[ccp4bb] Correcting 3-letter codes based on protonation states in a PDB file
Dear all - I'm working with a PDB file with explicit hydrogens where many of the histidines are in protonated form due to crystallization at low pH. Unfortunately, although the additional protons are present in the model for the positively charged histidines, the residues in question are indicated in both the SEQRES and the ATOM records as 3-letter code `HIS` regardless of protonation state (i.e. instead of `HIP` for positively charged, and `HID` or `HIE` for the neutral tautomers). Are there existing tools available to determine the proper 3-letter residue code for titratable amino acid residues based on which hydrogens are present, and output a corrected PDB file? Thank you in advance for your suggestions. Cheers, Jared Sampson Ph.D. Candidate Columbia University
[ccp4bb] Test system for binding energy predictions
Dear crystallographers - I've been trying without success to find a suitable system to test a method for predicting change in binding energy (delta-delta-G) due to mutations of protein-protein complexes that result in a change in net charge. In particular I'm looking for a system with the following features for a single mutation: * crystal structures and experimental binding affinity data available for both wild-type and mutant complexes * net change of charge of ±1 upon mutation (i.e. charged residue to neutral or vice versa--I'm not considering charge flipping at the moment) * non-trivial conformational change in the region around the mutated residue If you happen to know of any systems that may qualify, I would appreciate any information you could send my way. Thank you! Cheers, Jared -- Jared Sampson Ph.D. Candidate Honig/Shapiro and Friesner Labs Columbia University New York, NY
Re: [ccp4bb] pdbset
Hi Charlie - I'm not able to reproduce your issue. I tried this with a random PDB and, although the symmetry operation wasn't appropriate for that particular structure, I got normal-looking cartoon representations. One thing to consider might be that, if there are abnormalities in the numbering of your PDB residues (e.g. you have 2 residues with the same chain + residue number) this will break the cartoon representation, as PyMOL can no longer tell which N and C atoms should be bonded. To illustrate, try entering the following commands on the PyMOL command line: fab A, ala zoom as cartoon alter resi 3, resi=2 rebuild Is this something like what you see? If so, I would check the input (or output) file for sequence issues. Hope that helps. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Jun 26, 2015, at 11:33 AM, Carter, Charlie car...@med.unc.edumailto:car...@med.unc.edu wrote: I'm trying to generate an oligomer using pdbset with the script attached below. The rotated molecules appear to be oriented properly, but they cannot be viewed correctly in PYMOL because the cartoon option fails to connect many of the residues. What am I doing wrong? Thanks, Charlie pdbset XYZIN $1.pdb XYZOUT temp.pdb EOF-pdbset CHAIN A SYMGEN Y-0.5,-X+0.5,Z OUTPUT PDB END EOF-pdbset This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =
Re: [ccp4bb] 1.how to use pymol to choose all the residues that have polar contacts in the complex 2.how to draw a residues-DNA interaction picture
Hi Weifei - The first image looks like it was drawn using a vector drawing program like Adobe Illustrator or Inkscape. If you're looking for something automatically generated, two of the first hits from a Google search for protein interaction diagram are LigPlot+ (http://pubs.acs.org/doi/abs/10.1021/ci200227u) and LeView (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3765711/). For your second question, to show the residues on chain A within a cutoff distance (e.g. 3.5Å) of chain E, you could use two PyMOL commands like this: show sticks, br. (chain A and donors) within 3.5 of (chain E and acceptors) show sticks, br. (chain A and acceptors) within 3.5 of (chain E and donors) Check out http://www.pymolwiki.org/index.php/Selection_algebra and http://www.pymolwiki.org/index.php/Single-word_Selectors for more info. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On May 17, 2015, at 7:08 AM, weifei weife...@outlook.commailto:weife...@outlook.com wrote: Dear all, I am sorry to disturb you. I have two question to ask. The first one is how to draw a residue-DNA interaction picture looks like this one? Mail Attachment.png The second question is how to use pymol to select all the residues of a complex that interact with other protein or DNA by polar contacts? 1.I select chain E (DNA) and choose polar contacts --to other atoms in object. Mail Attachment.png 2.I can see polar contacts between ChainA(protein) and ChainE(DNA) but I want to show all the connected residue in ChainA. How to choose all the residues that have polar contacts in the Protein. Mail Attachment.png Mail Attachment.png Thank you so much for your answear. Best, Weifei
Re: [ccp4bb] off topic: pymol
Hi Almu - It's actually even easier than what Vincent wrote as well. :) You don't need to create multiple objects or worry about backbone selections--PyMOL has some built-in settings that will do this for you. # the PDB from your example fetch 3bwp # color however you like color blue, resi 1-100 color red, not resi 1-100 # show it as cartoon and use PyMOL's ring mode setting to show the bases as cartoon set cartoon_ring_mode, 3 # add transparency, adjust the thickness of the stick representation set cartoon_ring_transparency, 0.5 set cartoon_ring_width, 0.2 # color the rings the same as the rest set cartoon_ring_color, blue, resi 1-100 set cartoon_ring_color, red, not resi 1-100 Hope that helps. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Feb 25, 2015, at 6:58 AM, vincent Chaptal vincent.chap...@ibcp.frmailto:vincent.chap...@ibcp.fr wrote: Dear Almu, very easily: #load the same pdb twice and give it two different names: load xx.pdb, molA load xx.pdb, molB # show one as cartoon, the other as sticks: hide everything show cartoon, molA show sticks, molB #hide the backbone sticks of molB hide sticks, molB and name c+n+o (this is for proteins, for DNA you have to look what are the names to hide). best vincent Le 25/02/15 11:48, Almudena Ponce Salvatierra a écrit : Hi, does anybody know how to represent in pymol a combination of cartoon, with sticks, but without the sticks from the phosphate backbone? I am referring to something like it is in this figure (see attachment). I can get the sticks and the cartoon together for the nucleobases but I don't know how to remove the sticks from the backbone. All suggestions are welcome. Best, Almu -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug-resistance modulation and mechanism Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 07 http://www.ibcp.frhttp://www.ibcp.fr/
Re: [ccp4bb] Adding a residue with an insertion code
