[ccp4bb] Graphics software to show epitope foot-print
Dear colleagues, I am looking for a graphics software program that can make the following, easily. Make a surface representation of a macromolecule. That surface should be coloured according to some property. On, or close to, that surface the outer rim of a binding epitope from a second molecule should be indicated by a line or string, a foot-print representation, without altering the original colouring of the surface. Unfortunately I can not find out any program that can make it easily, or have not understood all features of the programs. Can anyone help? Kind regards Anders Svensson __ Anders Svensson Novo Nordisk A/S Denmark
Re: [ccp4bb] problem of crystallization
... your protein is the dream of any NMR spectroscopist. Small and ultra-soluble. Maybe just do the structure by NMR? It should be totally straightforward for any NMR lab. A. On May 13, 2008, at 18:16, Jennifer Han-Chun Tsai wrote: Hi, This topic is not related to CCP4. I am having problem of crystallizing one protein. It's a pretty small protein with size around 15kDa. I have stock concentration around 100mg/mL. Crystallization plates I set up are with concentration of 10mg/mL, 30mg/mL and 50mg/mL. All the plates had been set up at least one week. Only around 5 wells per plate or less formed precipitation. The rest of wells are pretty clear still. Is there any suggestion for reducing protein solubility or increasing the chance of getting crystals? Thanks for your time, Jennifer
[ccp4bb] any review on protein-protein complex crystallization?
Dear CCP4bb, Can anyone point me to good reviews or books which describe how to crystallize protein-protein complexes (or anyone willing to share his/her experience)? In particular I'm interested in: (1) which tests to perform on your complex before you even start thinking about crystallization (2) what should you take in account when you start to crystallize (any other than 'use the Radaev and Sun' screen) (3) how to increase the success rate of crystallization (cross linking? co-expression?) (4) any alternative techniques when crystallization fails (any other than NMR) I would be very grateful! Thanks in advance, Maarten __ Maarten Dewilde - PhD student Laboratory for Pharmaceutical Biology ON2 - PB 824 - Herestraat 49 3000 Leuven mailto:[EMAIL PROTECTED] [EMAIL PROTECTED] tel: +32 16 323434 fax: +32 16 323460 Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
[ccp4bb] Fixing waters around metal atom
Hi, I have a structure with a metal beautifully coordinated by 3 water molecules. However, every time I run automated water picking they get removed (due to combination of being too close to metal/too deep in the density). So far I've been manually reentering them into pdb but it becomes a bit frustrating. Is there a way to fix those waters during water picking? Regards, Andrzej -- Andrzej LYSKOWSKI, Ph.D. ([EMAIL PROTECTED]) Institute of Biotechnology - Structural Biology Biophysics P. O. Box 65, Viikinkaari 1 FIN-00014 University of HELSINKI, FINLAND TEL.: 358 9 191 58955 FAX : 358 9 191 59940
[ccp4bb] Call for synchrotron beam time at EMBL Hamburg
Dear Colleague, This is a gentle reminder of our call for beam time applications at EMBL Hamburg that we circulated a few weeks ago. We kindly ask you to complete your beam time proposal by the deadline of --- 16 May 2008 If you have already taken action, you can ignore this message. --- EMBL HAMBURG UNIT Call for access to Synchrotron Beamline Facilities 2008 We announce a call for synchrotron beam time applications in biological X-ray crystallography (PX) and small-angle scattering (SAXS). Up to 12 weeks of beam time will be available at the DORIS storage ring (DESY) during the period September 2008 until December 2008. The EMBL Outstation will operate the following beamlines: BeamlineTypeWavelength Scientist responsible X11 PX 0.80 A Paul Tucker X12 PX tuneable Manfred Weiss X13 PX 0.80 A Matthew Groves X33 SAXS1.5 A Dmitri Svergun, Manfred Roessle The deadline for submission of proposals is May 16th, 2008. An external Priorities Committee will assess the proposals. Electronic beam proposal forms and detailed description of the beamline facilities are available via the web links http://www.embl-hamburg.de and http://www.embl-hamburg.de/services In parallel, EMBL-Hamburg is constructing three new beamlines for applications in biological X-ray crystallography (PX) and small-angle scattering (SAXS) at