Re: [ccp4bb] Kabat, insertion codes refinement
Insertion codes are a commonly used part of the PDB specification. It's odd that they wouldn't be supported correctly. To take another similar case, what would you say of a program that couldn't handle negative residue numbers as is commonly done with N-terminal purification tags? All sequences must start with 1? (Not all antibodies are isolated from natural sources. Some are from human-designed libraries for example, so they are every bit as engineered as something with as His tag stuck on the end.) Cheers, Eric On Jun 16, 2014, at 7:23 AM, Ed Pozharski wrote: There is no actual requirement to use Kabat numbering, you can avoid it alrogether. Some argue that L27A is actually 28th amino acid in the protein sequence, and labeling it as L27A is simply incorrect. I would suggest doing refinement with plain numbering (no insertion codes) and changing it only for the final model if needed for comparative analysis. Ed Sent on a Sprint Samsung Galaxy S® III Original message From: Hargreaves, David Date:06/16/2014 6:07 AM (GMT-05:00) To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Kabat, insertion codes refinement Dear CCP4bb, I’m refining an antibody structure which requires Kabat residue numbering with insertion codes. My setup of Refmac5 and Buster both break peptide bonds between some (not all) of the residues with insertion codes. I was wondering whether there is a special way of handling these residues in refinement? Thanks, David David Hargreaves Associate Principal Scientist _ AstraZeneca Discovery Sciences, Structure Biophysics Mereside, 50F49, Alderley Park, Cheshire, SK10 4TF Tel +44 (0)01625 518521 Fax +44 (0) 1625 232693 David.Hargreaves @astrazeneca.com Please consider the environment before printing this e-mail AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking compliance with our Code of Conduct and policies. -- Eric Bennett, er...@pobox.com Always try to associate yourself with and learn as much as you can from those who know more than you do, who do better than you, who see more clearly than you. - Dwight Eisenhower
Re: [ccp4bb] Off topic: Homology modeling
One possible outcome is: (a) if the two proteins bind similar ligands and (b) you know which part of the xray structure of the solved protein is binding the ligand and (c) you can use this information to tweak the alignment and determine that there is higher identity/similarity in the ligand binding region, that would increase your confidence in the prediction of the ligand binding site relative to a case where these factors weren't present. The local sequence identity in the binding site could be more important than the overall sequence identity. Some models may be accurate enough for purposes such as identifying domain junctions, or identifying residues that are likely involved in the function of the protein (ie possible ligand binding residues), but not accurate enough for detailed inhibitor design. So whether you can draw reliable conclusions depends on the type of conclusions you are trying to draw. Another possible outcome is that the model is completely wrong. At low identity levels it would be very important to test any model against experimental data to make sure it isn't junk. Also make sure your alignment places gaps in sensible locations taking into account the structure of your template. As a real world example, the lowest identity useful model I've ever made for detailed inhibitor design was a kinase where the sequence identities in the kinase domain were in the very low 20s. The active site was more conserved though, and since kinase binding sites are very well studied there was additional information to help ensure the alignments in the ligand site were correct. Even in that case wasn't clear when we made the model if it was going to be useful or not; it was only during the course of inhibitor optimization that we gained more confidence in its accuracy. Cheers, Eric On May 22, 2014, at 3:48 PM, Theresa Hsu wrote: Dear all I am working with a membrane protein without known structure. The closest protein in PDB has 10% sequence identity/25% similarity to my protein. What is the best method and software to do homology modeling while I try to get the crystal? Is the ligand binding site prediction reliable? There is no available experimental data on this protein except to sugest it is some type of ion transport. Thank you. Theresa -- Eric Bennett, er...@pobox.com Always try to associate yourself with and learn as much as you can from those who know more than you do, who do better than you, who see more clearly than you. - Dwight Eisenhower
Re: [ccp4bb] Stereo monitor
Hi David, We have had success with the ASUS VG248QE connected with DisplayPort, on an HP Z620 running RHEL 6.4. We like to have dual stereo displays on Linux, and Nvidia is discontinuing many of the cheaper multi-DVI-port cards. We had no success trying to take two Acer DVI monitors and connect them to DP on a Quadro 4000 (not K4000) using various DP/DVI adapters. So we decided we had to switch entirely to native DP connections and chose the VG248QE.No built in emitter on this monitor, however. So I think if you want to use this on Linux, you will need the K4000 or higher. We bought a K5000 to test it with, assuming we could fall back to the K5000's dual DVI ports and our old DVI monitors if DP didn't work. But since we got DP to work, we will probably go with the K4000 for our next batch of Linux workstations, since it appears to be the minimum card that works on Linux with the 3-pin emitter, and also provides two DP connectors. We had problems getting the correct stereo 3-pin bracket adapter for these cards; our reseller initially sent us the wrong one that is apparently for older Nvidia cards (very nice of them to change the plug periodically!) but we were able to get the correct one by talking directly to HP. The card will drive the monitor at 144 Hz when stereo is disabled in the X server config file, but it drops to 120 Hz in stereo mode, which I assume is probably the maximum shutter speed on the 3D Vision Pro glasses. Cheers, Eric On Nov 21, 2013, at 9:52 AM, David Schuller wrote: On 11/21/13 07:50, mesters wrote: ...