Thanks to Paul and Zhijie for the suggestions. In the past, I’ve also renumbered everything from 1 (using pdbset) for the duration of refinement, then renumbered the structure at the end. For that, I would use either pdbset and a text editor (which is somewhat tedious, as there are several insertion positions in either the Kabat or Chothia numbering schemes, although Matt Franklin suggested to me off-list that their usage in new PDB deposits has been declining), or if I’m not feeling particularly secretive about the structure, via Andrew Martin's Abnum server (http://www.bioinf.org.uk/abs/abnum/), although that’s only good for antibody structures, of course. In any case, insertion codes are the exception to the rule, and I don’t particularly mind the workarounds every now and then. I just wanted to make sure I wasn’t missing an easier way to do it. :) Thanks again, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Jan 14, 2015, at 12:52 PM, Zhijie Li zhijie...@utoronto.camailto:zhijie...@utoronto.ca wrote: Hi Jared, The only thing that comes to my mind that might help a little is to use pdbset to renumber your residues. Then you only need to change residue 101 to 100A manually in a text editor (unfortunately I could not find a program that does that). Here are the steps I would take: 1) build the model with normal numbering, i.e., the concerned region would be 100,101,102; 2) manually change 101 to 100A in text editor; 3) pdbset xyzin old.pdb xyzout new.pdb renumber increment –1 102 to 500 chain A !move everything up starting from 102 end You can make a little shell script file for step 3, to save some typing/typo. (see attachment for an example) Zhijie From: Sampson, Jaredmailto:jared.samp...@nyumc.org Sent: Wednesday, January 14, 2015 11:04 AM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Adding a residue with an insertion code Along the same lines as Dialing’s recent post about inserting a residue, I’d like to ask: Is it possible to insert a residue with an insertion code in the residue number? For example, what’s the best way to insert residue 100A between residues 100 and 101? This situation arises frequently for me in antibody CDR loops, for example. I ran into it most recently just last week, and Coot wouldn’t allow this kind of insertion, even though the consecutively numbered residues were too far apart to be covalently linked. (In the terminal window, it explained that residue was not at a terminus.”) My workaround has been either to increment the residue numbers of the C-terminal portion of the chain, then renumber manually in a text editor; or, to position a lone amino acid in approximately the right spot, save the coordinates, copy them manually into the working PDB and adjust the numbering in a text editor, reload the PDB in Coot, and real space refine the loop with the insertion. Any suggestions for how to do this more efficiently? Thanks! Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Jan 14, 2015, at 9:54 AM, Emilia C. Arturo (Emily) ec...@drexel.edumailto:ec...@drexel.edu wrote: If the residues are consecutively numbered (Calculate Renumber residues), and are assigned the same chain ID (Calculate Change Chain ID), Coot might surprise you and link them on its own. On Wed, Jan 14, 2015 at 9:39 AM, Zhijie Li zhijie...@utoronto.camailto:zhijie...@utoronto.ca wrote: Have you done it? 1) Click “add residue...” 2) Click that “real space refine zone” button. You will see what will happen. From: Dialing Prettymailto:03f1d08ed29c-dmarc-requ...@jiscmail.ac.uk Sent: Wednesday, January 14, 2015 9:24 AM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Coot: How to connect N-terminal to neighbouring C-terminal Dear All, Suppose I delete a residue ( residue 100 for example) for outlier refinement, then I add the same residue at the C-terminal of residue 99 (by Add terminal residue function of the Coot). By coot, how can I connect the C-terminal of residue 100 to the N-terminal of residue 101? I am looking forward to getting your reply. DIaling renumber.sh
Re: [ccp4bb] Protein Crystallography challenges Standard Model precision
Greetings all - My interest in the rest of the discussion of experimental precision and error notwithstanding, and at the risk of stating explicitly what some might consider obvious, it seems to me that no one has actually (intentionally) asserted that they have determined the unit cell to 10^-20 meter precision. Rather, I find it far more likely that some program just output the floating point representation of a 3-decimal-place number without a proper 3-decimal-place format string (something like `printf(“%f”, _cell.length_a)` instead of `printf(“%5.3f”, _cell.length_a)`, perhaps). The extra digits are the “noise” of floating point rounding error. Notice the repeating 9’s and 0’s after 3 decimal places in each of the values in question: _cell.entry_id 4c69 _cell.length_a 100.152000427 == 100.152 _cell.length_b 58.3689994812 == 58.369 _cell.length_c 66.5449981689 == 66.545 _cell.angle_alpha 90.0 _cell.angle_beta99.2519989014 == 99.252 _cell.angle_gamma 90.0 Each of these “extra precise” numbers should simply have been output with only 3 decimal places. But I suppose this still doesn’t answer the original question of *which* program actually needs to be fixed. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Jul 23, 2014, at 5:44 PM, Bernhard Rupp hofkristall...@gmail.commailto:hofkristall...@gmail.com wrote: The representation is simply non-parsimonious. There is no meaning to the zepto-meter digits. Numquam ponenda est pluralitas sine necessitate. BR From: James Holton [mailto:jmhol...@lbl.gov] Sent: Wednesday, July 23, 2014 9:58 PM To: b...@hofkristallamt.orgmailto:b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Protein Crystallography challenges Standard Model precision Where is it written that compactness of representation and accuracy/precision are the same thing? Is 1/3 more or less precise than 0.333 ? If mmCIF were a binary floating-point format file, there would be more decimal places in the precision of the stored value for the unit cell, despite fitting into only 4 bytes instead of the 13 bytes of text some seem offended to see below. Would that be better? Or worse? -James Holton MAD Scientist On 7/22/2014 4:01 AM, Bernhard Rupp wrote: I am just morbidly curious what program(s) deliver/mutilate/divine these cell constants in recent cif files: data_r4c69sf # _audit.revision_id 1_0 _audit.creation_date ? _audit.update_record 'Initial release' # _cell.entry_id 4c69 _cell.length_a 100.152000427 _cell.length_b 58.3689994812 _cell.length_c 66.5449981689 _cell.angle_alpha 90.0 _cell.angle_beta99.2519989014 _cell.angle_gamma 90.0 # Maybe a little plausibility check during cif generation might be ok Best, BR PS: btw, 10^-20 meters (10^5 time smaller than a proton) in fact seriously challenges the Standard Model limits.. Bernhard Rupp k.-k. Hofkristallamt Crystallographiae Vindicis Militum Ordo b...@ruppweb.orgmailto:b...@ruppweb.org b...@hofkristallamt.org http://www.ruppweb.org/ --- This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =
Re: [ccp4bb] How to transfer non-frozen crystals with less disturbance?
