Re: [ccp4bb] Fwd: Citing Aimless
Dear all I am also looking for aimless reference. Which paper should I cite? Thanks for the powerful tools for the community. Best, Joe On Sun, Feb 24, 2013 at 9:58 PM, Morten Groftehauge m...@mb.au.dk wrote: Hi guys, In the log from Aimless the only reference mentioned is the 1994 CCP4 paper and then as well as any specific reference in the program write-up. First of all, is this the correct CCP4 reference to use? And second of all, since running Aimless through the interface always invokes Pointless and ctruncate, wouldn't I always cite those as well? I might not need Pointless to determine the space group but it doesn't hurt and doesn't Aimless use information from that run? Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University -- Morten K Grøftehauge, PhD Pohl Group Durham University
[ccp4bb] converting structure factor files to mtz files
Hi, Could anyone give a quick hint for the Fortran format for the following structure factor mmCIF file? or Is there any easy program or better way to convert it? I think I need to skip first 3 columns. Thanks in advance. Joe loop_ _refln.crystal_id _refln.wavelength_id _refln.scale_group_code _refln.index_h _refln.index_k _refln.index_l _refln.F_meas_au _refln.F_meas_sigma_au _refln.status 1 1 1200 617.50 5.41 o 1 1 1400 773.50 6.92 o 1 1 1600 62.30 3.19 o I am trying to view the electron density of a published structure. I downloaded the file from pdb and used cif2mtz in ccp4. I think the following output mtz is wrong. * Column Labels : H K L FREE FP SIGFP F(+) SIGF(+) F(-) SIGF(-) DP SIGDP I(+) SIGI(+) I(-) SIGI(-) * Column Types : H H H I F Q G L G L D Q K M K M * Associated datasets : 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 * Cell Dimensions : (obsolete - refer to dataset cell dimensions above) 88.0800 86.3600 80.7700 90. 95.7100 90. * Resolution Range : 0.000450.29217 ( 47.298 - 1.850 A ) * Sort Order : 1 2 3 0 0 * Space group = 'C 1 2 1' (number 5) OVERALL FILE STATISTICS for resolution range 0.000 - 0.292 === Col SortMinMaxNum % Mean Mean Resolution Type Column num order Missing complete abs. LowHigh label 1 ASC-47 47 0 100.00 -1.4 17.9 47.28 1.85 H H 2 NONE 0 46 0 100.00 17.2 17.2 47.28 1.85 H K 3 NONE 0 43 0 100.00 16.4 16.4 47.28 1.85 H L 4 NONE0.019.0 0 100.00 9.52 9.52 47.28 1.85 I FREE 5 NONE0.0 1566.050 99.90 162.85 162.85 47.28 1.85 F FP 6 NONE0.082.150 99.90 9.49 9.49 47.28 1.85 Q SIGFP 7 BOTH ? ? 513730.00 ?? -999.00 0.00 G F(+) 8 BOTH ? ? 513730.00 ?? -999.00 0.00 L SIGF(+) 9 BOTH ? ? 513730.00 ?? -999.00 0.00 G F(-) 10 BOTH ? ? 513730.00 ?? -999.00 0.00 L SIGF(-) 11 BOTH ? ? 513730.00 ?? -999.00 0.00 D DP 12 BOTH ? ? 513730.00 ?? -999.00 0.00 Q SIGDP 13 BOTH ? ? 513730.00 ?? -999.00 0.00 K I(+) 14 BOTH ? ? 513730.00 ?? -999.00 0.00 M SIGI(+) 15 BOTH ? ? 513730.00 ?? -999.00 0.00 K I(-) 16 BOTH ? ? 513730.00 ?? -999.00 0.00 M SIGI(-) No. of reflections used in FILE STATISTICS51373 LIST OF REFLECTIONS === -47 1 10.00 0.00 0.00 ? ? ? ? ? ? ? ? ? ? -47 1 20.00 0.00 0.00 ? ? ? ? ? ? ? ? ? ? -47 1 3 17.00 0.00 0.00 ? ? ? ? ? ? ? ? ?
