[ccp4bb] ... docking question
Dear all, I am risking life and limb here, and possibly wining a first row seat to 'Morten's Inferno' for modelers! I want a software that will do some docking of a flexible ligand to a rigid protein model. Consensus google search suggested me to use AutoDock 4/Vina. (I am looking for free software). However, what I want to do is 'non-standard': I know from a crystallographic structure (b) the position of a Vanadate, which has to be (give or take) the position of my phosphate atom in my substrate (I have a phosphodiesterase). Thus this point should get fixed in space (no translation, or ideally restrained translation of some sort), while rotation around it should be allowed, plus that point should be the 'root' of the torsion tree of the ligand to allow it to change conformation around it. AutoDock (but not Vina) seems to be able to do it in simulated annealing mode, by setting the translation to 0. However, my script does not work, there seems to be a bug is s-a mode (asking for keyword that in for the g-a mode!), and while I am waiting for some help from their BB (less lively that ccp4bb as it seems), would anyone have any other suggestion for a free docking software that can do what I want to do? Tassos
Re: [ccp4bb] refmac
Described at: http://www.ccp4.ac.uk/dist/html/refmac5/keywords/xray-principal.html#scal Simple scaling doesn't take into account the bulk solvent at all, whereas Babinet is a simple fix. A more sophisticated treatment of bulk solvent is given by the SOLVENT keyword: http://www.ccp4.ac.uk/dist/html/refmac5/keywords/xray-principal.html#solv which generates a solvent mask and calculates a contribution to Fcalc from that. In the GUI, this is the Calculate the contribution from the solvent region button in the Scaling folder. By default this is on, and scaling type is SIMPLE. In principle, Babinet scaling and solvent mask calculation are alternative treatments of bulk solvent. There was a time however when it seemed to be better to use both (presumably not as bad as it sounds because scale factors will adjust for double counting). I think that's no longer true, but its always possible to suck it and see ... The bottom line: if you've run with defaults, it's probably ok. With high solvent content, you certainly need to model the solvent one way or the other! Cheers Martyn -Original Message- From: CCP4 bulletin board on behalf of Alexandra Deaconescu Sent: Thu 11/19/2009 3:55 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] refmac Hi everyone: Can someone enlighten me as to the difference between simple scaling and Babinet scaling in Refmac? It seems to me that Babinet scaling is more similar to what is employed in CNS for bulk solvent correction (Ksolv, Bsolv search). Is that correct? Would you recommend the Babinet method for high solvent content/ low resolution structures? Thanks a lot, Alex -- Scanned by iCritical.
[ccp4bb] off-topic: crystal optimization without buffer
Hi everybody, sorry for my off-topic question. I got small initial crystals in 200mM NaSulfat and 20% PEG 3350. There is no buffer in this condition. How can I optimize these crystals? Just vary the PEG concentration? Or should I add a buffer; or vary the pH of the buffer the proteinsolution was in? Thank you and best regards, Katja
[ccp4bb] [Fwd: Re: [ccp4bb] off-topic: crystal optimization without buffer]
Forgot to hit the Reply all button (sorry :-( ) ---BeginMessage--- Katja Schleider wrote: Hi everybody, sorry for my off-topic question. I got small initial crystals in 200mM NaSulfat and 20% PEG 3350. There is no buffer in this condition. How can I optimize these crystals? Just vary the PEG concentration? Or should I add a buffer; or vary the pH of the buffer the proteinsolution was in? Thank you and best regards, Katja Hi Katja, What we usually do here (IBS/LBM) is optimisation manually in 24 wells plates. Usually pH vs precipitant concentration (for this you need a buffer). Since you have crystals already, I would try to see if varying the precipitant is enough (who knows, you might be lucky). If the crystals we obtain are not of sufficient quality, we go on with the 3 additive screens from Hampton Research, also manually (droplets of 2 microl + 2 microl + 0.5 microl additive). This (additive screen) can be done by robotics too. Fred. ---End Message---
Re: [ccp4bb] off-topic: crystal optimization without buffer
