Re: [ccp4bb] Direct method solution at 1.15A
At this resolution you may/ should be able to find anamalous scatterers using the anom signal from P and S. the SHELXC/D/(E) package is very good at this! Once you have the sites for the heavier atoms I would expect most direct methods programs couild extend that sub-structure. Certainly ACORN seems to work without resolution limits, and give excellent final maps. Eleanor On 09/24/2011 04:03 AM, Fan, Hai-fu wrote: Dear Yuri, If you have located all the heavy atoms (sulfur and phosphor) correctly, you could try sulfur-SAD phasing using the program OASIS. This program has a record of solving a 1206 residues protein with SAD signals from 22 sulfur atoms scattered under Cu-Ka radiation and a record of solving a 213 residues protein with SAD signals from 2 sulfur atoms scattered under Cr-Ka radiation. By the way please note that the OASIS in CCP4 6.2.x is not the uptodate version. You can get a better version from http://cryst.iphy.ac.cn. The latest version will be available on the website in the coming October. Best regards, Hai-fu On Sat, Sep 24, 2011 at 2:49 AM, Yuri Pompeuyuri.pom...@ufl.edu wrote: Hello everyone, I have a data set99% completeness to 1.15A This is a 400 amino acid long protein and it has 7 Met (Sulfur peaks around 20sigma) And a tightly bound phosphate (P peak around 22sigma) Could I try and solve this directly or is it crazy idea? If so what program should I try? thanks Yuri
[ccp4bb] Post-doctoral Position in Structural Biology and Membrane Trafficking: CIC bioGUNE, Bilbao, Spain
The position is available in the laboratory of Aitor Hierro to work in the area of *structural biology* and *membrane trafficking*. We study the interactions, in molecular mechanistic detail, that underlie the selectivity of cargo transport vesicles for recognizing the correct target membrane. We do this using a combination of structural, biochemical and biophysical approaches. The focus of the project is on a series of soluble and membrane associated proteins (and their complexes), which coordinate tethering and fusion of transport vesicles from endosomes to the Golgi apparatus (for references, see PMDIs: 20615984; 21183348 and 17891154). The position requires PhD. degree with a strong background in molecular biology for heterologous recombinant protein expression in different hosts such Escherichia coli, insect cell-baculovirus and mammalian cells. Previous experience in X-ray crystallography and the use of biophysical or biochemical techniques for the characterization of protein complexes would be an advantage. Local resources at the institute include shared state-of-the-art facilities for high throughput crystallization, and in-house X-ray data collection. We also have regular synchrotron beamtime. Other biophysical instrumentation such DLS, ITC, DSC, CD, SEC-MALLS and fluorescence spectrometers are also available. For testing our structural and *in vitro* analyses we have complementary collaborations with leading laboratories in the cell biology field. The institute is well-situated with numerous groups working in X-ray crystallography, NMR and EM that form a critical mass in the area of structural biology. This position offers an excellent opportunity for an experienced protein biochemist/biophysicist or cell biologist to complement his or her expertise in X-ray crystallography working at the juncture between structural biology and cell biology. The position is available beginning December 2011 and funded for 3+2 years. Applications will be accepted until the position is filled. * Interested candidates* please email a cover letter, your CV, and names (including email address) of at least two referees to *r...@cicbiogune.es* with *ref. 3131*in the subject.
