[ccp4bb] Mosquito Tips (4.5mm / 9.0mm)
Hello CCP4, Sorry for the labware related post, but I think this is the right audience. I have 4 new reels of mosquito tips with 4.5mm pitch (for 384 well setups, TTP labtech part number 4150-03010). I only use 96well format, thus am looking to swap these for 9mm pitch (part number 4150-03020). Anyone out there in the reverse situation or sitting on a surplus of 9mm tips? Thanks, --Paul -- Nothing can be more incorrect than the assumption one sometimes meets with, that physics has one method, chemistry another, and biology a third. --Thomas Huxley + Dr. Paul Smith Assistant Professor Department of Chemistry Fordham University 441 E. Fordham Road Bronx, NY 10458 phone: 718-817-4461 fax: 718-817-4432 email: psmit...@fordham.edu office: JMH 638 http://www.fordham.edu/academics/programs_at_fordham_/chemistry/index.asp http://www.fordham.edu/academics/sciences_at_fordham/
Re: [ccp4bb] REFMAC Riding Hydrogens
Hello CCP4bb, Firstly, thanks to all for your comments. However, I'm still unsure how to sort all of this riding hydrogen business out. Robbie's comments seem particularly apt: Because there were some reporting errors in the past (http://proteincrystallography.org/ccp4bb/message18808.html) it is hard to tell from the PDB when refinement with hydrogens became hip. Is there any foolproof way to know if a recently deposited file was refined with riding hydrogens in REFMAC, especially since some such structures do not yet have publications associated with them? How about the value of NON-BONDED CONTACTS OTHERS? If that is other than NULL, does that mean riding hydrogens were present? Also, how about refmac version numbers? Is there a clear demarcation when riding hydrogens a) became available, b) became default, or c) became default in the CCP4i GUI? Thanks again, --Paul From: Robbie Joosten robbie_joos...@hotmail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, March 6, 2012 4:26 AM Subject: Re: [ccp4bb] REFMAC Riding Hydrogens Hi Everyone, Pavel’s statement is likely a bit of an exaggeration, but he has a valid (yet hard to prove point). The default in CCP4i was (and is?) to use hydrogens only if present in the input file. This is IMO not a safe default. Because there were some reporting errors in the past (http://proteincrystallography.org/ccp4bb/message18808.html) it is hard to tell from the PDB when refinement with hydrogens became hip. Discussions on this BB show that at the use of riding hydrogens is still not fully accepted, especially at low resolution (where they actually help most). Cheers, Robbie From:CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Pavel Afonine Sent: Monday, March 05, 2012 21:53 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] REFMAC Riding Hydrogens Dear Tim, good catch, thanks; I could craft that phrase more carefully! Although often it may not be quite fair to take phrases out of context: this newsletter article was written in the context of macromolecular refinement. And yes, recently may be a broad term -:) All the best, Pavel On Mon, Mar 5, 2012 at 12:45 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Pavel, you may want to add to the structures mentioned in [1] one or two organic structures present in the Cambridge Database. Until recently it was customary to ignore hydrogen atoms throughout the process of crystallographic X-‐ray structure determination. [1] 'recently' as in 1997 [2]? Even though 1997 is probably a poor estimation of the corresponding year... Cheers, Tim [1] On contribution of hydrogen atoms to X-ray scattering http://www.phenix-online.org/newsletter/ [2] http://shelx.uni-ac.gwdg.de/SHELX/shelx.pdf On 03/05/2012 09:14 PM, Pavel Afonine wrote: Hi, On Mon, Mar 5, 2012 at 11:52 AM, Matthew Franklin mfrank...@nysbc.orgwrote: Adding the riding hydrogens generally gives you some improvement in R factors even with a good quality (i.e. stereochemically correct) model. and here are the results of more or less systematic test that prove this: see On contribution of hydrogen atoms to X-ray scattering here: http://www.phenix-online.org/newsletter/ Pavel - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPVSXkUxlJ7aRr7hoRAm1TAJ9Hyfhkl3yhD5QSKw9I4RSK58m0fACgmlxk YGILzeMam/3gQVmCeh0vQ8k= =3m2J -END PGP SIGNATURE-
[ccp4bb] REFMAC Riding Hydrogens
Hello CCP4 community, I'm posting at large regarding a previously raised issue for REFMAC for which I cannot find the conclusion in the old threads. Specifically, does REFMAC add riding hydrogens during default refinement? Though I've not requested that any hydrogens be added, only used if in the input, I see the following in the output header: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS Does anyone know exactly what this remark is referring to? Are riding hydrogens added for stereochemical restraints, or are their scattering contributions calculated regardless of they are explicitly defined? Can the hydrogen behavior in REFMAC be more explicitly controlled. Thanks, --Paul
