Re: [ccp4bb] Na vs K
Mitch,
For discernment of Sodium versus Potassium, you could also look at the bonding
distances and coordination of the metal present. Ran into this problem back in
the day. Check out Figure 6 C,D in the following pub:
https://pubs.acs.org/doi/10.1021/bi060653d
Scott
--
Scott Pegan
Professor
Division of Biomedical Sciences
School of Medicine
University of California Riverside
205 SOM Research Building
900 University Avenue
Riverside, CA 92521-0001
(951) 827 7907
sco...@medsch.ucr.edu
On 9/8/22, 9:51 AM, "CCP4 bulletin board on behalf of Mitchell D. Miller"
wrote:
You can also look at your anomalous maps. For most
energies/wavelengths used to
collect protein data, f" for K will be just under 2x the f" for S
while for Na f"
will be much less (0.2-0.25 of S). So you can use S atom anomalous as
an internal reference.
If you see anomalous peaks at your S atoms, then you would also expect
peaks at
K atoms but not at Na atoms.
Regards,
Mitch
$ echo 'Atom Wave (keV) f"' ; for atom in NA S K ; do echo -e
NWAV 5 0.9 1 1.2 1.4 1.7"\n"ATOM $atom"\nEND\n"| crossec | awk
'NF==4&&$2+1>1{printf "%3s %6.2f %6.2f %8.4f\n", $1, $2, 12.39842/$2,
$4}'; done | sort -k2,2n -k4n
Atom Wave (keV) f"
NA 0.90 13.78 0.0411
S 0.90 13.78 0.1982
K 0.90 13.78 0.3948
NA 1.00 12.40 0.0512
S 1.00 12.40 0.2439
K 1.00 12.40 0.4819
NA 1.20 10.33 0.0746
S 1.20 10.33 0.3474
K 1.20 10.33 0.6770
NA 1.40 8.86 0.1023
S 1.40 8.86 0.4656
K 1.40 8.86 0.8979
NA 1.70 7.29 0.1507
S 1.70 7.29 0.6677
K 1.70 7.29 1.2685
Quoting Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>:
> Is that the right way round? Atomic no K 19, Na 11
>
> Call something K when it should be NA - B factor will shoot to reduce the
> atom contribution.
> Call something Na when it should be K - B factor will become very small..
>
> As you say - check which fits best with the surrounding atoms..
>
>
>
> On Thu, 8 Sept 2022 at 14:16, Jon Cooper <
> 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Hello, K will always have a higher B-factor for a given piece of density
>> due to it having a larger atomic number. Is the K B-factor much higher
than
>> those of neighbouring atoms and, if not, it's probably the best
>> interpretation? Cheers, Jon.C.
>>
>>
>> Sent from ProtonMail mobile
>>
>>
>>
>> Original Message
>> On 8 Sep 2022, 14:07, smita yadav < sm...@rcb.res.in> wrote:
>>
>>
>> Dear Community,
>> Can you tell me. if we fit some metal in X-ray
>> structure and its geometry and other properties are satisfied but showing
>> some higher B-factor. does it validate to put that metal-ligand.ligand.
At
>> one site 2 metals such as K and NA fit, but K shows a higher B-factor,
but
>> other parameters such as geometry and other fit better for K instead of
NA.
>> So, out of the two ligands at the same site which one would be more
>> favorable to be fit.
>> --
>>
>> On Thu, Sep 8, 2022 at 6:35 PM smita yadav wrote:
>>
>>>
>>> Dear Community,
>>> Can you tell me. if we fit some metal in X-ray
>>> structure and its geometry and other properties are satisfied but
showing
>>> some higher B-factor. does it validate to put that metal-ligand.ligand.
At
>>> one site 2 metal such as K and NA fits, but K shows higher
>>> --
>>> Regards,
>>> Smita Yadav
>>> Ph.D SRF
>>> Regional Centre for biotechnology,
>>> Haryana-121001.
>>>
>>
>>
>> --
>> Regards,
>> Smita Yadav
>> Ph.D SRF
>> Regional Centre for biotechnology,
>> Haryana-121001.
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>>
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>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the foll
[ccp4bb] When does increased computer power come with diminishing returns for CCP4; Apple Silicon
CCP4bb, Looking for some thoughts related to the cost / benefit of the recently released Apple Silicon. Like many labs, the 27” iMacs have been the backbone of our computational power for structural biology in recent years. I bought a couple of the 24” iMacs with the M1 recently but had held off hoping for the 27” refresh this Spring before outfitting the lab further. As many might know as of yesterday, the refresh isn’t coming and the 27” iMac is being replaced with Mac Studio (tower – display). So, I wanted to tap into the collective wisdom of the CCP4bb to see if there were any thoughts on when the hardware starts to outpace the current and near-term software capabilities of CCP4. In other words, for the price what in the Apple line up makes the most sense. The 24” iMacs strike me as a bit anemic for future proofing, but the Ultra Mac Studio (plus monitor) Seems a bit overkill. Scott -- Scott Pegan Professor Division of Biomedical Sciences School of Medicine University of California Riverside 205 SOM Research Building 900 University Avenue Riverside, CA 92521-0001 (951) 827 7907 sco...@medsch.ucr.edu<mailto:sco...@medsch.ucr.edu> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Looking or Coot 0.9 or newer for OSX
Been looking for Coot 0.9 or better package install files for OSX, anyone know where to look? I seem to only find 0.8 or less through the web. Scott -- Scott Pegan Professor Division of Biomedical Sciences School of Medicine University of California Riverside 205 SOM Research Building 900 University Avenue Riverside, CA 92521-0001 (951) 827 7907 sco...@medsch.ucr.edu<mailto:sco...@medsch.ucr.edu> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Structural Biology - Infectious Disease Postdoc opening at University of California Riverside's School of Medicine
CCP4 Bulletin Board members, We have recently moved to the University of California Riverside’s School of Medicine. We are looking for a couple of postdoc fellows to join us on our federally sponsored projects dealing with structure based therapeutic development for nairoviruses and coronaviruses. The full add is attached and the follow webpage has additional information about our research efforts: https://profiles.ucr.edu/app/home/profile/scottp<https://urldefense.proofpoint.com/v2/url?u=https-3A__profiles.ucr.edu_app_home_profile_scottp=DwMGaQ=LsLxleeqPm1pgCNn-PN_bQ=OzMkUES-0z62ageiNePBE9Gpp3dgqAPNRz3VZzIHMro=Iz8lWyIbP3vL-NGKrg5yVkzo7s8ezLFTDapmmb1Ohx8=52YlnmPwBgb3lt5fqknA14rv_L5tgPK4suCKlO1nSWU=>. Come check us out! Scott -- Scott Pegan Professor Division of Biomedical Sciences School of Medicine University of California Riverside 205 SOM Research Building 900 University Avenue Riverside, CA 92521-0001 sco...@medsch.ucr.edu<mailto:sco...@medsch.ucr.edu> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ Postdoc Ad-2021-Pegan.pdf Description: Postdoc Ad-2021-Pegan.pdf
[ccp4bb] Any advice on specs for a new Mac Laptop to run CCP4 and other Xtal Software?