Re: [ccp4bb] Fwd: [ccp4bb] Occupancy refinement of substrate using refmac5
Hi, Ed I am dealing the similar problem. I checked CNS qindividual.inp. But how do I refine one compound with two or more possible conformations (mainly due to one bond rotation), each of wihich has a different occupancy? Thanks in advance. Joe On Dec 17, 2007 2:24 PM, Edward Berry [EMAIL PROTECTED] wrote: I think the correlation between occupancy and B-factor depends also on the size of the ligand (relative to resolution). Bob Stroud, I think, has estimated occupancy by comparing the integrated electron density of the ligand with that of a well-defined, isolated water (assumed to be at unit occuancy?). In principle the integrated electron density is not affected by applying a B-factor, it is just spread out over a wider area. In the case of a single atom at 3 A resolution, it is spread out under the neighboring atoms and effectively lost, so it is hard to distinguish high B-factor from low occupancy. In a large ligand most of the atoms are inside the ligand, so their spread-out density remains inside the ligand and gets counted in the integrated density. In that case high B-factor has a very different effect than low occupancy, as only the latter reduces the total electron density of the ligand. During a previous reincarnation of this thread I did the simple test of refining occupancy and B-factor for a stretch of the protein (holding the rest of the protein at unit occupancy) in CNS 1.1, and I felt the results were quite satisfactory (don't have the specifics now). Ed Anastassis Perrakis wrote: I have already changed occupancies as Eleanor mentioned, and got approximate values. But my hope is to try to get much precise ones if possible. I never expected to preach the 'Kleywegt Gospel' in the ccp4bb, but in this case what you need is more accurate answers, not more precise ones (or better both, but precision alone can be a problem, and you can easily get 'precise' but inaccurate data easily by making the wrong assumptions in your experiment) http://en.wikipedia.org/wiki/Accuracy I have heard from my colleague SHELX can refine occupancies, and got its license. I'll next try SHELX. I think that phenix.refine can also do occupancies ? The problem is not if the program can do it, but if at your specific case you have enough information to do that in a meaningful way. For a soaking experiment and 1.5 A data, I would say that Eleanor's suggestion of tuning Occ based on B, is as close as you would get, accurate enough given the data, although not necessarily too precise. Tassos
[ccp4bb] Calculate dipole moment of ligands from their coordinates
Hi, All Sorry about non-CCP4 questions. It is the best board I find so far to learn stuff related to structure biology. Could anyone suggest me any program that calculates dipole moment of a ligand from its coordinates? Thanks, sorry to bother others. Zheng
[ccp4bb] Question about freeR tag
Hi, All Could any tell me how CCP4 handle free R flag? I know It is important to select the same** FreeR reflections if I move to next step of refinement. But everytime I start from fresh, the freeR Flag remains unchanged. The Rwork and Rfree of my models are fine (20.7% and 22.9%). I thought Rfree was randomly generated. I asked more experienced people in the lab and neighbor labs, and didn't get a straight answer. Did I do something wrong? Thanks and sorry to bother others. Zheng (Joe)
Re: [ccp4bb] Question about freeR tag