Re: [ccp4bb] MOLREP fails when using input fixed model
Dear Zhong Chen and CCP4 users, I get the very same error on a Centos 5 box. Is there a solution yet? Best regards, Guenter Dear all, Recently, I used MOLREP to molecular replacement. My OS is fedora 14 and CCP4 version is the newest one ccp4-6.2.0 . When I run a pdb file and mtz by MOLREP without input fixed model, everything is right. However, when I run it by MOLREP when using input fixed model. The error is attached below. At line 1260 of file /usr/local/xtal/ccp4-6.2.0/src/molrep_/molrep.f Fortran runtime error: End of record Actually, my ccp4 is installed at /home/software/ccp4, not at /usr/local/xtal/ccp4-6.2.0/src/molrep_/molrep.f, which does not exist in my linux. In addition, I tried several published structures and tried to test MOLREP by input fixed model method .The error are same. Moreover, I tried to run it in windows XP using input fixed model, Molrep run well. I thought that it is a bug in this version of MOLREP. Any comments are welcome. with best wishes zhong chen -- zhongzhou chen Room 2071, research center in life sciences, No. 2 yuanmingyuan west road, Haidian District, Beijing, 100193 P.R. China Tel: (86)-10-62734078 -- PD Dr. Günter Fritz Fachbereich Biologie Universität Konstanz
[ccp4bb] Solved: [ccp4bb] MOLREP fails when using input fixed model
Sorry, I should have had a look also at the CCP4 site: updated version of molrep from Aug 8. http://www.ccp4.ac.uk/updates/linux/ccp4-6.2.0/bin/ Cheers Guenter Dear Zhong Chen and CCP4 users, I get the very same error on a Centos 5 box. Is there a solution yet? Best regards, Guenter Dear all, Recently, I used MOLREP to molecular replacement. My OS is fedora 14 and CCP4 version is the newest one ccp4-6.2.0 . When I run a pdb file and mtz by MOLREP without input fixed model, everything is right. However, when I run it by MOLREP when using input fixed model. The error is attached below. At line 1260 of file /usr/local/xtal/ccp4-6.2.0/src/molrep_/molrep.f Fortran runtime error: End of record Actually, my ccp4 is installed at /home/software/ccp4, not at /usr/local/xtal/ccp4-6.2.0/src/molrep_/molrep.f, which does not exist in my linux. In addition, I tried several published structures and tried to test MOLREP by input fixed model method .The error are same. Moreover, I tried to run it in windows XP using input fixed model, Molrep run well. I thought that it is a bug in this version of MOLREP. Any comments are welcome. with best wishes zhong chen -- zhongzhou chen Room 2071, research center in life sciences, No. 2 yuanmingyuan west road, Haidian District, Beijing, 100193 P.R. China Tel: (86)-10-62734078
Re: [ccp4bb] question regarding secondary-structure restraints
On Mon, Sep 26, 2011 at 1:53 AM, Dirk Kostrewa kostr...@genzentrum.lmu.dewrote: when I played with H-bond restraints for secondary structures for the refinement of a 4.3 A structure (only a few weeks before they were introduced in phenix), I've made the following observation: at low resolution without H-bond restraints for secondary structures, the carbonyl groups of these secondary structures take the liberty within their globbish electron densities to deviate from their ideal H-bond conformation, resulting in a tight belt of outliers around the preferred Ramachandran regions, with typical deviations of only a few degrees. Introducing the additional H-bond restraints for maintaining secondary structures pulls these outlier carbonyl groups back into the preferred Ramachandran regions. In my case, the number of Ramachandran outliers was reduced to less than one half! Although, these H-bond restraints do not directly include information about allowed Ramachandran regions, the Ramachandran plot is actually affected by these restraints. Thus, at least in my opinion, the Ramachandran plot is then not a truly independent measure for model quality, anymore. The same holds true for all geometrical restraints, of course. It depends on how strictly you assess the independence of validation criteria. The Ramachandran plot is considered valid in most cases because refinement programs traditionally do not restrain phi and psi angles, so we need to rely on the accuracy of the data (and our placement of atoms) and various complementary geometry restraints (especially nonbonded) to keep residues in the favorable regions of the plot. There are a variety of ways to make the plot better by modification of the model and/or restraints (adding hydrogens, increasing the weight on the nonbonded restraints, secondary structure restraints, etc.), none of which are as drastic as directly restraining the model to the plot. I don't really view this as biasing the plot, for two reasons: a) the quantity being measured is independent of the quantity restrained, and b) at least in my hands, these modifications never completely fix the problem of Ramachandran outliers. (It's the loop regions that are really awful.) Anyway, I don't think anyone should feel bad about using this kind of restraint at low resolution. The caveat is that of all the specialized restraints that we (Jeff Headd and I) have been testing for low-resolution refinement (in Phenix), nothing works nearly as well in preserving good geometry, and usually improving the R-factors, as restraining model parameters to a related high-resolution structure, when one is available. Fortunately, every modern refinement program has this ability in some form, and I expect that this is going to have the most impact in improving the overall quality of low-resolution structures. -Nat
Re: [ccp4bb] question regarding secondary-structure restraints
