[ccp4bb] [Fwd: [ccp4bb] accessible surface area of PISA at EBI]
Dear all, I understood what they mean. ASA -> Solvent accessible surface area BSA -> Buried area among Solvent accessible surface area when it make interaction Sorry for self-questioning and -answering. Best, Hyunchul Kim Forwarded Message > From: Hyunchul Kim <[EMAIL PROTECTED]> > Reply-To: Hyunchul Kim <[EMAIL PROTECTED]> > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] accessible surface area of PISA at EBI > Date: Wed, 18 Jul 2007 12:24:57 +0900 > > Dear all, > > Could you explain two terms of "Accessible Surface Area"(ASA) and > "Buried Surface Area"(BSA) of PISA at EBI ? > > I thought that > Standard accessible surface area = > Solvent accessible surface area + Buried surface area. > > When I looked up the result of PISA, ASA is always bigger than BSA > except "inaccessible residues". Thus, I think that ASA of PISA means > that "Standard accessible surface area" but one weird thing is that > those values of same type residues,i.e. Ala, are quite varied among one > chain. > > Also, "Inaccessible residues" has 0.00 square angstrom for both ASA and > BSA. How can this happen? I believe that ASA should be bigger than 0.00, > for instance, 100 angstrom square. > > Best, > > Hyunchul Kim > > Ph.D candidate > Bioinformatics program > Keio University, Japan >
[ccp4bb] accessible surface area of PISA at EBI
Dear all, Could you explain two terms of "Accessible Surface Area"(ASA) and "Buried Surface Area"(BSA) of PISA at EBI ? I thought that Standard accessible surface area = Solvent accessible surface area + Buried surface area. When I looked up the result of PISA, ASA is always bigger than BSA except "inaccessible residues". Thus, I think that ASA of PISA means that "Standard accessible surface area" but one weird thing is that those values of same type residues,i.e. Ala, are quite varied among one chain. Also, "Inaccessible residues" has 0.00 square angstrom for both ASA and BSA. How can this happen? I believe that ASA should be bigger than 0.00, for instance, 100 angstrom square. Best, Hyunchul Kim Ph.D candidate Bioinformatics program Keio University, Japan
Re: [ccp4bb] Combining MR and MAD phases
>If you want to combine though, I use the molrep phases to get all >heavy atoms >in an anomalous fourier map, then go to SHARP with these sites and >use the 'External phases' option >in the SHARP gui. Works well for me. This has worked well for me too...I highly recommend SHARP. Good luck- Steve -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Anastassis Perrakis Sent: Tuesday, July 17, 2007 12:56 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Combining MR and MAD phases I would be tempted to say that you don't need to combine; with 1.7 A data, refinement should do it with no trouble. And, yes, of course ARP/wARP (7.0) would be the best way to do it ;-) If you want to combine though, I use the molrep phases to get all heavy atoms in an anomalous fourier map, then go to SHARP with these sites and use the 'External phases' option in the SHARP gui. Works well for me. I also recall that Phaser has an option for exactly do that, but with SAD data only. But, again, if you have 1.7 A data good old refinement and auto- building will (likely) do the job in a glance. Tassos PS If you dont want to install arp/warp locally why not try: http://cluster.embl-hamburg.de/ARPwARP/remote-http.html PS2 Apologies for the shameless promotion of ARP/wARP ;-) On 17 Jul 2007, at 18:22, Joe Batchelor wrote: > Hi, > > I have a 1.7 A native dataset, a good MR solution for 2/3 of the > protein, and MAD phases to 3 A. How should I combine the MR phases > with the MAD phases? > > Thanks, > Joe -- Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. --
Re: [ccp4bb] ARP_wARP 7.0 release