Sorry that I didn't explain the situation clearly. I used only one output.sca file from HLK2000. I ran the scalepack2mtz (in CCP4i, data reduction, import merged data) several times, on both linux Fedora and window XP, the same computer though. For the next step refinement, I mean add H2O, ion, ligands, double check certain sidechains In those refmac runs, I always use the same mtz file, which I generated from the beginning. I am as surprised as you are the Rfree flags are identical from those different first runs. Thanks On Jan 23, 2008 9:50 AM, Zheng Zhou [EMAIL PROTECTED] wrote: Hi, All Could any tell me how CCP4 handle free R flag? I know It is important to select the same** FreeR reflections if I move to next step of refinement. But everytime I start from fresh, the freeR Flag remains unchanged. The Rwork and Rfree of my models are fine ( 20.7% and 22.9%). I thought Rfree was randomly generated. I asked more experienced people in the lab and neighbor labs, and didn't get a straight answer. Did I do something wrong? Thanks and sorry to bother others. Zheng (Joe) I cant understand this. Do you mean you have multiple data sets and they all generate the same FreeRs? If you have EXACTLY the same reflection list, and generate FreeR flags on the same machine I guess they would be the same.. but it would be surprising Or if you are using the same file which already has FreeR flags then they wont change of course - the default is always to use the reflections flagged with FreeR = 0. (Thats as it should be..) By the by - your agreement between R and FreeR seems unusually low unless you have very high resolution data or a great deal of non-crystallographic symmetry. Eleanor Zheng - I am not sure what you are doing, but as long as you work with one dataset only, you generate the free reflections at the very beginning when you import your data into CCP4. Then use the resulting mtz file for all following refinement steps. There are situations where one will have to deviate from this scheme, but those are rare. If you feel you have such a case, then tell us more about it. Hope that helps. Best - MM Joe, can you explain a bit clearer your problem? what do you mean the 'next step of refinement'? are you just doing another round of refinement? what program are you using, REFMAC5? also, R/Rfree of 20.7/22.9 is pretty good, depending on resolution. yes, you are right, Rfree flags are generated randomly and can be anywhere from 5-10% of your reflections (your choice). then, once the Rfree flagged reflections are selected, they will not change (nor be refined) throughout the rest of your structure determination. they should have their own column in your *.mtz file called RfreeFlag or something like this (in CCP4 that is). other programs handle this relatively the same, but may use various naming conventions. one caveat is that CCP4 flags reflections using 0 by default (meaning 5% of your reflections are flagged with 0 and are the Rfree set). Other programs such as CNS and PHENIX use 1 by default, so be careful when switching back and forth. You can tell either program which to use for Rfree set, but needs to be set, since it is not default. again, not exactly sure what the problem is, but i hope some of this helps. feel free to email with further questions if needed. best of luck! cheers, nick
Re: [ccp4bb] Question about freeR tag
Thank you all for fast replying. The reason that I am trying to use a different set of FreeR flag from the very beginning of the refinement is that for some data set, my colleague's CNS refinement gave converged Rfree and R work, 3% difference. However both my CNS and CCP4 refinement gave a difference of about 7%. I was trying to use the same parameter settings as my colleague in simulated annealing. His program is from his previous lab and all the input files for CNS are modified as a batch file. But mine are just individual files downloaded from CNS website. Among those things I tried, I thought about looking at the true input data for computing Rfree and Rwork. It appeared to me the FreeR flags in my First runs are never randomized. Thanks for your reply, I guess I could use a different flag number other than 0 (I know I am not supposed to change this in the middle of a refinement). I even tried to use my colleague's cross-validation file .cv for CNS. It still diverge in my runs. Anyone met similar problem before, where CNS and CCP4 give a quite different R factors? Thanks for your insight. Zheng (Joe) On Jan 23, 2008 9:50 AM, Zheng Zhou [EMAIL PROTECTED] wrote: Hi, All Could any tell me how CCP4 handle free R flag? I know It is important to select the same** FreeR reflections if I move to next step of refinement. But everytime I start from fresh, the freeR Flag remains unchanged. The Rwork and Rfree of my models are fine ( 20.7% and 22.9%). I thought Rfree was randomly generated. I asked more experienced people in the lab and neighbor labs, and didn't get a straight answer. Did I do something wrong? Thanks and sorry to bother others. Zheng (Joe)
