Re: [ccp4bb] How to make a structure-based multiple sequence alignment on DALI server?
Hi, I would suggest the indonesia program... easy to use and very flexible. http://xray.bmc.uu.se/dennis/ Cheers Dave david wu wrote: > Hi all， > > I want to produce structure-based multiple sequence alignment of my protein > with five of its homologs on DALI server. However, when I tried the "Database > Search Form", only one homolog was picked up from PDB. If I align my protein > with each homolog by the "DaliLite Pairwise comparison", how can I combine > them together? > > Thanks in advance. > > > Best regards, > > Sincerely, > > Dalei Wu > Drug Discovery and Design Center > Shanghai Institute of Materia Medica > Shanghai Institutes for Biological Sciences > Chinese Academy of Sciences > 555 Zu Chongzhi Road, Shanghai, 201203, China > [EMAIL PROTECTED] > 2007-12-05
Re: [ccp4bb] How to make a structure-based multiple sequence alignment on DALI server?
POSA at the Godzik lab does exactly what you are after, flexibly! http://fatcat.burnham.org/POSA/ Hi all=A3=AC I want to produce structure-based multiple sequence alignment of my =20= protein with five of its homologs on DALI server. However, when I =20 tried the "Database Search Form", only one homolog was picked up =20 from PDB. If I align my protein with each homolog by the "DaliLite =20 Pairwise comparison", how can I combine them together? Thanks in advance. Best regards, =09 Sincerely, Dalei Wu Drug Discovery and Design Center Shanghai Institute of Materia Medica Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 555 Zu Chongzhi Road, Shanghai, 201203, China [EMAIL PROTECTED] 2007-12-05
Re: [ccp4bb] refmac5.3 vs refmac5.4
On Dec 5, 2007, at 14:05, Jianghai Zhu wrote: Hi all, I updated refmac5.3 to refmac5.4 and found out that the reported RMSDs are quite different from these two versions even the refining protocols are the same. refmac5.3 rmsBOND rmsANGLE rmsCHIRAL 0.006 0.694 0.046 refmac5.4 rmsBOND rmsANGLE rmsCHIRAL 0.015 1.150 0.004 The R and Rfree are very similar from these two versions of refmac5. Does refmac5.4 have different geometry weights from refmac5.3? Which one is more reasonable? besides the obvious answer that Garib gave (I agree...5.4 is better), it might be good to remind (without going to the long previous discussions about the best rmsBOND), that its the users responsibility to choose correct weights. having said this, its good to say that half the people will think 0.015 is better, and half that 0.006 is better. what I find strange is the discrepancy in CHIRAL volumes rms, which I can attribute either to a bug fix, a print error, or drastically changed internal weighting between bonds and chiral volumes. A. Thanks. Jianghai +++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++
[ccp4bb] ccp4 study weekend registration closes this Friday
Dear All the registration for the CCP4 study weekend closes on this Friday (7th) at 5pm GMT. Details for this/early next years event on "Low Resolution Structure Determination and Validation" are at http://www.cse.scitech.ac.uk/events/CCP4_2008/ so if you would like to join 400 souls in Leeds (UK) on the 3-5 January (2008) you had better hurry. Charles Ballard on behalf of Shirley Miller and Damian Jones.
[ccp4bb] coot: Show Symmetry
--- Hi All i want to display symmetry molecules in COOT, but regularly getting the following warning: There are no model molecules that can display symmetry (Cryst1 problem). How to troubleshoot this Cryst1 problem thanks in advance Vineet gaur --- This problem can also happen if the cryst card is given with a 'shorthand' spacegroup notation. For instance, in CNS, spacegroup 'C2' is written 'C2' on the output file. Coot wants to see all axes defined, ie/ C 1 2 1. If it doesn't see the fuller notation, it gives a 'cryst1 problem' type error. -- Byron DeLaBarre, Ph.D. Structural Biology Group Millennium Pharmaceuticals Cambridge, MA
[ccp4bb] SeMet peptide synthesis
Dear all, Does anyone know a reliable company that could perform a peptide synthesis including a SeMet residue? Thanks a lot in advance for your answers, Alfredo. Alfredo Torres-Larios, PhD Instituto de Fisiologia Celular, UNAM Mexico This message was sent using IMP, the Internet Messaging Program.