the Petra-III synchrotron storage ring, with an expected opening in 2010/11. Further information can be obtained under http://www.embl-hamburg.de/services/petra. Two of the DORIS-III beamlines (BW7A, BW7B) will be used as test beamlines for future Petra-III applications. Depending on circumstances, they may become temporarily available to the external user community. Applications to use the EMBL-Hamburg high-throughput crystallisation facility can be made at any time at http://www.embl-hamburg.de/services/crystallisation Further information can be obtained by tel. +49-40-89902-110, (fax +49-40-89902-149), Email [EMAIL PROTECTED] (PX), [EMAIL PROTECTED] (SAXS). Access to the EMBL Hamburg facilities is supported by the European Commission, Research Infrastructure Action under the FP6 'Structuring the European Research Area Specific Programme', Contract Number RII3-CT-2004-506008. ---
[ccp4bb] refinement problem
Hi, I have one structural refinement problem. I am working on a protein crystals which diffracted to 2.8 Å. But when I refine through REFMAC5, with 0.1 wt(geometry to x-ray terms), I get high B-factors around 70. But if I do TLS refinement, the R-factors lower down and B-factors come down to 40. My question is; Are TLS refined B-factors real?? Can I trust them? or what else could be done to lower down the B.factors? BR vimal
Re: [ccp4bb] pdb format
Hi Raja You can use a command-line script like this one: #!/bin/tcsh sed -e /ATOM/ s/'/*/g -e /ATOM/ s/O5T/O3T/ -e /ATOM/ s/ADE/ DA/g -e /ATOM/ s/CYT/ DC/g -e /ATOM/ s/GUA/ DG/g -e /ATOM/ s/THY/ DT/g $1refmacok_$1 cat refmacok_$1|grep ATOM|more/dev/tty Save the script in a new file (ex:DNArefmac.sh) and make sure it is executable on your computer (in a terminal type chmod -x DNArefmac.sh). I used it for rna to convert from CNS format to refmac, and adapted it for dna. Just put it in the same directory with your pdb then run it (ie: sh DNArefmac.sh thing.pdb). It will normally produce a new pdb suitable for refmac.called refmacok_thing.pdb and also display it on the terminal. Hope this will help. Nicolas Raja Dey wrote: Hi, The out pdb file from 'CNS' or from 'O' is not readable in 'CCP4'. I have dna and protein in my pdb file. Do you the best way to convert the pdb file I got from 'CNS or from 'O' into 'CCP4' format? Especially CCP4 follows 1 letter code for dna whereas CNS and O follow 3 letter code. Looking forward to hearing from you Thanks... Raja BMR - a key player in weight issues. Know more. http://in.rd.yahoo.com/tagline_glue_4/*http://in.search.yahoo.com/search?fr=na_onnetwork_mail_taglinesei=UTF-8rd=r1p=basal+metabolic+rate -- Nicolas Soler Institut de Chimie des Substances Naturelles 91190 Gif-sur-Yvette tel 33-1-69823764 fax 33-1-69823784 http://perso.nicodam.org/
Re: [ccp4bb] problem of crystallization
I would suggest to open the wells, add some hefty precipitant to the reservoir, and close the wells again. The point is to drive the equilibrium further towards high concentration by drawing more water into the reservoir. It therefore does not matter what the supplemental precipitant is. Concentrated AMS, PEG, whatever as long as it has no volatile component which might uncontrollably affect pH in the drop. BR -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Anastassis Perrakis Sent: Wednesday, May 14, 2008 1:28 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] problem of crystallization ... your protein is the dream of any NMR spectroscopist. Small and ultra-soluble. Maybe just do the structure by NMR? It should be totally straightforward for any NMR lab. A. On May 13, 2008, at 18:16, Jennifer Han-Chun Tsai wrote: Hi, This topic is not related to CCP4. I am having problem of crystallizing one protein. It's a pretty small protein with size around 15kDa. I have stock concentration around 100mg/mL. Crystallization plates I set up are with concentration of 10mg/mL, 30mg/mL and 50mg/mL. All the plates had been set up at least one week. Only around 5 wells per plate or less formed precipitation. The rest of wells are pretty clear still. Is there any suggestion for reducing protein solubility or increasing the chance of getting crystals? Thanks for your time, Jennifer
[ccp4bb] looking for software
Dear all, I am looking for some software (computer program) that would take a full PDB file (including waters) and that would output a list of the water networks (including the names of the atoms) at the surface of a protein. Thank you in advance, Fred. begin:vcard fn:Fred. Vellieux (Ph.D) n:Vellieux (Ph.D);Fred. email;internet:[EMAIL PROTECTED] tel;work:+33 438789605 version:2.1 end:vcard