[ccp4bb] Absorption correction in HKL2000
Hi, everyone I have a question about HKL2000 too. During scaling, there is a check option call absorption correction. I processed the data with and without it checked. With absorption correction checked, my rejection file is only 0.4%. When I leave it out, the rejection file is 0.8%. I read through the HKL2000 online manual and only find direction cosines produce information that can be read by an outside absorption correction program, such as Shelx. The need for it will disappear as the HKL-2000 absorption correction routines are implemented. So do I need to use the absorption correction routinely or just for some trouble dataset. Obviously I don't want to incorporate bad spots. Thanks for your input. Best, Zheng On Sat, Apr 11, 2009 at 7:36 PM, Engin Ozkan eoz...@stanford.edu wrote: Hi everyone, I have recently been plagued by incomplete data according to HKL2000. My last dataset, which is 360 degrees of images, with 0.1% rejected during scaling, and no overlaps during indexing/integration, keeps on scaling in HKL2000 as incomplete. It is reported incomplete only at higher resolution (see stats below, in my case 5 Angstroems is usually high resolution). This is really odd, because (1) the data is 360 degrees, (2) if the beamstop was the culprit, I would expect incompleteness at low res., not high, and not 35% incomplete, (3) at this resolution the blind region outside the Ewald sphere should be insignificant (not 35%), (4) and there are no overlaps (thanks to the detector being sent to Outer Mongolia, according to our synchrotron host), and (5) there are no overloads. Moreover, mosflm thinks the data is 100.0% complete. I have had similar incompleteness issues on other unrelated low resolution data in the last year or two with HKL2000. So before I lose it because of HKL2000, I have two questions, and I'd appreciate any answers to either: 1. Can there be another reason for incompleteness that I am missing (other than blind region at higher res., overlaps, overloads, and not enough many frames)? 2. Has anyone been experiencing similar phenomena with HKL2000 (v0.98.698o)? Especially with anisotropic data? Thanks, Engin Shell Summary of observation redundancies: Lower Upper % of reflections with given No. of observations limit limit 0 1 2 3 4 5-6 7-8 9-12 13-19 19 total 50.00 11.49 0.1 0.1 3.7 2.9 93.3 0.0 0.0 0.0 0.0 0.0 99.9 11.49 9.14 0.0 0.0 1.7 2.3 96.0 0.0 0.0 0.0 0.0 0.0 100.0 9.14 7.99 0.0 0.0 1.5 2.8 95.7 0.0 0.0 0.0 0.0 0.0 100.0 7.99 7.26 0.0 0.0 1.5 2.8 95.7 0.0 0.0 0.0 0.0 0.0 100.0 7.26 6.74 0.0 0.0 1.3 2.2 96.6 0.0 0.0 0.0 0.0 0.0 100.0 6.74 6.35 0.0 0.3 1.3 4.1 94.3 0.0 0.0 0.0 0.0 0.0 100.0 6.35 6.03 2.1 3.6 4.0 7.3 83.0 0.0 0.0 0.0 0.0 0.0 97.9 6.03 5.77 8.9 6.2 5.1 10.2 69.6 0.0 0.0 0.0 0.0 0.0 91.1 5.77 5.54 16.0 6.1 6.6 9.4 61.9 0.0 0.0 0.0 0.0 0.0 84.0 5.54 5.35 20.6 7.3 6.5 6.4 59.2 0.0 0.0 0.0 0.0 0.0 79.4 5.35 5.19 25.7 6.8 6.6 7.9 52.9 0.0 0.0 0.0 0.0 0.0 74.3 5.19 5.04 26.1 5.9 6.2 7.2 54.6 0.0 0.0 0.0 0.0 0.0 73.9 5.04 4.91 28.7 7.9 6.2 7.0 50.2 0.0 0.0 0.0 0.0 0.0 71.3 4.91 4.79 29.0 7.7 5.8 7.3 50.2 0.0 0.0 0.0 0.0 0.0 71.0 4.79 4.68 32.4 7.2 7.0 7.2 46.3 0.0 0.0 0.0 0.0 0.0 67.6 4.68 4.58 31.8 9.2 7.5 6.6 44.9 0.0 0.0 0.0 0.0 0.0 68.2 4.58 4.49 35.1 9.7 6.1 6.1 43.0 0.0 0.0 0.0 0.0 0.0 64.9 4.49 4.40 33.8 11.2 7.0 6.4 41.7 0.0 0.0 0.0 0.0 0.0 66.2 4.40 4.32 37.9 9.4 7.7 7.8 37.3 0.0 0.0 0.0 0.0 0.0 62.1 4.32 4.25 36.7 11.5 8.5 6.8 36.4 0.0 0.0 0.0 0.0 0.0 63.3 All hkl 18.3 5.5 5.1 6.0 65.1 0.0 0.0 0.0 0.0 0.0 81.7
Re: [ccp4bb] coot