Finally looking to replace my 2014 Mac Pro lap (duo core; 16 gb RAM. I would welcome any input or being put in the direction of some related to the following: 13" versus 16" I know the 16" has a better and standalone GPU. Is there anyone using a 13" that finds that it works well? If so, what were the specs Memory for the 16" Torn between 16 gb and 32 gb RAM for the next computer. Apple asks a premium for the 32 gb, but some say that now with the SSD's it's not as big of a deal. Any thoughts? GPU For the 15", apple has two 4 gb and an 8 gb. Does anyone have any experience on these for running CCP4 and other Xtal software on these? Thanks for your help in advance, looking to get something that is a Mac, robust to last a while spec wise. However, not looking to buy something that is the equivalent of a small car in price and overkill. Scott To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] University of Georgia post-doctoral fellowship in structural biology with an emphasis on experience with NMR and X-ray crystallography techniques
Seeking Post-Doctoral candidates for my rapidly expanding laboratory located in the University of Georgia's Department of Pharmaceutical Biomedical Sciences. In this recently available positions, the individual will assist in my ongoing NIH funded infectious disease related projects that involve the use of NMR, molecular biology, protein purification, enzymology, structural biology (X-ray) as well as other biophysical techniques. Although basic NMR experience (protein assignment) is required, the project will also feature additional opportunities for advance X-ray crystallographic experience. My laboratory, and UGA at large, possesses significant Structural Biology and protein science resources including a robust wet lab infrastructure, an X-ray home source, crystallization robotics, liquid handling robots, multiple high field magnets and regular access to the SER-CAT at APS. More information on my laboratory can be found at: http://pbs.rx.uga.edu/index.php/people/faculty/scott_pegan/ Recent graduates that have basic NMR experience are encouraged to apply. Starting date for the position is in the May - June timeframe. Significant track record working with viral proteins, expressing/refolding recombinant proteins and/or performing enzymology will be a plus. Also, preference will be given to those applicants with one, or more first author publications. Interested parties please send a single PDF file with your CV, with publication list included, and a minimum of two references. Please submit to spe...@uga.edu.
[ccp4bb] New Structural Biology/Drug Discovery Postdoctoral Position at the University of Georgia
Seeking Post-Doctoral candidates for a position in my laboratory located in the University of Georgia's Department of Pharmaceutical Biomedical Sciences. In this newly added position, the individual will assist in my ongoing USDA funded infectious disease related projects that involve the use of structural biology (X-ray) as well as other drug discovery and biophysical techniques. My laboratory, and UGA at large, possesses significant Structural Biology resources including a home source, crystallization robotics, liquid handling robots and regular access to the SER-CAT at APS. More information on my laboratory can be found at: http://pbs.rx.uga.edu/index.php/people/faculty/scott_pegan/ Recent graduates encouraged. X-ray experience a plus as well as having a first, or second author publication. Ideal start date would be as early as February 1st. Interested parties please send a single PDF file with your CV, with publication list included, and a minimum of contact information for two references. Please submit to spe...@uga.edu.
Re: [ccp4bb] Guard columns from FPLC
Anita, From your description, you most likely are looking for a prefilter6000. http://www.gelifesciences.com/webapp/wcs/stores/servlet/productById/en/GELifeSciences/18458201 Scott Scott D. Pegan, Ph.D. Associate Professor Pharmaceutical and Biomedical Sciences College of Pharmacy University of Georgia 240 W. Green St. Athens, GA, USA, 30602 phone: 706-542-3435 On Tue, Sep 16, 2014 at 4:29 AM, Anita P crystals...@gmail.com wrote: Hi All, Sorry for this off topic. I have heard that there are these little columns called guard columns which can be attached to AKTA purifiers. These columns prevent the incoming huge aggregates to be deposited and blocking of the gel filtration columns. Can any one advice me regarding where to purchase these columns. I could not find them in GE website. We have Superdex 16/60 on AKTA purifier. Thanks in advance. Have a good day Anita
[ccp4bb] off topic: Crystallization robots
In the process of acquiring a crystallography robot for the laboratory. I have narrowed along capability and budgetary constraints to either an Formulatrix NT8, or a Art Robbins Gryphon. I know the Art Robbins instrument characteristics pretty well, does anyone have any experience/advice on the NT8? Scott
[ccp4bb] Postdoctoral Position available at the University of Georgia
Seeking Post-Doctoral candidates for a position in my laboratory located in the University of Georgia's Department of Pharmaceutical Biomedical Sciences. This individual will assist in my ongoing NIH funded infectious disease related projects that involve the use of structural biology (X-ray/NMR) as well as other drug discovery and biophysical techniques. My laboratory, and UGA at large, possesses significant Structural Biology resources including a home source, several high field magnets, crystallization robotics, liquid handling robots and regular access to the SER-CAT at APS. More information on my laboratory can be found at: http://pbs.rx.uga.edu/index.php/people/faculty/scott_pegan/ Recent graduates encouraged. X-ray, or NMR, experience a plus. Ideal start date would be July 1, 2014. Interested parties please send a single PDF file with your CV, with publication list included, and a minimum of information for two references. Please submit to spe...@uga.edu. Scott
[ccp4bb] Structural Biology/Drug Discovery Post Doctoral Position Available at the University of Georgia's College of Pharmacy
Dear CCP4 Bulletin Board Members, I am looking for Post-Doctoral candidates for a position in my laboratory located in the University of Georgia's Department of Pharmaceutical Biomedical Sciences. This position will assist in my ongoing NIH funded infectious disease related projects that involve the use of structural biology (X-ray/NMR) as well as other drug discovery and biophysical techniques. My laboratory, and UGA at large, possesses significant Structural Biology resources including a home source, several high field magnets, crystallization robotics, and regular access to the SER-CAT at APS. Ideal start date would be July 1, 2014 Qualifications: 1) Candidates should hold a Ph.D. or have one by July 1, 2014 2) Have at least one first author peer-reviewed paper dealing with enzymology, drug discovery, X-ray crystallography, or use of NMR. Any interested parties, please send a single PDF file with your CV, with publication list included, and a minimum of two references. Please submit to spe...@uga.edu. Scott -- Scott D. Pegan, Ph.D. Associate Professor Department of Pharmaceutical Biomedical Sciences Pharmacy South College of Pharmacy University of Georgia Athens, GA 30602
Re: [ccp4bb] delete subject