Re: [ccp4bb] problem of crystallization
A few ideas: 1) go even higher with protein concentration. Some ultra-soluble proteins may need 100 mg/mL. You may have to set up drops at higher ratios of protein:precipitant to achieve this. e.g. 3:1 or more. Use a test such as the Hampton PCT to tell you when you are in the right concentration range. 2) reductive methylation of lysine residues as Stephen suggested. This often reduces the solubility of proteins and will change the surface properties. 3) get rid of any glycosylation as the surface sugars increase solubility (and are flexible anyway and so bad for crystallization) 4) check the few drops which have precipitate and look for common factor e.g. 2M Ammonium Sulphate. You could then add a small amount of this ingredient (e.g. 100mM Ammonium Sulphate) to your protein and then re-screen. 5) Wait a bit longer. One week is still early days. Good luck Tom ** Tom Walter B.Sc. M.Res. ** ** Oxford Protein Production FacilityTel: +44 (0)1865 287747 ** ** Wellcome Trust Centre for Human Genetics Fax: +44 (0)1865 287547 ** ** Roosevelt Drive [EMAIL PROTECTED] ** ** Headington, Oxford OX3 7BNhttp://www.oppf.ox.ac.uk ** Original message Date: Tue, 13 May 2008 11:16:41 -0500 From: Jennifer Han-Chun Tsai [EMAIL PROTECTED] Subject: [ccp4bb] problem of crystallization To: CCP4BB@JISCMAIL.AC.UK Hi, This topic is not related to CCP4. I am having problem of crystallizing one protein. It's a pretty small protein with size around 15kDa. I have stock concentration around 100mg/mL. Crystallization plates I set up are with concentration of 10mg/mL, 30mg/mL and 50mg/mL. All the plates had been set up at least one week. Only around 5 wells per plate or less formed precipitation. The rest of wells are pretty clear still. Is there any suggestion for reducing protein solubility or increasing the chance of getting crystals? Thanks for your time, Jennifer
[ccp4bb] Oxford cryostream 700 series to give away
Dear BBorders, the lab is giving away a complete and perfectly functional Oxford Cryosystems Cryostream 700 series. For more information, please contact me outside the bulletin, please. Best regards Adriana Erica Miele - Adriana E. Miele, Ph.D. Dipartimento di Scienze Biochimiche Sapienza Universita' di Roma P.le A. Moro 5 00185 Roma tel.: +3906 49910713 fax: +3906 4440062 eMail: [EMAIL PROTECTED]
Re: [ccp4bb] Graphics software to show epitope foot-print
Hi Anders and CCP4bb Would something like http://www.ysbl.york.ac.uk/~ccp4mg/index_info_5.html (done with CCP4mg) be useful? In that image the molecule surface is coloured by electrostatics (but could be any other property) and the contact area to a ligand is indicated by dots on the surface. Liz On Wednesday 14 May 2008 08:34, ANSV (Anders Svensson) wrote: Dear colleagues, I am looking for a graphics software program that can make the following, easily. Make a surface representation of a macromolecule. That surface should be coloured according to some property. On, or close to, that surface the outer rim of a binding epitope from a second molecule should be indicated by a line or string, a foot-print representation, without altering the original colouring of the surface. Unfortunately I can not find out any program that can make it easily, or have not understood all features of the programs. Can anyone help? Kind regards Anders Svensson __ Anders Svensson Novo Nordisk A/S Denmark
[ccp4bb] Alternate Ligand Conformations
Hello. I am trying to refine a structure that has 2 ligand conformations as seen in the electron density. I tried to put both conformations in Coot and format the PDB similar to a residue alternate conformation and changing the occupancies to 0.50 for each conformation. This formatting did not work when I ran Refmac5 for the Refinement. Has anyone had this issue before? And can anyone suggest a PDB format that will work in Refmac5? Thanks, Kathleen
Re: [ccp4bb] Graphics software to show epitope foot-print