Hi Meisam - We do this frequently, using pieces of spongy foam to pad the inside of a sturdy styrofoam shipping box, which keeps the temperature from fluctuating too much. This is then carried in a reusable grocery bag by one person whose sole responsibility it is to ensure it isn’t subjected to any jarring movements during the trip. We haven’t used anything quite so large as your 10+ μl drops, but this setup works fine with 24-well plates of ~2-4 μl hanging drops for the 1.5-hour drive to our friendly neighborhood synchrotron. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Jul 2, 2014, at 4:17 PM, Meisam Nosrati meisam.nosr...@gmail.commailto:meisam.nosr...@gmail.com wrote: Dear CCP4ers I need to transfer some crystals mainly in sitting drops to the site of data collection without freezing them. I do not know what is the best solution to secure the boxes in their place to minimize the disturbance. I am using the 24 well VDX plates with 10-80 microliter sitting drops. I have one or two hanging drop boxes as well with 10 microliter size drops. If you have any experience about this matter, I greatly appreciate, if you share it with me. Thanks Meisam Nosrati This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =
Re: [ccp4bb] Kabat, insertion codes refinement
Hi David - Your input files for Refmac (I’m not sure about Buster) should have LINKR records of the form: LINKRGLY L 95 THR L 95A gap This has worked fine for me in the past. The file I happened to excerpt here was refined with Refmac 5.6.0117 a few years back, but I doubt this has changed since then. I’d say to make sure you have all the appropriate LINKRs present (typically located between SSBOND and CRYST1 records) and try again. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Jun 16, 2014, at 6:07 AM, Hargreaves, David david.hargrea...@astrazeneca.commailto:david.hargrea...@astrazeneca.com wrote: 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.commailto:name.surn...@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. This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =
Re: [ccp4bb] HisTrap Trap
Hi Bernhard - Like Zhijie, we have also been using a Tangential Flow Filtration (TFF) system to address this same issue with serum-free 293 Freestyle media. Ours is the Minimate TFF system from Pall; there is also the Millipore Labscale system, and I’m sure others as well. I’ve done only limited direct testing, but I have seen 2- to 3-fold increased yield from a TFF’ed sample in comparison to a non-TFF'ed sample from the same batch of media. I concentrate the media 10x, then change the buffer by continuous diafiltration with 5-6 volumes of Ni-NTA loading/wash buffer. The advantages of TFF over plain dialysis are that it’s faster and uses less dialysis buffer, and due to the continuous agitation, the membrane is less likely to become clogged. On the downside, the membrane capsules are rather pricey, and although it’s mostly hands-off time, the process can still take quite a while, especially with lower-MWCO membranes. Good luck! Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On May 19, 2014, at 1:54 PM, Zhijie Li zhijie...@utoronto.camailto:zhijie...@utoronto.ca wrote: Hi Bernhard, I too suspect that it is some kind of metal chelating reagent causing the problem (possibly used in medium for carrying Fe2+, as the free Fe2+ is toxic to cells). One simple test would be to load a liter of the unused medium to the Ni2+ column and see what happens. Do you concentrate your medium before pull-down? If it is the chelating reagent in the medium, then concentrating the medium 10-30x may help a lot (also helps yield, since every affinity binding has a Kd). We do that regularly on tangential flow filter columns. It is a little weird that your first run was OK but the later ones suffered from Ni2+ loss. I wonder if you can try stripping the column with EDTA first and then loading it again with fresh NiCl2, every time before loading the medium. The reason to strip it is that I also worry that some Ni2+ on your column might have been partially replaced by some metal ions from the medium. (Loading 1L medium to a 1mL column does not sound like a great idea to me anyways...) Zhijie From: Bernhard Ruppmailto:hofkristall...@gmail.com Sent: Monday, May 19, 2014 10:13 AM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] HisTrap Trap Hi Fellows, my lab mates successfully expressed a glycoprotein in CHO cells in serum free medium, and the protein captures nicely on HisTrap Excel 1ml columns (obviously, high yield is not my problem…). We load ca 1L supernatant at 0.5 ml/min, and eluate with a steep imidazole gradient. 20mM Imidazole buffer for regeneration. Works fine (and often…see yield remark). Overcome by common crystallographers’ greed (nor creed), we switched to stable xfected HEK293, and cell free medium Gibco CD 293. The first run gave high final yields cheers. The second run less of either, because the small HisTrap column essentially dissolved – the medium collapsed, Ni leaches out, kaput as kaput goes. A 3rd run on a similar previously working column lead to the same result. Only thing changed was the cells and medium. Same buffers, same gradients, same Akta equipment, same lab techs. Before I improve the statistics by ruining further columns, has anybody experienced such a calamity that might be blamable on secret media components or similar? There is a mysterious ‘proprietary dispersant’ preventing cell adhesion quoted…. Best wishes, BR Bernhard Rupp b...@ruppweb.orgmailto:b...@ruppweb.org b...@hofkristallamt.orgmailto:b...@hofkristallamt.org http://www.ruppweb.org/ --- This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =
Re: [ccp4bb] [PyMOL] Farewell
Jason - I’d also like to express my appreciation for all you’ve done to benefit the PyMOL community. You have, time and again, proven yourself to be an extremely responsive and helpful leader both in developing the software and in enabling others to learn to use it. Like many on these lists, I’m sure, after hearing of Warren’s untimely passing 5 years ago, I was saddened of course, but also concerned about what would happen to PyMOL without him. Fortunately, it couldn’t have landed in better hands. I wish you all the best in your new endeavor. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Apr 24, 2014, at 9:29 AM, Thomas Holder thomas.hol...@schrodinger.commailto:thomas.hol...@schrodinger.com wrote: Dear Jason, thank you so much for you deep commitment and your invaluable contributions to PyMOL and the PyMOL community. You assumed responsibility for PyMOL and managed to give it a new home at Schrödinger. We are sorry to see you leave and will truly miss you here. To me personally, you have been a great mentor and guide and I can hardly enumerate what I learned from you. I owe you deep gratitude. It is my honour to now take the lead on PyMOL and serve the community and our sponsors as best as I can. The PyMOL team at Schrödinger is strongly dedicated to continuously improve PyMOL and keep the PyMOL spirit alive. Cheers, Thomas On 24 Apr 2014, at 05:00, Jason Vertrees jason.vertr...@gmail.commailto:jason.vertr...@gmail.com wrote: Greetings PyMOLers and CCP4ers worldwide, It has been my great pleasure to serve the PyMOL community both in a volunteer and professional capacity for the past decade. I have recently been given an offer I can't refuse—to follow one of my dreams—helping lead technology and science at a new startup. March 30th marked my last day at Schrödinger and supporting PyMOL. Because of my great fondness for PyMOL and its community, I will continue to operate the PyMOLWiki until I find it a suitable home. I started the PyMOLWiki in 2005 and since then it's been visited over 15,289,590 times! (If you would like to sponsor or host the wiki feel free to email me.) Now I can't imagine the PyMOL community without it. Last, I am truly humbled to have followed in the footsteps of Warren DeLano. He was an amazing man whose ideas and actions have touched the lives of millions, whether they know it or not. He is missed. It's been great fun. I wish you all the best. Cheers, -- Jason -- Jason Vertrees, PhD (e) jason.vertr...@gmail.commailto:jason.vertr...@gmail.com (o) +1 (603) 374-7120 -- Thomas Holder PyMOL Developer Schrödinger, Inc. This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =
Re: [ccp4bb] PyMol and Schrodinger