(both handle the dual link DVI-D standard)... Are there any monitors on the market yet which can produce stereo 3D from a Displayport 1.2 input? With or without a built-in emitter. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu -- Eric Bennett, er...@pobox.com Always try to associate yourself with and learn as much as you can from those who know more than you do, who do better than you, who see more clearly than you. - Dwight Eisenhower
Re: [ccp4bb] delete subject
Scott, I'm not sure I understand your last paragraph. Once researchers have had their data pass peer review (which I interpret as meaning a journal has accepted it), how often do you think it happens that it does not immediately get published? Just depositing data in the PDB, or posting it on a public web site, is not meet[ing] the veracity of peer review. There is something to be said for giving credit to the first people who have subjected their data to peer review and had the data pass that step, otherwise people will be tempted to just post data of dubious quality to stake a public claim before the quality of the data has been independently checked. In a case where this initial public non-peer-reviewed posting is of unacceptable data quality, that would dilute credit granted to another person who later obtained good data. An unfortunate number of problematic structures still sneak through peer review. Relaxing quality review standards that must be passed before a scientist gets to claim credit for a discovery is a step backwards IMO. Cheers, Eric On Mar 28, 2013, at 5:06 PM, Scott Pegan wrote: 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
Re: [ccp4bb] Off-topic: Best Scripting Language
On Sep 12, 2012, at 2:28 PM, Ethan Merritt wrote: Why are you dis-ing python? Seems everybody loves it... I'm sure you can google for many reasons I hate Python lists. Mine would start 1) sensitive to white space == fail 2) dynamic typing makes it nearly impossible to verify program correctness, and very hard to debug problems that arise from unexpected input or a mismatch between caller and callee. 3) the language developers don't care about backward compatibility; it seems version 2.n+1 always breaks code written for version 2.n, and let's not even talk about version 3 4) slw unless you use it simply as a wrapper for C++, in which case why not just use C++ or C to begin with? 5) not thread-safe you did ask... Ethan While I agree generally with your points and try to avoid python if at all possible, I'm not sure about what you mean with point 5, since it's certainly possible to write threaded python scripts. Another point that is purely personal taste is the language philosophy that there is one official way to do something in Python, as contrasted with Perl (which is my choice) where the language philosophy is that there are many ways of doing any given task and the language is not designed to force you into a particular way of doing it. Ed adds: While indeed 1/3=0 (but so it will be in C), I think it's a bit of an overstatement that python code execution is nearly impossible to verify. Another goal of python is to accelerate implementation, and dynamic/duck typing supposedly helps that. The argument is simply that weak typing favours strong testing, which should be a good thing. Actually it's a bit of a hindrance. In Perl I can call the int function on anything and get a sensible answer. In python if you call int on a string that contains a floating point number the default behavior is that it will crash: [woz:~] bennette% cat pytest.py example_string = 10.3 number = int(example_string) [woz:~] bennette% /Library/Frameworks/Python.framework/Versions/2.6/bin/python pytest.py Traceback (most recent call last): File pytest.py, line 2, in module number = int(example_string) ValueError: invalid literal for int() with base 10: '10.3' That's brain dead. IMHO of course. Cheers, Eric
Re: [ccp4bb] very informative - Trends in Data Fabrication
I doubt many people completely fail to archive data but maintaining data archives can be a pain so I'm not sure what the useful age of the average archive is. Do people who archived to tape keep their tapes in a format that can be read by modern tape drives? Do people who archived data to a hard drive 10 years ago have something that can still read an Irix EFS-formatted SCSI hard drive today and, if not, did they bother to move the data to some other storage medium? -Eric On Apr 5, 2012, at 9:08 AM, Roger Rowlett wrote: FYI, every NSF grant proposal now must have a data management plan that describes how all experimental data will be archived and in what formats. I'm not sure how seriously these plans are monitored, but a plan must be provided nevertheless. Is anyone NOT archiving their original data in some way? Roger Rowlett