Hey everyone, Both Mark and Fred make some good points. I totally agree with Nat (beat me to the send button). Although in an ideal world with all the advancements in crowd sourcing and electronic media, one might think that posting data on a bulletin board might be considered marking one's turf and protect the scientist place in that pathway towards discoveries. Regrettably, the current reality doesn't' support this case. As structural biologists, we are still in the mode of first to publish gets the bulk of the glory and potentially future funding on the topic. For instance, when I was in graduate school, the lab I was in had KcsA crystals at the same time as a couple of competing groups. Several groups including the one I belong to had initial diffraction data. One group was able to solve KcsA, the first K channel trans-membrane protein structure, first. That group was led by Roderick Mackinnon, now a Noble Laureate partly because of this work. Now imagine if one of Mackinnon's student would have put up the web their initial diffraction data and another group would have used it to assist in their interpretation of their own data and either solved the structure before Mackinnon, or at least published it prior. Even if they acknowledged Mackinnion for the assistance of his data (as they should), Mackinnion and the other scientists in his lab would likely not have received the broad acclaim that they received and justly deserved. Also, ask Rosalind Franklin how data sharing worked out for her. Times haven't changed that much since ~10 years ago. Actually, as many have mentioned, things have potentially gotten worse. Worse in the respect that the scientific impact of structure is increasingly largely tide to the biochemical/biological studies that accompany the structure. In other words, the discoveries based on the insights the structure provides. Understandably, this increasing emphasis on follow up experiments to get into high impact journals in many cases increases the time between solving the structure and publishing it. During this gap, the group who solved the structure first is vulnerable to being scoped. Once scoped unless the interpretation of the structure and the conclusion of the follow up experiments are largely and justifiably divergent from the initial publications, there is usually a significant difficulty getting the article published in a top tier journal. Many might argue that they deposited it first, but I haven't seen anyone win that argument either. Because follow up articles will cite the publication describing the structure, not the PDB entry. Naturally, many could and should argue that this isn't they way it should be. We could rapidly move science ahead in many cases if research groups were entirely transparent and made available their discovers as soon as they could meet the veracity of peer-review. However, this is not the current reality or model we operate in. So, until this changes, one might be cautious about tipping your competition off whether they be another structural biology group looking to publish their already solved structure, or biology group that could use insights gathered by your structure information for a publication that might limit your own ability to publish. Fortunately, for Tom his structure sounds like it is only important to a pretty specific scientific question that many folks might not be working on exactly. Scott On Thu, Mar 28, 2013 at 12:28 PM, mjvdwo...@netscape.net wrote: No. :-) When you are a reviewer for structural papers in journals (I do this work sometimes), and when you see an article that has (in this example) Tom's structure in it, but he and/or his mentor is not an author, then you call the editor and tell them you may have a problem. I realize that the casemay not be closed with that statement because the manuscript could indeed be totally legitimate and genuine, but it would be a signal in my mind to watch for. A friend could not just run with the data and publish. A competing group could take advantage and get ahead in their project inexpensively (provided that the posted data are what you think they are). But that is sort of the point of publishing result (I must remember to leave my idealism at home tomorrow). Our old approach is to keep a lid on all your data until the paper is published. Although it is hard to imagine, there could be a mechanism by which you make all your data public, immediately when you get it and this public record shows who owns it. The advantage (in my mind) of such a system would be that you would also make public the data that does not make sense to you (it does not fit your scientific model) and this could (and has) lead to great discoveries. The disadvantage to the method is that you will sometimes post experiments that are just completely wrong (you did not measure what you said you measured) and this might make you look dumb (not really, this
[ccp4bb] Off Topic: Maltose Binding Protein Purification
CCP4, I will be doing some MBP fusion purification in the near future and I was wondering if anyone knew what the most cost effective MBP trapping resin to use. So, far I have seen the following two products, are there any others I should consider? GE* Healthcare MBPTrap HP ColumnsNew England Amylose Resin High Flow Scott -- Scott D. Pegan, Ph.D. Assistant Professor Chemistry Biochemistry University of Denver Office: 303 871 2533 Fax: 303 871 2254
Re: [ccp4bb] Off Topic: Isothermal Titration Calorimetry (ITC)
Dear Jose, Last year we acquired a TA instruments nanoITC after evaluating it and a Microcal model. For the price, the TA instrument was a considerable steal, was ~$50,000 cheaper the the Microcal Model. We didn't see or have since seen any issues with quality of the instrument. Software between the two differ does differ. TA instruments has a nice prediction model to assist with setting up the experiment, but is just in the throws of getting all the models put into practice for their analysis software (they provide all of their updates for free). Where as Microcal has a mature analysis software, but lacks the prediction component. Scott On Tue, Jan 17, 2012 at 9:24 AM, Michael Hothorn mich...@hothorn.de wrote: Dear Jose, I used both instruments for a number of years, first the VP ITC and later on the ITC 200. I personally find the ITC 200 much more demanding to operate. I think Microcal managed to improve the sensitivity of the ITC 200 about 2-3 fold compared to the VP ITC, but they decided to decrease the volumes by a factor of 6-7. This means that you have to work at higher sample concentrations in the cell and in the syringe to get decent signals. In addition the instrument is rather fragile (especially the glass syringe) and more difficult to clean and maintain. I decided to go back to the VP ITC. I cannot comment on other instruments. best wishes Michael On 01/17/2012 05:02 PM, Jose Artur Brito wrote: Dear All, sorry for this off-topic questions but I would like to have some feed-back from you on Isothermal Titration Calorimetry (ITC) equipments. We have a very nice quotation for an iTC200 from GE Healthcare. We wanted this one because it uses ~200uL sample per measurement (really nice when your dealing with precious samples, ie., proteins with low expression yields). However, I was told that, although consuming much less sample, is not as good (sensitivity, mixing issues, bubbles, ...), as the VP-ITC (it uses ~1.4mL per measurement, seven times more than the iTC200). Does anyone has experience with these two equipments? Would you prefer one over the other (please state your reasons)? Would you suggest another equipment/brand for the ITC (like the NanoITC from TA Instruments)? Thanks in advance, Jose Artur Brito -- Scott D. Pegan, Ph.D. Assistant Professor Chemistry Biochemistry University of Denver Office: 303 871 2533 Fax: 303 871 2254
[ccp4bb] Lithium versus Sodium
Hey all, Does anyone know of a good article that deals with differentiating between a lithium ion and sodium ion for density in a X-ray structures? Scott -- Scott D. Pegan, Ph.D. Assistant Professor Chemistry Biochemistry University of Denver Office: 303 871 2533 Fax: 303 871 2254
Re: [ccp4bb] Off topic: Kendrew Model
Yeah, maybe if he got down to 1.0 Angstrom he could get it in the front door. Scott On Tue, Nov 1, 2011 at 8:39 AM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Maybe you could refine it using our new-fangled methods to improve the model? (Couldn't resist such irony!) Jacob On Tue, Nov 1, 2011 at 9:34 AM, Katherine Sippel katherine.sip...@gmail.com wrote: Hi all, I'm going to interject into the middle of this rousing though protracted debate to pick your brains. I am in possession of a rather large and intact brass scale Kendrew model (sans mirrors). Due to facility restructuring we no longer have room for it. I have approached the local health science and natural science museums but have gotten nothing but the run around. This amazing model is in need of a forever home and I'm stumped as far as alternative ideas. I am seriously considering suspending a Mars bars in the sugar binding cleft, calling it MBP, and trying to spin it to the art museum as a modernist piece commenting on the diets in Western civilization. Either that or putting it in my dining room if I can get it in the door. Any suggestions would be appreciated. Cheers, Katherine -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** -- Scott D. Pegan, Ph.D. Assistant Professor Chemistry Biochemistry University of Denver Office: 303 871 2533 Fax: 303 871 2254
Re: [ccp4bb] Nanodrop versus Nanophotomter Pearl versus good old Bradford.