Hi Katja, Sodium sulphate forms a solution of neutral pH in water. 200 mM of Na2SO4 will buffer the crystallization solution at pH 7, in addition to acting as a salt. You could try varying the concentration of PEG and Sod.sulphate now to see if the crystals get better. Sometimes using potassium or calcium sulphate instead of Sodium at the same concentration can also yield good results. You could also screen for additives. In my opinion, varying the pH of the protein solution at this stage is not a good idea, as it has already been optimised during purification. regards Ganesh On Thu, 19 Nov 2009 09:33:57 +, Katja Schleider wrote: Hi everybody, sorry for my off-topic question. I got small initial crystals in 200mM NaSulfat and 20% PEG 3350. There is no buffer in this condition. How can I optimize these crystals? Just vary the PEG concentration? Or should I add a buffer; or vary the pH of the buffer the proteinsolution was in? Thank you and best regards, Katja
[ccp4bb] FW: Blip
Hi all, I'm using the distributed Refmac version 5.5.0109 (OS = Centos 4.6) and I get this cryptic error message at the end of cycle 13: 1 0.3931933 1.013090 8.5092507E-02 -2.2578495E-02 -0.1768152 -0.1084905 2.9251081E-04 2.0343070E-03 3.6935641E-03 -8.4393099E-04 3.7736616E-05 -8.1993081E-04 1.7520475E-03 6.3033602E-03 8.0644749E-03 1.2155819E-03 -2.8136030E-03 -1.0205148E-02 1.1736480E-02 -2.7233852E-02 -3.6240614E-03 Problem xyz10446 1.977153 -4.287523 4.657890 -3.8452903E-03 0.5033807 0.8756923 0.1101464 -6.6662721E-02 - 0.1923930 -0.1637010 -3.8452903E-03 0.5818514 0.9112133 -0.3702289 -0.9259773 -7.4138783E-02 The first few lines of numbers look like TLS tensors to me, so it looks like it comes from this piece of code in tls_allocate.f : 1596 call find_min_eigen(u_aniso(1,ia),u_min) 1597 if(u_min.lt.0.0) then 1598 write(*,*)im 1599 write(*,*)tmat(1:6,idom) 1600 write(*,*)lmat(1:6,idom) 1601 write(*,*)smat(1:8,idom) 1602 write(*,*)uover_atom 1603 write(*,*)'Problem' 1604 write(*,*)'xyz ',ia,x,y,z,u_min, 1605 u_aniso(1:6,ia),evalue,uaniso0(1,1:3) 1606 stop 1607 endif Looks like it's complaining about a negative eigenvalue of the Uaniso tensor but I thought Refmac could handle those?? Any thoughts? Cheers -- 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 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
[ccp4bb] AW: [ccp4bb] off-topic: crystal optimization without buffer
Hi Katja, it makes perfect sense to add a buffer to your assay. Of course for the beginning something which buffers well around pH 7 like HEPES, BTP, etc. would be appropriate. If your purification protocol is optimized I would not change the conditions of the purification buffer. But this might change maybe if your crystallization experiments give you some more hints about the solubility of the protein. Good luck, Jan --- Katja Schleider katjaschlei...@yahoo.de schrieb am Do, 19.11.2009: Von: Katja Schleider katjaschlei...@yahoo.de Betreff: [ccp4bb] off-topic: crystal optimization without buffer An: CCP4BB@JISCMAIL.AC.UK Datum: Donnerstag, 19. November 2009, 10:33 Hi everybody, sorry for my off-topic question. I got small initial crystals in 200mM NaSulfat and 20% PEG 3350. There is no buffer in this condition. How can I optimize these crystals? Just vary the PEG concentration? Or should I add a buffer; or vary the pH of the buffer the proteinsolution was in? Thank you and best regards, Katja
[ccp4bb] Postdoctoral positions at NIH, Research Triangle Park, North Carolina, USA
Two postdoctoral positions are available in the Genome Stability Structural Biology group (Williams Laboratory) of the National Institute of Environmental Health Sciences (NIEHS/NIH), Research Triangle Park, North Carolina. Related research projects will investigate structural and functional aspects of DNA repair and maintenance of genome integrity using X-ray crystallography, small angle X-ray scattering (SAXS) and biochemical methods, with collaborative in vivo analysis of targeted systems. The Williams group is in the Laboratory (i.e., department) of Structural Biology (LSB) in the Division of Intramural Research, with investigators renowned for their contributions to the area of genome stability, protein-DNA, and protein-RNA structural biology and biochemistry. The exceptional training environment within the LSB is coupled to the strong NIEHS/NIH infrastructure, and offers a highly supportive and interactive scientific environment