Hi Tracy - Thats actually a warning message (sorry to use the word error there ...) and it should not stop the program from running. I believe, you dont have to take any action. If the procedure however stops indeed, please send us detailed log files and more complete output to try and solve it. Thanks for the bug report - Tassos On 17 Jul 2007, at 19:48, Tracy Arakaki wrote: Hello, I just tried running the new version of ARP/wARP (Classic) and got the following error message: :1: parser error : Document is empty XMLOutputFilename = 'snow_log.xml' ^ snow - WRNG* : CConfig::processStream File isn't in proper XML format Any ideas on how to fix this so that ARP/wARP will successfully run? Thanks, -Tracy Tracy Arakaki, Ph.D. University of Washington Dept. of Biochemistry MS 357742 Seattle, WA 98195-7742 On Mon, 16 Jul 2007, Victor Lamzin wrote: Dear all, We are happy to announce the release of ARP/wARP version 7.0 Please visit http://www.arp-warp.org for details and software download. The major improvements are: • A new module for ultra-fast low resolution tracing of helical and beta-stranded fragments at resolution down to 4.5 A. • Improved and faster chain tracing, working at lower resolution than before, for both 'Classic' and 'flex-wARP' modules. • Flex-wARP, a control system which automatically defines the sequence of the steps to be taken during iterative model building. • Considerably advanced automated ligand building with ~80% success in site identification and ~70% in ligand constructions. • An option for ‘cocktail screening’; the most likely ligand is identified and built from a list of potential compounds. • Improved fragment sequence docking with empirical targets extracted from experimental datasets. • A validation program ElAl (originated from G. Kleywegt) based on statistical density targets from the EDS implemented in flex-wARP. • A standalone module for side chain building and refinement. • A module for building loops between fragments implemented in flex-wARP and provided standalone. • The solvent building module with incremental improvements as a dedicated module. • Remote job submission at the EMBL Hamburg cluster directly from the web in addition to the CCP4i GUI. • Command-line job submission for most ARP/wARP tasks. • ARP/wARP is now running on Mac powerpc, Mac Intel, some flavours of Linuxes (i32 and 64-bit ) as well as alpha-Tru64 and mips-IRIX64. Victor and Tassos on behalf of the ARP/wARP developers' team.
Re: [ccp4bb] ARP_wARP 7.0 release
Hello, I just tried running the new version of ARP/wARP (Classic) and got the following error message: :1: parser error : Document is empty XMLOutputFilename = 'snow_log.xml' ^ snow - WRNG* : CConfig::processStream File isn't in proper XML format Any ideas on how to fix this so that ARP/wARP will successfully run? Thanks, -Tracy Tracy Arakaki, Ph.D. University of Washington Dept. of Biochemistry MS 357742 Seattle, WA 98195-7742 On Mon, 16 Jul 2007, Victor Lamzin wrote: Dear all, We are happy to announce the release of ARP/wARP version 7.0 Please visit http://www.arp-warp.org for details and software download. The major improvements are: • A new module for ultra-fast low resolution tracing of helical and beta-stranded fragments at resolution down to 4.5 A. • Improved and faster chain tracing, working at lower resolution than before, for both 'Classic' and 'flex-wARP' modules. • Flex-wARP, a control system which automatically defines the sequence of the steps to be taken during iterative model building. • Considerably advanced automated ligand building with ~80% success in site identification and ~70% in ligand constructions. • An option for ‘cocktail screening’; the most likely ligand is identified and built from a list of potential compounds. • Improved fragment sequence docking with empirical targets extracted from experimental datasets. • A validation program ElAl (originated from G. Kleywegt) based on statistical density targets from the EDS implemented in flex-wARP. • A standalone module for side chain building and refinement. • A module for building loops between fragments implemented in flex-wARP and provided standalone. • The solvent building module with incremental improvements as a dedicated module. • Remote job submission at the EMBL Hamburg cluster directly from the web in addition to the CCP4i GUI. • Command-line job submission for most ARP/wARP tasks. • ARP/wARP is now running on Mac powerpc, Mac Intel, some flavours of Linuxes (i32 and 64-bit ) as well as alpha-Tru64 and mips-IRIX64. Victor and Tassos on behalf of the ARP/wARP developers' team.