Here is also a very effective method: 1Gill, S. Hippel, P. v. Calculation of protein extinction coefficients from amino acid sequence data. Analytical Biochemistry 182, 319-326, (1989). On Thu, Jun 16, 2011 at 5:56 PM, Filip Van Petegem filip.vanpete...@gmail.com wrote: A convenient fast way is the earlier mentioned Edelhoch method, as described in this paper which is referenced on the popular Protparam tool: http://onlinelibrary.wiley.com/doi/10.1002/pro.5560041120/pdf Filip On Thu, Jun 16, 2011 at 4:45 PM, aaleshin aales...@burnham.org wrote: Mischa, You intrigued me. What is the experimental technique for the Extinction Coefficient measurement (which requires knowledge of protein concentration)? Let me guess, Bradford? Protein evaporation and weighing? Alex On Jun 16, 2011, at 4:22 PM, Machius, Mischa Christian wrote: With respect to the Edelhoch method and the ProtParam server, I would strongly recommend determining extinction coefficients experimentally and not rely on the ProtParam values. The reason is that the underlying extinction coefficients in the formula used by ProtParam and referenced there are statistical averages. They may or may not be valid for a given protein. I have seen differences of more than 20% between the theoretical and experimental extinction coefficients, particularly for proteins with few Trp and Tyr residues. When relying on relative concentrations, this inaccuracy is not detrimental, but when absolute concentrations are needed (CD, AUC, ITC, any binding experiment, etc.), such a difference would be considered huge. Determining an extinction coefficient experimentally takes but a few minutes. Cheers! MM On Jun 16, 2011, at 6:22 PM, Petr Leiman wrote: Totally support the statements below. We have had several proteins with A280 absorbance of 0.1 or less (at 1 mg/ml). You _have_ to use Bradford in the Nanodrop or whatnot to measure the concentration. Before purchasing the Nanodrop we used a Hellma TrayCell and a normal UV/Vis instrument. Similar to the Nanodrop, the sample volume in TrayCell is 2-3 ul. Traycell works well at a fraction of the Nanodrop cost, but Nanodrop is a lot more convenient to use for high concentration quick measurements (especially if you need to measure several things in succession), so you get what you pay for. Petr P.S. Expasy's Protparam tool has been around for ages (10-12+ years?). That plus the Nanodrop are two essential and synergetic tools of a protein chemist/crystallographer. On Jun 16, 2011, at 10:31 PM, Edward A. Berry wrote: Bradford is an assay, Nanodrop is a spectrophotometer. Both the A280 and Bradford methods are strongly dependent on amino acid composition, so unless you correct A280 for that as mentioned by Filip, either one is semiquantitative. Occasionally you come across a protein with no tryptophan which will have a much lower extinction coefficient. Try making a 1 g/l solution of gelatin (collagen?) and see what its A280 is! I noticed recently the protparam tool at http://ca.expasy.org/cgi-bin/protparam estimates the extinction coefficient given a sequence. David Briggs wrote: ~~~ I wouldn't touch Bradford with a barge-pole. I've found it to be wildly inaccurate for certain proteins I've handled, where as the OD280 measurements have been fine. One wonders what does fine mean, like same as with Biuret or Kjeldahl nitrogen, or solution made up by weight? --- Mischa Machius, PhD Director, Center for Structural Biology Assoc. Professor, Dept. of Pharmacology Member, Lineberger Comprehensive Cancer Center University of North Carolina 4079 Genetic Medicine CB#7365 120 Mason Farm Road Chapel Hill, NC 27599-7365, U.S.A. tel: +1-919-843-4485 fax: +1-919-966-5640 email: mach...@unc.edu mach...@med.unc.edu -- Filip Van Petegem, PhD Assistant Professor The University of British Columbia Dept. of Biochemistry and Molecular Biology 2350 Health Sciences Mall - Rm 2.356 Vancouver, V6T 1Z3 phone: +1 604 827 4267 email: filip.vanpete...@gmail.com http://crg.ubc.ca/VanPetegem/ -- Scott D. Pegan, Ph.D. Assistant Professor Chemistry Biochemistry University of Denver Office: 303 871 2533 Fax: 303 871 2254
[ccp4bb] Calculating Difference Maps Between an RCSB data set and an mtz (Different Ligand)
Trying to calculate a difference map from a dataset downloaded from the RCSB and one I have. The following applies: Object find the difference between two bound ligands of the same structure in the same space group. My following work path has been: 1) Convert mmCIF to mtz (RCSB data set) 2) Use CAD to combine them 3) Use FFT to generate the diff map If I remember correctly, I think I am missing a scaling step somewhere. Any thoughts? Scott -- Scott D. Pegan, Ph.D. Assistant Professor Chemistry Biochemistry University of Denver Office: 303 871 2533 Fax: 303 871 2254
Re: [ccp4bb] composite maps
Rakesh, Composite maps are used in publications some times however many folks also publish the 2Fo-Fc or even better the 1Fo-Fc. These can be obtained by selecting a button in refmac to export the maps and then visualize them in pymol. Scott On Mon, Aug 9, 2010 at 8:37 AM, Rakesh Joshi rjo...@purdue.edu wrote: Hi all, I wanted to know the best way to make a composite file using ccp4. I have tried the SF-check program GUI; but it does not give me an option to construct composite maps. Also, is it true that when one does molecular replacement, if one wants to show an electron density map in a publication, it has to be composite map and not a 2Fo-Fc map? Thanks to all in advance Rakesh -- Scott D. Pegan, Ph.D. Assistant Professor Chemistry Biochemistry University of Denver Office: 303 871 2533 Fax: 303 871 2254
Re: [ccp4bb] thread protein sequence using pdb coordinates that are not avaliable on RCSB?