Re: [ccp4bb] Akta Prime / FPLC Options / Off Topic
Michael, Unfortunately, I actually don't know who serves these machines apart from GE. Because you brought up the subject of GE equipment and service, I thought I would ask the community about the best options for routine crystallographic scale FPLC. In my opinion, following the takeover of Pharmacia by GE the the price of GE machines, replacement parts, and service has skyrocketed and GE service reps seem determined to squeeze and extort every dollar they can. Personally, I'd love to never do business with GE again. However, in some ways, they are the only game in town. GE is the de facto standard for our line of work and the Akta line are very good machines. However, GE's consistent price gouging and outright crooked service practices encourage me look elsewhere. I've used systems from AP-biotech (junk) and have heard some good things about Bio-rad. What does the community at large think? Are there other good options? Does anyone have some spare millions and manufacturing connections in India/China to consider starting a competing company? Sorry to hijack your thread Michael. Let me know what you find out. The less money I send to GE the better. --Paul From: Michael Colaneri colane...@gmail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, October 12, 2011 2:28 PM Subject: [ccp4bb] Akta Prime Dear all, We have an AktaPrime and GE Lifesciences stop servicing these instruments because they are getting old. Does anyone know of a third party company that gives contracts to maintain these instruments? Thank you. Mike Colaneri
Re: [ccp4bb] Windows 7 and Xtal Software
Okay then, Here's the plan for all the software developers out there: 1) backport cctbx to fortran (preferably F77) and include all subroutines inline to avoid the use of any external libraries whatsoever 2) ditch all gui support or, from scratch, develop a gui front-end that uses none of the following: Qt, Ruby, Perl, Python, TK/TCl, etc. This gui must compile and run on all mainstream hardware on all major operating systems. The custom gui might also need a custom driver for maximizing the capabilities of modern GPU's for 3D work, but shouldn't make use of any existing shading/tiling/rendering methods (like openGL). 3) scratch all binary formats (mtz,ccp4map,etc.) due to interoperability issues/dependencies. Everything in flat text (if you like, all variables can have four letters and can be followed by a flag/switch consisting of an integer or two, perhaps negative, to control software behavior). 4) abandon rapid software development afforded by modular, object oriented programming. Sounds good to me. Seriously however, I do like how well-coded monolithic executables simply work once compiled without fuss. I also like the speed and power afforded by using a well thought out toolkit of practical modules, a la PHENIX. I guess I can't have it all. Personally, if you really need windows, I second the idea of a VM running a linux environment. It's vastly simpler to install mature linux binaries within a VM then fight to get all of modern crystallographic software to run under windows. Even better, the other way around -- run linux native and windows in a VM. For the record: Shelx is awesome Fortran is a perfectly good programming language I keep a slide rule in my desk. --Paul Paul Smith, Ph.D. -- p...@smithops.net - Memorial Sloan-Kettering Cancer Center - New York Institute of Technology - www.paladinscientific.com --- On Mon, 8/29/11, George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: From: George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de Subject: Re: [ccp4bb] Windows 7 and Xtal Software To: CCP4BB@JISCMAIL.AC.UK Date: Monday, August 29, 2011, 3:12 PM It is simply a result of the 'zero dependency' philosophy. In other words, the exact opposite of current trends in crystallographic computing (e.g. Phenix/CCTBX). George On Mon, Aug 29, 2011 at 12:39:16PM -0500, Jacob Keller wrote: You know, why does your software always seem so clean? Was it something about the punch cards? Jacob On Mon, Aug 29, 2011 at 12:29 PM, George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: The current SHELX binaries (including the beta-test multi-CPU SHELXD) all appear to run fine under Windows 7. There is no need to use a virtual box etc. George On Sun, Aug 28, 2011 at 11:53:05PM -0700, Nat Echols wrote: On Sun, Aug 28, 2011 at 7:23 PM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: are there any additional problems or known issues running ccp4 or other xtal software on windows 7 (beyond those of Vista, etc.?) Phenix, ARP/wARP, and HKL2000 do not run on Windows. I'm pretty sure none of Global Phasing's software does either (aside from web interfaces). -Nat -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu *** -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582