Re: [ccp4bb] very informative - Trends in Data Fabrication
Then everyone's data can be lost at once in the next cloud failure. Progress! The hardware failed in such a way that we could not forensically restore the data. What we were able to recover has been made available via a snapshot, although the data is in such a state that it may have little to no utility... -Amazon to some of its cloud customers following their major crash last year http://articles.businessinsider.com/2011-04-28/tech/29958976_1_amazon-customer-customers-data-data-loss -Eric On Apr 3, 2012, at 9:22 PM, Zhijie Li wrote: Hi, Regarding the online image file storage issue, I just googled cloud storage and had a look at the current pricing of such services. To my surprise, some companies are offering unlimited storage for as low as $5 a month. So that's $600 for 10 years. I am afraid that these companies will feel really sorry to learn that there are some monsters called crystallographers living on our planet. In our lab, some pre-21st century data sets were stored on tapes, newer ones on DVD discs and IDE hard drives. All these media have become or will become obsolete pretty soon. Not to mention the positive relationship of getting CRC errors with the medium's age. Admittedly, it may become quite a job to upload all image files that the whole crystallographic community generates per year. But for individual labs, I think clouding data might become something worth thinking of. Zhijie
Re: [ccp4bb] All-D World
Jacob, I wish it were that cheery. Do not forget the darker side of history. The prefix L- stands for levorotary. The levo comes from the Latin wording for left side. Left handedness is also known as sinistrality, from the Latin sinistra which also meant the left side, but over time took on the connotations that we currently associate with the word sinister. The latter word, of course, is generally associated with dark and evil. It is therefore erroneous to attribute the L amino acid to the Almighty. The L amino acid is in fact a diabolical corruption of cellular processes that begin with the D-nucleotide (D- meaning rotating to the right, but derived from dexter, meaning dextrous and skillful). The instrument which causes this perversion of God's perfect righteousness into a sign of evil deserves our strongest moral condemnation... I am referring, of course, to that devilish piece of cellular machinery known as the ribosome. The discovery of the ribosome was a significant blow to the success of what Charles Baudelaire famously called the devil's greatest trick. For years now, his acolytes have attempted to hide the truth about the ribosome by referring to its work with the neutral, innocent-sounding phrase translation. Don't be fooled, but instead pray for the development of the next generation of ribosome inhibitors, or at least dissolve the current generation in holy water before ingesting. -Eric On Feb 15, 2012, at 7:24 PM, Jacob Keller wrote: G-d is right-handed, so to speak: Ex 15:6 Thy right hand, O LORD, is become glorious in power: thy right hand, O LORD, hath dashed in pieces the enemy. Since we are made in His image, and our (chiral) molecules are the cause of making most of us right-handed, which enantiomer to use was not a real choice but rather flowed logically from His (right-handed) Essence. Our chirality is dictated by His, whatever that means! JPK On Wed, Feb 15, 2012 at 4:48 PM, William G. Scott wgsc...@ucsc.edu wrote: Hi Jacob: After giving this a great deal of reflection ….. I realized that you would face the same paradox that God had to resolve six thousand years ago at the Dawn of Creation, i.e., He needed D-deoxyribose DNA to code for L-amino acid proteins, and vice versa. Likewise, you would probably be faced with a situation where you need L-deoxyribose DNA to code for D-amino acid proteins, so once again, you need a ribozyme self-replicase to escape the Irreducible Complexity(™). (The Central Dogma at least is achiral.) At least it can be done six thousand years, which isn't unreasonable for a Ph.D. thesis project (especially when combined with an M.D.), and you, unlike Him, have access to a Sigma catalogue. All the best, Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA On Feb 15, 2012, at 10:28 AM, Jacob Keller wrote: So who out there wants to start an all-D microbial culture by total synthesis, a la the bacterium with the synthetic genome a while back? Could it work, I wonder? I guess that would be a certain benchmark for Man's conquest of nature. JPK ps maybe if there is a broadly-acting amino-acid isomerase or set of isomerases of appropriate properties, this could be helpful for getting the culture started--or even for preying on the L world? On Wed, Feb 15, 2012 at 12:17 PM, David Schuller dj...@cornell.edu wrote: On 02/15/12 12:41, Jacob Keller wrote: Are there any all-D proteins out there, of known structure or otherwise? If so, do enantiomer-specific catalyses become inverted? JPK What do you mean by Out There? If you mean in the PDB, then yes. As of two weeks ago, there are ~ 14 racemic structures deposited; most in space group P -1, with one outlier in space group I -4 C 2. This includes RNA, DNA, and PNA, but 6 entries are actually protein. The longest is over 80 residues. Theoretically, enantiomer-specific catalysis ought to be inverted, but most of the structures solved are not enzymes. kaliotoxin, plectasin, antifreeze protein, monellin, villin, and a designed peptide. On the other hand, if by out there you meant in nature outside of biochemistry and organic chemistry labs; then no, I am not aware of any all-D proteins. There are a few protein/peptides which include a small number of D-residues, which is marked up to nonribosomal synthesis. The first paper I managed to Google: http://jb.asm.org/content/185/24/7036.full Learning from Nature's Drug Factories: Nonribosomal Synthesis of Macrocyclic Peptides doi: 10.1128/JB.185.24.7036-7043.2003 J. Bacteriol. December 2003 vol. 185 no. 24 7036-7043 If racemic crystallization isn't exciting enough for you, look into quasi-racemic crystallization. On Wed, Feb 15, 2012 at 8:05 AM,