Kelly, You can do it with swiss-model, just have to use the alignment mode. I will ask for a pdb or RCSB code. Also, in the past I have found Jigsaw 3D model server to be a comparable tool. Scott On Wed, May 12, 2010 at 10:10 AM, Kelly Daughtry kddau...@bu.edu wrote: Hello all, I would like to thread one protein sequence onto a structure I recently solved, and has not been submitted to the pdb. I found the swiss-model website, which is an excellent tool for inputing a template sequence and target sequence (which is what I want to do), but it only allows you to select a PDB ID, and not to upload your own pdb file. Does anyone know where I can do this online? I'm thisclose to just changing each amino acid in coot (with the amount of searching I've done, it's about equal time!). Thanks in advance, Kelly Daughtry *** Kelly Daughtry PhD Candidate Department of Physiology and Biophysics Boston University School of Medicine 590 Commonwealth Ave R 390 Boston MA, 02215 (P) 617-358-5548 *** -- Scott D. Pegan, Ph.D. Assistant Professor Chemistry Biochemistry University of Denver
Re: [ccp4bb] freezing crystals grown in isopropanol condition
Nat, A few years ago I had K channel crystals that formed under similar conditions. I found that using MPD as a cryo-protectant worked best. As for the evaporation issue, I had a little extra time as I was performing the mounting in a cold room. Scott Pegan S, Arrabit C, Zhou W, Kwiatkowski W, Collins A, Slesinger PA, Choe S. Nat Neurosci. 2005 Mar;8(3):279-87. Epub 2005 Feb 20. On Fri, Apr 9, 2010 at 9:59 AM, James Holton jmhol...@lbl.gov wrote: Yes, oil is great, but you have to be careful to choose an oil in which the alcohol is not soluble, or the oil will suck it out of your drop, (just like air). This is particularly annoying with detergents, which are almost all soluble in oil. I've always thought that maybe some synthetic motor oils (which your auto mechanic will tell you are immiscible with petroleum-based oils) might be a good thing to try with membrane proteins. It is a common trick, however, to pre-saturate the oil by vortexing it with an excess of the reservoir solution before applying it to the drop. Obviously, however, this trick can get expensive when working with detergents... -James Holton MAD Scientist Nathaniel Clark wrote: I have wondered if placing a layer of oil over the drop would help solve the problem of the crystals moving around. Haven't tried it, but don't people harvest from a microbatch tray by dragging the loop and crystal through oil? Nat On Fri, Apr 9, 2010 at 11:21 AM, James Holton jmhol...@lbl.gov wrote: Yes, isopropanol is a cryoprotectant, and a relatively good one. So are the other alcohols. It was even popular in the olden days when we would typically set up drops that were 5-10 microliters in volume (each!). These take a while (minutes) to evaporate, giving you enough working time to mount the crystal before the alcohol concentration changed too much. Modern nanoliter-scale drops have largely made alcohol additives impractical, which is a shame. A potentially general way to deal with evaporating drops is to bathe the work area in a stream of air or nitrogen that has been pre-saturated with the reservoir solution. That is, run the gas line in and out of a jar of say about 50-100 mL of replicated reservoir solution (bubbling the gas through the solution in the jar) and then route the end of the hose to under your dissecting microscope and point it at your crystallization well just before you crack it open. This should give you a nice, long working time, and similar devices have already been reported in the literature: http://dx.doi.org/10.1107/S0021889801020702 That, or you can try to just work really quickly! -James Holton MAD Scientist Chris Meier wrote: Dear all, I have a protein which crystallizes in 25% isopropanol, at pH4.5. Does anyone have experience freezing crystals grown in such a condition? What cryoprotectants should I try? Can isopropanol itself act as a cryoprotectant? Any suggestions on how to deal with isopropanol evaporation during mounting? Many thanks and best wishes, Chris -- Scott D. Pegan, Ph.D. Assistant Professor Chemistry Biochemistry University of Denver
Re: [ccp4bb] units of the B factor
Nice Scott On Mon, Nov 23, 2009 at 1:07 PM, Ed Pozharski epozh...@umaryland.eduwrote: Ian, On Mon, 2009-11-23 at 17:34 +, Ian Tickle wrote: Ed, For instance, if angles are measured in degrees and x1 sin x ~ pi * x / 180 sin x ~ x Your equations cannot simultaneously be true in fact the 1st one is obviously wrong, the 2nd is right. In the 1st case I think you meant (substituting 'x*deg' for 'x' in your correct 2nd equation): Hmm... It's not the same x in these two equations - one is measured in degrees, the other in radians. Just one: it's a=b=c. In any case, this comment is analogous to Henry Ford's famous sales pitch for the Model T: You can have a car in any colour so long as it's black. Tell me, which would you say makes more sense: a) 1 person spends 10 secs adding 10 lines to the syminfo file once and for all, or b) many people post queries to CCP4BB about re-indexing their MTZ files because the processing mis-identified 2-fold screw axes from the systematic absences? Tough call. On one hand, refusing P22121's right to exist is discrimination, on the other - these are the subtleties that help understanding so this has some educational value. Then there is Ockham's razor (which I personally believe people sometimes take too far). I think you pose the question in the way which pushes towards certain answer, let me try it differently: Which one makes more sense: 1) people learning more about space groups and reading the manuals of the software they are using to process data or 2) adding more space groups and using more paper to print the International Tables for Crystallography (gently hugs an imaginary tree)? Seriously though, I think it makes sense to keep just P21212, because you don't get a different crystal form by axes permutation. PS. By the way, did you notice that pi^2 ~ g ? I ... and did you notice that e^(i*pi) + 1 = 0 connects the 5 fundamental mathematical constants? - that also has nothing whatsoever to do with this thread ;-). Oh yeah - e^(i*pi)=-1 is my favorite meditation object :-) Nicely connects arithmetics, geometry, calculus and complex analysis. Cheers, Ed. -- -- Scott D. Pegan, Ph.D. Assistant Professor Chemistry Biochemistry University of Denver
[ccp4bb] Looking for a good review of successful SBDD.
