[ccp4bb] loading maps in coot using EDS
Hi all, I was trying to get maps using the *fetch PDB and Map using EDS option* in coot, however the map would not open I am using coot version 0.6.2 was wondering if anybody else had similar problems and how to fix this, the following is the error message I get. It used to work fine with a previous version of coot. CCP4MTZfile: open_read - File missing or corrupted: coot-download/3tvn_sigmaa.mtz INFO:: not an mtz file: coot-download/3tvn_sigmaa.mtz ERROR: no f_cols! ERROR: no phi_cols! valid_labels(coot-download/3tvn_sigmaa.mtz,FOFCWT,PHFOFCWT,,0) returns 0 CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read System signal 0:Success (Error) raised in ccp4_file_rarch CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read System signal 0:Success (Error) raised in ccp4_file_readchar CCP4 library signal mtz:Read failed (Error) raised in MtzGet CCP4MTZfile: open_read - File missing or corrupted: coot-download/3tvn_sigmaa.mtz INFO:: not an mtz file: coot-download/3tvn_sigmaa.mtz ERROR: no f_cols! ERROR: no phi_cols! WARNING:: label(s) not found in mtz file coot-download/3tvn_sigmaa.mtz FOFCWT PHFOFCWT WARNING:: -1 is not a valid molecule in set_scrollable_map thanks, Shya
Re: [ccp4bb] loading maps in coot using EDS
Hi, Thanks, I think the problem is with the EDS server as I tried numerous pdb files (not just the 3TVN) and none of them worked so far. Shya On Wed, Aug 8, 2012 at 5:47 PM, Paul Emsley paul.ems...@bioch.ox.ac.ukwrote: On 08/08/12 21:39, Shya Biswas wrote: Hi all, I was trying to get maps using the *fetch PDB and Map using EDS option* in coot, however the map would not open I am using coot version 0.6.2 was wondering if anybody else had similar problems and how to fix this, the following is the error message I get. It used to work fine with a previous version of coot. If you have 0.7-pre Extensions - Get from PDBe (I like to keep my refmac pretty up to date). On 08/08/12 22:28, Dale Tronrud wrote: It appears that the Electron Density Server could not calculate a map for 3TVN. The EDS doesn't speak to me at all. Maybe I am asking in the wrong places... These cryptic messages are what you get from Coot when there is no map on the server. ... no mtz file on the server (which probably amounts to the same thing). I can see from the RCSB web page that there is no EDS link in the Experimental Details section, which also happens when the EDS comes up empty. When the EDS fails to calculate a reasonable map for an entry they do not tell us why. Coot downloads the web page too and parses it for message referring to the non-existence of a reliable map. It lets you know if it finds such a thing. If they knew what the problem was they would fix it themselves. They remain silent hoping that the authors of the entry will contact them and give them some help. It is absolutely amazing that they can calculate as many maps as they do. wwPDBs are better at making parsable/convertible data these days (in my experience). Paul.
[ccp4bb] MR solution
Hi all, I have a dataset that I scaled in p212121 with cell dimension a=28.9 b=67.1 and c=93.5 however I do not get a right MR solution with this. So I went back and scaled it in p222 space group and asked phaser to find the right spacegroup solution for it, this time phaser gave me the right solution and in p212121 space group. By right solution I mean the molecule is a dimer and has to be oriented in a particular way, which I get only when I use p222 scaled data. I am puzzled and would like to know if anyone can explain this. thanks, Shya
Re: [ccp4bb] Questions on unknown density?
Hi, Try modeling a zinc close to the histidine and then do one round of refinement the density will improve close to that area, generally a zinc ion coordinated to histidine also has a water molecule close to the zinc. HTH, Shya On Tue, Jun 19, 2012 at 5:47 AM, Lianying Jiao bio...@gmail.com wrote: Dear all, As in *Screenshot2.png*, some unknown density exists around a histidine. The crystallization condition contains Zn(OAc)2, PEG3350, pH4.5. Do anyone tell me what is it? Thanks in advance. Sincerely, Lianying Jiao
Re: [ccp4bb] pdb and cif file generation from smiles string
Hi Paul The pdb file that you send me does not have the right geometry, have tried phenix elbow, same problem not the right geometry however in consultation with Nigel it looks like a special symbol had to be inserted in smiles, he send me a file that looks like correct. thanks to all who helped, Shya On Wed, May 9, 2012 at 12:55 PM, Paul Emsley paul.ems...@bioch.ox.ac.ukwrote: On 09/05/12 17:08, Shya Biswas wrote: Hi all, I am having trouble generating a pdb and cif file from the following smiles string: O=C(C[N+]23CN1CN(CN(C1)C2)C3)**c45c45 Prodrg fails to run when i draw the molecule in JME editor was wondering if anyone knows a better program which does this kind of job. I believe that this is supposed to work: cprodrg XYZIN mol.smi XYZOUT mol.pdb LIBOUT mol.cif ! MINI PREP END ! (it went boom when I tried it though - but perhaps you can compile it better - or otherwise make it work. I should add, for balance, that I use MDL molfiles with cprodrg and they work considerably more robustly). Paul.