Dear Nat, yes, I fully agree - all these restraints that improve the geometry either by restraining to high-resolution structures or by introducing H-bond restraints for secondary structures are very useful for low-resolution structures! I see your argument with the Ramachandran plot. But imagine a set of very strong non-bonding/bonding restraints that would result in an absolutely clean Ramachandran plot for any structure, then the Ramachandran plot would become useless even in the absence of any phi/psi-restraints. So, I prefer to err a bit on the safe side here by saying not a truly independent measure. Personally, I think, that ALL refinement programs, including the real-space refinement in Coot, would benefit from inclusion of proper H-bonding terms (something, that for instance the very old X-Plor version did), since this would automatically restrain secondary structures and other hydrophilic interactions to some reasonable geometry, even at very low resolution. Best regards, Dirk. Am 26.09.11 16:17, schrieb Nat Echols: On Mon, Sep 26, 2011 at 1:53 AM, Dirk Kostrewa kostr...@genzentrum.lmu.de mailto:kostr...@genzentrum.lmu.de wrote: when I played with H-bond restraints for secondary structures for the refinement of a 4.3 A structure (only a few weeks before they were introduced in phenix), I've made the following observation: at low resolution without H-bond restraints for secondary structures, the carbonyl groups of these secondary structures take the liberty within their globbish electron densities to deviate from their ideal H-bond conformation, resulting in a tight belt of outliers around the preferred Ramachandran regions, with typical deviations of only a few degrees. Introducing the additional H-bond restraints for maintaining secondary structures pulls these outlier carbonyl groups back into the preferred Ramachandran regions. In my case, the number of Ramachandran outliers was reduced to less than one half! Although, these H-bond restraints do not directly include information about allowed Ramachandran regions, the Ramachandran plot is actually affected by these restraints. Thus, at least in my opinion, the Ramachandran plot is then not a truly independent measure for model quality, anymore. The same holds true for all geometrical restraints, of course. It depends on how strictly you assess the independence of validation criteria. The Ramachandran plot is considered valid in most cases because refinement programs traditionally do not restrain phi and psi angles, so we need to rely on the accuracy of the data (and our placement of atoms) and various complementary geometry restraints (especially nonbonded) to keep residues in the favorable regions of the plot. There are a variety of ways to make the plot better by modification of the model and/or restraints (adding hydrogens, increasing the weight on the nonbonded restraints, secondary structure restraints, etc.), none of which are as drastic as directly restraining the model to the plot. I don't really view this as biasing the plot, for two reasons: a) the quantity being measured is independent of the quantity restrained, and b) at least in my hands, these modifications never completely fix the problem of Ramachandran outliers. (It's the loop regions that are really awful.) Anyway, I don't think anyone should feel bad about using this kind of restraint at low resolution. The caveat is that of all the specialized restraints that we (Jeff Headd and I) have been testing for low-resolution refinement (in Phenix), nothing works nearly as well in preserving good geometry, and usually improving the R-factors, as restraining model parameters to a related high-resolution structure, when one is available. Fortunately, every modern refinement program has this ability in some form, and I expect that this is going to have the most impact in improving the overall quality of low-resolution structures. -Nat -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] STFC consultation on advisory panels
Frank, I don't have a plan, but as the consultation seeks the views of the community. I would urge those with views to write to to STFC expressing them, and mention this to their friends/colleagues/students/PI. Although I suspect that the views of people from industry will have more weight than than those of provincial academics, a significant volume of responses expressing the anxiety that we will be under-represented in the new structures should(?) mean the plans are reconsidered. Perhaps, as you seem to suggest, people might also like to make their views public through the BB? This might lessen the activation energy of those intending to write something to STFC. Peter On 24 September 2011 22:32, Peter Moody pcem1bigfi...@gmail.com wrote: Could I draw (especially) UK users of STFC facilities (such as Diamond) to the STFC's proposals and consultation? http://www.stfc.ac.uk/About+STFC/36187.aspx Please note the composition of the Science Board and the research interests of the members, and with this in mind consider the question of the future of advisory panels. Facility users might remember the recent Programmatic Review and need for our community to fully inform the STFC of the importance of our work. I worry that we will be under represented in future discussions about resources (by we I mean macromolecular crystallographers, but this applies to biological scientists and indeed anyone interested in things smaller than planets and larger than sub-atomic particles). The closing date for the consultation is 14 October best wishes, Peter Moody, Leicester (PS don't reply to me at this address, I don't always give it the attention it deserves!)