Hi Liz, Yes, that's a smart solution. I will have a try on my own data. Many thanks. Anders -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Liz Potterton Sent: 14. maj 2008 14:10 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Graphics software to show epitope foot-print Hi Anders and CCP4bb Would something like http://www.ysbl.york.ac.uk/~ccp4mg/index_info_5.html (done with CCP4mg) be useful? In that image the molecule surface is coloured by electrostatics (but could be any other property) and the contact area to a ligand is indicated by dots on the surface. Liz On Wednesday 14 May 2008 08:34, ANSV (Anders Svensson) wrote: Dear colleagues, I am looking for a graphics software program that can make the following, easily. Make a surface representation of a macromolecule. That surface should be coloured according to some property. On, or close to, that surface the outer rim of a binding epitope from a second molecule should be indicated by a line or string, a foot-print representation, without altering the original colouring of the surface. Unfortunately I can not find out any program that can make it easily, or have not understood all features of the programs. Can anyone help? Kind regards Anders Svensson __ Anders Svensson Novo Nordisk A/S Denmark
Re: [ccp4bb] looking for software
Vellieux Frederic wrote: Dear all, I am looking for some software (computer program) that would take a full PDB file (including waters) and that would output a list of the water networks (including the names of the atoms) at the surface of a protein. Thank you in advance, Fred. watertidy does something like this - it produces a bastard format but it does give meaningful names.. eleanor
Re: [ccp4bb] refinement problem
parkash wrote: Hi, I have one structural refinement problem. I am working on a protein crystals which diffracted to 2.8 Å. But when I refine through REFMAC5, with 0.1 wt(geometry to x-ray terms), I get high B-factors around 70. But if I do TLS refinement, the R-factors lower down and B-factors come down to 40. My question is; Are TLS refined B-factors real?? Can I trust them? or what else could be done to lower down the B.factors? BR vimal This is or should be a FAQ - all B factors after TLS are relative to the TLS restraints Try running TLSANL and that should give you back a more meaningful overall B Eleanor
[ccp4bb] Metal-Ligand Link tag
Hello all, I have a structure that has a Ni coordinated by an Asp residue and the backbone of two other residues. When I try to include Link statements for this in my pdb, refmac fails and says that a new ligand has been found. I was wondering if anyone knew what proper tag for these interactions might be; what library file might actually contain them; or how to generate a new ligand in sketcher that includes at least some part of the existing residue definitions. Thank you in advance, Eric Salgado
[ccp4bb] poll: cutoff for high resolution
At what refinement resolution or resolution ranges would you call a structure high resolution vs. low resolution? I realize that this may boil down to semantics (e.g. some may classify structures as medium resolution), but I wanted to get an opinion from the pros.
Re: [ccp4bb] poll: cutoff for high resolution
I don't think you can give a resolution range - you could argue that it depends on molecular weight, i.e. high resolution for insulin and high resolution for the ribosome are going to be very different numbers. Other than that, my answer would be that you know it when you've got it :) Cheers, Eddie. Edward Snell Ph.D. Assistant Prof. Department of Structural Biology, SUNY Buffalo, Hauptman-Woodward Medical Research Institute 700 Ellicott Street, Buffalo, NY 14203-1102 Phone: (716) 898 8631 Fax: (716) 898 8660 Email: [EMAIL PROTECTED] Telepathy: 42.2 GHz Heisenberg was probably here! -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Mark Del Campo Sent: Wednesday, May 14, 2008 3:28 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] poll: cutoff for high resolution At what refinement resolution or resolution ranges would you call a structure high resolution vs. low resolution? I realize that this may boil down to semantics (e.g. some may classify structures as medium resolution), but I wanted to get an opinion from the pros.
Re: [ccp4bb] poll: cutoff for high resolution
I think this is coupled with the data completeness. Say you have a data 50.0-1.0A resolution, but the completeness in say 3.0-1.0A resolution range is equal to 10%, and it is 100% complete in 50.0-3.0A. Pavel. On 5/14/2008 12:28 PM, Mark Del Campo wrote: At what refinement resolution or resolution ranges would you call a structure high resolution vs. low resolution? I realize that this may boil down to semantics (e.g. some may classify structures as medium resolution), but I wanted to get an opinion from the pros.