I am looking for a good review on SBDD that includes a few successful attempts. Anyone know one? Thanks, Scott -- Scott D. Pegan, Ph.D. Assistant Professor Chemistry Biochemistry University of Denver
[ccp4bb] Off Topic: Stereo Microscope Recommendations
Starting a new lab and looking for an inexpensive stereo microscope to support my crystallography. Any thoughts or recommendations? Would like for it to have a way to take a photo of the crystals either through an eyepiece or dedicated camera port. As any new lab, a cheap option won't be bad. Scott -- Scott D. Pegan, Ph.D. Assistant Professor Chemistry Biochemistry University of Denver
[ccp4bb] Issue with installing CCP4 on OS X
Recently tried to install ccp4-6.1.1-i386 on a leopard 10.5.7 system Installer worked Then I corrected the ccp4.setup-sh file to reflect the location of bltwish /usr/local/X11/bin Ran ccp4i and it worked once. Every-time after that it opened and closed immediately. Using X11 2.3.3.2. Anyone seen this? Scott -- Scott D. Pegan, Ph.D. Research Assistant Professor Center for Pharmaceutical Biotechnology Department of Medicinal Chemistry Pharmacognosy University of Illinois at Chicago
Re: [ccp4bb] tutorial / pipeline for ligand fitting, refinement?
Andy, We do a lot of liganding fitting with CCP4. This is the general order of steps we take (post initial solution of the protein itself): 1) Build the potential ligand in CCP4 Sketcher a) Rename all the Hydrogens to H#, CCP4 Refmac has some issues with Hydrogens marked OH1, NH1, etc. To simplify things I normally just renumber all the Hydrogens starting from 1. Also makes for less hassle when using the definition file, as the labels in the definition file has to match the pdb of the ligand (this will be more important below). b) Use the regularize function with Refmac 2) Using Coot, load the protein and maps 3) Load the ligand and definition file (_mon_lib.cif) 4) Use the find ligand function in Coot (find it under other modeling tools) a) select the protein, map you want to search 5) If you find results you desire, merge those ligands with the main pdb 6) Run Refmac on the merged PDB with the library for the ligand in the library input space. Hope this helps, Scott On Thu, Feb 5, 2009 at 9:27 AM, ANDY DODDS andy.dod...@googlemail.comwrote: Hello, does anyone know of a tutorial which lays out some sort of pipeline, hopefully using CCP4 packages, to fit and refine a small molecule ligand please? cheers andy -- Scott D. Pegan, Ph.D. Senior Research Specialist Center for Pharmaceutical Biotechnology University of Illinois at Chicago
Re: [ccp4bb] Nvidia 3D
Warren, If we are buying a system from scratch, can I get the GeForce 2 card and 3D bundle and have it work for winCoot? Scott On Tue, Jan 27, 2009 at 2:58 PM, Warren DeLano war...@delsci.com wrote: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0901L=CCP4BBT=0F=S =P=192056https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0901L=CCP4BBT=0F=S=P=192056 https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0901L=CCP4BBT=0F=; S=P=192056https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0901L=CCP4BBT=0F=S=P=192056 -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Chris Waddling Sent: Tuesday, January 27, 2009 12:56 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Nvidia 3D Has anyone taken the plunge and tried this setup with Coot or PyMol? Seems interesting: http://www.nvidia.com/object/GeForce_3D_Vision_Main.html Chris -- Dr. Christopher A. Waddling, Ph.D. University of California at San Francisco MC 2140 S126C 600 16th St., San Francisco, CA 94158-2517 (415) 476-8288 (office) (415) 502-7779 (lab) (415) 514-4142 (fax) (415) 810-7556 (cell) waddl...@msg.ucsf.edu AIM duckie2k1 Skype chriswaddling -- Scott D. Pegan, Ph.D. Senior Research Specialist Center for Pharmaceutical Biotechnology University of Illinois at Chicago
Re: [ccp4bb] CCP4i: P212121 to P22121 conversion
Jacob, You could also just use reindex app in CCP4 to change the original MTZ to a P22121 MTZ. Scott On Sat, Nov 8, 2008 at 1:46 AM, Kay Diederichs [EMAIL PROTECTED] wrote: Jacob, you could use, for refinement, the FP SIGFP columns from the .mtz-file that PHASER writes out, together with the .pdb-file of the best solution. One caveat: the resolution of the data in that file is what you chose for the PHASER calculation, so you might need to re-run PHASER with the full resolution (no need to do the full calculation again, there are shortcuts possible using the known solution). HTH, Kay -- Scott D. Pegan, Ph.D. Senior Research Specialist Center for Pharmaceutical Biotechnology University of Illinois at Chicago
Re: [ccp4bb] Putting ligand in the protein structure
The best why that I have put inhibitors in is by using the sketcher program in CCP4. Its a little unwieldy at first but if you get the hang of it, it provides pdb's and library files that can be directly inputed into refmac and Coot. The Coot ligand find function does a pretty good job of initially placing inhibitors in density. The only thing to be careful of is that sketcher tends to label hydrogens in a problematic way for large ligands. It labels the hydrogen based on the carbon number that it is attached too. Problems tend to occur if the hydrogens get three digit labels. Refmac won't necessarily recognize these causing problems with the cif file. If this problem occurs re-label the hydrogens to two digit numbers. Unless your using a ligand that requires more than 100 hydrogens. Then you will have to build it a different way. Scott On Wed, Oct 1, 2008 at 3:38 PM, Anastassis Perrakis [EMAIL PROTECTED]wrote: On Sep 30, 2008, at 9:56, Anshul Awasthi wrote: Hi all the crystallographers, I am trying to solve a structure of a protein with some inhibitor. I want to know how I can put in my inhibitor in the density map of the data i got. I can see some density in the active site where the inhibitor should be. I generated the topoly file of the inhibitor (in both pdba nd refmac5 top formats) from the Dundee PRODRG server. Now do i need to incorporate the structure of the inhibitor in ccp4 or can i do in coot?? I am not sure of how to do it. As one of many alternatives you can use ARP/wARP Ligand Fit from the CCP4I (provided you downloaded and installed the current version of ARP/wARP) and then input your protein structure, the observed data, and the PDB of your ligand. The script will calculate the mFo-DFc map, find the most likely site for the ligand, and then fir the ligand there, and refine it in real space. Tassos ANy sugegstion will be very valuable for me. -- Scott D. Pegan, Ph.D. Senior Research Specialist Center for Pharmaceutical Biotechnology University of Illinois at Chicago
Re: [ccp4bb] Progresss with Stereo 3D under Mac OS X Leopard
