Re: [ccp4bb] pdb file deposition
Hi, What happens usually is that some solvent atoms are in fact closer to a symmetry-related molecule than the one you are working on. The PDB has programs to reposition these water molecules closer to the correct macromolecule or subunit, and they will provide you with the modified waters and ask you to approve (or not). So I personally ignore these warning messages until I receive news from the PDB. HTH, Fred. Azadeh Shahsavar wrote: Dear All, In depositing a pdb file, after validation step, an error comes up: *Solvent Atoms* The following solvent molecules lie farther than expected from the protein. Can any one give me some advice about it? deleting these water molecules results in a large increase of R factor, by the way. Thank you in advance, A
[ccp4bb] Any simple way to scale 2 MTZ?
Hello, Is there a magic tool doing the job of scaling 2 MTZ to the same scale? For the moment I know with ccp4: rwcontents then wilson then mtzutils with phenix: lsq_scale (in fact I am lying, I was forced to run ccp4's cad before) Is there a simpler way with ccp4? As I am not a crystallographer, I am afraid I can do many different stupid errors when I have to use many tools for just one task. Regards, Francois.
Re: [ccp4bb] Any simple way to scale 2 MTZ?
Hi Francois, SCALEIT in CCP4 sounds like the tool you want - this is for scaling e.g. native and derivitive data sets together. You will need to cad together the two files first though. This is illustrated in the tutorials here: http://www.ccp4.ac.uk/dist/examples/tutorial/html/heavy-tutorial-mad.html#step_4a Best wishes, Graeme On 12 March 2010 08:17, Francois Berenger beren...@riken.jp wrote: Hello, Is there a magic tool doing the job of scaling 2 MTZ to the same scale? For the moment I know with ccp4: rwcontents then wilson then mtzutils with phenix: lsq_scale (in fact I am lying, I was forced to run ccp4's cad before) Is there a simpler way with ccp4? As I am not a crystallographer, I am afraid I can do many different stupid errors when I have to use many tools for just one task. Regards, Francois.
[ccp4bb] protein crystallization problem
Dear All, I have several proteins that share a common problem. When crystallization, once the precipitant is PEG, the protein will be precipitated in seconds. Even the protein concentration is just 2 mg/ml. But if the precipitant is salt such as NH2SO4. The drop is clear for months, even higher protein concentration (50 mg/ml) . After screening more than 1000 conditions, I concluded this problem. Is anyone has the same problem? Any suggestions are welcome. Thanks Regards, George
Re: [ccp4bb] Any simple way to scale 2 MTZ?
Graeme Winter wrote: Hi Francois, SCALEIT in CCP4 sounds like the tool you want - this is for scaling e.g. native and derivitive data sets together. You will need to cad together the two files first though. My crystallographer colleague tells me that if we use scaleit there is a risk if there are multiple copies in the ASU. So, we should scale both data sets to absolute scale. This is illustrated in the tutorials here: http://www.ccp4.ac.uk/dist/examples/tutorial/html/heavy-tutorial-mad.html#step_4a Best wishes, Graeme On 12 March 2010 08:17, Francois Berenger beren...@riken.jp wrote: Hello, Is there a magic tool doing the job of scaling 2 MTZ to the same scale? For the moment I know with ccp4: rwcontents then wilson then mtzutils with phenix: lsq_scale (in fact I am lying, I was forced to run ccp4's cad before) Is there a simpler way with ccp4? As I am not a crystallographer, I am afraid I can do many different stupid errors when I have to use many tools for just one task. Regards, Francois.
Re: [ccp4bb] Any simple way to scale 2 MTZ?