Hi, Stefanie Are those 6 molecules related by NCS? If so, you can model one first, and use transform_coords_molecule (imol, rtop) to generate others. I used to do this five times for a pentamer: output_pdb='template' for i in range (2,6): transform_coords_molecule (1, [[x1, y1, z1, x2, y2, z2, x3, y3, z3], [a, b, c]]) filename=output_pdb+str(i)+'.pdb' save_coordinates (1, filename) I think you can write all the the tranformation matrix out instead of the loop if they differ significantly. Others may have more experience. Best, Joe On Mon, Feb 28, 2011 at 6:32 PM, FREITAG-POHL S. stefanie.freitag-p...@durham.ac.uk wrote: Hello everybody, Currently I am refining my 6 x 220 amino acid structure and I was wondering if COOT is automatically writing a kind of protocol what I am changing in my pdb file when I am fitting-in new residues or mutate amino acids. If so where can I find it? Thanks a lot, Stefanie Dr. Stefanie Freitag-Pohl Durham University Chemistry Dept South Road Durham. DH1 3LE Tel: 0191 3342143 Email: stefanie.freitag-p...@durham.ac.uk
Re: [ccp4bb] Protein aggregation and crystallization
Hi, Anita If you could find a way to test the elute's activity/binding to its' substrat/cofactor, then you will learn much more about your target. If the function assay is elusive, you could try superose column (5KDa-5MKDa). Does your light scattering tell you about the estimated size and MW? Best, Joe On Sat, Aug 27, 2011 at 1:29 AM, anita p crystals...@gmail.com wrote: Hi Yury, I have done dynamic light scattering and it shows its polydispersed. Please let me know if it is still ok for setting trays. reg. anita On Fri, Aug 26, 2011 at 10:21 PM, Yuriy Patskovsky yuriy.patskov...@einstein.yu.edu wrote: Anita, an assembly may be quite large - I would check it somehow, maybe by light scattering or centrifugation Good luck Yury -- *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of anita p [crystals...@gmail.com] *Sent:* Friday, August 26, 2011 3:03 AM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] Protein aggregation and crystallization Hi All, I am working on a protein which has a membrane spanning region and as cytosolic domain.I have made various deletion constructs of the protein, so that I can have a crystallizable fragment. There is no homologues mentioned in the pdb for this protein. All of these constructs are purified successfully but when concentrated and loaded on a gel filtration column Superdex-200, they elute in the void volume. But the proteins donot precipitate out !! Is it worth while to go ahead for crystallization trials?? Any other suggestion is most welcome. Thanks Anita
[ccp4bb] Does imosflm do pre-refine
Dear all
I am new to imosflm. Thanks for the online tutorial for imosflm. I am
also checking the mosflm 7.0.4 user guide. It is mentioned in the
manual that
From version 6.2.5 onwards, there are some optional questions, based
on whether the user wants extra output to help decide between similar
solutions.
and
For expert users, iMosflm now has the option of specifying ipmosflm
keywords for the very specialised options that are only rarely used
and are not yet included in the iMosflm GUI explicitly.
How do I turn on those options? Is there any way to do this in the
windows version? Thanks.
Best,
Joe
On Thu, Mar 19, 2009 at 7:46 PM, Harry Powell ha...@mrc-lmb.cam.ac.uk wrote:
Hi folks
The real problem here is that the imosflm you run by default after
installing the latest CCP4 is a shell script in $CBIN (i.e. where all the
compiled programs are), which doesn't actually set things up properly. This
has been addressed by the guys in Daresbury and the fix will appear in the
next release (after which you should be able to ignore the rest of this
message).
If, on the other hand, you run the imosflm in the directory
$CCP4/ccp4i/imosflm/src, everything should be hunky-dory - you can do this
by setting your PATH environment variable so it finds this script first,
e.g. in tcsh -
setenv PATH $CCP4/ccp4i/imosflm/src:$PATH
_after_ doing the normal source'ing ccp4.setup; then imosflm on the
command line should work.