Just to put my two cents in on this as I would fall into that new generation so to speak: I started out with the SGI and linux systems with stereo, O, and dials about eight years ago. Never used the dials and rarely seen anyone else use them. Over the past few years I have transition to coot, pc, and now have a MAC. The freedom of not having a bulky system that I have to build on is a huge plus for many of the reasons you described. However, My colleagues and I I DO WANT STEREO. I have nearly perfected building without IT not out of choice but mostly out of lack of one. I feel as many of my colleagues do, that if we had the stereo option on our flat panels we most undoubtedly would use it. We just don't those type of options right know. As a result, I wholeheartedly support anyone trying to get us this added capability. Scott Steve Lane wrote: Warren et al.: The following is based largely on a survey conducted here about 6 months ago (the survey questions are at the bottom of this msg). Among the older generation of PIs, there is a strong perception that stereo and SGI dials are very important to users. This perception is not at all borne out among users themselves (20+ grad students and postdocs, plus one or two junior faculty) - no one uses the dials (see below for why), and stereo is used very infrequently to never. The consensus among the users regarding stereo seems to be some version of the following: if it's available, I might use it occasionally for a particularly difficult part of a molecule, but not otherwise; if it's not available, that's fine. Reasons for not using it seem to be based primarily on: inconvenience (we use StereoGraphics glasses and emitters - in spite of having many pairs available, and efforts by the admins here to keep them functional, it can be difficult for a user to find a pair that works, either because of dead batteries or because they're just broken); discomfort (wearing the glasses themselves is a pain, people complain of headaches, and the ambient lighting situation can make using them difficult under some circumstances and cause eye strain); and lack of need. No one uses the dials because no one in our environment is building with O, and this is the only piece of software we have that supports the dials (we have a Linux-only environment). *Everyone* here builds with Coot. I believe (based on somewhat anecdotal evidence) that if Coot supported the dials people would use them more, but they seem quite happy without them; they are certainly not enough reason for people to learn to use O (or go back to using it). The above perception vs reality dichotomy seems to stem largely from a generation gap: users who learned to build using SGIs running O are firm believers in the need for stereo and dials (even though, for the most part, they are no longer actively building); users who learned to build on Linux boxes using Coot simply don't see the need, for the most part. Note that these are, for the most part, users who have never used O, but who *do* actively build, spending hours and days at a time sitting in front of the workstation doing so. In addition, many/most users these days do alot of their building using their own laptops (many/most of which are Macs running OS X), often but not always in conjunction with an external flat panel display. When doing so, they don't use stereo or dials, and again, this doesn't seem to be a huge loss to them, especially given the convenience of being able to work where they want (i.e. at home, in coffee shops libraries, outdoors, etc.) Users also like to be able to sit in front of a flat-panel display to do their work. This seems to be a combination of two factors: the extra space available on the work surface that isn't taken up by a huge CRT; and the absence of the huge, heavy, space-hogging CRT sitting in front of them all day (i.e. a psychological lightness provided by a flat-panel display - this seems hard to quantify, but I experienced it myself when switching from a CRT to a flat-panel, and others I have talked to have reported similar feelings). Obviously, if a reasonably-priced flat-panel stereo solution were to become available this would influence decisions about stereo. I've included our survey questions below my .sig - please feel free to use or adapt them as you like. -- Steve Lane System, Network and Security Administrator Doudna Lab Biomolecular Structure and Mechanism Group UC Berkeley == Greetings. This is a semi-informal survey of recent crystallography workstation users. Please take a minute to respond. Your answers will help us improve the crystallography computing environment. 1) Have you recently (past few months) used a crystallography workstation for molecular model building and/or visualization? YES NO Answer: 2) If yes to (1), which model building software did you use
Re: [ccp4bb] Coot and OS X Leopard
I just recently purchased a Mac Pro Intel with Leopard. I was able to install, Coot and ccp4. Both were not as straight forward as I would have hoped but still possible. For Coot: Go to: http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Coot-0.5-pre-1-968_for_Intel_10.5_only Download : coot-10.5-pre-1-968-intel-April20_2008.tgzhttp://sage.ucsc.edu/%7Ewgscott/xtal/coot/coot-10.5-pre-1-968-intel-April20_2008.tgz Follow instructions on the page. Beware, when I down loaded it, OSX immediately unzipped it. I am not a guru for OSX, so I just gzipped it prior to running the command: sudo tar xvfz coot-10.5-pre-1-968-intel-April20_2008.tar.gz As you probably experienced, coot wouldn't run at this point. No fear, you will need to install the X11.pkg version 2.20.1. Follow the instructions on the page: http://trac.macosforge.org/projects/xquartz Once you restart the computer, download the CootAutoOpenerhttp://sage.ucsc.edu/%7Ewgscott/xtal/coot/CootAutoOpener.dmg.gz. If you placed Coot in the directory as the instructions state, it should run. Note. Tried the CCP4 coot download page and that coot version didn't work. For CCP4: Was a little tricky. I had to get some help on this one for the proper unix commands. Go to the CCP4 site and download the OSX version. Install BOTH the TLK/BLK programs and CCP4 site. Next, I couldn't find anywhere, had to run the following commands in the bin directory to get it to work: source ccp4i.sh # (for bash shell; sets up ccp4's directories, make sure that the paths in this file accurately reflect reality; had an issue here) Then should be able to run: ccp4i When I ran it, I had to source the file every time prior to execution. There may be a better way to do this but I just created an executable script to run it for me. Hope this helps, Scott http://sage.ucsc.edu/%7Ewgscott/xtal/coot/coot-10.5-pre-1-968-intel-April20_2008.tgz On Wed, Aug 20, 2008 at 9:33 AM, Paul Emsley [EMAIL PROTECTED]wrote: Winter, G (Graeme) wrote: I have an OS X leopard machine which I would really like to get coot working on, but it appears to involve messing with the X system and / or fink, neither of which I really fancy. Now I appreciate that there is something broken about the X window (no idea what though) but I was wondering if it is possible to get coot working with it anyway? I looked at the X window update on Bill Scott's page, but the idea of having to reinstall it every time Apple decide to update my machine didn't really appeal. Doesn't Bill provide a stand-alone version? If not that then the answer, I think, is no not yet - I intend to make such a thing after returning from IUCr. You are not alone. Paul. -- Scott D. Pegan, Ph.D. Senior Research Specialist Center for Pharmaceutical Biotechnology University of Illinois at Chicago