Re: [ccp4bb] pdb and cif file generation from smiles string
does not give correct files needed to insert special symbol @ after N+ Shya On Wed, May 9, 2012 at 2:57 PM, Pavel Afonine pafon...@gmail.com wrote: Shya, Elbow command: phenix.elbow --smiles=O=C(C[N+]23CN1CN(CN(C1)C2)C3)c45c45 will give you CIF and PDB files. I just tried, it took 5 minutes to calculate them on my mac. Pavel On Wed, May 9, 2012 at 9:08 AM, Shya Biswas shyabis...@gmail.com wrote: Hi all, I am having trouble generating a pdb and cif file from the following smiles string: O=C(C[N+]23CN1CN(CN(C1)C2)C3)c45c45 Prodrg fails to run when i draw the molecule in JME editor was wondering if anyone knows a better program which does this kind of job. thanks in advance, shya
[ccp4bb] P21221 to P21212 conversion
Hi all, I was wondering if anyone knows how to convert the P21221 to P21212 spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I got a correct MR solution in P21221 spacegroup. I have a script file that runs with scalepack but was wondering if there is an easier way to do it with HKL2000 gui mode. thanks, Shya
Re: [ccp4bb] P21221 to P21212 conversion
Hi, My case is old b is changed to c (scenario 2 as you explained) or hkl is changed to hlk. Thanks for the help Shya On Mon, May 7, 2012 at 4:33 PM, Ethan Merritt merr...@u.washington.eduwrote: On Monday, May 07, 2012 01:09:25 pm Shya Biswas wrote: Hi all, I was wondering if anyone knows how to convert the P21221 to P21212 spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I got a correct MR solution in P21221 spacegroup. Shya: Scaling is done in a point group, not a space group. The point group P222 contains both space groups P2(1)22(1) and P2(1)2(1)2, so your original scaling is correct in either case. It is not clear from your query which of two things happened: 1) The MR solution kept the same a, b, and c axis assignments but made a different call on whether each axis did or did not correspond to a 2(1) screw. In this case you don't need to do anything to your files. Just make sure that you keep the new space group as you go forward into refinement. 2) The MR solution kept the orginal screw-axis identifications but permuted the axes to the standard setting (non-screw axis is labelled c). In this case you will need to construct a file containing the permuted indices. For example, the reflection originally labeled (h=1 k=2 l=3) is now (h=3 k=1 l=2). There are several programs that can help you do this, including the HKL2000 GUI. But you do not need to go back into HKL if you don't want to. You could, for example, use the ccp4i GUI to select - Reflection Data Utilities - Reindex Reflections Define Transformation Matrix by entering reflection transformation h=l k=h l=k Ethan I have a script file that runs with scalepack but was wondering if there is an easier way to do it with HKL2000 gui mode. thanks, Shya -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] P21221 to P21212 conversion
Hi Matt, It worked really well in HKL 2000 reindex option, sorry about the confusion before, I wanted hkl to lhk. as you pointed out the second one gave me what I wanted. thanks, Shya On Mon, May 7, 2012 at 4:47 PM, Matthew Franklin mfrank...@nysbc.orgwrote: On 5/7/12 4:09 PM, Shya Biswas wrote: Hi all, I was wondering if anyone knows how to convert the P21221 to P21212 spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I got a correct MR solution in P21221 spacegroup. I have a script file that runs with scalepack but was wondering if there is an easier way to do it with HKL2000 gui mode. thanks, Shya Hi Shya - Under the Scale tab of HKL2000, you'll see a button near the bottom labeled Reindex. Clicking this brings up a dialog box with the reindexing conventions appropriate to your spacegroup. For P orthorhombic, there are only two choices: hkl - klh, or hkl - lhk. If you have P21221, and want to go to P21212, you want hkl -lhk. HOWEVER, there seems to be a bug in this particular reindexing (or maybe the options are written confusingly). You want to choose the wrong option (number 2 in the list presented), as the two options seem to be reversed. You'll know that you got it right by inspection of the scaling log file - look at the systematic absence table at the bottom. Also check that the unit cell axes were permuted in the correct way - you want your old b axis to be your new c axis. Once you select the correct reindexing (make sure you apply it to all datasets being scaled at the same time), you click Reindex in the popup dialog, and this triggers another round of scaling with the reindexing included. This reindexing is sticky - you don't need to select it again for subsequent rounds of scaling. Hope that helps - feel free to contact me if you want more explanation. - Matt -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374