Re: [ccp4bb] refmac5.3 vs refmac5.4
Weights are the same. 5.4 has a lot of small bug fixes and performance enhancement and some added stability things. And some new features I am planning to announce soon. Since I am responsible, my extremely biased view is that 5.4 is better. Garib On 5 Dec 2007, at 13:05, Jianghai Zhu wrote: Hi all, I updated refmac5.3 to refmac5.4 and found out that the reported RMSDs are quite different from these two versions even the refining protocols are the same. refmac5.3 rmsBOND rmsANGLE rmsCHIRAL 0.006 0.694 0.046 refmac5.4 rmsBOND rmsANGLE rmsCHIRAL 0.015 1.150 0.004 The R and Rfree are very similar from these two versions of refmac5. Does refmac5.4 have different geometry weights from refmac5.3? Which one is more reasonable? Thanks. Jianghai +++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++
Re: [ccp4bb] refmac5.3 vs refmac5.4
> -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Anastassis Perrakis > Sent: 05 December 2007 13:45 > To: Jianghai Zhu > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] refmac5.3 vs refmac5.4 > > > On Dec 5, 2007, at 14:05, Jianghai Zhu wrote: > > > Hi all, > > I updated refmac5.3 to refmac5.4 and found out that the > reported RMSDs are quite different from these two versions > even the refining protocols are the same. > > refmac5.3 > rmsBOND rmsANGLE rmsCHIRAL > 0.006 0.694 0.046 > > > refmac5.4 > rmsBOND rmsANGLE rmsCHIRAL > 0.015 1.150 0.004 > > > The R and Rfree are very similar from these two > versions of refmac5. Does refmac5.4 have different geometry > weights from refmac5.3? Which one is more reasonable? > > > > besides the obvious answer that Garib gave (I agree...5.4 is > better), it might be good to remind (without going to the > long previous discussions about the best > rmsBOND), that its the users responsibility to choose correct weights. Tassos, whilst not wishing to rerun this argument all over again (in any case I have nothing further to add to it), I should point out that this month's Acta D contains a letter I wrote in response to an earlier article on this subject: http://journals.iucr.org/d/issues/2007/05/00/wd5076/wd5076.pdf My letter is here: http://journals.iucr.org/d/issues/2007/12/00/gx5119/gx5119.pdf and for the opposing view also see: http://journals.iucr.org/d/issues/2007/12/00/be5098/be5098.pdf This is also relevant: http://journals.iucr.org/d/issues/2007/10/00/be5093/be5093.pdf As you said, it's the user's responsibility to make up his/her own mind based on the theoretical arguments and the experimental evidence. -- Ian 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] PhD Position in Wuerzburg / Germany
A PhD position in structural biology is available in the group of Prof. Utz Fischer at the Institute of Biochemistry, Biocentre of the Julius Maximilans University, Wuerzburg/Germany. The successful applicant will work on the crystallographic structure determination of the Survival Motor Neuron (SMN) complex, the key player during the pathogenesis of Spinal Muscular Atrophy (SMA). Techniques for bacterial expression and reconstitution of the SMN complex are already established and first crystals available. Please send your application including a letter of interest, Curriculum vitae, academic certificates and the name and contact detail of one referee to Dr. Clemens Grimm e-mail: [EMAIL PROTECTED] Institut fuer Biochemie Biozentrum der Universitaet Wuerzburg Am Hubland D-97074 Wuerzburg
[ccp4bb] refmac5.3 vs refmac5.4
Hi all, I updated refmac5.3 to refmac5.4 and found out that the reported RMSDs are quite different from these two versions even the refining protocols are the same. refmac5.3 rmsBOND rmsANGLE rmsCHIRAL 0.006 0.694 0.046 refmac5.4 rmsBOND rmsANGLE rmsCHIRAL 0.015 1.150 0.004 The R and Rfree are very similar from these two versions of refmac5. Does refmac5.4 have different geometry weights from refmac5.3? Which one is more reasonable? Thanks. Jianghai +++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++
Re: [ccp4bb] PEG MW vs. cryoprotectivity
In our recent experience, larger PEGs work similarly to smaller PEGs as far as vitrification goes. Additionally, transferring crystals to a solution of increased PEG concentration (as compared to mother liquor) can substantially reduce the amount of cryo needed for freezing and can be more gentle on crystals than just using a high concentration of cryo. Here is a reference that tests cryoprotective ability of PEG 2000 & 2. J. Appl. Cryst. (2006) 39, 244-251 ** Check out AOL's list of 2007's hottest products. (http://money.aol.com/special/hot-products-2007?NCID=aoltop000301)
Re: [ccp4bb] How to make a structure-based multiple sequence alignment on DALI server?
Christoph Gille's program STRAP generates structure-based multiple sequence alignment, which can be combined with sequences for which no structure is available. http://www.charite.de/bioinf/strap/ Klaus - Klaus Fütterer, Ph.D. School of Biosciences P: +44-(0)-121-414 5895 University of Birmingham F: +44-(0)-121-414 5925 Edgbaston E: [EMAIL PROTECTED] Birmingham, B15 2TT, UK W: www.biochemistry.bham.ac.uk/klaus/ - On 5 Dec 2007, at 05:03, david wu wrote: Hi all， I want to produce structure-based multiple sequence alignment of my protein with five of its homologs on DALI server. However, when I tried the "Database Search Form", only one homolog was picked up from PDB. If I align my protein with each homolog by the "DaliLite Pairwise comparison", how can I combine them together? Thanks in advance. Best regards, Sincerely, Dalei Wu Drug Discovery and Design Center Shanghai Institute of Materia Medica Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 555 Zu Chongzhi Road, Shanghai, 201203, China [EMAIL PROTECTED] 2007-12-05