[ccp4bb] Superpose, SSM
Dear CCP4 users, I am using the ccp4i version 6.2.0 under windows 7. I've come across a problem with superpose. The outputfile appears to have additional line feeds (see picture) which, however are not seen in the windows notepad. The structure can also be opened in coot and pymol. However, it is not possible to use it within CCP4, eg. for a subsequent superposition. Is this problem known to anybody and is there a simple workaround available? I need to compare hell of a lot of relative domain orientations... I did not have this problem on a second computer with ccp4 6.1.2. When I updated to 6.2.0, the situation was as described above. Any help will be highly appreciated, Thanks, Matthias attachment: superpose.png
Re: [ccp4bb] Superpose, SSM
On Mon, 2011-09-26 at 20:42 +0100, Matthias Zebisch wrote: However, it is not possible to use it within CCP4, eg. for a subsequent superposition. What do you mean by that? Do you get an error when you use the superpose output pdb with some other program? -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] Superpose, SSM
I vaguely recall notepad doing something wacky with files in certain cases...why don't you get the excellent text editor NoteTab Light [sic] (I use it all the time--free and works great), then take a look at your files and see whether MS notepad altered the files. JPK On Mon, Sep 26, 2011 at 2:42 PM, Matthias Zebisch matthias.zebi...@bbz.uni-leipzig.de wrote: Dear CCP4 users, I am using the ccp4i version 6.2.0 under windows 7. I've come across a problem with superpose. The outputfile appears to have additional line feeds (see picture) which, however are not seen in the windows notepad. The structure can also be opened in coot and pymol. However, it is not possible to use it within CCP4, eg. for a subsequent superposition. Is this problem known to anybody and is there a simple workaround available? I need to compare hell of a lot of relative domain orientations... I did not have this problem on a second computer with ccp4 6.1.2. When I updated to 6.2.0, the situation was as described above. Any help will be highly appreciated, Thanks, Matthias -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] question regarding secondary-structure restraints
-Just to make a note, there has actually been some discussion in the published literature recently (ok maybe past ten years) about what terms; simply steric (as originally) or hydrogen bonding etc might be needed to explain observed backbone angular values. Tommi On Sep 26, 2011, at 5:44 PM, Dirk Kostrewa wrote: Dear Nat, yes, I fully agree - all these restraints that improve the geometry either by restraining to high-resolution structures or by introducing H-bond restraints for secondary structures are very useful for low-resolution structures! I see your argument with the Ramachandran plot. But imagine a set of very strong non-bonding/bonding restraints that would result in an absolutely clean Ramachandran plot for any structure, then the Ramachandran plot would become useless even in the absence of any phi/psi-restraints. So, I prefer to err a bit on the safe side here by saying not a truly independent measure. Personally, I think, that ALL refinement programs, including the real-space refinement in Coot, would benefit from inclusion of proper H-bonding terms (something, that for instance the very old X- Plor version did), since this would automatically restrain secondary structures and other hydrophilic interactions to some reasonable geometry, even at very low resolution. Best regards, Dirk. Am 26.09.11 16:17, schrieb Nat Echols: On Mon, Sep 26, 2011 at 1:53 AM, Dirk Kostrewa kostr...