Re: [ccp4bb] Computer encryption matters
John, Since so many people have said it's flawless, I'd like to point out this is not always the case. The particular version of the particular package that we have installs some system libraries that caused a program I use on a moderately frequent basis to crash every time I tried to open a file on a network drive. It took me about 9 months to figure out what the cause was, during which time I had to manually copy things to the local drive before I could open them in that particular program. The vendor of the encryption software has a newer version but our IT department is using an older version. There is another workaround but it's kind of a hack. So I'd say problems are very rare, but if you run into strange behavior, don't rule out encryption as a possible cause. -Eric On Aug 17, 2011, at 3:13 PM, Jrh wrote: Dear Colleagues, My institution is introducing concerted measures for improved security via encryption of files. A laudable plan in case of loss or theft of a computer with official files eg exams or student records type of information stored on it. Files, folders or a whole disk drive can be encrypted. Whilst I can target specific files, this could get messy and time consuming to target them and keep track of new to-be-encrypted files. It is tempting therefore to agree to complete encryption. However, as my laptop is my calculations' workbench, as well as office tasks, I am concerned that unexpected runtime errors may occur from encryption and there may be difficulties of transferability of data files to colleagues and students, and to eg PDB. Does anyone have experience of encryption? Are my anxieties misplaced? If not, will I need to plan to separate office files, which could then all be encrypted, from crystallographic data files/calculations, which could be left unencrypted. If separate treatment is the best plan does one need two computers once more, rather than the one laptop? A different solution would be to try to insist on an institutional repository keeping such files. In anticipation, Thankyou, John Prof John R Helliwell DSc
Re: [ccp4bb] more Computer encryption matters
For anything other than the most intensive I/O operations, recent processors will give you very respectable performance. I don't encrypt whole drives but I do have some AES-encrypted disk images in Snow Leopard, and I get about 38 MB/sec throughput copying (using cp) and 60 MB/sec reading (while also calculating cksum) for files of several hundred megabytes in size. I only have one drive, so the write test includes the time it takes to read the data from the unencrypted hard drive before writing back to the disk image on the same volume. The process that handles the encryption only hits about 30% CPU use while writing and 40% while reading so I assume my hard drive is the limiting factor. If I repeat the read test, so presumably the encrypted data is already cached, it hits over 90 MB/sec throughput and about 60% of a single core is busy. These numbers are for a 2.93 GHz core i7 iMac with the HDS722020ALA330 Hitachi drive. I believe this is the 870 series chip which does _not_ have the new AES instruction set on-chip. -Eric On Aug 18, 2011, at 5:50 PM, William G. Scott wrote: OS X 10.7 enables you to do whole-drive encryption. Here is a description from Arse Technica: http://arstechnica.com/apple/reviews/2011/07/mac-os-x-10-7.ars/13 I ain't never tried it myself. 10.7 seems to run slow enough as it is. -- Bill
Re: [ccp4bb] unusual sighting of a crystal structure
It would be even scarier if they used an NMR structure. -Eric On Jul 16, 2011, at 1:20 PM, Robbie Joosten wrote: Hi Artem, Thank for that nice example of a protein structure used to pimp a movie. Ribbon representations are always the scariest. Cheers, Robbie
Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro'
Nvidia lists that monitor on their list of supported hardware: http://www.nvidia.com/object/3d-vision-requirements.html They even sell some Acer monitors in their online store although they are labeled in conflicting ways. I tried upgrading the driver yesterday to the 270.41.06 version but it didn't make any difference, still only 100 Hz. Are you using Windows or Linux? We're using the 64-bit Linux driver. -Eric On May 9, 2011, at 4:26 AM, Takaaki Fukami wrote: not seen a working 120 Hz stereo setup working on the Acer GD235 monitor. if you ask the Nvidia driver or the monitor, it reports 100 Hz instead This is what I encountered on Dell Alienware OptX AW2310 with Quadro FX3800, which has been fixed by nVIDIA Linux driver update (in 256.44). I don't know if the Acer monitor is compatible or not, it seems better to ask NVIDIA directly. see: http://twitter.com/#!/NVIDIAQuadro/status/65188179753435137 Takaaki Fukami - Discovery Platform Technology Dept. Gr.5 Chugai Pharmaceutical Co.,Ltd.
Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro'
We recently had issues setting up a 3D projector and have tried lots of combinations of monitors, drivers, cards, glasses, etc. The answer seems to be that interchangeability is very complicated and you won't know unless you try it. For example, with the last version of the Nvidia driver I tested, the driver refused to put out an Nvidia 3D Vision sync signal (stereo 10 in xorg.conf) unless there was a 3D capable LCD attached. I don't know of any technical reason the Nvidia 3D Vision couldn't be used with a CRT but Nvidia has apparently chosen to disable it (or at least make it hard to enable) in the Linux driver. Going the other direction, using RealD with and LCD system, it might be possible but you probably have to match your RealD emitter with RealD glasses. Older CrystalEyes glasses (CE3 and earlier) generally do not work with LCD monitors because of the polarization in the glasses. We recently got some CE4 glasses and they don't seem to have that problem although in practice we are using them with a projector, not LCD monitors. But I don't really like the CE4's, there is too much of my field of vision under the glasses that they don't cover. We've observed some really weird configurations that appear to mostly work, such as plugging in a RealD emitter and glasses when the driver is configured to output a signal for Nvidia 3D Vision (stereo 10 option under Linux). You don't say whether you are using Windows or Linux and there may be variations in the drivers, variations by card, etc. Regarding card to card variations, we've observed 3D setups in conference rooms with multiple emitters where some Nvidia cards happily drive multiple emitters with particular splitters boosters, but other Nvidia cards don't. The bottom line is if you mix hardware you might have problems and vendors are unlikely to help you. If you have CE4 glasses already, you can try it with an LCD and it may work. Otherwise, if you have to buy new glasses (ie, you have CE3 or older), you might as well get the Nvidia package with the emitter included. 3D Vision Pro uses the 2.4 GHz band instead of IR to transmit the sync signal so if you were setting up a conference room in theory the Pro version might be less likely to leave dead zones in the conference room. For a single user workstation it's very unlikely that you would get any benefit. Just to muddy the waters a bit, I have not seen a working 120 Hz stereo setup working on the Acer GD235 monitor. We have a bunch of them set up, and we put a 120 Hz mode line in xorg.conf. If you ask X11 it says it's running at 120. But if you ask the Nvidia driver or the monitor, it reports 100 Hz instead, and visually there is enough flickering that the monitor and the driver seem to have the correct number. I'm curious if anyone else here has looked in detail to make sure their Acer-based system is running at 120 and found that it is actually doing what people claim it can do. I find the 100 Hz LCD flicker annoying over long periods so I am still a neanderthal CRT user. My coworkers were convinced their LCD systems were running at 120, when they were actually only running at 100. I'm not sure if this is a driver problem or a monitor problem. -Eric On May 6, 2011, at 11:27 AM, zhang yu wrote: Dear colleagues, Sorry to present the stereo issue to the board again. Since my old SGI CRT monitor only has 75 HZ refresh rate, the flickering in stereo mode bothered me a lot. Recently, I want to update my old CRT to 120 HZ LCD. I have a Nvidia Quadro FX3800 in my workstation. I would like to make sure some issues before I make the upgrade. 1. Can I apply the previous stereo emitter (Purchased from Real D, Model #E-2) to 120HZ LCD? Although the company told me this emitter is not compatible with LCD, could some one tell me why? Is it true that the Nvidia 3D vision is the only solution for the stereo in LCD? 2. Nvidia supply two kinds of 3D emitters. One of them is 3D vision, while the other one is 3D vision pro. Which one is sufficient for crystallographier user? (3D vision pro is much more expensive than 3D vision) It seems that 3D vision is for home user and powered by the Nvidia GeForce series graphic cards. While 3D vision pro is for professional user and powered by Nvidia Quardro series graphic card . 3. It looks that the Nvidia 3D glasses are very compact. Is it comfortable for someone like me already with eyeglasses? Thanks Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
Re: [ccp4bb] what to do with disordered side chains