In addition to what has been mentioned by others, Open-Source PyMOL installation instructions for various platforms are available on the PyMOL Wiki: http://pymolwiki.org/index.php/Linux_Install http://pymolwiki.org/index.php/MAC_Install http://pymolwiki.org/index.php/Windows_Install Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Apr 23, 2014, at 1:02 PM, Guenter Fritz guenter.fr...@uni-konstanz.demailto:guenter.fr...@uni-konstanz.de wrote: Hi, if one is hesitant to compile it it, pymol is easily installed on a Linux box via yum ; enable EPEL repo ( in Redhat derivatives e.g. fedora, Centos, SciLinux) yum install pymol will install version 1.6 (latest version by Schrödinger is 1.7) Best, Guenter Hi, I have inquired at Schrodinger about the licensing for PyMol. I was surprised by their answer. The access to PyMol is only through a yearly licence. They do not offer the option of purchasing the software and using the obtained version without time limitation. This policy is very different from many other software packages, which one can use without continuing licensing fees and additional fees are only when an upgrade is needed. At least I believe that Office, EndNote, Photoshop and others are distributed this way. I also remember very vividly the Warren’s reason for developing PyMol, and that was the free access to the source code. He later implemented fees for downloading binary code specific for one’s operating system but there were no time restrictions on its use. As far as I recollect, Schrodinger took over PyMol distribution and development promising to continue in the same spirit. Please correct me if I am wrong. I find the constant yearly licensing policy disturbing and will be looking for alternatives. I would like to hear if you have had the same experience and what you think about the Schrodinger policy. Best wishes, Mirek This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =
Re: [ccp4bb] coloring by RMSD
Hi Tim - There is a script on the PyMOL Wiki that does just this: http://pymolwiki.org/index.php/ColorByRMSD. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Avenue New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Jan 29, 2014, at 12:43 PM, Colussi, Timothy timothy.colu...@ucdenver.edumailto:timothy.colu...@ucdenver.edu wrote: I was wondering if anybody knows of a program or script that you can run that will calculate local RMSDs between 2 superposed pdbs and color based on those local RMSDs or allow for the ability to color based on RMSD? I have a molecule that is similar in some aspects to another molecule but also very different in others and thought this would be a good way to show this graphically. Tim Colussi This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =
Re: [ccp4bb] making high res image in pymol
Hi Alex - You can also try reducing the value of `hash_max`http://www.pymolwiki.org/index.php/Hash_max (e.g. `set hash_max, 50`). The default value is 130; a lower number reduces the memory PyMOL tries to obtain for ray tracing. The trace will take longer, but hopefully will get you through without crashing. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.eduhttp://kong.med.nyu.edu/ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of A K [alek6...@gmail.com] Sent: Tuesday, January 28, 2014 10:27 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] making high res image in pymol Hi all, I am trying to generate a high resolution figure of a molecule together with its symmetry mates (250 A readius) for a poster. If I try to ray it, the pymol session crashes (perhaps too many molecules are open). Using png xxx.png, dpi=300 or dpi=600 command doesn't make any difference; the image is still kind of low resolution for A0 or A1. Any idea how I can generate this in pymol? (I am using the free version of pymol) Thank you in advance, Alex This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =
Re: [ccp4bb] Two P1 xtals with same xtal contacts give 2 different asymmetric units
Hi Gabriel - If the crystal contacts really are all the same, it sounds to me like your MR program may have just placed the monomers in different but equivalent symmetry-related positions between the two structures. Try moving the outlying monomers to the symmetrically related positions that would complete the tetramer. The PISA server may help with this. You could also do this from within COOT (Extensions PISA... PISA Assemblies...). Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Avenue New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Jan 22, 2014, at 3:50 PM, Gabriel Moreno gabe.li...@gmail.com wrote: Dear CCP4 Contributors, I have a bit of a mystery: Two co-crystals that I picked up from the same grid tray (the two conditions vary slightly in %PEG and [salt], both indexed as P1 (apo structure normally crystallizes in P3221). One dataset was indexed, integrated and scaled with HKL2000. The other was processed with MOSFILM (could not process in HKL2000). Downstream processing for both sets was done exactly the same in PHENIX. Though both asymmetric units contain two complete tetramers, the interesting thing is that the configuration of monomers is different between the solutions. One contains one complete tetramer, one trimer (with a void where the fourth monomer would be), and one monomer on off on its own. The asymmetric unit of the other dataset solution also contains a complete tetramer, but then has two dimers. Close analysis of contacts between symmetrically related molecules reveals that the crystal packing is exactly the same between the two solutions from the two datasets. Also, the Rwork and Rfree for both models are 0.18 and 0.20. Other quality indices are also comparable between the two sets. Here's my question: Does this phenomenon reveal anything important, or is this type of thing just seen sometimes with P1 solutions from crystals of the same protein and condition (more or less). I hope I have been clear. Thanks! Gabriel This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =
Re: [ccp4bb] how to get off a mailing list
In particular, selecting the option in your favorite email program to view all headers should reveal the following lines: List-Help: https://www.jiscmail.ac.uk/cgi-bin/webadmin?LIST=CCP4BB, mailto:lists...@jiscmail.ac.uk?body=INFO%20CCP4BB List-Unsubscribe: mailto:ccp4bb-unsubscribe-requ...@jiscmail.ac.uk List-Subscribe: mailto:ccp4bb-subscribe-requ...@jiscmail.ac.uk List-Owner: mailto:ccp4bb-requ...@jiscmail.ac.uk List-Archive: https://www.jiscmail.ac.uk/cgi-bin/webadmin?LIST=CCP4BB Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Avenue New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Dec 10, 2013, at 9:10 PM, Frances C. Bernstein f...@bernstein-plus-sons.com wrote: ANYONE ELSE WHO WANTS TO UNSUBSCRIBE SHOULD READ THIS FIRST. There are two aspects to any mailing list - the messages that are sent to everyone on the list and the management of the list. You told evryone subscribed to the list that you are not intereested in the discussions. If you look at the end of messages from a list you might see how to manage your subscription. Or you can google the name of the list and get to a web page where you can manage your subscription. Frances = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =
Re: [ccp4bb] Extracting .pdb info with python
Hi Grant - In addition to the other good suggestions, there is also the Biopython project's PDB parser. http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc148 Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center Old Public Health Building, Room 610 341 East 25th Street New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Jun 6, 2013, at 12:37 AM, GRANT MILLS gdmi...@students.latrobe.edu.aumailto:gdmi...@students.latrobe.edu.au wrote: Dear CCP4BB, I'm trying to write a simple python script to retrieve and manipulate PDB data using the following code: #for line in open(PDBfile.pdb): #if ATOM in line: #column=line.split() #c4=column[4] and then writing to a new document with: #with open(selection.pdb, a) as myfile: #myfile.write(c4+\n) Except for if the PDB contains columns which run together such as the occupancy and B-factor in the following: ATOM608 SG CYS A 47 12.866 -28.741 -1.611 1.00201.10 S ATOM609 OXT CYS A 47 14.622 -24.151 -1.842 1.00100.24 O My script seems to miscount the columns and read the two as one column, does anyone know how to avoid this? (PS, I've googled this like crazy but I either don't understand or the link is irrelevant) Any advice would help. Thanks for your time, Grant
Re: [ccp4bb] Best practice for transformed PDB coordinates?