@genzentrum.lmu.de wrote: when I played with H-bond restraints for secondary structures for the refinement of a 4.3 A structure (only a few weeks before they were introduced in phenix), I've made the following observation: at low resolution without H-bond restraints for secondary structures, the carbonyl groups of these secondary structures take the liberty within their globbish electron densities to deviate from their ideal H-bond conformation, resulting in a tight belt of outliers around the preferred Ramachandran regions, with typical deviations of only a few degrees. Introducing the additional H-bond restraints for maintaining secondary structures pulls these outlier carbonyl groups back into the preferred Ramachandran regions. In my case, the number of Ramachandran outliers was reduced to less than one half! Although, these H-bond restraints do not directly include information about allowed Ramachandran regions, the Ramachandran plot is actually affected by these restraints. Thus, at least in my opinion, the Ramachandran plot is then not a truly independent measure for model quality, anymore. The same holds true for all geometrical restraints, of course. It depends on how strictly you assess the independence of validation criteria. The Ramachandran plot is considered valid in most cases because refinement programs traditionally do not restrain phi and psi angles, so we need to rely on the accuracy of the data (and our placement of atoms) and various complementary geometry restraints (especially nonbonded) to keep residues in the favorable regions of the plot. There are a variety of ways to make the plot better by modification of the model and/or restraints (adding hydrogens, increasing the weight on the nonbonded restraints, secondary structure restraints, etc.), none of which are as drastic as directly restraining the model to the plot. I don't really view this as biasing the plot, for two reasons: a) the quantity being measured is independent of the quantity restrained, and b) at least in my hands, these modifications never completely fix the problem of Ramachandran outliers. (It's the loop regions that are really awful.) Anyway, I don't think anyone should feel bad about using this kind of restraint at low resolution. The caveat is that of all the specialized restraints that we (Jeff Headd and I) have been testing for low-resolution refinement (in Phenix), nothing works nearly as well in preserving good geometry, and usually improving the R- factors, as restraining model parameters to a related high- resolution structure, when one is available. Fortunately, every modern refinement program has this ability in some form, and I expect that this is going to have the most impact in improving the overall quality of low-resolution structures. -Nat -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de *** Tommi Kajander, Ph.D. Structural Biology and Biophysics Institute of Biotechnology University of Helsinki Viikinkaari 1 (P.O. Box 65) 00014 Helsinki Finland p. +358-9-19158903 tommi.kajan...@helsinki.fi
Re: [ccp4bb] Superpose, SSM
Hi again, Thanks for your quick replies but I think I made myself not clear. here is what I'm doing: 1) superpose proteinA.pdb onto proteinB.pdb : works, but gives out proteinA_lsq1.pdb with extra empty lines (not the anisou lines ;o) ) 2) superpose proteinA_lsq1.pdb onto proteinC.pdb : doesnt work because proteinA_lsq1.pdb cannot be read Any ideas? Even if there is some compatibility issue between CCP4 and windows, I guess superpose should be able to read its own files, shouldnt it? Thanks, Matthias On 9/26/2011 9:13 PM, Jacob Keller wrote: I vaguely recall notepad doing something wacky with files in certain cases...why don't you get the excellent text editor NoteTab Light [sic] (I use it all the time--free and works great), then take a look at your files and see whether MS notepad altered the files. JPK On Mon, Sep 26, 2011 at 2:42 PM, Matthias Zebisch matthias.zebi...