Re: [ccp4bb] finding I/Sigma(I) from HKL Scalepack
Hello Evette, I've encountered the same problem. I have a perl utility that does much of what you would like. It will run scalepack for you iteratively until the number of rejections converges, or it will parse scalepack output. The output has I/sigI by shell gleaned from the scale log with the same resolution bins used in scaling. The usage for parsing is autoscale.pl -e scale.log See if this is of any use. Best, --Paul --- On Mon, 11/1/10, Radisky, Evette S., Ph.D. radisky.eve...@mayo.edu wrote: From: Radisky, Evette S., Ph.D. radisky.eve...@mayo.edu Subject: [ccp4bb] finding I/Sigma(I) from HKL Scalepack To: CCP4BB@JISCMAIL.AC.UK Date: Monday, November 1, 2010, 4:18 PM finding I/Sigma(I) from HKL Scalepack Dear all, I have previously used SCALA for data reduction, and in publications and pdb depositions, reported the Mn(I/sd) output from SCALA for the whole data set and for the highest resolution shell. We now have some data that has instead been reduced using the HKL suite, and I am confused about how to find the value that would be equivalent to Mn(I/sd) from SCALA. For I/Sigma(I) I've been advised by a colleague more familiar with HKL to manually calculate from average I divided by average error (sigma). As pointed out in a previous ccp4bb thread, this would give me I/Sigma(I), which is not the same as I/Sigma(I). Two questions: (1) Is this I/Sigma(I) what is generally reported in the literature for data processed with the HKL suite? (2) Since I would also like to know the Mn(I/sd) by shell anyway so that I can compare to previous data sets, is there a way to extract this value from the scalepack log, or is there a simple reflection file analysis utility that could read the .sca or .mtz file to extract this information? Thanks for any clarifications or suggestions! Evette Evette S. Radisky, Ph.D. Assistant Professor Mayo Clinic Cancer Center Griffin Cancer Research Building, Rm 310 4500 San Pablo Road Jacksonville, FL 32224 (904) 953-6372 autoscale.pl Description: Perl program
Re: [ccp4bb] which Linux workstation for crystallography to buy?
Stefano, I second the previous posts. Essential is a solid NVIDIA graphics card - quadro or geforce and not something low end. Vendors don't matter so much, we use both Dell and Hp and both are fine (essentially the same hardware inside). Also, linux version doesn't matter. We use both Suse and Ubuntu (and, yes, you can have a root account on Ubuntu, just use the sudo su command to log in as root, set a password, and Bob's your uncle). For laptop, I recommend the Dell precision portable workstation in i5/nvidia configuration. For desktop, I recommend HP proliant quad-core servers with a third-party nvidia graphics card. Avoid AMD hardware - often the linux drivers aren't stable. Feel free to contact me if you would like more specifics. --Paul --- On Tue, 10/12/10, Benini Stefano (P) stefano.ben...@unibz.it wrote: From: Benini Stefano (P) stefano.ben...@unibz.it Subject: [ccp4bb] which Linux workstation for crystallography to buy? To: CCP4BB@JISCMAIL.AC.UK Date: Tuesday, October 12, 2010, 4:28 AM Dear All, I need to buy a Linux workstation to run crystallographic software and graphics like ccp4, mosflm, coot., etc., Could you please suggest me a good combination of hardware and which linux operating system to install (ubuntu?)? I can spend about 1500€ Technology evolves so fast that I really want to be up to date not to be already late! Thank you very much in advance Stefano Stefano Benini, Ph.D. Assistant Professor http://pro.unibz.it/staff2/sbenini/ Bio-organic Chemistry Laboratory Faculty of Science and Technology Free University of Bolzano Piazza Università, 5 39100 Bolzano, Italy Office (room K2.11): +39 0471 017128 Laboratory (room E.012): +39 0471 017901 Fax: +39 0471 017009 ***
[ccp4bb] Home Source Options