Re: [ccp4bb] P21221 to P21212 conversion
Hi, i just repeated the MR using the reindexed dataset (hkl to lhk) and it gave me the right solution. thanks, Shya On Mon, May 7, 2012 at 5:39 PM, Edward A. Berry ber...@upstate.edu wrote: Now given that the MR soluiton was obtained in the (preparing to duck) nonstandard setting, what is the transform to apply to that solution in pdbset to get the solution in the standard setting? Or is it easier to just repeat the MR? eab Shya Biswas wrote: Hi Matt, It worked really well in HKL 2000 reindex option, sorry about the confusion before, I wanted hkl to lhk. as you pointed out the second one gave me what I wanted. thanks, Shya On Mon, May 7, 2012 at 4:47 PM, Matthew Franklin mfrank...@nysbc.org mailto:mfrank...@nysbc.org wrote: On 5/7/12 4:09 PM, Shya Biswas wrote: Hi all, I was wondering if anyone knows how to convert the P21221 to P21212 spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I got a correct MR solution in P21221 spacegroup. I have a script file that runs with scalepack but was wondering if there is an easier way to do it with HKL2000 gui mode. thanks, Shya Hi Shya - Under the Scale tab of HKL2000, you'll see a button near the bottom labeled Reindex. Clicking this brings up a dialog box with the reindexing conventions appropriate to your spacegroup. For P orthorhombic, there are only two choices: hkl - klh, or hkl - lhk. If you have P21221, and want to go to P21212, you want hkl -lhk. HOWEVER, there seems to be a bug in this particular reindexing (or maybe the options are written confusingly). You want to choose the wrong option (number 2 in the list presented), as the two options seem to be reversed. You'll know that you got it right by inspection of the scaling log file - look at the systematic absence table at the bottom. Also check that the unit cell axes were permuted in the correct way - you want your old b axis to be your new c axis. Once you select the correct reindexing (make sure you apply it to all datasets being scaled at the same time), you click Reindex in the popup dialog, and this triggers another round of scaling with the reindexing included. This reindexing is sticky - you don't need to select it again for subsequent rounds of scaling. Hope that helps - feel free to contact me if you want more explanation. - Matt -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374 tel:%28212%29%20939-0660%**20ext.%209374
[ccp4bb] JME editor in PRODRG
Hi all, I was wondering if anyone had problems with drawing molecule using JME editor in PRODRG? If yes then how do I fix it? I could not draw molecule in the JME editor in the PRODRG webpage recently and JAVA is already installed in my computer. thanks, Shya
Re: [ccp4bb] Aggregated protein for crystallization
Hi, Did you try using a different column like Superose 6? This column works well to separate large molecular weight proteins including oligomers. Ideally if your solution is not cloudy (coming out of void volume) those are not aggregates those might be oligomers. HTH, Shya On Tue, Feb 21, 2012 at 6:21 PM, Raji Edayathumangalam r...@brandeis.eduwrote: Hi Folks, As crazy as it sounds, if you have crystallized and managed to solve the structure of a protein from aggregated protein, please could you share your experience. After many constructs, many many expression schemes and after the usual rigmarole of optimization that is also often discussed on ccp4bb (buffers, glycerol, salt concentrations, pH, detergent, additives etc.), I now have a decently expressing truncated construct for my protein (80 kDa) that is pure but aggregated (elutes in the void volume from a Superdex200 column). I am tempted to make a boatload of aggregated protein and set up some crystal trays (after perhaps testing by CD). So I'd like to hear from folks who have been successful in solving structures from aggregates when many many known and tested optimization methods still leave one with aggregated protein. Thanks. Raji -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University
Re: [ccp4bb] Manually setting 96 wells plates with lower volume samples!