@bbz.uni-leipzig.de wrote: Dear CCP4 users, I am using the ccp4i version 6.2.0 under windows 7. I've come across a problem with superpose. The outputfile appears to have additional line feeds (see picture) which, however are not seen in the windows notepad. The structure can also be opened in coot and pymol. However, it is not possible to use it within CCP4, eg. for a subsequent superposition. Is this problem known to anybody and is there a simple workaround available? I need to compare hell of a lot of relative domain orientations... I did not have this problem on a second computer with ccp4 6.1.2. When I updated to 6.2.0, the situation was as described above. Any help will be highly appreciated, Thanks, Matthias
Re: [ccp4bb] Superpose, SSM
The outputfile appears to have additional line feeds (see picture) which, however are not seen in the windows notepad. What application ARE the extra lines seen in? Sounds like a problem with different newline conventions- CR vs LF vs CRLF - although I shouldn't have thought extra carriage returns and linefeeds would confuse a program reading a PDB. Maybe the latest update uses the windows CRLF on output but still unix LF for input Anyway, to help the developers debug, it would be good to provide a hex dump of a portion of the pdb file. If you don't have a windows hex editor you can use debug (I assume it still exists in windows 7) Open a dos shell and cd to the directory where the peculiar file is, and debug lsq1.pdb d 100 200 that is dump from the beginning of the file (which is loaded starting hex 100) to hex 200. If there is a big header you may want to skip down to the ATOM records, d 1000 1100 or such. this gives hex dump on left and ascii on the right like below. Lines are separated by two dots in the ascii which correspond to 0D 0A in the hex dump- -d 100 200 0B05:0100 57 79 61 72 74 69 74 65-3A 20 42 75 72 6E 73 20 Wyartite: Burns 0B05:0110 61 6E 64 20 46 69 6E 63-68 2C 20 41 6D 20 4D 69 and Finch, Am Mi 0B05:0120 6E 20 38 34 20 28 31 39-39 39 29 20 31 34 35 36 n 84 (1999) 1456 0B05:0130 2D 31 34 36 30 0D 0A 57-79 61 72 74 69 74 65 3A -1460..Wyartite: 0B05:0140 20 43 72 79 73 74 61 6C-6C 6F 67 72 61 70 68 69Crystallographi 0B05:0150 63 20 65 76 69 64 65 6E-63 65 20 66 6F 72 20 74 c evidence for t 0B05:0160 68 65 20 66 69 72 73 74-20 70 65 6E 74 61 76 61 he first pentava 0B05:0170 6C 65 6E 74 2D 75 72 61-6E 69 75 6D 0D 0A 20 6D lent-uranium.. m 0B05:0180 69 6E 65 72 61 6C 0D 0A-31 31 2E 32 37 30 36 20 ineral..11.2706 0B05:0190 37 2E 31 30 35 35 20 32-30 2E 38 30 37 20 39 30 7.1055 20.807 90 0B05:01A0 20 39 30 20 39 30 20 50-32 32 32 0D 0A 55 31 0D90 90 P222..U1. 0B05:01B0 0A 2E 36 31 31 20 2E 33-31 30 20 2E 31 35 34 20 ..611 .310 .154 0B05:01C0 33 0D 0A 43 0D 0A 2E 35-31 31 20 2E 34 31 30 20 3..C...511 .410 0B05:01D0 2E 31 35 34 20 32 0D 0A-61 6E 69 6F 6E 73 0D 0A .154 2..anions.. 0B05:01E0 4F 31 0D 0A 2E 35 31 31-20 2E 33 31 30 20 2E 31 O1...511 .310 .1 0B05:01F0 35 34 0D 0A 65 6E 64 F0-97 01 75 03 E8 CE E0 3C 54..end...u 0B05:0200 2E Matthias Zebisch wrote: Hi again, Thanks for your quick replies but I think I made myself not clear. here is what I'm doing: 1) superpose proteinA.pdb onto proteinB.pdb : works, but gives out proteinA_lsq1.pdb with extra empty lines (not the anisou lines ;o) ) 2) superpose proteinA_lsq1.pdb onto proteinC.pdb : doesnt work because proteinA_lsq1.pdb cannot be read Any ideas? Even if there is some compatibility issue between CCP4 and windows, I guess superpose should be able to read its own files, shouldnt it? Thanks, Matthias On 9/26/2011 9:13 PM, Jacob Keller wrote: I vaguely recall notepad doing something wacky with files in certain cases...why don't you get the excellent text editor NoteTab Light [sic] (I use it all the time--free and works great), then take a look at your files and see whether MS notepad altered the files. JPK On Mon, Sep 26, 2011 at 2:42 PM, Matthias Zebisch matthias.zebi...