Hi Francois, As I understand this, they (the F's) should be already on an absolute scale as determined by the Wilson stats as TRUNCATE does this scaling. What SCALEIT does is to scale the data sets together in terms of an overall (or anisotropic) temperature factor and overall scale, so that the differences between related observations can be interpreted more sensibly. I am sure by now that the authors of these programs will be online and able to provide a more authoritative answer. I guess what would be helpful here is to know what you are trying to achieve in this scaling. Best wishes, Graeme On 12 March 2010 09:27, Francois Berenger beren...@riken.jp wrote: Graeme Winter wrote: Hi Francois, SCALEIT in CCP4 sounds like the tool you want - this is for scaling e.g. native and derivitive data sets together. You will need to cad together the two files first though. My crystallographer colleague tells me that if we use scaleit there is a risk if there are multiple copies in the ASU. So, we should scale both data sets to absolute scale. This is illustrated in the tutorials here: http://www.ccp4.ac.uk/dist/examples/tutorial/html/heavy-tutorial-mad.html#step_4a Best wishes, Graeme On 12 March 2010 08:17, Francois Berenger beren...@riken.jp wrote: Hello, Is there a magic tool doing the job of scaling 2 MTZ to the same scale? For the moment I know with ccp4: rwcontents then wilson then mtzutils with phenix: lsq_scale (in fact I am lying, I was forced to run ccp4's cad before) Is there a simpler way with ccp4? As I am not a crystallographer, I am afraid I can do many different stupid errors when I have to use many tools for just one task. Regards, Francois.
Re: [ccp4bb] protein crystallization problem
Have you ever tried the condition of AS as precipitant and PEG as the additive? They have opposite functions on your protein's solubility:one increases and decrease it. Maybe you can vary the ratio of them to control your protein's solubility. And the xtals may be seen in some conditions. Good luck! leo Xingding Zhou wrote: Dear All, I have several proteins that share a common problem. When crystallization, once the precipitant is PEG, the protein will be precipitated in seconds. Even the protein concentration is just 2 mg/ml. But if the precipitant is salt such as NH2SO4. The drop is clear for months, even higher protein concentration (50 mg/ml) . After screening more than 1000 conditions, I concluded this problem. Is anyone has the same problem? Any suggestions are welcome. Thanks Regards, George
[ccp4bb] Soaking at pH 4.0 ?
Hi, I am trying to soak some sugars in my crystals, but the cystallization condition has a pH of 4.0. Does anybody has any experience with acidic oxidation in such a case. I think I can´t avoid oxidation at this pH? Any suggestions, or do I have to screen for other conditions? Thanks, P.
Re: [ccp4bb] Soaking at pH 4.0 ?
Hi, I have soaked various crystals at that pH with various sugars and never had a problem with oxidation of the sugar. I wouldn't worry about it. What group do you think will be oxidized? Nat On Fri, Mar 12, 2010 at 5:35 AM, Paul Lindblom lindblom.p...@googlemail.com wrote: Hi, I am trying to soak some sugars in my crystals, but the cystallization condition has a pH of 4.0. Does anybody has any experience with acidic oxidation in such a case. I think I can´t avoid oxidation at this pH? Any suggestions, or do I have to screen for other conditions? Thanks, P.
[ccp4bb] pdb dep
Dear all, in the process of pdb file deposition, after some error removal, suddenly pdbdep made errors on the covalent bond angles of all PRO residues. Does any one has any suggestion? :( Regards, Azadeh
[ccp4bb] Postdoctoral position at NIH: Membrane-associated protein complexes
A postdoctoral position is available for a skilled protein crystallographer interested in challenging projects in the Hurley lab, NIDDK, NIH. We are seeking to understand the structure and function of membrane-associated multiprotein complexes involved in protein and lipid trafficking. Some of these complexes include one or more integral membrane proteins. We offer a superbly equipped facility and an interdiscplinary evironment that encourages skill and career development both within and beyond crystallographic structure determination. The lab integrates techniques from yeast cell biology to reconstitution of membrane trafficking along with structural analysis. See http://www-mslmb.niddk.nih.gov/hurley/index.html for more information. Experience is required in crystallizing challenging integral membrane proteins and/or multiprotein complexes expressed in eukaryotic systems. Substantial experience in crystallographic data collection, processing, phasing, and refinement is required. Candidates should have less than five years previous postdoctoral experience. Send cv and names of three references to hur...@helix.nih.gov.