The other option would be to install imosflm from our web-pages and run
that, but since this is currently the one that ccp4 distribute there's no
obvious advantage to that, other than removing the ambiguity.
HTH
On 19 Mar 2009, at 10:03, Williams, MA (Mark) wrote:
imosflm also takes the command line switch --startdir so you could try
an alias of
alias imosflm='imosflm --startdir $PWD'
Mark
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
William G. Scott
Sent: 18 March 2009 17:17
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] imosflm STARTDIR
You could try something like this (bash/zsh/sh):
alias imosflm='MOSDIR=${PWD} imosflm'
The single quotes are required for it to do the right thing.
Bill
On Mar 18, 2009, at 6:49 AM, James Foadi wrote:
Dear MOSFLM/IMOSFLM people,
when I start the new version of imosflm I expect it to dump files and
to search all files starting from the current directory. This doesn't
seem to be the case. It appears it always starts from MOSDIR. I my
imosflm.tcl the line related to STARTDIR is:
set STARTDIR [pwd]
Perhaps somebody else has written about this, but if this is the case,
I have missed the thread.
Can somebody help me with this?
J
Dr James Foadi PhD
Membrane Protein Laboratory
Diamond Light Source Ltd.
Diamond House
Harwell Science and Innovation Campus
Didcot
Oxfordshire
OX11 0DE
United Kingdom
office email: james.fo...@diamond.ac.uk alternative email:
j.fo...@imperial.ac.uk
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Scanned by iCritical.
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Road, Cambridge, CB2 0QH
[ccp4bb] delocalized bond or aromatic bond
Dear all I ran into a problem with monomer sketcher. One of my compounds has a benzimidazole group. C12=CC=CC=C1N=CN2 When I used monomer sketcher regularizing with refmac, the C-C bond that connect the benzene ring and the imidazole has a length of 1.49 A. I defined them as delocalized bond. When I used PRODRG server, it refined to 1.39A and defined as aromatic bond Then I checked PDB entry with similar group 1D0S. 1JHM, 1KXM, L5F, 1RYC. They all have 1.38-1.39A. Then I though about load the monomer directly into coot with code name BZI, the bond length is 1.48. Is there a clear definition of delocalized bond or armatic bond? I tried to look for the manual of monomer sketcher. Thanks for your suggestion in advance. Best, Joe
Re: [ccp4bb] delocalized bond or aromatic bond
Thanks Bill for clarifying the notion of aromatic bonds I think the C-C bond shared by the benzene and imidazole ring should be close to a double bond distance http://en.wikipedia.org/wiki/Benzimidazole How come calculation from monomer sketcher and the BZI entry in the library has a distance close to a single bond? Joe On Thu, Sep 24, 2009 at 12:36 PM, William G. Scott wgsc...@chemistry.ucsc.edu wrote: On Sep 23, 2009, at 5:03 PM, Zheng Zhou wrote: Is there a clear definition of delocalized bond or armatic bond? Hi Zheng: Aromatic bonds only occur in planar cyclic molecules that have 4n +2 pi electrons. Aromatic interactions give energetic stabilization beyond that observed for delocalized conjugated systems, for example, the aromatic stabilization of benzene is the energy difference between real benzene and a hypothetical set of resonance structures representing delocalized 1,3,5-cyclohexatriene. Similarly, anti-aromatic interactions occur in planar cyclic molecules having 4n pi electrons; they are destabilized relative to their hypothetical cycloalkene counterparts. (If you allow for perpendicular aromatic interactions, Hoffmann and Goldstein in 1971 demonstrated that 4n pi electrons in that case are also stabilizing, due to the different topology of the pi electron interactions, something that may be of relevance to aromatic side chain clusters.) HTH, Bill
Re: [ccp4bb] Reg Protein purification