@bbz.uni-leipzig.de wrote: Dear CCP4 users, I am using the ccp4i version 6.2.0 under windows 7. I've come across a problem with superpose. The outputfile appears to have additional line feeds (see picture) which, however are not seen in the windows notepad. The structure can also be opened in coot and pymol. However, it is not possible to use it within CCP4, eg. for a subsequent superposition. Is this problem known to anybody and is there a simple workaround available? I need to compare hell of a lot of relative domain orientations... I did not have this problem on a second computer with ccp4 6.1.2. When I updated to 6.2.0, the situation was as described above. Any help will be highly appreciated, Thanks, Matthias
Re: [ccp4bb] Local refinement strategy
Hi Zhiyi, I am trying to refine a structure with two domains. The electron density of one domain is reasonable, but that of the other domain is poor. So, I am wondering whether the refinement by Phenix or Refmac can be done locally with two parts, the first domain is refined with normal restrains, the second domain is refined by rigid body and group B? yes, you can do it in Phenix. Such functionality is exemplified for example here: see page 6: http://www.phenix-online.org/presentations/latest/pavel_phenix_refine.pdf Let me know if you have any questions. Pavel
[ccp4bb] renaming an holo PDB after the alo one
Hello, I have one bound complexe (a ligand + a protein in holo conformation). I also have the apo structure for a very similar protein. Is there a tool to create a new PDB, whose coordinates are taken from the holo structure but residue names and numbers are taken from the alo structure (by looking at the corresponding residues in the output of a sequence alignment program)? I thought about doing a script using clustalw for the alignment part, but the task seems not trivial. Thanks a lot, Francois.
Re: [ccp4bb] renaming an holo PDB after the alo one
Hi François, Chainsaw should do the job for you if you input a clustal alignment. Cheers David Le 26 sept. 2011 à 17:44, Francois Berenger a écrit : Hello, I have one bound complexe (a ligand + a protein in holo conformation). I also have the apo structure for a very similar protein. Is there a tool to create a new PDB, whose coordinates are taken from the holo structure but residue names and numbers are taken from the alo structure (by looking at the corresponding residues in the output of a sequence alignment program)? I thought about doing a script using clustalw for the alignment part, but the task seems not trivial. Thanks a lot, Francois.
Re: [ccp4bb] renaming an holo PDB after the alo one
On 09/27/2011 09:55 AM, David Veesler wrote: Hi François, Chainsaw should do the job for you if you input a clustal alignment. Cheers David Thanks! I'm happy I asked. I'll give a try at chainsaw. Hope to not cut one of my fingers during the process... Le 26 sept. 2011 à 17:44, Francois Berenger a écrit : Hello, I have one bound complexe (a ligand + a protein in holo conformation). I also have the apo structure for a very similar protein. Is there a tool to create a new PDB, whose coordinates are taken from the holo structure but residue names and numbers are taken from the alo structure (by looking at the corresponding residues in the output of a sequence alignment program)? I thought about doing a script using clustalw for the alignment part, but the task seems not trivial. Thanks a lot, Francois.
Re: [ccp4bb] Desmond 3.0 Tutorial, Oct 5 in Boston, MA
On Sep 22, 2011, at 9:29 AM, Ben Eisenbraun wrote: Desmond 3.0 Tutorial 2.2 was quite impressive. (sorry.)