[ccp4bb] phenix target weight refinement
Dear All, In every refinement round the wxc and wcu are out of control, although I modify the def file and change the values of wxc=1 and wxu=1 so they are tightly restrained, but it failed to fix the problem, wxc and wxu values keep fluctuating, in my latest refinement round wxc=256!! wxu=3. The Stereochemistry looks very loosely restrained and the gap between R-free and R-work is too big. I've been using phenix for almost 4 years and never had this problem, or once I set the values of wxc and wxu that will be it, never change. I also tried to fix wxc from the command line and didn't work either (phenix.refine refine.def fix_wxc=1.0). I will certainly appreciate any help. Thanks, Mohd ** Mohd A. Salameh, Ph.D. Mayo Clinic Cancer Center Griffin Cancer Research building,Rm 331 4500 San Pablo Rd Jacksonville, FL 32224 Tel: (904) 953-0046 Fax: (904) 953-0277 salameh.m...@mayo.edu **
Re: [ccp4bb] Soaking at pH 4.0 ?
Could you transfer your crystals in a higher pH buffer? Maia Paul Lindblom wrote: Hi, I am trying to soak some sugars in my crystals, but the cystallization condition has a pH of 4.0. Does anybody has any experience with acidic oxidation in such a case. I think I can´t avoid oxidation at this pH? Any suggestions, or do I have to screen for other conditions? Thanks, P.
Re: [ccp4bb] phenix target weight refinement
Yes Im using wxc_scale and wxu_scale but I also use tls refinement,so in this case if the weights need to be tightly restrained, I should not use tls refinement! ** Mohd A. Salameh, Ph.D. Mayo Clinic Cancer Center Griffin Cancer Research building,Rm 331 4500 San Pablo Rd Jacksonville, FL 32224 Tel: (904) 953-0046 Fax: (904) 953-0277 salameh.m...@mayo.edu ** -Original Message- From: Phil Jeffrey [mailto:pjeff...@princeton.edu] Sent: Friday, March 12, 2010 12:37 PM To: Salameh, Mohd A., Ph.D. Subject: Re: [ccp4bb] phenix target weight refinement Use wxc_scale and wxu_scale not wxc and wxu. If you're doing TLS it will ignore wxu_scale either way. Salameh, Mohd A., Ph.D. wrote: *Dear All,* *In every** refinement** round** the** wxc and wcu** are out of control, although I modify the def file and** change the values** ** of** wxc=1 and wxu=1** so they are tightly restrained**, but it fail**ed** to** fix the problem,** wxc and wxu** values keep fluctuating, in my latest** refinement** round wxc=256!!** wxu=3. The** Stereochemistry looks** very** loosely restrained** and the** gap between R-free and R-work** is** too big**. I**'**ve been using phenix for almost 4 years and** never had this problem,** or once** I** set the values of wxc and wxu that will be it, never change.** I** also tried to fix wxc from the command line and** didn't** work either (phenix.**refine refine.def fix_wxc=1.0). I** will certainly** appreciate** any help**. Thanks, Mohd ** * ** *Mohd A. Salameh, Ph.D.* Mayo Clinic Cancer Center Griffin Cancer Research building,Rm 331 4500 San Pablo Rd Jacksonville, FL 32224 Tel: (904) 953-0046 Fax: (904) 953-0277 salameh.m...@mayo.edu
[ccp4bb] inexpensive source of DDM
Hello, I am looking for an inexpensive US source for large quantities of dodecylmaltoside. Can anyone help me? Thank you!