Hi James - If you need the transformed coordinates in the original form for another program, this may not help, but if you just want to compare the packing between structures, have a look at PyMOL's matrix_copy command (http://pymolwiki.org/index.php/Matrix_copy). # load your files load file1.pdb load file2.pdb # generate symmetry mates for each file symexp file1_sym_, file1, file1, cutoff=10 symexp file2_sym_, file2, file2, cutoff=10 # group them together to keep things tidy group file1_sym, file1_sym* group file2_sym, file2_sym* # superimpose file2 onto file1 super file2, file1 # bring along file2_sym matrix_copy file2, file2_sym Hope that helps! Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center Old Public Health Building, Room 610 341 East 25th Street New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Mar 13, 2013, at 8:57 AM, James Davidson j.david...@vernalis.commailto:j.david...@vernalis.com wrote: Dear All, This is my first post to the group – so “Hello”! I have searched with not much success to find an answer to my question, so I thought I would try posting here for some expert advice. I should start by saying that I am not a crystallographer, but please don’t hold that against me! I am working with PDB files that are being aligned to reference structures, indirectly by (a) using the alignment tools in PyMOL, then (b) extracting the transformation matrix and re-applying this to the ATOM / HETATM entries outside of PyMOL (to avoid atom reordering / atom charging / etc that occurs when directly exporting from PyMOL). Anyway, what I wanted to know is is there a way that I could (or should?) reference that the PDB file coordinates have been transformed? Is there a way of preserving the ability of tools (eg PyMOL) to legitimately recreate the symmetry mates from the transformed coordinates if I eg apply the same transform to some of the data in CRYST1 and SCALE1, SCALE2, SCALE3? Or should I instead be adding ORIGX1, ORIGX2, ORIGX3 entries to show that a transformation has been applied? Or, indeed, should I just accept that my aligned coordinates should no longer be expected to recreate the packing environment? I have read through what I think is the correct section of the PDB documentation, but I must confess that my lack of expertise means I am in danger of approaching an old(?) problem through naïve trial and error! Any help / advice greatly appreciated. Kind regards James __ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.commailto:postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies 100 Berkshire Place Wharfedale Road Winnersh, Berkshire RG41 5RD, England Tel: +44 (0)118 938 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.comhttp://www.vernalis.com and click on the Company address and registration details link at the bottom of the page.. __
Re: [ccp4bb] Any tool to calculate surface accessible by ... another protein?
Hi Emmanuel - You might consider using MSMS. If you wish to visualize it, there is a PyMOL script available: http://pymolwiki.org/index.php/Msms. Relatedly, one should keep in mind that, while a 10 or 50 Angstrom probe will give you a general idea of accessible surface, if there is any shape complimentarity between two interacting proteins, it won't provide the whole picture. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center Old Public Health Building, Room 610 341 East 25th Street New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Feb 12, 2013, at 2:51 PM, Emmanuel Levy emmanuel.l...@gmail.commailto:emmanuel.l...@gmail.com wrote: Hello, I have been looking for a tool to measure the Protein accessible surface area, which could be defined exactly as the solvent ASA except with a probe of larger radius. Most tools that calculate ASA however do not work with a probe radius of a size equal to 10 or 50 Angstroms. Plus, ideally one would like to know the largest probe size that can access each atom or residue. So using classic ASA programs means one would have to run it ~30 times, each time with different probe radius for each protein. So my question is, do you know of a tool that could help us in obtaining this type of information? Thanks in advance for any hint, All the best, Emmanuel
Re: [ccp4bb] Coot 0.7 Saving Dialog opens behind main window
Terrific! I always thought it was X11-related as well. Thanks to Paul and Bernhard for the fix. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Ave MSB 398 New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Nov 7, 2012, at 1:53 PM, Jon Agirre jon.agi...@gmail.commailto:jon.agi...@gmail.com wrote: Thanks for the heads-up. Bernhard and I have fixed several of these window-order problems, but this one slipped by us (neither of us use a Mac :-). Fixed in 0.7.1 That's great news, Paul. Thank you for fixing it and others for pointing it out. I've been always quite convinced that it was an XQuartz.app (aka X11 for OS X) related bug and therefore never reported it. Jon -- Jon Agirre, PhD Unit of Biophysics (CSIC-UPV/EHU) http://www.ehu.es/jon.agirre http://sourceforge.net/projects/projectrecon/ +34656756888
Re: [ccp4bb] Coot 0.7 Saving Dialog opens behind main window
I agree, this is a frustrating feature. I tend to work around this by pressing Cmd-` (back-tick) to cycle through the X11 windows (this works for other applications as well), or by running Coot from within the directory containing the PDB file and using Ctrl-S to save with auto-incremented (e.g. -coot-0.pdb) filenames without having to open the Save dialog. Cheers, Jared Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center kong.med.nyu.edu From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eike Schulz [eike.sch...@embl.de] Sent: Tuesday, October 30, 2012 11:32 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Coot 0.7 Saving Dialog opens behind main window Dear Coot-users, I am running Coot-0.7 on OSX 10.6.8. Installation from the 'Scott'-package was no problem at all it runs very smoothly. However, whenever I want to save the coordinates the saving dialog open -behind- the main window. To be more precise: the coordinate molecule selector opens in front of it but the -file name selector- opens behind the main window. This is over the time a bit frustrating when you have to minimize/move the main window every time you want to save your structure. Does it happen to others as well, or is this specific to my system? If its possible, how could it be changed to open in front of the main window? Best regards Eike
Re: [ccp4bb] Stereo Microscope