Most non-structural users are familiar with the sequence of the proteins they are studying, and most software does at least display residue identity if you select an atom in a residue, so usually it is not necessary to do any cross checking besides selecting an atom in the residue and seeing what its residue name is. The chance of somebody misinterpreting a truncated Lys as Ala is, in my experience, much much lower than the chance they will trust the xyz coordinates of atoms with zero occupancy or high B factors. What worries me the most is somebody designing a whole biological experiment around an over-interpretation of details that are implied by xyz coordinates of atoms, even if those atoms were not resolved in the maps. When this sort of error occurs it is a level of pain and wasted effort that makes the pain associated with having to build back in missing side chains look completely trivial. As long as the PDB file format is the way users get structural data, there is really no good way to communicate atom exists with no reliable coordinates to the user, given the diversity of software packages out there for reading PDB files and the historical lack of any standard way of dealing with this issue. Even if the file format is hacked there is no way to force all the existing software out there to understand the hack. A file format that isn't designed with this sort of feature from day one is not going to be fixable as a practical matter after so much legacy code has accumulated. -Eric On Apr 3, 2011, at 2:20 PM, Jacob Keller wrote: To the delete-the-atom-nik's: do you propose deleting the whole residue or just the side chain? I can understand deleting the whole residue, but deleting only the side chain seems to me to be placing a stumbling block also, and even possibly confusing for an experienced crystallographer: the .pdb says lys but it looks like an ala? Which is it? I could imagine a lot of frustration-hours arising from this practice, with people cross-checking sequences, looking in the methods sections for mutations... JPK
Re: [ccp4bb] The meaning of B-factor, was Re: [ccp4bb] what to do with disordered side chains
Personally I think it is a _good_ thing that those missing atoms are a pain, because it helps ensure you are aware of the problem. As somebody who is in the business of supplying non-structural people with models, and seeing how those models are sometimes (mis)interpreted, I think it's better to inflict that pain than it is to present a model that non-structural people are likely to over-interpret. The PDB provides various manipulated versions of crystal structures, such as biological assemblies. I don't think it would necessarily be a bad idea to build missing atoms back into those sorts of processed files but for the main deposited entry the best way to make sure the model is not abused is to leave out atoms that can't be modeled accurately. Just as an example since you mention surfaces, some of the people I work with calculate solvent accessible surface areas of individual residues for purposes such as engineering cysteines for chemical conjugation, and if residues are modeled into bogus positions just to say all the atoms are there, software that calculates per-residue SASA has to have a reliable way of knowing to ignore those atoms when calculating the area of neighboring residues. Ad hoc solutions like putting very large values in the B column are not clear cut for such a software program to interpret. Leaving the atom out completely is pretty unambiguous. -Eric On Mar 31, 2011, at 7:34 PM, Scott Pegan wrote: I agree with Zbyszek with the modeling of side chains and stress the following points: 1) It drives me nuts when I find that PDB is missing atoms from side chains. This requires me to rebuild them to get any use out of the PDB such as relevant surface renderings or electropotential plots. I am an experienced structural biologist so that I can immediately identify that they have been removed and can rebuild them. I feel sorry for my fellow scientists from other biological fields that can't perform this task readability, thus removing these atoms from a model limits their usefulness to a wider scientific audience. 2) Not sure if any one has documented the percentage of actual side chains missing from radiation damage versus heterogeneity in confirmation (i.e. dissolved a crystal after collection and sent it to Mass Spec). Although the former likely happens occasionally, my gut tells me that the latter is significantly more predominant. As a result, absence of atoms from a side chain in the PDB where the main chain is clearly visible in the electron density might make for the best statistics for an experimental model, but does not reflect a reality. Scott
Re: [ccp4bb] Question on calculation of RMSD