[ccp4bb] While on the subject of stereo
OK, so we weren't on this subject, and all of you are tired of me asking. However, the following link came to me and I wanted to see some programmers opinions on this one. The thing I'm wondering is, what needs to be done on the programming end to make this something that we could use in a classroom to show molecules in stereo. It seems like it would be fun, and I actually think it would work well, though I don't know if it would work with more than one person looking at the screen at a time (now that I really think about it, probably not - nevermind). If it only works with one person, can we use this for modeling? Just curious www.ted.com/index.php/talks/view/id/245 Dave
Re: [ccp4bb] While on the subject of stereo
Hi David, This has already been done with PyMOL. There's a video at: http://molviz.cs.toronto.edu/molviz/ and the code is downloadable. The stereo effect isn't so great with both eyes open, but I do think there is potential for use of head or object tracking as a means of controlling rotation. Cheers, Warren From: CCP4 bulletin board on behalf of David Roberts Sent: Wed 5/14/2008 12:59 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] While on the subject of stereo OK, so we weren't on this subject, and all of you are tired of me asking. However, the following link came to me and I wanted to see some programmers opinions on this one. The thing I'm wondering is, what needs to be done on the programming end to make this something that we could use in a classroom to show molecules in stereo. It seems like it would be fun, and I actually think it would work well, though I don't know if it would work with more than one person looking at the screen at a time (now that I really think about it, probably not - nevermind). If it only works with one person, can we use this for modeling? Just curious www.ted.com/index.php/talks/view/id/245 Dave
Re: [ccp4bb] poll: cutoff for high resolution
On May 14, 2008, at 12:28 PM, Mark Del Campo wrote: At what refinement resolution or resolution ranges would you call a structure high resolution vs. low resolution? I realize that this may boil down to semantics (e.g. some may classify structures as medium resolution), but I wanted to get an opinion from the pros. This really needs to take into account the numerical resolution vs. inherent-coolness-factor tradeoff matrix. For example, if the macromolecule is comprised of 100% amino acids and catalyzes a reaction in the Krebs cycle, high resolution is 0.5*(C=C), the carbon-carbon double-bond length. If it is a snRNP, 7Å is moderate resolution.
[ccp4bb] User proposal submission for Collaborative Crystallography at BCSB
Dear Users, The Berkeley Center for Structural Biology (BCSB) is pleased to announce the launch of a Collaborative Crystallography Pilot Program (CC) at the Advanced Light Source in Berkeley. Through this program, scientists will be able to send protein crystals to BCSB staff researchers for data collection and analysis. The CC Pilot Program can provide an number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; * Reduced travel costs. Thumbnail Description: == The Collaborative Crystallography program will be piloted on beamlines 5.0.1 and 5.0.2 for one year; if successful it will be implemented on a permanent basis. CC proposals will go through the egular ALS General User proposal review process for beamtime allocation. Proposals will be reviewed and ranked by the Proposal Study Panel, and beamtime will be allocated accordingly. BCSB staff will schedule the projects to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography How To Apply: = To submit a proposal, go to: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize For question 3 select Collaborative PX 501/502. For question 9, please describe a specific research project with a clear end point. In order to request CC time for July/August, 2008, proposals must be submitted by May 15, 2008. The deadline for CC proposals for the time period September/October 2008 is July 15, 2008. Regards, Banumathi Sankaran
[ccp4bb] Position in protein crystallography, Novartis. Insts. for Biomedical Research - Emeryville