Dear Sivaraman I worked on some protein with DNA contamination recently. Adding DNase and increasing IMAC wash volume at the same time changed 280/260 ratio and yield reproducible protein crystals, not high resolution yetIn case your protein can't stand other treatment... (Sorry Tommi, I hit the wrong reply button.) Best, Zheng (Joe) Zhou On Sat, Mar 6, 2010 at 8:23 PM, Sivaraman Padavattan s.padavat...@gmail.com wrote: Dear All, We are trying to purify an enzyme, which requires the co-factor NAD+ during catalysis by affinity column (Ni-NTA). After induction, the bacterial cells were harvested and lysed with 20 mM Tris pH 7.2, 500 mM NaCl, 5% glycerol, 5 MM B-ME. The resultant supernatant was passed through Ni-NTA and bound protein eluted with increasing concentration of Imidazole. The eluted proteins was concentrated and load onto gelfiltration (Superdex S-75 16/60) column. Our protein eluted as a aggregate along with other protein, where A260 was much greater than A280, indicative of large fraction of nucleic acid contamination. The eluant also appeared as a smear on 1% agarose gel electrophoresis. We introduced 1M NaCl in the lysis buffer to prevent the nucleic acid interaction. But most of our protein went in pellet after cell lysis. We look forward to your valuable suggestion to purify the protein free of nucleic acid contamination. Thanks in advance, Sivaraman Padavattan
[ccp4bb] Blend error
Hi, all I am running Blend on a new machine (Redhat 6.9 Santiago) and met the following X11 module and R code error. Thanks for your help. When I run $ X -version It returns: X.Org X Server 1.17.4 Release Date: 2015-10-28 X Protocol Version 11, Revision 0 Build ID: xorg-x11-server 1.17.4-16.el6 Current version of pixman: 0.32.8 I checked that libpng12.so.0 is in /usr/lib64 *** * Information from CCP4Interface script *** The program run with command: ccp4-7.0/bin/blend -a data has failed with error message Error in png(file = "./tree.png", height = 1000, width = 1000) : X11 module cannot be loaded Execution halted EXECUTION ERROR! An error occurred in the execution of R code associated with BLEND. *** #CCP4I TERMINATION STATUS 0 "Error in png(file = "./tree.png", height = 1000, width = 1000) :X11 module cannot be loaded Execution halted EXECUTION ERROR! An error occurred in the execution of R code associated with BLEND." #CCP4I TERMINATION TIME 03 Jun 2017 22:33:34
Re: [ccp4bb] secondary structure prediction
Thanks for many advices. I was not clear in the previous email. I know the close homologous protein (20% identity, total 500aa), but the fragment hits (30~40aa, identity 40~50%) are from other proteins in PDB. I am trying to see whether the fragments from non-homologous proteins may help the secondary structure prediction. Best, Z On Wed, Dec 6, 2017 at 10:14 PM, zheng zhou <zhengzho...@gmail.com> wrote: > Dear CCP4 community, > > Sorry for the off-topic question. I am trying to design constructs for > structure studies. It only has a homolog structure in PDB with > sequence identity ~20%. When I blast against PDB sequence, there are > quite a few motif hits (30~40aa, identity 40~50%). Any prediction > tools utilize this information? > > Thanks for your advice in advance. > > Best, > > Zheng
[ccp4bb] secondary structure prediction
Dear CCP4 community, Sorry for the off-topic question. I am trying to design constructs for structure studies. It only has a homolog structure in PDB with sequence identity ~20%. When I blast against PDB sequence, there are quite a few motif hits (30~40aa, identity 40~50%). Any prediction tools utilize this information? Thanks for your advice in advance. Best, Zheng
[ccp4bb] RMS bond and angle
Hi all Just finishing up a new structure at 2.4A. Buster refine gives RMS bond 0.008 and angle 1.13, while MolProbity gives 0.01 and 1.83 degree. I checked the 4 outliers from molprobity……>4sigma. After manual correction, warning goes off, but RMS angle only goes down to 1.82 I am using Phenix 1.13 and buster2.11.6 Could not figure out what went wrong. Sorry for not CCP4 related questions. Thanks Joe To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