with many diverse areas of expertise. The group has a fully equipped molecular biology and protein chemistry laboratory and access to superb in house X-ray crystallographic data collection and crystallization robotics equipment. NIEHS is located in an especially attractive part of North Carolina that is central to prominent research institutions, and within driving distance of the beautiful North Carolina coast to the East and the Appalachian mountains to the West. Applicants must possess a doctoral level degree. While candidates with less than five years of relevant postdoctoral research experience are eligible, recent graduates are encouraged to apply. Experienced applicants with skills in molecular biology, protein chemistry, and/or backgrounds in protein structure are preferred. Motivated individuals looking to expand their skill set to include crystallographic methods are also encouraged to apply. Starting postdoctoral salary is $46,800, plus medical benefits. For additional information please see: http://www.niehs.nih.gov/research/atniehs/labs/lsb/index.cfm http://www.niehs.nih.gov/research/atniehs/labs/lsb/genome/index.cfm To apply, please visit: www.training.nih.gov/apps/publicForms/postdoctoral/forms/adIndex.aspx?strSearch Job ID: PD-4663 Or send CV and names of 3 references to: R. Scott Williams Laboratory of Structural Biology NIH/NIEHS, Maildrop F3-03 111 TW Alexander Dr RTP, NC 27709 william...@niehs.nih.gov The National Institute of Environmental Health Sciences (NIEHS) is located in Research Triangle Park, North Carolina. The NIH is dedicated to building a diverse community in its training and employment programs.
Re: [ccp4bb] trouble with protein storage
Marie-Helene-- We have included 3-5% 1,2-propanediol in the protein buffer (as a substitute for glycerol) to stabilize proteins and have seen improvement in the long term storage in many cases. Hope this helps! annie Annie Hassell Glaxo Smithkline 5 Moore Drive RTP, NC 27709 919/483-3228 919/483-0368 (FAX) annie.m.hass...@gsk.com LEDU Marie-Helene 16 marie-helene.l...@cea.fr Sent by: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK 18-Nov-2009 03:45 Please respond to LEDU Marie-Helene 16 marie-helene.l...@cea.fr To CCP4BB@JISCMAIL.AC.UK cc Subject [ccp4bb] trouble with protein storage Hello, Sorry for the unrelated question. We encounter important storage problem of our favorite protein. We can not freeze it without a lost of 50 to 90 %, and can not use glycerol without precipitation. Would anybody have suggestions or references that could help us ? Thanks a lot in advance. Marie-Helene Dr Marie-Hélène LeDu CEA/DSV/IBITEC-S/LBSR bat 144, CE Saclay 91191 Gif-sur-Yvette FRANCE tel 01 69 08 71 35 emel : marie-helene.l...@cea.fr
[ccp4bb] Stereo 3D notebook
http://www.xbitlabs.com/news/mobile/display/20091118173434_Nvidia_Adds_Stereo_3D_Vision_to_Notebooks.html Nvidia Adds Stereo 3D Vision to Notebooks. Asustek Computer to Add Stereo 3D to Mobile PCs This is the 120 Hz LCD technology. But still, no Linux drivers. - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
[ccp4bb] refmac5/ccp4i GUI error
Howdy All,
The refmac5 ccp4i GUI is barfing for one of my users. The GUI error is:
can't read array(NATOMS): no such element in array
can't read array(NATOMS): no such element in array
while executing
if {$array(N_DEPFRAMES_$def_proc0) = 0 $array($indexVar) 0 } {
append array(UPDATE_SCRIPTS) update_toggleframe $def_proc0 0 $arrayname
$in...
(procedure CreateToggleFrame line 98)
invoked from within
CreateToggleFrame NATOMS atom_proc Add another atomic form factor Atomic
form factors Add Atom [list ATOM ATOM_FP ATOM_FPP ]
(procedure refmac5_task_window line 97)
invoked from within
refmac5_task_window refmac5_T347B1L
(eval body line 1)
invoked from within
eval $cmd
(procedure RunTask line 109)
invoked from within
RunTask refmac5
invoked from within
.module.menu.action.canvas.frame.t.f_5 invoke
(uplevel body line 1)
invoked from within
uplevel #0 [list $w invoke]
(procedure tk::ButtonUp line 22)
invoked from within
tk::ButtonUp .module.menu.action.canvas.frame.t.f_5
(command bound to event)
==
And the shell prints out:
ERROR no type for TWINREF_TYPE
ERROR no type for F+
ERROR no type for F-
ERROR no type for WAVELENGTH
==
This is CCP4 6.1.2 on linux. Does anyone have any ideas on what is going
wrong? I see one similar message in the archives, but there were no
responses at that time.