Re: [ccp4bb] Vista
Deena, If you are going to run windows, have to use XP. I tried vista, and the software wouldn't work. Scott On Wed, February 20, 2008 2:44 pm, Paul Paukstelis wrote: Or don't buy an OS at all. There are a number of vendors out there that sell OEM notebooks without OSs. I picked up a Compal IF90 with WSXGA+ (1680x1050) for a good price. --paul Yi Zhou wrote: I think we are all using Linux, so just choose the cheaper OS (you have to delete it anyway). Yi On Wed, 2008-02-20 at 15:11 -0500, deena wrote: Hi All, I am about to buy a laptop and find that the XP is twice the price of Vista. Does anyone have positive experience using Vista for crystallographic packages: CCP4, Coot, O, X-plor? or must I still avoid it? Thanks, Deena Deena Abells Oren, PhD Manager, Structural Biology Resource Center Rockefeller University 1230 York Avenue New York, NY 10065-6399 phone: 212- 327-7429 fax: 212-327-7389 -- Paul Paukstelis, Ph.D. Research Associate Institute for Cellular and Molecular Biology The University of Texas at Austin P: 512-471-4778, F: 512-232-3420 [EMAIL PROTECTED] -- Scott D. Pegan, Ph.D. Visiting Senior Research Specialist Center for Pharmaceutical Biotechnology University of Illinois at Chicago
Re: [ccp4bb] Vista
My attempt was a desktop installation. This was ~1 month ago. Scott On Wed, February 20, 2008 3:34 pm, Flip Hoedemaeker wrote: Strange, CCP4 and Coot run just fine on my Vista laptop... Have not tried all programs though. Flip -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Scott Pegan Sent: Wednesday, February 20, 2008 22:04 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Vista Deena, If you are going to run windows, have to use XP. I tried vista, and the software wouldn't work. Scott On Wed, February 20, 2008 2:44 pm, Paul Paukstelis wrote: Or don't buy an OS at all. There are a number of vendors out there that sell OEM notebooks without OSs. I picked up a Compal IF90 with WSXGA+ (1680x1050) for a good price. --paul Yi Zhou wrote: I think we are all using Linux, so just choose the cheaper OS (you have to delete it anyway). Yi On Wed, 2008-02-20 at 15:11 -0500, deena wrote: Hi All, I am about to buy a laptop and find that the XP is twice the price of Vista. Does anyone have positive experience using Vista for crystallographic packages: CCP4, Coot, O, X-plor? or must I still avoid it? Thanks, Deena Deena Abells Oren, PhD Manager, Structural Biology Resource Center Rockefeller University 1230 York Avenue New York, NY 10065-6399 phone: 212- 327-7429 fax: 212-327-7389 -- Paul Paukstelis, Ph.D. Research Associate Institute for Cellular and Molecular Biology The University of Texas at Austin P: 512-471-4778, F: 512-232-3420 [EMAIL PROTECTED] -- Scott D. Pegan, Ph.D. Visiting Senior Research Specialist Center for Pharmaceutical Biotechnology University of Illinois at Chicago -- Scott D. Pegan, Ph.D. Visiting Senior Research Specialist Center for Pharmaceutical Biotechnology University of Illinois at Chicago
Re: [ccp4bb] how to change a membrane protein into a water soluble protein?
Don't know if anyone has mentioned this paper but its an exact example how to make a K channel soluble. Roosild TP, Choe S. Redesigning an integral membrane K+ channel into a soluble protein. Protein Eng Des Sel. 2005 Feb;18(2):79-84. Epub 2005 Mar 23. PMID: 15788421 [PubMed - indexed for MEDLINE] Scott On Tue, December 4, 2007 4:04 am, Brenda Patterson wrote: Another option is refolding which can increase soluble protein content and is used routinely to achieve soluble protein such as the TIMPs http://peds.oxfordjournals.org/cgi/content/abstract/7/8/1035 http://www.proteinscience.org/cgi/reprint/11/10/2493.pdf?ck=nck that said, this is not true of all membrane proteins. Addition of a fusion partner, MBP, to the normally membrane associated FMO3 has been shown to generate stable, soluble protein and the addition of a fusion protein allows purification downstream more easily. Here is a paper where they did as the original poster suggested and tried mutagenesis of hydrophobic regions, including a truncation of a membrane anchor. They achieved increased solubility with this in combination with use of detergents. Krueger SK, Siddens LK, Henderson MC, VanDyke JE, Karplus PA, Pereira CB, Williams DE. Abstract C-Terminal truncation of rabbit flavin-containing monooxygenase isoform 2 enhances solubility. Arch Biochem Biophys. 2006 Jun 15;450(2):149-56. Epub 2006 Mar 29. cheers Quoting Bil Clemons [EMAIL PROTECTED]: There is also the soluble KcsA. Computational design of water-soluble analogues of the potassium channel KcsA. A. M. Slovic, H. Kono, J. D. Lear, J. G. Saven, and W. F. DeGrado (2004) PNAS 101, 1828-1833 Bil Bil Clemons, PhD Assistant Professor of Biochemistry Caltech 157 Broad Center MC 114-96 Pasadena, CA 91125 (626) 395-1796 [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] From: Thomas J Magliery PhD [EMAIL PROTECTED] Reply-To: Thomas J Magliery PhD [EMAIL PROTECTED] Date: Mon, 3 Dec 2007 16:50:03 -0500 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] how to change a membrane protein into a water solub= le protein? =20 It's hard. See: =20 J Mol Biol. 2005 May 6;348(3):777-87. X-ray structure of a water-soluble analog of the membrane protein phospholamban:=20 sequence determinants defining the topology of tetrameric and pentameric coiled coils. Slovic AM, Stayrook SE, North B, Degrado WF. =20 Slovic, A. M., Summa, C. M., Lear, J. D. DeGrado, W. F. (2002). Computational design of a water-soluble analog of phospholamban. Protein Sci. 12, 337=AD348. =20 Li, H., Cocco, M. J., Steitz, T. A. Engelman, D. E. (2001). Conversion of phospholamban into a soluble pentameric helical bundle. Biochemistry, 40, 6636=AD6645. =20 Frank, S., Kammerer, R. A., Hellstern, S., Pegoraro, S., Stetefeld, J., Lustig, A. et al. (2000). Toward a high resolution structure of phospholamban: design of soluble transmembrane domain mutants. Biochemistry, 39, 6825=AD6831. =20 Tom =20 =20 Daniel Jin wrote: Hi, I am wondering whether there is a way to turn a membrane protein with known crystal structure into a water soluble protein by systematic mutagenesis. I guess it should be doable if we introduce enough hydrophilic residues on the surface. Has anyone tested this crazy idea before? Thank you for your help. Best, Chen =20 Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now.=20 http://us.rd.yahoo.com/evt=3D51733/*http://mobile.yahoo.com/;_ylt=3DAhu06i6= 2sR8H DtDypao8Wcj9tAcJ%20 =20 =20 --=20 Thomas J. Magliery, Ph.D. Assistant Professor Department of Chemistry Department of Biochemistry The Ohio State University 1043 Evans Laboratory 100 West 18th Ave. Columbus, OH 43210-1185 =20 (614) 247-8425 office (614) 292-1685 fax [EMAIL PROTECTED] http://www.chemistry.ohio-state.edu/~magliery =20 -- Scott D. Pegan, Ph.D. Visiting Senior Research Specialist Center for Pharmaceutical Biotechnology University of Illinois at Chicago