I'm interested in opinions/advice on home source systems. As synchrotron beamlines are more powerful and more accessible than ever, a home source is really only needed for crystal screening, if at all. With that idea in mind, what are options out there for buying and running a home source in the most cost friendly way possible? I'm aware of most of the options from the big players (Rigaku, Oxford, Bruker), but I would like input on which setups cost the least to buy, run year in and year out, and require the least in terms of facilities setup (cooling water, power supply, etc.) Any positive/negative experiences worth sharing? Thanks, --Paul
Re: [ccp4bb] problem in heavy metal soaking
Hi Seema, In theory, Ammonium Sulfate contains some small fraction of neutral ammonia which can act as a strong nucleophile and react with many heavy metal compounds. That being said, I recently phased two structures with mercury soaks, both of which contained ammonium sulfate. The first was a thimerisol soak with 2M AmSO4 in the mother liquor, and the second with a MeHgCl soak with 0.2M AmSO4. Both were fairly routine. I think others will agree that with heavy metals, logic and theory can go right out the window. There is no way of knowing if it will work, you just have to try. One tip I can offer is to use fresh stocks of metals dissolved at saturating concentrations in water and used on the same day. The fresher the better in my experience, but it could just be voodoo. Good luck! --Paul --- On Sun, 9/26/10, Seema Nath seema.n...@saha.ac.in wrote: From: Seema Nath seema.n...@saha.ac.in Subject: [ccp4bb] problem in heavy metal soaking To: CCP4BB@JISCMAIL.AC.UK Date: Sunday, September 26, 2010, 9:00 AM I'm working with a protein which crystallizes in a mixture of PEG6K with 0.2M AmSO4,my question is if there's any problem if I want to soak heavy metal derivatives in this crystallizing condition? Does AmSO4 interfere in heavy-metal soaking ? if yes, what's the reason? Thank you in advance.
Re: [ccp4bb] Recommendations for (linux) crystallography workstation, server?
Hi Ed, Yes, the entire core line is great for crystallography setups. As has been mentioned, there are often issues with AMD processors as the occasional binary that is distributed has been compiled with intel CPU optimizations. I'm particularly fond of Dell's entry level servers with Quad-core Xeon processors. You can get a base T110 unit for $400 with and a fully tricked out model for less than $1000 Be sure to use NVIDIA graphics cards (Quadro, but not the NVS series) as NVIDIA has superior linux support. NFS is built in to the modern kernel distributions and is fully compliant with all other NFS setups (mac, unix, windows, etc.). You don't need to install anything, just configure /etc/exports (server side) and /etc/fstab (client side) correctly and you're set. NIS is still a supported package and can easily be added onto any linux distribution, but other options such as Kerberos and/or LDAP may be more secure up to date. Personally, I would just skip network authentication, mount home areas on NFS shares, and copy login info (/etc/passwd and /etc/shadow) entries from a central machine. Be sure to keep your network behind a firewall. Also, read up on NFS tuning. Getting the most out of network shares can often require asynchronous mounting, eliminating atime modification, and increasing block size from NFS defaults. Also, XFS is preferred to Reiser and possibly ext3 filesystems for NFS export. If you have a lot of users, be sure to set quotas, blah, blah, blah. In short, by Intel (basic Xeons are great), NVIDIA graphics, tune NFS properly, skip NIS, and use a good firewall. Happy Computing! Paul --Paladin Scientific (www.paladinscientific.com) --- On Thu, 6/3/10, Edward A. Berry ber...@upstate.edu wrote: From: Edward A. Berry ber...@upstate.edu Subject: [ccp4bb] Recommendations for (linux) crystallography workstation, server? To: CCP4BB@JISCMAIL.AC.UK Date: Thursday, June 3, 2010, 5:08 PM A colleague is interested in purchasing computers for structural biology. On the CCP4 wiki Kay reports good results with core i7 940 processor in Dell desktops. Is i7 still a good choice? is it worth upgrading now to i7 960 (3.2 GHz vs 2.66, for + $467) or i7 980 (3.33 ghz and more L2 cache for + $999)? Any particular Dell model, disk configuration? Any recommendations for a linux NFS and NIS server that would have user's home directories and software installs for 20 - 30 linux and Mac workstations? In a building with 1GHz network. Any suggestions, success reports, or horror stories would be appreciated. Ed
Re: [ccp4bb] About solvent flattening