Andrew Martin's ProFit program is another option: http://www.bioinf.org.uk/software/profit/doc/node11.html Having fitted the structures using the ZONE and ATOMS commands to specify which residues and atoms should be included in the fitting, the RMS deviation may then be calculated over a different region of the structure and/or a different atom set. This is achieved using the RZONE and RATOMS commands. The syntax of these commands is identical to that of the ZONE and ATOMS commands described in Sections 8 and 9. -Eric -Original Message- From: E rajakumar Sent: Monday, November 15, 2010 6:52 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Question on calculation of RMSD Dear All I have two structures of homo-dimeric protein complex with different DNA. I want to calculate RMS deviation between second monomer from these two complexes by fixing superposed first monomer. This I require to know what is the effect of DNA on relative orientation of two monomers in the dimer. Previously I was using MOLEMAN2 to do this calculation. Please can you suggest me any other program to do this calculation. Thanking you Raj E. Rajakumara Postdoctoral Fellow Strcutural Biology Program Memorial Sloan-Kettering Cancer Center New York-10021 NY 001 212 639 7986 (Lab) 001 917 674 6266 (Mobile) -- -- Eric Bennett, er...@pobox.com Drawing on my fine command of the language, I said nothing. -Robert Benchley
Re: [ccp4bb] Rosetta vs Modeller
Subhendu wrote: Hi everyone, I am currently in the process of solving some antigen-antibody complex structures. I was wondering if people here have used Modeller and Rosetta for homology modeling and have any recommendations.I would like to build the model of the antigen/antibody to the known structure of the antibody/antigen ( to get a model of the complex while my crystallization/structure solving process continues).I have experience in Modller but I have not tried Rosetta or the newer PyRosetta (which looks interesting). In the event of docking a protein to another are there any great programs that people here have used/recommend? Because Modeller is a general purpose tool while RosettaAntibody has some specialized knowledge of antibodies you might want to consider giving Rosetta a try. A couple reasons: (1) Modeller operates at the local level of structure. It isn't written to specifically optimize relative domain orientations, such as between VL and VH. RosettaAb includes a specific step for optimizing domain orientation, which could improve your chances with MR if you intend to use the homology model for that purpose. (2) For identifying templates, if you use the sort of global sequence alignment tools in Modeller to choose a template, you may end up with a template that has high identity in the framework region but the CDR loop lengths are not the same. Rosetta takes a more sensible piecemeal approach where it will identify a template for the framework, and other templates for the CDRs based on the loop length. Of course, you can do this manually if you want to use Modeller since Modeller supports multiple templates, but it's more work. -Eric --
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....?
Dear Fred, People have already done this for all PDB entries: - http://eds.bmc.uu.se/eds/ : maps and many crystallographic stats - http://www.cmbi.ru.nl/pdb_redo : maps and re-refinement. And yes, the stats and maps do improve most of the time, unfortunately also for structures that are not old (but to a lesser extent). Except it doesn't work for _all_ PDB entries, even when SF are available. On your site, for example, the Current entries link on the home page seems to be broken and entry 3G6A (which was released 8 months ago) is not available for some unspecified reason. For some cases (like twinned structures) EDS won't have a map. Rather than relying on availability of a third party server to enable viewing the map, it would be a much cleaner solution if authors just deposited their own maps in the PDB. --
[ccp4bb] map deposition (was: Retraction of 12 Structures...)
Robbie Joosten wrote: I think the deposition of maps is a waste of space. Maps may describe what the depositors paranoidwant you to think they/paranoid have looked at. But that does not mean they looked at the right thing. Who knows what they did to the maps in terms of (unwarrented) density modefication to make them look cleaner? The advantage of the EDS is that it is impartial and uniform. The maps are generated in a clear and well-described way. For those who want to do bulk statistical analyses, the automated servers with uniform settings are unquestionably a good tool to have. They're also useful for the rare cases where somebody is cheating. I don't think deposited maps should replace the servers. But for most structures, where we do not suspect the crystallographer was intentionally cheating, I'd rather have the map as calculated with settings determined by the person who is most familiar with each specific data set. Are default settings really smarter than the average crystallographer? My personal opinion is that in most cases, when non-default settings have been used, there was probably a valid reason. --
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....