Please note that qualified B.S. and M.S. level research associates are invited to apply. Structural Chemistry, Structure-Based Drug Design Discovery Novartis Institutes for BioMedical Research, Emeryville, California Use your scientific expertise to aid us in our structure-based drug design efforts. Your task will be the determination of high-resolution, three-dimensional structures of macromolecular drug targets (typically proteins), including crystallization and structure solution of medically important structures and target-ligand complexes. As a part of an integrated team you will interact with computational chemists and medicinal chemists to design new scaffolds and improve lead compounds. The ideal candidate will have a B.S. or M.S. degree and 2 or more years of work experience, or a Ph.D. and 2 or more years of postdoctoral and/or work experience. Degrees in Biochemistry, Chemistry, or Molecular Biophysics are acceptable. Experience in protein biochemistry, protein crystallization, and crystallographic methods are necessary and pharmaceutical industry experience is a plus. Strong computational and molecular modeling skills, experience in solution studies (calorimetry, NMR, etc.) and/or experience in structure-based drug design would be useful. You should have excellent verbal and written communication skills and the ability to work in large, multidisciplinary project teams. To join our global team, please submit your CV online at http://www.novartisvaccines.com/jobs http://www.novartisvaccines.com/jobs , referencing Brassring requisition number 2294. Any questions about the position should be sent to [EMAIL PROTECTED]
Re: [ccp4bb] refinement problem
Hi, It would be nice if you mention more clearly how you have done TLS..i.e.,domains or individual residues or molecules !! You should keep in mind that you have 2.8A data. I would do TLSANL with domains or molecules. Best regards, Krishna Ch PhD Student Hannover Medical school Germany On Wed, May 14, 2008 at 11:36 AM, parkash [EMAIL PROTECTED] wrote: Hi, I have one structural refinement problem. I am working on a protein crystals which diffracted to 2.8 Å. But when I refine through REFMAC5, with 0.1 wt(geometry to x-ray terms), I get high B-factors around 70. But if I do TLS refinement, the R-factors lower down and B-factors come down to 40. My question is; Are TLS refined B-factors real?? Can I trust them? or what else could be done to lower down the B.factors? BR vimal
Re: [ccp4bb] any review on protein-protein complex crystallization?
This may be obvious, but I would run a size-exclusion column on the complex first. This will give you an idea as to how well these two proteins stick together. On Wed, May 14, 2008 at 4:34 AM, Maarten Dewilde [EMAIL PROTECTED] wrote: Dear CCP4bb, Can anyone point me to good reviews or books which describe how to crystallize protein-protein complexes (or anyone willing to share his/her experience)? In particular I'm interested in: (1) which tests to perform on your complex before you even start thinking about crystallization (2) what should you take in account when you start to crystallize (any other than 'use the Radaev and Sun' screen) (3) how to increase the success rate of crystallization (cross linking? co-expression?) (4) any alternative techniques when crystallization fails (any other than NMR) I would be very grateful! Thanks in advance, Maarten __ Maarten Dewilde - PhD student Laboratory for Pharmaceutical Biology ON2 - PB 824 - Herestraat 49 3000 Leuven [EMAIL PROTECTED] tel: +32 16 323434 fax: +32 16 323460 Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm for more information.
[ccp4bb] UV light source for protein xtal detection
Dear all, Here's another non CCP4 question: does anyone know a cheap alternative to set up a UV source at 280 nm? I'd really like to have one :), but I really don't have the $20K Dlls needed to buy a UV/white light source from the crystallographic vendors :(. Thanks so much in advance for your answers, Alfredo. Alfredo Torres-Larios, PhD Assistant Professor Instituto de Fisiologia Celular, UNAM. Ciudad Universitaria, Mexico This message was sent using IMP, the Internet Messaging Program.
Re: [ccp4bb] looking for software
Hi, Please try the following web based tool to get a list of the water networks in a given PDB file. http://iris.physics.iisc.ernet.in/psap/ Please click on the option Display water Bridges. regards, Sekar Dear all, I am looking for some software (computer program) that would take a full PDB file (including waters) and that would output a list of the water networks (including the names of the atoms) at the surface of a protein. Thank you in advance, Fred. -- 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. Could you kindly confirm the safe receipt of this mail please All best wishes and regards, Yours sincerely, Sekar, K. Ph.D. Bioinformatics Centre (Centre of Excellance in Structural Biology and Bio-computing) Supercomputer Education and Research Centre Indian Insitute of Science Bangalore 560 012 INDIA E-mail: [EMAIL PROTECTED] and [EMAIL PROTECTED] Tel: 91-(0)80-23601409, 22933059, 22932469 Fax: 91-(0)80-23600683, 23600551 Homepage: http://www.physics.iisc.ernet.in/~dichome/sekhome/index.html -- 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.