Hi Hailiang, Be sure to include PARTIAL WCMB in your sigmaa script. This option outputs something more like a conventional FOM for use in DM. Also, I would allow DM to run more cycles and suggest starting with default parameters for solvent masking and density levels and then looking at the resulting maps. You have also specified ncsmask parameters without specifying ncs or asking the program to utilize ncs. Try the CCP4i GUI, it avoids many of these technical problems. Best, --Paul --- On Wed, 6/2/10, Hailiang Zhang zhan...@umbc.edu wrote: From: Hailiang Zhang zhan...@umbc.edu Subject: [ccp4bb] About solvent flattening To: CCP4BB@JISCMAIL.AC.UK Date: Wednesday, June 2, 2010, 3:04 PM Hi, I wanted to do solvent flattening for my map using Wang's method. I used CCP4-DM, and now have several questions: 1. DM seems requiring the FOM, so I generated FOM using SIGMAA by providing FP, FC and SIFFP using the following: sigmaa HKLIN in.mtz HKLOUT out-sigmaa.mtz eof title tt labin FP=FP SIGFP=SIGFP FC=FC PHIC=PHIC labout DELFWT=DELFWT FWT=FWT WCMB=WCMB symmetry $spcgrp END eof # I think the output FOM should be in range between 0 to 1; however, it produced FOM between -1 to 1 based on my in.mtz. This leads to complaints by the following DM calculation, and I am not sure whether I could avoid this. 2. My DM script is as follows: # dm HKLIN ./1KP8-NewSharpRescaleB0-sigmaa-oriB.mtz HKLOUT ./1KP8-NewSharpRescaleB0-sigmaa-oriB_dm.mtzdmtest mode - SOLV - NOHIST combine PERT scheme ALL ncycles - 1 solc 0.6 solmask - frac 0.6 - 0.4 - radius 3.0 2 ncsmask LABIN FP = FWT SIGFP = SIGFP PHIO = PHIC FOMO = WCMB LABOUT FDM=FDM PHIDM=PHIDM FOMDM=FOMDM FCDM=FCDM PHICDM=PHICDM END dmtest ## I am not sure whether there the above is ok for the purpose of a simple real-space solvent flattening using Wang's method. By the way, my map is at resolution 2.0, and I am not sure what is the best radius for this resolution. 2. Based on Wang's paper (Wang, B. C. (1985) Methods in Enzymology 115, 90-112), the solvent flattening is carried out in real space, and since my goal it simply modify my map, and I don't think I need FOM etc. So, can CCP4 (or anyother packages like Phenix, CNS, UPPSALA...,) provide a simple real-space solvent flattening without too much complications? Thanks a lot for any hints. Best Regards, Hailiang
Re: [ccp4bb] Refining against images instead of only reflections
Hi Jacob, I see you're still in the crystallography business. While you have an interesting idea, I doubt refining structures against entire images would be of any use in obtaining higher quality macromolecular structures. Much of what you see on the screen is a function of parameters completely unrelated or irrelevant to the structure being studied. Diffuse scattering can come from the cryo liquid surrounding the crystal as well as the fibers of the mounting loop itself. Background scattering is related to beam collimation. Spot size/shape is a function of crystal morphology among other things. In addition, every detector has its own peculiarities that make the intensities observed apart from diffraction spots particular to that detector. Also, you would have to take into account other physical properties such as ambient temperature, detector dark current fluctuations, variations in air absorption, etc. So, you could conceivably fit all of these various parameters to the images on hand, but none of them give you any actual information about your structure. As always, if you want more information about your structure, get higher resolution data. Nonetheless, I do think some thought could be put in to exactly how data are reduced. Perhaps the impending era of real time detector readout will help us rethink about spot profiles and intensity integration in a more sophisticated way. We may see a return to thinking about ccd readouts like an area detector which makes the process of analyzing images moot. --Paul --- On Wed, 1/20/10, Jacob Keller j-kell...@md.northwestern.edu wrote: From: Jacob Keller j-kell...@md.northwestern.edu Subject: [ccp4bb] Refining against images instead of only reflections To: CCP4BB@JISCMAIL.AC.UK Date: Wednesday, January 20, 2010, 12:47 PM Dear Crystallographers, One can see from many posts on this listserve that in any given x-ray diffraction experiment, there are more data than merely the diffraction spots. Given that we now have vastly increased computational power and data storage capability, does it make sense to think about changing the paradigm for model refinements? Do we need to reduce data anymore? One could imagine applying various functions to model the intensity observed at every single pixel on the detector. This might be unneccesary in many cases, but in some cases, in which there is a lot of diffuse scattering or other phenomena, perhaps modelling all of the pixels would really be more true to the underlying phenomena? Further, it might be that the gap in R values between high- and low-resolution structures would be narrowed significantly, because we would be able to model the data, i.e., reproduce the images from the models, equally well for all cases. More information about the nature of the underlying macromolecules might really be gleaned this way. Has this been discussed yet? Regards, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] NADP - ADP binding