[ccp4bb] MrBUMP version 0.4.0 release
Dear All, We're pleased to announce the latest release of MrBUMP. Pre-release version 0.4.0 is now available from the MrBUMP website: http://www.ccp4.ac.uk/MrBUMP The new features include: - The inclusion of the new CCP4i DBviewer, a graphical interface for viewing CCP4i jobs. This will form part of the upcoming 6.1 release of CCP4. We are grateful to Wanjuan (Wendy)Yang and Peter Briggs for letting us include it in MrBUMP. - Support for installing the scripts on Windows. - Removed the requirement for inputting an MTZ file when running in "Model generation only" mode. Sequence file is all that is required now. Kind regards, Ronan and Martyn
Re: [ccp4bb] Combining MR and MAD phases
I would be tempted to say that you don't need to combine; with 1.7 A data, refinement should do it with no trouble. And, yes, of course ARP/wARP (7.0) would be the best way to do it ;-) If you want to combine though, I use the molrep phases to get all heavy atoms in an anomalous fourier map, then go to SHARP with these sites and use the 'External phases' option in the SHARP gui. Works well for me. I also recall that Phaser has an option for exactly do that, but with SAD data only. But, again, if you have 1.7 A data good old refinement and auto- building will (likely) do the job in a glance. Tassos PS If you dont want to install arp/warp locally why not try: http://cluster.embl-hamburg.de/ARPwARP/remote-http.html PS2 Apologies for the shameless promotion of ARP/wARP ;-) On 17 Jul 2007, at 18:22, Joe Batchelor wrote: Hi, I have a 1.7 A native dataset, a good MR solution for 2/3 of the protein, and MAD phases to 3 A. How should I combine the MR phases with the MAD phases? Thanks, Joe
[ccp4bb] Combining MR and MAD phases
Hi, I have a 1.7 A native dataset, a good MR solution for 2/3 of the protein, and MAD phases to 3 A. How should I combine the MR phases with the MAD phases? Thanks, Joe
[ccp4bb] aspherical atom refinement against F and F^2
Dear all: I am working on the aspherical atom refinement of a small molecule using the XD package. The program provides you with the option of selecting a refinement strategy against F or F^2. I have noticed that the R-factors and GOFs calculated based on F^2 are larger in magnitude compared to those computed based on F. Why is it so? Any comments or suggestions in this regard is welcome. Sincerely, Tuhin. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
[ccp4bb] Sad news; Emeritus Professor Durward W J Cruickshank
Dear Colleagues, I am very sorry to convey the news below. Durward W J Cruickshank FRS, Professor of Chemistry at UMIST (1967-1983; Emeritus thereafter), died on Friday July 13th at Alderley Edge, near Manchester, aged 83. There will be a private family funeral this week. A memorial service will be held at a later date, details to follow. Best wishes, Yours sincerely, John -- John R Helliwell Professor of Structural Chemistry, The University of Manchester; Visiting Scientist at STFC Daresbury Laboratory.
Re: [ccp4bb] calculate B-factor of individual parts
baverage xyzin prot.pdb end Will give you something of what you want.. Eleanor fang sheng wrote: Dear all, The refmac output lists B-factor of each individual atom. But how can I get the B-factor of each set of group, say, protein, ligand A, B, and all 300 waters? suzi _ http://liveearth.msn.com
Re: [ccp4bb] need help for viewing hardware stereo
Venky, have a look at your Xorg.config file in /etc/X11 directory. Make sure to set the options correct (Option "Stereo" "3")!: Section "Device" BoardName"Quadro FX 3450" BusID"1:0:0" Driver "nvidia" Identifier "Device[0]" Option "IgnoreEDID" Option "Stereo" "3" Screen 0 VendorName "NVidia" EndSection Jeroen. venkadesan krishnan wrote: > Hello everyone, > We have bought a new Dell Precision Workstation > 690 (32-bit) and installed Fedora core 6. We are having problem while > viewing molecules in harware stereo mode using programs coot, pymol, etc. > The graphics card came with system is, 256MB PClex16 nVidia Quadro Fx > 3450, Dual DVI or Dual VGA or DVI + VGA. In coot it shows the > following message in the terminal, > > WARNING:: Can't enable stereo visual - falling back > INFO:: Hardware stereo widget opened successfully > INFO:: switch to hardware_stereo_mode succeeded > > In pymol, though it doesn't show any message nothing happened in the view. > > If anyone experienced similar problem previously or knew solutions, > help us to solve this problem. > Thanks in advance > venky > > >