Thanks.
-ben
--
| Ben Eisenbraun | Software Sysadmin |
| Structural Biology Grid | http://sbgrid.org |
| Harvard Medical School | http://hms.harvard.edu |
Re: [ccp4bb] refmac5/ccp4i GUI error
Mmmm. This rings a bell. It is either:
1) an infelicity re-running an old job - start from a new task window
2) the user has a file ~/.CCP4/CCP4I_TOP/tasks/refmac5.def - delete it
If it is really only one of your users, then it is probably the
second ...
HTH
Martyn
On Thu, 2009-11-19 at 13:59 -0500, Ben Eisenbraun wrote:
Howdy All,
The refmac5 ccp4i GUI is barfing for one of my users. The GUI error is:
can't read array(NATOMS): no such element in array
can't read array(NATOMS): no such element in array
while executing
if {$array(N_DEPFRAMES_$def_proc0) = 0 $array($indexVar) 0 } {
append array(UPDATE_SCRIPTS) update_toggleframe $def_proc0 0 $arrayname
$in...
(procedure CreateToggleFrame line 98)
invoked from within
CreateToggleFrame NATOMS atom_proc Add another atomic form factor Atomic
form factors Add Atom [list ATOM ATOM_FP ATOM_FPP ]
(procedure refmac5_task_window line 97)
invoked from within
refmac5_task_window refmac5_T347B1L
(eval body line 1)
invoked from within
eval $cmd
(procedure RunTask line 109)
invoked from within
RunTask refmac5
invoked from within
.module.menu.action.canvas.frame.t.f_5 invoke
(uplevel body line 1)
invoked from within
uplevel #0 [list $w invoke]
(procedure tk::ButtonUp line 22)
invoked from within
tk::ButtonUp .module.menu.action.canvas.frame.t.f_5
(command bound to event)
==
And the shell prints out:
ERROR no type for TWINREF_TYPE
ERROR no type for F+
ERROR no type for F-
ERROR no type for WAVELENGTH
==
This is CCP4 6.1.2 on linux. Does anyone have any ideas on what is going
wrong? I see one similar message in the archives, but there were no
responses at that time.
Thanks.
-ben
--
| Ben Eisenbraun | Software Sysadmin |
| Structural Biology Grid | http://sbgrid.org |
| Harvard Medical School | http://hms.harvard.edu |
--
***
* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. *
* Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
* Fax: +44 1925 603825Skype name: martyn.winn *
* URL: http://www.ccp4.ac.uk/martyn/ *
***
[ccp4bb] units of the B factor
Many textbooks describe the B factor as having units of square Angstrom (A^2), but then again, so does the mean square atomic displacement u^2, and B = 8*pi^2*u^2. This can become confusing if one starts to look at derived units that have started to come out of the radiation damage field like A^2/MGy, which relates how much the B factor of a crystal changes after absorbing a given dose. Or is it the atomic displacement after a given dose? Depends on which paper you are looking at. It seems to me that the units of B and u^2 cannot both be A^2 any more than 1 radian can be equated to 1 degree. You need a scale factor. Kind of like trying to express something in terms of 1/100 cm^2 without the benefit of mm^2. Yes, mm^2 have the dimensions of cm^2, but you can't just say 1 cm^2 when you really mean 1 mm^2! That would be silly. However, we often say B = 80 A^2, when we really mean is 1 A^2 of square atomic displacements. The B units, which are ~1/80th of a A^2, do not have a name. So, I think we have a new unit? It is A^2/(8pi^2) and it is the units of the B factor that we all know and love. What should we call it? I nominate the Born after Max Born who did so much fundamental and far-reaching work on the nature of disorder in crystal lattices. The unit then has the symbol B, which will make it easy to say that the B factor was 80 B. This might be very handy indeed if, say, you had an editor who insists that all reported values have units? Anyone disagree or have a better name? -James Holton MAD Scientist