Our setup is an Olympus SZX-10 with both 1x and 2x objectives and 10x eyepieces. It's nice having the different objectives for different things--a close up look at a tiny crystal requires the 2x, but the 1x is less bulky and has better depth-of-field, so it's better for freezing crystals. The DP21 camera is also nice, and provides for simple save-to-USB-drive photos and movies and scale bars, and also displays the field of view on an LCD monitor, which is nice for teaching and discussion among lab members. (To get the right value for the scale with a zoom microscope, though, it needs to be set up with the objectives as the zoom knob stop values and the adapter setting as the actual objective lens magnification. A bit of a workaround, but it's been fine for us.) Cheers, -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Ave MSB 398 New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Jul 18, 2012, at 2:26 PM, Roger Rowlett wrote: We have an Olympus SZX-12 microscope and are running a 1X objective (with polarizer) and a 10 X eyepiece. The scope will zoom from approximately 10X-90X magnification. At 90X a 400 nL drop in a 96-well plate will nearly fill the field. Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edumailto:rrowl...@colgate.edu On 7/18/2012 1:03 PM, PRASENJIT BHAUMIK wrote: Hello, I am planning to purchase a stereo microscope for visualizing crystallization drops. I would be very grateful if someone let me know the “objective” and “binocular eyepiece” specifications for SZX-7 or SZ-61 (Olympus) to get good magnification. Thank you. Regards, Prasenjit
[ccp4bb] NCONT chain selection issue
Hello all - Short version: NCONT from CCP4 v6.2.0 doesn't properly recognize comma-separated chain IDs with the source or target keyword. I'm trying to use NCONT to determine contacts between antibody chains and their bound epitope as part of a programmatic workflow. I'm using a Biopython Bio.Application.AbstractCommandline subclass to generate the command to be executed. It ends up looking something like this: ncont xyzin /path/to/.pdb eof source L,H target P maxdist 4 eof The problem is, the output only identifies the contacts between chains L and P. If I switch the order of the source to H,L it only identifies contacts between H and P. Similarly, if I switch the source and target selections (i.e. source P, target L,H) I see the same behavior. I'm using NCONT from CCP4 v6.2.0 on Mac OS 10.7.3 installed via Fink. A quick archives search produced a 2006 discussion about having the wrong ncont in the user's path, but mine appears to be correct: $ which ncont /sw/share/xtal/ccp4-6.2.0/bin/ncont Any suggestions on what might be going on here? I've pasted the full NCONT output below in case that might shed any light on the issue. Of course, I could work around this by running each pair of chains separately, but I'd prefer to do it in one fell swoop. Many thanks, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Ave MSB 329/398 New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ Here's the full output from NCONT with a test antibody-peptide complex from 1Q1J, first with L,H then with H,L as the source selections. $ ncont xyzin 1Q1J.pdb eof source P target L,H maxdist 4 eof ### ### ### ### CCP4 6.2: NCONTversion 6.2 : ## ### User: jared Run date: 1/ 3/2012 Run time: 14:22:07 Please reference: Collaborative Computational Project, Number 4. 1994. The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up. -- PDB file 1Q1J.pdb has been read in. -- Input cards Data line--- source P Data line--- target L,H Data line--- maxdist 4 -- Selected 73 source atoms Selected 1611 target atoms -- 23 contacts found: SOURCE ATOMS TARGET ATOMS DISTANCE /1/P/ 309(ILE). / CG2[ C]: /1/L/ 91(TRP). / CH2[ C]: 3.78 /1/L/ 32(TYR). / CG [ C]: 3.93 /1/L/ 32(TYR). / CD1[ C]: 3.47 /1/L/ 32(TYR). / CE1[ C]: 3.86 /1/P/ 312(GLY). / N [ N]: /1/L/ 91(TRP). / CH2[ C]: 3.97 /1/P/ 312(GLY). / CA [ C]: /1/L/ 91(TRP). / CH2[ C]: 4.00 /1/P/ 313(PRO). / N [ N]: /1/L/ 91(TRP). / CD2[ C]: 3.96 /1/P/ 313(PRO). / CA [ C]: /1/L/ 91(TRP). / CD1[ C]: 3.94 /1/P/ 313(PRO). / CB [ C]: /1/L/ 91(TRP). / CB [ C]: 3.82 /1/L/ 95(ALA).B/ O [ O]: 3.49 /1/L/ 91(TRP). / CG [ C]: 3.93 /1/P/ 313(PRO). / CG [ C]: /1/L/ 96(TRP). / NE1[ N]: 3.57 /1/L/ 91(TRP). / CB [ C]: 3.95 /1/L/ 96(TRP). / CD2[ C]: 3.73 /1/L/ 96(TRP). / CE2[ C]: 3.27 /1/L/ 96(TRP). / CZ2[ C]: 3.39 /1/L/ 96(TRP). / CH2[ C]: 3.90 /1/P/ 313(PRO). / CD [ C]: /1/L/ 91(TRP). / CE3[ C]: 3.91 /1/L/ 96(TRP). / CE2[ C]: 3.95 /1/L/ 96(TRP). / CZ2[ C]: 3.51 /1/L/ 96(TRP). / CH2[ C]: 3.65 /1/L/ 91(TRP). / CD2[ C]: 3.90 /1/P/ 314(GLY). / N [ N]: /1/L/ 95(ALA).B/ CB [ C]: 3.91 Total 23 contacts -- NCONT: Normal termination Times: User: 0.0s System:0.0s Elapsed: 0:00 $ ncont xyzin 1Q1J.pdb eof source P target H,L maxdist 4 eof ### ### ### ### CCP4 6.2: NCONTversion 6.2 : ## ### User: jared Run date: 1/ 3/2012 Run time: 14:22:26 Please reference: Collaborative Computational Project,
Re: [ccp4bb] NCONT chain selection issue
Thanks to Pius for the tip that I can use more than one source keyword. ncont xyzin my.pdb eof source L source H target P eof works like a charm! -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Ave MSB 329/398 New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Mar 1, 2012, at 4:47 PM, Pius Padayatti wrote: what if you add as follows ncont xyzin /path/to/.pdb eof source L,H target P maxdist 4 source H,L target P maxdist 4 eof will it run? and give both? just a thought This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =
Re: [ccp4bb] Off topic: vector map editing and DNA sequence alignment software
Hi Florian - I've used Geneious for a few years now and been pleased with it. Also a freemium business model: Basic version is free, and Pro version price depends on the term and type of license (student, academic/government, or commercial). I find the Basic version suits my limited molecular biology needs pretty well. They also have occasional Geneious Days (today happens to be one!) when the Basic version can use all the features of the Pro version. Available for Linux/Mac/Windows in both 32- and 64-bit. http://www.geneious.com/ -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Ave MSB 329 New York, NY 10016 212-263-7898 On Sep 27, 2011, at 2:32 PM, Luca Jovine wrote: Hi Florian, Have a look at Serial Cloner - it's free, runs on OS X, Linux and Windows, and is really quite powerful - including the ability to export single or multiple sequences to FASTA format text files (however, it can only align two sequences at the time I'm afraid): http://serialbasics.free.fr/Serial_Cloner.html HTH, Luca Luca Jovine, Ph.D. Assistant Professor EMBO Young Investigator Karolinska Institutet Department of Biosciences and Nutrition Center for Biosciences Hälsovägen 7, SE-141 83 Huddinge, Sweden Voice: +46.(0)8.524-81136 FAX: +46.(0)8.6081-501 E-mail: luca.jov...@ki.semailto:luca.jov...@ki.se W3: http://jovinelab.orghttp://jovinelab.org/ On 27 Sep 2011, at 17:42 , Florian Schmitzberger wrote: Dear All, What type of software are people commonly using these days for vector/plasmid map editing, making/visualizing vector maps, and aligning (small to medium size) DNA sequencing data? Preferably, it should not be too expensive and be able to write text files, readable by other programs. I am familiar with VectorNTI, which is great for vector visualization and editing; but I find it somewhat expensive. Sequencher seems good to quickly align DNA sequences (such as from DNA sequencing) with templates, but is not free. I have been using ApE for while for alignments, but aligning many sequences is more cumbersome than in Sequencher; I have not tested if Sequencher is good at visualizing and editing plasmid maps. Ideally, I would like to have a single program for both purposes (vector editing and DNA sequence comparison). Does something like that exist? What are the alternatives to above programs? Thank you in advance. Florian --- Florian Schmitzberger, PhD Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, Seeley G. Mudd 123 Boston, MA 02115, US Tel: 001 617 432 5603 /PRE html body br / This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.br / = /body /html PRE