Hello, I'm not entirely sure I know what you mean, but what came to my mind was malic enzyme. Check out Liang Tong's summary of structural data: http://como.bio.columbia.edu/tong/Research/me.html This protein has 2 nucleotide binding sites, one in a canonical Rossman fold and another on the surface that is believed to be an allosteric site. However, I could be remembering this story wrong. --Paul --- On Tue, 10/20/09, Mark Brooks mark.bro...@u-psud.fr wrote: From: Mark Brooks mark.bro...@u-psud.fr Subject: Re: [ccp4bb] NADP - ADP binding To: CCP4BB@JISCMAIL.AC.UK Date: Tuesday, October 20, 2009, 7:42 AM This is a good start for Rossmann folds, I find. (I'm not sure if this is what you want though.) Chemical and biological evolution of a nucleotide-binding protein. Michael G. Rossmann, Dino Moras Kenneth W. Olsen. Nature Vol. 250 July 19 1974, p194. (Structural alignments in 1974 - wow!) If anyone has votes for other favourite papers of this ilk, I'm all ears! Mark 2009/10/20 Vellieux Frederic frederic.velli...@ibs.fr: Michael Rossmann and colleagues did some work on the binding of fragments of cofactors to dogfish lactate dehydrogenase. In the 70's I think. Can be found on google scholar. Perhaps that's what you are after? Can't find the reference right now (it's in one of my drawers but I don't know which one...). I passed the reference on to Nicolas Coquelle @ualberta (coque...@ualberta.ca) a few days ago but that was from my home e-mail address so I don't have it here in the office. Fred. sajid akthar wrote: Dear All Can any one mention some reference regarding the binding of NADPH or ADP in the surface of the protein. Is there any rules that dominate these two cofactors to select the surface istead of typical Rossmann fold. Thank you Sajid Yahoo! India has a new look. Take a sneak peek http://in.yahoo.com/trynew -- Mark Brooks, IBBMC, UMR8619 - Bâtiment 430, Université de Paris-Sud, 91405 Orsay, France. Tel: (33) 169157968 Fax: (33) 169853715 Skype: markabrooks
Re: [ccp4bb] Format issue with TLSIN/TLSOUT files
Also, TLS parameters can be converted to conventional B-factors with both an isotropic and an anisotropic component which can then represented in conventional PDB format. PHENIX does this automatically, but I'm sure other software can perform the conversion as well. --Paul
[ccp4bb] Crystallization Reagent
Does anyone know of a source of AMP-N-PP? Thanks, --Paul
Re: [ccp4bb] Ligand PDB
Mariah, Try ChemDraw-3D, you can draw any chemical structure conceivable and write it out as a pdb. It can also do a wide variety of energy minimizations for you. Best, --Paul --- On Tue, 7/21/09, protein.chemist protein.chemist pp73...@gmail.com wrote: From: protein.chemist protein.chemist pp73...@gmail.com Subject: [ccp4bb] Ligand PDB To: CCP4BB@JISCMAIL.AC.UK Date: Tuesday, July 21, 2009, 4:23 PM Dear All, What is the best way to find the coordinates of a ligand. I do not find teh ligand in Pdb.org. I am trying to draw it in prodrug but the server is showing error. Also if I draw it how do I make sure that the geometry is correct. Thanks, Mariah -- Mariah Jones Department of Biochemistry University of Florida
Re: [ccp4bb] more than one ligands for CNS generate.inp and refine.inp files
Jacob,
In CNS/XPLOR all topology files are created equal. You are free to combine all
topology into a single file and read that into CNS. Do you have two copies of
the same ligand or two different ligands? If you have two different ligands,
you can use prodrg or xplo2d/hic-up to generate unique nomenclature for the
topology of each (different chemical identifier characters) and combine the
output to a single file and read that in. If you look how topology files are
read in:
topology
if ( BLANK%prot_topology_infile = false ) then
@@prot_topology_infile
end if
if ( BLANK%nucl_topology_infile = false ) then
@@nucl_topology_infile
end if
if ( BLANK%water_topology_infile = false ) then
@@water_topology_infile
end if
if ( BLANK%carbo_topology_infile = false ) then
@@carbo_topology_infile
end if
if ( BLANK%prost_topology_infile = false ) then
@@prost_topology_infile
end if
if ( BLANK%lig_topology_infile = false ) then
@@lig_topology_infile
end if
if ( BLANK%ion_topology_infile = false ) then
@@ion_topology_infile
end if
end
you'll see that no distinction is made anywhere as to what is ligand water
ion etc.