Fred V wrote: I personally like to visualise the electron density as well, however, I do think that a non-crystallographer will go through the trouble of downloading the structure factors, installing ccp4/coot etc. Fred. They shouldn't have to go through some of that trouble. Maps should be deposited. Even if you have good crystallography knowledge can you exactly reproduce the map the authors were looking at? Software algorithms change over the years... the software version the authors used might not even be compilable on modern systems... some authors may not fully specify all software settings required to get the same map (perhaps they used NCS but you have to re-determine the NCS yourself)... etc. -- Eric Bennett, er...@pobox.com
Re: [ccp4bb] Rfree in similar data set
Ian Tickle wrote: For that to be true it would have to be possible to arrive at a different unbiased Rfree from another starting point. But provided your starting point wasn't a local maximum LL and you haven't gotten into a local maximum along the way, convergence will be to a unique global maximum of the LL, so the Rfree must be the same whatever starting point is used (within the radius of convergence of course). But if you're using a different set of data the minima and maxima of the function aren't necessarily going to be in the same place. Rfree is supposed to inform about overfitting. In an overfitting situation there are multiple possible models which describe the data well and which overfit solution you end up with could be sensitive to the data set used. The provisions that you haven't gotten stuck in a local maximum and are within radius of convergence don't seem safe considering historical situations that led to the introduction of Rfree. What algorithm is going to converge main chain tracing errors to the correct maximum? Thinking about that situation, isn't part of the goal of Rfree to give you a hint in situations where you have, in fact, gotten stuck in a local maximum due to a significant error in the model that places it outside the radius of convergence of the refinement algorithm? -Eric --
Re: [ccp4bb] images
Kay Diederichs wrote: In this case the structure factors were deposited, but these do not have a column for the anomalous signal. Re-refinement with these structure factors was inconclusive. If I could have downloaded the images, I could have investigated this easily, because there's a large difference in the f of those two metals. So to me access to images sometimes may help to answer a scientific question. I would add a plea to those considering an image deposition system: accept MAPS too! At the very least it would be nice to see the initial and final maps the crystallographer used. Even if I have the structure factors I'm not necessarily an expert on the ins and outs of what someone had to do to refine a twinned or otherwise troublesome structure, and I don't want to have to learn the specific refinement program you used to be able to reproduce the exact map you saw. (For very old structures, it may no longer be possible to compile the specific version of the refinement software on new processors/OSes, or someone may have used a commercial refinement package.) And of course, there are non-crystallographers who use structures and it is absurd to expect them to learn x-ray refinement to see the relevant map for a twinned structure that EDS couldn't process. I love EDS. But even though it usually has a map for a given structure, seeing the actual map generated by the crystallographer who was the expert on the project would be better. Once a system is designed that is large enough to handle images, maps would not significantly increase the required storage space. I've poked a couple people to suggest that even now the PDB ought to be accepting maps. -- -Eric
Re: [ccp4bb] fake images
Bernhard Rupp wrote: I only scratched the surface and I think it would be hard work to fake the images in a way that later expert forensics would not readily provide evidence. Also, there are 'watermarks' available from cryptographic methods that are even 'post-processing' resistant. A practical question is, even if it could be detected in theory, is anyone looking for it in practice? How many journal reviewers are going to audit this information? Today some structures still don't get deposited with structure factors. Not all journals enforce deposition policies well. Even if some future image repository can do automated image auditing, people who want to commit overt fraud will pick a journal that doesn't enforce deposition requirements, and decline to provide their images. A watermark or statistical analysis won't help you if you don't have access to the image. This discussion started regarding a place for people who _want_ to deposit images; unfortunately some people aren't going to do it voluntarily. -Eric --
Re: [ccp4bb] stereo with Nvidia Quadro
Dear David, thank you for your answer. Do you (or anyone on the list) know if any FX-card would work with NuVision 60GX (like FX370, FX570), or only the dear ones (FX1400 and above)? Nvidia has been progressively dropping support from their lower-end cards. For example the older FX1100 has stereo, but the newer FX1700 does not. Currently you have to buy the FX 3500 or above to get stereo. Look at this chart under the row Display Connectors for cards which have Stereo listed: http://www.nvidia.com/object/IO_11761.html The 3500 series is moderately expensive. If you are on a budget maybe you could snag an older used card online somewhere. -- -- Eric Bennett Hofstadter's Law: It always takes longer than you expect, even when you take into account Hofstadter's Law.