[ccp4bb] Rigaku high voltage tank
Hi Citizens: We seem to run through high voltage tanks on our Raxis IV like guano goes through a goose. Has anyone else had this problem, and, more importantly, what is the best way to protect them. I am assuming it might have something to do with our electrical supply, which is a bit unreliable. Also, does anyone have an extra used functional one they want to get rid of? We've run out of 7-11s to rob to pay for this, and our friendly and helpful radiation safety staff think the best way to deal with this problem is to hack apart the power cable, so it is a current (so to speak) source of frustration. Thanks in advance. 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
[ccp4bb] Post-doctoral position in macromolecular crystallography at the Australian Synchrotron
Dear all, A two year post-doctoral position associated with the macromolecular crystallography group at the Australian Synchrotron is currently open for applications. To read the position description and application instructions please go to http://www.synchrotron.org.au/index.php/about-us/working-at-the-synchrotron/employment-opportunities Regards Christine
Re: [ccp4bb] Superpose, SSM
One would assume that Windows software would read DOS/Windows type text files... Open the file in Wordpad. Unlike Notepad, it is able to work with Windows and Unix type text files. If you edit something and save the file, it will be in Windows style. If Superpose stops on that, it should really be updated. I'm sure that there are Windows versions op the programs Unix2dos and Dos2unix which were the programs to use to convert one type to the other. You can also use Word to search and replace the linefeeds. Good luck with this very retro problem. Cheers, Robbie Date: Mon, 26 Sep 2011 17:07:50 -0600 From: xtald...@gmail.com Subject: Re: [ccp4bb] Superpose, SSM To: CCP4BB@JISCMAIL.AC.UK I think something in your workflow is inserting dos line feeds (\n\r or \r\n, I can't remember which). If I have guessed correctly, you want to remove those \rs before proceeding (or never let them get in there in the first place). You claim to open it with MS something, which would insert dos line feeds as part of Operation Vendor Lock. Did you happen to save it, perhaps by habit? That would do the trick. It might even do something insidious and insert those linefeeds without your purposefully saving the document. Your best bet to fix the file after corruption is vim (used to be that crystallographers could use real text editors). The command in vim is: :%s/\r//g You might find some third party utility that fixes linefeeds for $30.00 somewhere, if vim is too retro. Otherwise, you may want to start over, skip checking it out in MS something, and go straight to superpose. James On Sep 26, 2011, at 2:51 PM, Matthias Zebisch wrote: Hi again, Thanks for your quick replies but I think I made myself not clear. here is what I'm doing: 1) superpose proteinA.pdb onto proteinB.pdb : works, but gives out proteinA_lsq1.pdb with extra empty lines (not the anisou lines ;o) ) 2) superpose proteinA_lsq1.pdb onto proteinC.pdb : doesnt work because proteinA_lsq1.pdb cannot be read Any ideas? Even if there is some compatibility issue between CCP4 and windows, I guess superpose should be able to read its own files, shouldnt it? Thanks, Matthias On 9/26/2011 9:13 PM, Jacob Keller wrote: I vaguely recall notepad doing something wacky with files in certain cases...why don't you get the excellent text editor NoteTab Light [sic] (I use it all the time--free and works great), then take a look at your files and see whether MS notepad altered the files. JPK On Mon, Sep 26, 2011 at 2:42 PM, Matthias Zebisch matthias.zebi...@bbz.uni-leipzig.de wrote: Dear CCP4 users, I am using the ccp4i version 6.2.0 under windows 7. I've come across a problem with superpose. The outputfile appears to have additional line feeds (see picture) which, however are not seen in the windows notepad. The structure can also be opened in coot and pymol. However, it is not possible to use it within CCP4, eg. for a subsequent superposition. Is this problem known to anybody and is there a simple workaround available? I need to compare hell of a lot of relative domain orientations... I did not have this problem on a second computer with ccp4 6.1.2. When I updated to 6.2.0, the situation was as described above. Any help will be highly appreciated, Thanks, Matthias
[ccp4bb] Lectureship in Structural Biology at the University of Adelaide, Australia
Dear All Applications are invited from scientists in the fields of X-ray crystallography or Structural Biology. You will have a strong commitment to excellence in research and teaching, be expected to develop an active, externally funded research group and contribute to the undergraduate teaching responsibilities of the School of Molecular and Biomedical Science at the University of Adelaide, Australia. Further information about the position can be viewed at http://www.adelaide.edu.au/jobs/current/16987/ or from the Head of School, Professor David Adelson, telephone +61 8 83135328 or email head@adelaide.edu.au Applications close: 26 October 2011 best wishes Grant Booker