Hi, I am routinely using the gryphon robot from Art Robbins.This instrument can dispense 0.02microlitre at minimum. Your drops can dry out if you use such low volumes you have to be really fast. You can set up 0.2 to 0.1 micro litre drops using this for 96 well plates however the instrument needs to be calibrated well sometimes with low volume drop the robot dispenses the protein at one corner of the well and the precipitant at another end so eventually the outcome is the mixing of the precipitant with your protein is not happening. However with 0.2micro litre drop or higher this is less of a problem. HTH, shya On Fri, Nov 18, 2011 at 9:34 AM, xaravich ivan xaravich.i...@gmail.comwrote: Hi, I apologize in advance as it is not a ccp4 related question, but over the years, CCP4bb is synonymous with protein crystallographers virtual university, at least for me. Ok, now I do not have an easy access to crystallization robot, so I was hoping if someone here have ever used the 96 well plates for manually setting drops with much lower solution/sample volumes (0.1-0.2micro litres). I heard about a clicker syringe that can be used to manually add lesser volumes but I am not sure how to go about it. Please let me know if you are aware of or are routinely setting 96 well trays with much lower volumes of crystallization solutions as well as samples, manually. thanks in advance, ivan
Re: [ccp4bb] Manually setting 96 wells plates with lower volume samples!
sorry totally misunderstood your question, however if you can ship your protein i can always try to setup a tray for you. Shya On Fri, Nov 18, 2011 at 9:34 AM, xaravich ivan xaravich.i...@gmail.comwrote: Hi, I apologize in advance as it is not a ccp4 related question, but over the years, CCP4bb is synonymous with protein crystallographers virtual university, at least for me. Ok, now I do not have an easy access to crystallization robot, so I was hoping if someone here have ever used the 96 well plates for manually setting drops with much lower solution/sample volumes (0.1-0.2micro litres). I heard about a clicker syringe that can be used to manually add lesser volumes but I am not sure how to go about it. Please let me know if you are aware of or are routinely setting 96 well trays with much lower volumes of crystallization solutions as well as samples, manually. thanks in advance, ivan
Re: [ccp4bb] COOT library
Hi Eric, Once you merge the ligand coordinates to your model and do one round of refinement, the next time you open up coot and try using the real space refinement it never works (even if you import cif dictionary of your ligand) so not sure if its a problem with coot. Did anyone else had similar problems? thanks, Shya On Wed, Aug 17, 2011 at 12:10 PM, Eric Karg harvard...@yahoo.com wrote: Thanks for the suggestions. I could solve the problem by using the setenv command to the coot directory,but I still cannot use the Real Space Refine Zone in Coot because the names are not compatible. I'm trying to build an RNA molecule by the way. Any suggestions? Eric
Re: [ccp4bb] output individual redundancies
Hi, I was wondering if anyone knows what HKL 2000 does? Does it merge all partials and treat it as one, because often times I noticed with increase in partials the redundancy increases. Shya On Fri, Jul 15, 2011 at 1:24 PM, James Holton jmhol...@lbl.gov wrote: At the risk of asking a question to which I should already know the answer: do partials count as redundancy? That is, in SCALA, is the number of observations the number of recorded spots? Or is it the number of recorded spots after adding partials? If it is the latter, what happens if you collect more than 360 degrees of data? Does the second pass through a given unmerged hkl index count as more partials or is it now somehow upgraded to an independent observation? Then again, in Eastern English the word redundancy has a negative connotation, and the output of SCALA actually uses the word multiplicity. I wonder if that makes unmerged partials redundant? -James Holton MAD Scientist On 7/15/2011 8:09 AM, Ed Pozharski wrote: On Fri, 2011-07-15 at 09:26 +0100, Phil Evans wrote: Ed. You could count them from the unmerged output as you say, or I could make you a special version of SCALA or Aimless maybe next week Phil, that would be fantastic! Hope there is broader interest in such option (beyond Robbie and myself). I'll try unmerged output in the meantime. Ed.