[ccp4bb] Computational Systems Biology Postdoctoral Positions
Computational Systems Biology Postdoctoral Positions Center for the Study of Systems Biology at the Georgia Institute of Technology Outstanding Postdoctoral applicants are sought in Computational Systems Biology to work with Professor Jeffrey Skolnick at the Georgia Tech Center for the Study of Systems Biology in the following areas: · Proteome scale virtual ligand screening. · Prediction of off-target drug interactions. · Development of algorithms to predict metabolites with anticancer properties. · Structure prediction of GPCRs followed by virtual ligand screening. · Prediction of protein-protein and protein-DNA interactions. · Development of algorithms for protein structure refinement. · Development of multiscale modeling approaches for the simulation of virtual cells. Highly creative, outstanding individuals are sought with the following qualifications: · Demonstrated ability to do high quality research in protein structural modeling, virtual ligand screening, large scale simulations, bioinformatics, or computational genomics. · A track record of publication in high quality international journals. · Ability to work in a team, yet think independently. · Extensive computer code development experience in programming using languages such as Fortran, C, C++, and/or Perl. To apply please send your CV to: skoln...@gatech.edu.
Re: [ccp4bb] inexpensive source of DDM
You get what you pay for, and this is not a cheap detergent! If your application is not sensitive to a little bit of the alpha- anomer, try Anatrace sol-grade, 25 g for $803.01: http://www.affymetrix.com/estore/browse/brand/anatrace/product.jsp?productId=131630categoryId=35662#1_1 If you find something cheaper, I'd like to know. Ed Tony Wu wrote: Hello, I am looking for an inexpensive US source for large quantities of dodecylmaltoside. Can anyone help me? Thank you!
Re: [ccp4bb] phenix target weight refinement
Which version did you use? I remember the old version of phenix (1.3) will automatically change your setting (wxc and wxu) each round. And v1.5 will automatically choose wxu if you use tls. I haven't tried 1.6 yet. Maybe there are some bugs associated with it? The default wxc is 0.5 and wxu is 1. So the default has tighter weight than your specification. Just use default setting instead. Nian Huang, Ph.D. UT Southwestern Medical Center On Fri, Mar 12, 2010 at 11:59 AM, Salameh, Mohd A., Ph.D. salameh.m...@mayo.edu wrote: Yes Im using wxc_scale and wxu_scale but I also use tls refinement,so in this case if the weights need to be tightly restrained, I should not use tls refinement! ** Mohd A. Salameh, Ph.D. Mayo Clinic Cancer Center Griffin Cancer Research building,Rm 331 4500 San Pablo Rd Jacksonville, FL 32224 Tel: (904) 953-0046 Fax: (904) 953-0277 salameh.m...@mayo.edu ** -Original Message- From: Phil Jeffrey [mailto:pjeff...@princeton.edu] Sent: Friday, March 12, 2010 12:37 PM To: Salameh, Mohd A., Ph.D. Subject: Re: [ccp4bb] phenix target weight refinement Use wxc_scale and wxu_scale not wxc and wxu. If you're doing TLS it will ignore wxu_scale either way. Salameh, Mohd A., Ph.D. wrote: *Dear All,* *In every** refinement** round** the** wxc and wcu** are out of control, although I modify the def file and** change the values** ** of** wxc=1 and wxu=1** so they are tightly restrained**, but it fail**ed** to** fix the problem,** wxc and wxu** values keep fluctuating, in my latest** refinement** round wxc=256!!** wxu=3. The** Stereochemistry looks** very** loosely restrained** and the** gap between R-free and R-work** is** too big**. I**'**ve been using phenix for almost 4 years and** never had this problem,** or once** I** set the values of wxc and wxu that will be it, never change.** I** also tried to fix wxc from the command line and** didn't** work either (phenix.**refine refine.def fix_wxc=1.0). I** will certainly** appreciate** any help**. Thanks, Mohd ** * ** *Mohd A. Salameh, Ph.D.* Mayo Clinic Cancer Center Griffin Cancer Research building,Rm 331 4500 San Pablo Rd Jacksonville, FL 32224 Tel: (904) 953-0046 Fax: (904) 953-0277 salameh.m...@mayo.edu