Your later problem during refinement is coming from missing parameter data, not
topology files. CNS knows the topology, but it doesn't have values for the
NONBONDED terms for the atoms in your ligand. Be sure you also read in the
parameter files with the relevant VDW information into the refine.inp script.
That should do it.
Best,
--Paul
--- On Tue, 7/21/09, Jacob Wong jacob.j.w...@gmail.com wrote:
From: Jacob Wong jacob.j.w...@gmail.com
Subject: [ccp4bb] more than one ligands for CNS generate.inp and refine.inp
files
To: CCP4BB@JISCMAIL.AC.UK
Date: Tuesday, July 21, 2009, 3:03 PM
Dear colleagues, please help
me with a CNS syntax. In the refine.inp, I could provide as
many topology (or parameter) files as
necessary:
{refine.inp}
{* topology files *}{===}
topology_infile_1=CNS_TOPPAR:protein.top;{===}
topology_infile_2=CNS_TOPPAR:dna-rna.top;{===}
topology_infile_3=CNS_TOPPAR:water.top;
{===}
topology_infile_4=CNS_TOPPAR:ion.top;{===}
topology_infile_5=../data/ligand1.top;{===}
topology_infile_6=../data/ligand2.top;
But in the generate.inp file, there is only one
input option for ligand (among others like
protein,
water, carbohydrate:{generate.inp}{*
ligand topology file *}
{===}
ligand_topology_infile=../data/ligand1.top;
As I'm
having two ligands in the structure, how do I get around
with the generate.inp syntax?
Thank
you in advance, -jacob
Re: [ccp4bb] is my crystal twinned or not?
Matthew, Here's my $0.02: Try more sophisticated twin tests such as xtriage from phenix or Ctruncate from the latest CCP4 distro. Both programs include multiple twining tests. Second, your R-factors seem very reasonable for a well refined structure missing 20% of a not-so-well ordered domain. If it ain't broke? Thirdly, if you do have a true twin fraction of 0.5, you have a hemihedral twin which cannot be detwinned -- I believe much of the detwinned data results in F = 0, could be wrong about that. Also, is your data anisotropic (your cell constants seem to be)? Anisotropy can interfere with twinning analysis. Lastly, think about optimizing your solvent envelope - this can make weak density stronger and improve R-factors as well (the latest CNS has a good implementation of optimized solvent flattening). Best of luck, --Paul --- On Wed, 7/22/09, Matthew Franklin matthew.frank...@imclone.com wrote: From: Matthew Franklin matthew.frank...@imclone.com Subject: [ccp4bb] is my crystal twinned or not? To: CCP4BB@JISCMAIL.AC.UK Date: Wednesday, July 22, 2009, 6:02 PM Hi all - I'm trying to solve the structure of an antibody-receptor complex, and I've hit a wall which may be due to a twinned crystal form. This crystal has the apparent space group P43212, with cell constants a=64.02 c=274.83. Solvent content analysis using this space group suggests 1 mol/asu, with 47% solvent, which would be fairly consistent with the diffraction limit of about 2.8 A. I've been able to place the antibody using molecular replacement and refine it to R=0.289, Rf=0.338. There is some density for the receptor, which represents about 20% of the mass of the complex, but not clear enough to build into, and all efforts to improve the density or place the receptor by molecular replacement have failed. Well, tough luck, you might say, but I noticed at the very beginning of the process that this crystal form may be a perfect twin. The 4th moment of E graph from Truncate shows nearly all resolution bins with values of 1.4 - 1.6, except in the very topmost few bins where the values rise up to 2. The other moment graphs are likewise at their perfect twin values across the resolution range. The cumulative intensity distribution graph shows the observed values are about 30% lower than the expected values for both acentric and centric reflections. As I understand it, both of these are strong indicators of twinning, and the twin fraction analysis in DETWIN suggests a twin fraction of ~0.5. So what do I do now? I think I'm supposed to reprocess the data in the space group without the twin transformation (which would be P43), then run molecular replacement which should show me solutions for both halves of the twin. However, all I'm seeing is two copies of the antibody in the (P43) asymmetric unit, which don't overlap, and both of which need to be present in the same unit cell in order to form a 3-dimensional lattice. This is exactly what I would expect to see if there were no twinning present. So my question is, is this crystal form twinned or not? Is there some way that the intensity statistics could be misleading me? On the other side, am I doing something wrong with the structure determination if the crystal is twinned? How should I proceed? Thanks for any help anyone can provide. - Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems, a wholly owned subsidiary of Eli Lilly Company 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.