Re: [ccp4bb] Coot Bad magic number errors
Hi Bill - Thanks for the fix. I'll make the changes on the affected computers. Alternatively, I may just have them download the newest package, which appears to work fine on my machine. Thanks again for the help, and for providing these builds to the community! Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center New York, NY 10016 212-263-7898 On Mar 10, 2011, at 5:46 PM, William G. Scott wrote: Sorry about this. Issue the command sudo perl -pi -e 's|/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6\:/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5\:||g' /Library/Coot/bin/coot and that will fix it. I'll make a new one. Bill On Mar 10, 2011, at 7:55 AM, Sampson, Jared wrote: Hi all - Two of the grad students in our structural biology course are having similar problems installing Coot on their Mac computers using the stand-alone packageshttp://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot from Bill Scott's Crystallography on OS X website. I've pasted the Terminal outputs below from each of their machines below. They're both getting Python magic number errors, which from what I know result from one Python version trying to run a .pyc file created with another Python version, but I'm not sure exactly how to work around it in the context of the stand-alone package. The students aren't planning to do much in the structural realm outside the course, and I don't want to have to go through installing Xcode and Fink to compile on their own, since they probably won't need it much past this one assignment. Any suggestions would be greatly appreciated. Thanks! Jared Sampson First student (3 week-old Macbook Pro, 10.6.6, stand-alone package for Version 0.6.2-pre-1-3250) $ coot Acquiring application resources from /Library/Coot/share/coot/cootrc INFO:: splash_screen_pixmap_dir /Library/Coot/share/coot/pixmaps INFO:: Colours file: /Library/Coot/share/coot/colours.def loaded There are 118 data in /Library/Coot/share/coot/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ALA.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ASP.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ASN.cif [... and a bunch more monomers ...] There are 2 data in /Library/Coot/share/coot/lib/data/monomers/u/UR.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/h/HOH.cif There are 1 data in /Library/Coot/share/coot/lib/data/monomers/ener_lib.cif sbase monomer dir: /share/sbase sbase files not found in /share/sbase Reading coordinate file: /Library/Coot/share/coot/standard-residues.pdb PDB file /Library/Coot/share/coot/standard-residues.pdb has been read. Spacegroup: P 1 Cell: 40.631 109.18 93.243 90 90 90 initalize graphics molecules...done. (filter-fileselection-filenames-state) (get-active-map-drag-flag) ImportError: Bad magic number in /System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site.pyc second student (Macbook, 10.6.5, also Version 0.6.2-pre-1-3250) $ /usr/local/bin/coot Acquiring application resources from /Library/Coot/share/coot/cootrc INFO:: splash_screen_pixmap_dir /Library/Coot/share/coot/pixmaps INFO:: Colours file: /Library/Coot/share/coot/colours.def loaded There are 118 data in /Library/Coot/share/coot/lib/data/monomers/list/mon_lib_list.cif/ There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ALA.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ASP.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ASN.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/c/CYS.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/g/GLN.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/g/GLY.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/g/GLU.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/p/PHE.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/h/HIS.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/i/ILE.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/l/LYS.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/l/LEU.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/m/MET.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/e/ETH.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/c/CIT.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/AR.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/AD.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/c/CR.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/c/CD.cif There are 2 data in /Library
[ccp4bb] Coot Bad magic number errors
Hi all - Two of the grad students in our structural biology course are having similar problems installing Coot on their Mac computers using the stand-alone packageshttp://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot from Bill Scott's Crystallography on OS X website. I've pasted the Terminal outputs below from each of their machines below. They're both getting Python magic number errors, which from what I know result from one Python version trying to run a .pyc file created with another Python version, but I'm not sure exactly how to work around it in the context of the stand-alone package. The students aren't planning to do much in the structural realm outside the course, and I don't want to have to go through installing Xcode and Fink to compile on their own, since they probably won't need it much past this one assignment. Any suggestions would be greatly appreciated. Thanks! Jared Sampson First student (3 week-old Macbook Pro, 10.6.6, stand-alone package for Version 0.6.2-pre-1-3250) $ coot Acquiring application resources from /Library/Coot/share/coot/cootrc INFO:: splash_screen_pixmap_dir /Library/Coot/share/coot/pixmaps INFO:: Colours file: /Library/Coot/share/coot/colours.def loaded There are 118 data in /Library/Coot/share/coot/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ALA.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ASP.