp4-6.1 on RHEL 5.2. The
installation (after automated download) went well and all works, except:
imosflm from within ccp4i doesn't start and outputs the following error:
MOSDIR is
Error in startup script: can't create directory "": no such file or
directory
while executing
"file mkdir $env(MOSDIR)"
invoked from within
"if { ! [file exists $env(MOSDIR)] } {
file mkdir $env(MOSDIR)
} {
if { ! [file isdirectory $env(MOSDIR)] } {
puts "stop here; the directory f..."
(file
"/csb/soft/Linux/src/ccp4-6.1.0/ccp4-6.1.0/ccp4i/imosflm/imosflm.tcl"
line 51)
imosflm from the command line works well. How do I get imosflm to work
from within ccp4i?
Two more issues that doesn't affect usability of ccp4.
Why is IMOSFLM_VERSION set to 0.6.1 in ccp4.setup? This should be
1.0.0, shouldn't it?
The last line of ccp4-others.setup sources
ccp4-6.1.0/src/phaser/phaser-2.1.4/build/intel-linux/setpaths.csh. This
file does not exist.
Thank you.
Andreas
--
Andreas Förster, Research Associate
Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