Re: [ccp4bb] model completion after MR with partial model
Jerry,
In similar situations, I've tried various solvent flattening approaches.
Programs such as DM allow input of a manually created solvent mask. If you
edit the mask created around your MR solution to include where you think
additional protein density should be (using for example MAPMASK with the
border and combine options), missing density can become stronger and not be
washed out during solvent flattening.
Also, the newer versions of CNS can optimize a solvent mask that may avoid
flattening out weak density.
Personally, I would try DM using a wide range of different protein and solvent
density levels along with a custom mask and look at the resulting maps
(including NCS averaging) to see what's best.
Good Luck!
Paul Smith, Ph.D.
--- On Wed, 7/22/09, Jerry McCully for-crystallizai...@hotmail.com wrote:
From: Jerry McCully for-crystallizai...@hotmail.com
Subject: [ccp4bb] model completion after MR with partial model
To: CCP4BB@JISCMAIL.AC.UK
Date: Wednesday, July 22, 2009, 6:15 PM
#yiv2140568612 .hmmessage P
{
margin:0px;padding:0px;}
#yiv2140568612 {
font-size:10pt;font-family:Verdana;}
Dear ALL:
Thanks a lot for the
input about EPMR statistics. After struggling for several
days, I finally got a promising solution from Phaser with a
partial poly-Ala model with 50% completeness.
two molecules in one ASU:
solu set RFZ=4.2 TFZ=5.9 PAK=0 LLG=23 RFZ 3.8
TFZ=19.0 PAK=3 LLG=110 LLG=123
After some initial refinement, some side chains have been
assigned with R-factor 50% and R-free 52%. In addition,
there are some extra density at two termini.
We tried NCS averaging to improve the map but it did not
help that much.
Now we are trying to build more residues in with 2.6A
data.
Any suggestions will be highly appreciated.
Jerry McCully
Windows Live™ Hotmail®: Celebrate the moment
with your favorite sports pics. Check
it out.
[ccp4bb] Charge vs. pH plot Isoelectric titration curve ascii plotter
Hello all, I had the worst time the other day finding an online tool to calculate charge versus pH values for an input protein sequence. There are many programs for calculating the isoelectric point (pI), put not many that output a complete titration curve. Because such information is often useful in protein purification and crystallization, I coded up a quick perl program I would like to share with the CCP4 community. The code is attached. It is pretty self-explanatory. Input a FASTA file as a command line arguement and the program outputs charge vs. pH value pairs (unsorted). The constants defined in the program header can be used to alter the pKa values used, titration starting and ending points, and grid sampling. Please feel free to use, distribute, and modify freely. Also attached is a ASCII plotting tool that takes paired values from a file or STDIN and plots them to STDOUT in ascii using automatically determining ranges and binning values. These two programs work well like so: ./titrate.pl FASTA.seq | ./plot.pl to produce a nice ascii plot of charge vs. pH. I hope these are helpful to someone. Best, Paul Smith Paladin Scientific paladinscientific.com titrate.pl Description: Perl program plot.pl Description: Perl program