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ASN.cif [... and a bunch more monomers ...] There are 2 data in /Library/Coot/share/coot/lib/data/monomers/u/UR.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/h/HOH.cif There are 1 data in /Library/Coot/share/coot/lib/data/monomers/ener_lib.cif sbase monomer dir: /share/sbase sbase files not found in /share/sbase Reading coordinate file: /Library/Coot/share/coot/standard-residues.pdb PDB file /Library/Coot/share/coot/standard-residues.pdb has been read. Spacegroup: P 1 Cell: 40.631 109.18 93.243 90 90 90 initalize graphics molecules...done. (filter-fileselection-filenames-state) (get-active-map-drag-flag) ImportError: Bad magic number in /System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site.pyc second student (Macbook, 10.6.5, also Version 0.6.2-pre-1-3250) $ /usr/local/bin/coot Acquiring application resources from /Library/Coot/share/coot/cootrc INFO:: splash_screen_pixmap_dir /Library/Coot/share/coot/pixmaps INFO:: Colours file: /Library/Coot/share/coot/colours.def loaded There are 118 data in /Library/Coot/share/coot/lib/data/monomers/list/mon_lib_list.cif/ There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ALA.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ASP.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/ASN.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/c/CYS.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/g/GLN.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/g/GLY.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/g/GLU.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/p/PHE.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/h/HIS.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/i/ILE.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/l/LYS.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/l/LEU.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/m/MET.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/e/ETH.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/c/CIT.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/AR.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/a/AD.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/c/CR.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/c/CD.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/g/GR.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/g/GD.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/t/TD.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/u/UR.cif There are 2 data in /Library/Coot/share/coot/lib/data/monomers/h/HOH.cif There are 1 data in /Library/Coot/share/coot/lib/data/monomers/ener_lib.cif sbase monomer dir: /share/sbase sbase files not found in /share/sbase Reading coordinate file: /Library/Coot/share/coot/standard-residues.pdb PDB file /Library/Coot/share/coot/standard-residues.pdb has been read. Spacegroup: P 1 Cell: 40.631 109.18 93.243 90 90 90 initalize graphics molecules...done. (filter-fileselection-filenames-state) (get-active-map-drag-flag) ImportError: Bad magic number in
Re: [ccp4bb] Coot Bad magic number errors
Hi Ben and Pete - I did think about deleting (or moving) the .pyc files, but in
the newer of the two students' computers (3 weeks out of the box), there wasn't
a site.py file in that directory, only .pyc and .pyo, so I figured I'd better
not mess with it.
Thanks for the suggestions so far. I'll see if I can get the students back
here again and try editing the wrapper script.
Cheers,
Jared
On Mar 10, 2011, at 12:05 PM, Pete Meyer wrote:
Ben Eisenbraun wrote:
Hi Pete,
Usually python will regenerate pyc files as needed (assuming the source
files are available). So find $COOTDIR -name *.pyc -exec rm {} \;
might be worth a try.
This is true, but the import error is being generated by Coot trying to
read the _system_ .pyc files:
Whoops - missed that.
ImportError: Bad magic number in
/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site.pyc
ImportError: Bad magic number in
/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site.pyc
And I would be hesitant to delete those. That said, in theory it really
shouldn't matter.
-ben
--
| Ben Eisenbraun
| SBGrid Consortium | http://sbgrid.org |
| Harvard Medical School | http://hms.harvard.edu |
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Re: [ccp4bb] Stereo Microscope advice
Hi Kevin - 1) I can only imagine that LEDs would produce vastly less heat than halogen lamps. In general, they are small, efficient, long-lasting and don't produce a lot of heat. Here's a start for more information http://en.wikipedia.org/wiki/Light-emitting_diode . Also, a quick search got me this page http://www.tedpella.com/mscope_html/2282.htm which has what appears to be all the options you mentioned. I'm sure other manufacturers have similar models. 2) We are generally satisfied with our older model Olympus . If you will be looking at drops smaller than 1μl total volume (e.g. from a mosquito or other sub-μl liquid handler) I'd recommend at least a 2x objective lens. Some models (like the one linked above) have an option to direct the light to a camera mount instead of the eyepieces--get one of these if possible! Trying to hold a camera (or smartphone) steady in front of one of the eyepieces gets old after a while. Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center New York, NY 10016 212-263-7898 On Jan 23, 2011, at 8:35 PM, Kevin Corbett wrote: Hi everyone, I'm looking to buy a new stereo microscope for looking at crystal trays, and was wondering if anyone could help me answer a few questions: 1) Does anyone have experience with LED illumination in the microscope base? I'm worried that there might be excessive heating of the base, as this is a huge problem with integrated halogen lamps. Also, can these stands with LED's accommodate polarizers? 2) Any really good (or really bad) experiences with specific manufacturer/models? Any advice is much appreciated. Thanks very much, Kevin Kevin Corbett, Ph.D. Stephen C. Harrison Lab Harvard University Medical School corbett (at) crystal.harvard.edu (617)-432-5605 This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =
Re: [ccp4bb] pyMol--set up view through one axis of the unit cell
Hi Jerry, If your protein has an NCS symmetry axis parallel to a cell edge, you can try using the “orient” command. http://www.pymolwiki.org/index.php/Orient Best, Jared On 9/3/10 7:31 PM, James Stroud xtald...@gmail.com wrote: On Sep 3, 2010, at 4:03 PM, Jerry McCully wrote: It is a Pymol question. How can I set up the view through one axis of the unit cell? By eye. Use orthoscopic view to help. Show the unit cell as a guide: http://www.pymolwiki.org/index.php/Cell James -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center New York, NY 10016 (212) 263-7898 This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =
