Re: [ccp4bb] dm: Error in opening input map file.
i should rtfm but don't you just need a mask per domain? On 16 May 2012 22:54, Yu Feng yufengc...@gmail.com wrote: Hi Eleanor, If you have a large protein and want to apply different ncs operations to different domains, then you might need to give multiple masks and matrices. Yu On Wed, May 16, 2012 at 8:26 AM, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: It is a long time since I did this, but don't you need just one master mask - then that is converted using your rotation matrix to mask the related part of the structure ? Eleanor Dodson On 15 May 2012 15:56, Yu Feng yufengc...@gmail.com wrote: Dear De-Feng Li, Thank you for your reply. Actually, I already used the script. The script and the log file are at the bottom of the email. Best wishes, Yu On Tue, May 15, 2012 at 3:18 AM, lidefeng lidef...@moon.ibp.ac.cnwrote: Dear Yu Feng, You could try it in script, but not in the CCP4i. The same problem could be found in DMMulti. Your sincerely De-Feng Li 2012-05-15 De-Feng Li, Ph.D, National Laboratory of Biomacromolecules Institute of Biophysics, Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101, PR China === 2012-05-15 18:44:48 You writed in your letter:=== Dear CCP4ers, I have a problem when I use DM to do NCS averaging. If I input 9 NCS averaging masks, DM works OK. However, if I input 10 NCS averaging masks, DM can not open input map file. The masks should be OK because they are generated by the same method. Do you have any idea how to solve the problem? Thank you in advance! Yu DM script is as below: /usr/share/CCP4-6.0.2/ccp4-6.2.0/bin/dm \ hklin /home/crystal/Documents/Ecoli/datasets/F111062011/130_10/reprocess/DM/x_refine33_phase.mtz \ ncsin1 E.msk \ ncsin2 F1.msk \ ncsin3 F2.msk \ ncsin4 D4.msk \ ncsin5 D5.msk \ ncsin6 D3.msk \ ncsin7 D2.msk \ ncsin8 D1.msk \ ncsin9 C5.msk \ ncsin10 C6.msk \ hklout x_dm.mtz EOF-dm SOLC 0.62 #RESOL 50 4.0 #NCSMASK SIZE 1 #NCSMASK UPDATE 3 #GRID 144 144 144 MODE SOLV hist AVER MULTI combine weight 0.15 combine pert scheme res from 4.5 NCYCLE 10 ncsmask overlap AVER DOMAIN 1 REFINE ROTATE EULER 0.0000.0000.000 TRANSLATION0.0000.0000.000 AVER DOMAIN 1 REFINE ROTA MATRIX -0.26665 0.52763 0.80654 0.60893 -0.55642 0.56533 0.74706 0.64187 -0.17293 TRAN -31.41600 172.23766 -96.59856 AVER DOMAIN 1 REFINE ROTA MATRIX 0.82271 0.34200 -0.45406 -0.55866 0.63407 -0.53465 0.10506 0.69353 0.71272 TRAN -141.48692 39.40455 -17.81890 AVER DOMAIN 1 REFINE ROTA MATRIX -0.35001 0.06658 0.93438 0.03939 -0.99554 0.08569 0.93592 0.06679 0.34582 TRAN -75.12174 220.50938 35.16329 AVER DOMAIN 2 REFIN ROTATE EULER 0.0000.0000.000 TRANSLATION0.0000.0000.000 AVER DOMAIN 2 REFINE ROTA MATRIX -0.42731 0.24363 0.87066 0.39149 -0.81818 0.42109 0.81494 0.52080 0.25424 TRAN -7.42336 185.84557 -68.83428 AVER DOMAIN 2 REFINE ROTA MATRIX -0.42918 0.04126 0.90228 0.01801 -0.99837 0.05422 0.90304 0.03952 0.42774 TRAN -74.51554 219.69878 39.63858 AVER DOMAIN 2 REFINE ROTA MATRIX 0.94716 0.32039 -0.01558 -0.30765 0.89358 -0.32691 -0.09082 0.31442 0.94493 TRAN -121.99072 28.41423 20.60830 AVER DOMAIN 3 REFINE ROTATE EULER 0.0000.0000.000 TRANSLATION0.0000.0000.000 AVER DOMAIN 3 REFINE ROTA MATRIX -0.42590 0.08845 0.90044 -0.00887 -0.99557 0.09361 0.90473 0.03188 0.42480 TRAN -77.38764 220.87816 40.52480 AVER DOMAIN 4 REFINE ROTATE EULER 0.0000.0000.000 TRANSLATION0.0000.0000.000 AVER DOMAIN 4 REFINE ROTA MATRIX -0.34404 0.07038 0.93631 -0.03070 -0.99750 0.06370 0.93845 -0.00683 0.34534 TRAN -79.74300 222.43433 43.52758 AVER DOMAIN 5 REFINE ROTATE EULER 0.0000.0000.000 TRANSLATION0.0000.0000.000 AVER DOMAIN 5 REFINE ROTA MATRIX -0.35957 -0.00781 0.93309 -0.00716 -0.1 -0.01113 0.93309 -0.01068 0.35948 TRAN -70.14525 224.81303 43.77335 AVER DOMAIN 6 REFINE ROTATE EULER 0.0000.0000.000 TRANSLATION0.0000.0000.000 AVER DOMAIN 6 REFINE ROTA MATRIX -0.35957 -0.00781 0.93309 -0.00716 -0.1 -0.01113 0.93309 -0.01068 0.35948 TRAN -70.14525 224.81303 43.77335 AVER DOMAIN 7 REFINE ROTATE EULER 0.0000.0000.000 TRANSLATION0.0000.0000.000 AVER DOMAIN 7 REFINE ROTA MATRIX -0.35957 -0.00781 0.93309 -0.00716 -0.1 -0.01113 0.93309 -0.01068 0.35948 TRAN -70.14525 224.81303 43.77335 AVER DOMAIN 8 REFINE ROTATE EULER 0.0000.0000.000 TRANSLATION0.0000.0000.000 AVER DOMAIN 8 REFINE ROTA MATRIX
[ccp4bb]
Dear All I have one query, i have solved one structure where in which near cys residues i can see density for beta mercaptoethanol (which i have used in my crystallization cocktail ). i have one query when i am taking BME from coot library, i can fit it in density but i do not know how to make disulphide bond ie to connect cysteine with bme. -- Regards Faisal School of Life Sciences JNU
[ccp4bb]
Hi, I think you'll find the Jligand tutorial on the York site very helpful in that regard. It's well worth trying. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Faisal Tarique [faisaltari...@gmail.com] Sent: Thursday, May 17, 2012 11:43 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Dear All I have one query, i have solved one structure where in which near cys residues i can see density for beta mercaptoethanol (which i have used in my crystallization cocktail ). i have one query when i am taking BME from coot library, i can fit it in density but i do not know how to make disulphide bond ie toconnectcysteine with bme. -- Regards Faisal School of Life Sciences JNU
[ccp4bb] Drawing plt and libXaw lib
Dear all, in Fedora 15 I am having troubles to get the .plt outputs drawn. The complaint is Using CCP4 programs from /protein/ccp4-6.2/ccp4-6.2.0/bin xplot84driver: error while loading shared libraries: libXaw.so.7: cannot open shared object file: No such file or directory libXaw.so.7 is in the system - the 64 bit version though. Anybody knows the way out? Jan Dohnalek -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 340 Fax: +420 296 809 410
Re: [ccp4bb] Drawing plt and libXaw lib
On 17/05/12 11:44, Jan Dohnalek wrote: Dear all, in Fedora 15 I am having troubles to get the .plt outputs drawn. The complaint is Using CCP4 programs from /protein/ccp4-6.2/ccp4-6.2.0/bin xplot84driver: error while loading shared libraries: libXaw.so.7: cannot open shared object file: No such file or directory libXaw.so.7 is in the system - the 64 bit version though. If that is a i386 binary then you need to yum install libXaw.i386 do you not?
Re: [ccp4bb] Drawing plt and libXaw lib
On 17/05/12 11:44, Jan Dohnalek wrote: Dear all, in Fedora 15 I am having troubles to get the .plt outputs drawn. The complaint is Using CCP4 programs from /protein/ccp4-6.2/ccp4-6.2.0/bin xplot84driver: error while loading shared libraries: libXaw.so.7: cannot open shared object file: No such file or directory libXaw.so.7 is in the system - the 64 bit version though. Anybody knows the way out? Jan Dohnalek Dear Jan, Does, yum install libXaw.i386 help? Stuart
Re: [ccp4bb] CYS-BME link
On 17/05/12 14:48, Ed Pozharski wrote: On Thu, 2012-05-17 at 14:13 +0530, Faisal Tarique wrote: to make disulphide bond ie to connect cysteine with bme While I believe that CYS+BME is a correct choice ideologically (you had cysteine and bme reacted with it), note that you can use CME monomer (it's listed as peptide in monomer libraries, so will incorporate fine). On the other hand, I have added BME a number of times in coot and had no problems. Yes, the bond is not showing, likely because coot decides which bonds to draw without much attention to atom type In Coot 0.7, to draw a bond between monomers that don't have an implicit connection due their serial number, you need a LINK record. You can add a LINK using Extensions - Modelling. Coot 0.7 has an interface to (recent versions of) JLigand to make the generation and transfer of bespoke link information considerably more straightforward (and in so doing will generate a LINK for you). Paul.
Re: [ccp4bb] CYS-BME link
On Thu, 2012-05-17 at 15:12 +0100, Paul Emsley wrote: In Coot 0.7, to draw a bond between monomers that don't have an implicit connection due their serial number, you need a LINK record. You can add a LINK using Extensions - Modelling. Thanks - is there some way to remove the link (other than deleting and re-inserting a residue)? -- Coot verendus est
Re: [ccp4bb] CSX
Dear All; Thank you very much for your comments and advices. My protein is homo-tetramer. Based on difference density, only one cysteine (among the four catalytic cysteins) has observed two positive density along SG-group. This one could be modeled into OCS, while the rest will be modeled as non-oxidized. I very much appreciate for all your inputs regards Uma On Fri, May 4, 2012 at 6:09 PM, Savvas Savvides savvas.savvi...@ugent.bewrote: Dear Uma Your modeling of a Cysteine sulfenic group (SOH) is reasonable given the observed difference density but do keep in mind that sulfenic groups are very susceptible to further oxidation to sulfinic and sulfonic acids. Stabilization of sulfenic and sulfinic groups in enzyme active sites is possible as shown crystallographically by Becker et al Nat Struct Biol 5:267-271 (1998). Also make sure that you flip the Histidine in the active site that faces the SOH group to account for a possible hydrogen bond. Best regards Savvas On 04 May 2012, at 20:24, Uma Ratu rosiso2...@gmail.com wrote: Dear All: Thank you very much for your advices and comments. Following your instructions, I am able to change the CYS to CSX. Both Get Monomer and Replace Residue work well. I have the refined conformation CSX (by real space refinment ) attached (named as M-CSX-1). The Fo-Fc map is shown with sigma @2.0. Is this conformation reasonable? Why there are two bond conformation there? Thank you for comments. Uma On Fri, May 4, 2012 at 12:10 PM, Hugo Correia h.corr...@campus.fct.unl.pt wrote: Dear Uma, You can do this using coot. Go to Extensions Modelling Replace Residue... and enter the three letter code. Cheers Hugo Correia 2012/5/4 Uma Ratu rosiso2...@gmail.com Dear All: My protein has a key cysteine residue involved in catalytic activity. The template structure used for the modeling has the same key cysteine. In the template structure, this key cysteine residue is assigned as CSX based on the observation from its electronic density. I compared the electron density from the template as well as my model. I can't tell if the cysteine in my model is oxidized or not. The ones from the template also looks different from each other, although both assigned as CSX. I have the snapshots of these cysteines attached. The ones from my model named as M-, and the ones from the template named as T-. Plus, how to change the residue label from Cys to CSX if the cystein is oxidized? In coot, I could not find such function. Thank you very much for your advice Uma M-CSX-1.tif
[ccp4bb] Covert Structure Factor to mtz
Dear All: I try to convert the .cif files (the structure factor files from PDB) to mtz file. From ccp4i, I chose convert to/modify/extend mtz for this purpose. But program keep complanining: no cell information in keywords or files I open the .cif file in text, and could not find any information about cell information. Is there a easy way to convert the .cif file from PDB to mtz? Thank you for advice Uma
Re: [ccp4bb] completeness in scala
Maybe it's including covert structure factors? See recent ccp4bb post subject... JPK On Tue, May 15, 2012 at 4:28 PM, case c...@biomaps.rutgers.edu wrote: On Tue, May 15, 2012, Toth, Eric wrote: In sports, maximal effort is considered to be 110%, so you're actually 9.9% short of getting everything you could out of that crystal at its resolution limit. All things considered, that's not bad. In (U.S.) politics, the standard continues to be the 1000% support given by presidential candidate George McGovern to vice-presidential candidate Thomas Eagleton, shortly before dropping him from the ticket. Sounds to me like you need to re-examine the statistics of this particular crystal to try to see why it is diffracting so poorly. ...dave case -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Covert Structure Factor to mtz
Reflection cif files from the PDB do not always have cell and symmetry information in them, particularly the older ones, and it sounds like this is your case. In that case, you need to manually copy the cell information from the PDB web page into the ccp4i interface before running. HTH Martyn From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Uma Ratu Sent: 17 May 2012 20:04 To: ccp4bb Subject: [ccp4bb] Covert Structure Factor to mtz Dear All: I try to convert the .cif files (the structure factor files from PDB) to mtz file. From ccp4i, I chose convert to/modify/extend mtz for this purpose. But program keep complanining: no cell information in keywords or files I open the .cif file in text, and could not find any information about cell information. Is there a easy way to convert the .cif file from PDB to mtz? Thank you for advice Uma
Re: [ccp4bb] Covert Structure Factor to mtz
It works! Thank you very much Uma On Thu, May 17, 2012 at 3:16 PM, martyn.w...@stfc.ac.uk wrote: Reflection cif files from the PDB do not always have cell and symmetry information in them, particularly the older ones, and it sounds like this is your case. In that case, you need to manually copy the cell information from the PDB web page into the ccp4i interface before running. HTH Martyn From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Uma Ratu Sent: 17 May 2012 20:04 To: ccp4bb Subject: [ccp4bb] Covert Structure Factor to mtz Dear All: I try to convert the .cif files (the structure factor files from PDB) to mtz file. From ccp4i, I chose convert to/modify/extend mtz for this purpose. But program keep complanining: no cell information in keywords or files I open the .cif file in text, and could not find any information about cell information. Is there a easy way to convert the .cif file from PDB to mtz? Thank you for advice Uma
Re: [ccp4bb] Covert Structure Factor to mtz
It would be desirable to actually HAVE the cell information in the cif file, if simply for assuring/checking consistency between model and data. Maybe something for the PDB to contemplate BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of martyn.w...@stfc.ac.uk Sent: Thursday, May 17, 2012 12:16 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Covert Structure Factor to mtz Reflection cif files from the PDB do not always have cell and symmetry information in them, particularly the older ones, and it sounds like this is your case. In that case, you need to manually copy the cell information from the PDB web page into the ccp4i interface before running. HTH Martyn
Re: [ccp4bb] question on metal refinement in a protein structure
I am not familiar with CNS restraints, but whatever the program restraints are - if you do a omit map, or just set the occupancies of the metal and its surroundings to 0.00 and do a few cycles of refinement, I believe any model bias will disappear and what you see will be pretty accurate description of the metal. When you include that atom in the refinement it is usually necessary to at least set distance restraints up - otherwise the heavier metal density will tend to swallow any water molecules around about Eleanor On 14 May 2012 15:19, Ed Pozharski epozh...@umaryland.edu wrote: On Sat, 2012-05-12 at 08:48 -0400, Dave Roberts wrote: However, I just want to make sure the metal environment is not due to the fact that I did something wrong in my refinement script - thus making it tetrahedral because it was refined as tetrahedral. ... I don't use CCP4 for refinement, I use CNS, but I'm hoping somebody will be able to guide me here. AFAIK, CNS does not generate any geometry restraints for metal ions *automatically*. You may want to make sure (if you didn't yet) that you use a correct residue name, e.g. NI2 (and atom name NI+2) for Ni++. CNS libraries would use different values for the radii and scattering factors of these. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] question on metal refinement in a protein structure
On 17 May 2012 21:27, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: I am not familiar with CNS restraints, but whatever the program restraints are - if you do a omit map, or just set the occupancies of the metal and its surroundings to 0.00 and do a few cycles of refinement, I believe any model bias will disappear and what you see will be pretty accurate description of the metal. When you include that atom in the refinement it is usually necessary to at least set distance restraints up - otherwise the heavier metal density will tend to swallow any water molecules around about Eleanor On 14 May 2012 15:19, Ed Pozharski epozh...@umaryland.edu wrote: On Sat, 2012-05-12 at 08:48 -0400, Dave Roberts wrote: However, I just want to make sure the metal environment is not due to the fact that I did something wrong in my refinement script - thus making it tetrahedral because it was refined as tetrahedral. ... I don't use CCP4 for refinement, I use CNS, but I'm hoping somebody will be able to guide me here. AFAIK, CNS does not generate any geometry restraints for metal ions *automatically*. You may want to make sure (if you didn't yet) that you use a correct residue name, e.g. NI2 (and atom name NI+2) for Ni++. CNS libraries would use different values for the radii and scattering factors of these. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] how to ignore spot overlap in imosflm?
Hi, there are two points in Herman's post that I'd like to comment upon: 1) in case of XDS, there are two modes of reporting the completeness: one is triggered with FRIEDEL'S_LAW=TRUE, and the other with FRIEDEL'S_LAW=FALSE. Obviously the reported completeness will differ between these two modes, since the latter mode treats Friedel pairs as separate reflection, whereas the former doesn't. However, the XDS_ASCII.HKL file which has the reflections' intensities and standard deviations for downstream usage is almost the same (except for small differences in scaling) in both cases. This means that the actual completeness of the isomorphous signal (which implicitly does not care about whether an intensity is I+ or I-) is the same in both modes, which has the consequence that for molecular replacement and refinement calculations it does not matter which mode was used for producing XDS_ASCII.HKL . In other words, only concerning the numbers in the famous Table 1 you have to pay attention in which mode you produce the statistics reported in CORRECT.LP/XSCALE.LP, not for calculations which make no use of the anomalous signal. 2) to lie to the program by specifying a very low REFLECTING_RANGE_E.S.D. is _not_ the best way to make XDS produce a more complete dataset! The right way is to specify a lower MINPK than the default of 75 - see http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/INTEGRATE HTH, Kay
[ccp4bb] Post-doc position available
A position is available now in the laboratory of Wim Hol, as described below. Please respond to the address at the end of the advertisement. Postdoctoral Position Available Laboratory of Wim Hol Department of Biochemistry, School of Medicine University of Washington, Seattle, USA Structural Biology of the type II secretion system from pathogenic bacteria The projects in Wim Hol’s protein crystallography group at the University of Washington are all focused on providing a basis for development of new therapeutics for tropical diseases. This particular available postdoctoral position is part of a major effort to unravel the architecture, mechanism of action and biogenesis of the “type II secretion system” (T2SS). The sophisticated T2SS occurs in many pathogenic bacteria. This machinery is responsible for translocating a wide variety of proteins in a folded state from the periplasm across the outer membrane into the extracellular milieu. One of these proteins is cholera toxin which has been studied intensively in the Hol lab. The large T2SS consists of multiple copies of ~14 different proteins that span the inner and the outer membrane, and is associated with a secretion ATPase in the cytoplasm which provides the energy for the secretion process. Another remarkable feature of the T2SS is a helical sub-assembly in the periplasm which is likely serving as a piston pushing cholera toxin and other exoproteins through a pore in the outer membrane. The successful candidate will have the opportunity to: (i) carry out protein _expression_ and protein chemistry studies to obtain insight into protein-protein interactions involving the T2SS from pathogenic bacteria like Vibrio cholera, enterotoxigenic E. coli, and other bacteria; (ii) purify and characterize multi-protein and multi-membrane protein complexes; (iii) determine high resolution crystal structures of these complexes; (iv) analyze these structures and combine this with other biochemical data; (v) interact with several collaborating groups which are using other methods to obtain structural and functional insight into the mechanism of this sophisticated secretion system. For more information regarding the laboratory of Wim Hol see the following website: http://www.bmsc.washington.edu/WimHol/ For more information regarding the type II secretion system see our recent review: Korotkov, K. V., Sandkvist, M. and Hol, W. G. J. The type II secretion system: biogenesis, molecular architecture and mechanism. Nature Reviews Microbiology 10, 336-351 (2012) START DATE: Immediately INSTITUTION: Department of Biochemistry Biomolecular Structure Center School of Medicine Box 357742 University of Washington Seattle, WA, 98195 USA Requirements Experience with membrane protein preparation, including molecular biology techniques, membrane protein characterization and protein crystallography. Application If you are interested, please send your CV, including a description of your experience and technical know-how, a list of publications and presentations, and names and email addresses of three references able to assess your scientific experience and capabilities to: wg...@u.washington.edu
Re: [ccp4bb] CYS-BME link
On 17/05/12 15:29, Ed Pozharski wrote: On Thu, 2012-05-17 at 15:12 +0100, Paul Emsley wrote: In Coot 0.7, to draw a bond between monomers that don't have an implicit connection due their serial number, you need a LINK record. You can add a LINK using Extensions - Modelling. is there some way to remove the link If you click on the wrong residue(s) there's always Ctrl-Z. Other than that, no :( (other than deleting and re-inserting a residue)? Not sure that (even) that'll do it (can't say that I've tried though). Paul.
Re: [ccp4bb] Covert Structure Factor to mtz
On 17/05/12 20:16, martyn.w...@stfc.ac.uk wrote: Reflection cif files from the PDB do not always have cell and symmetry information in them, particularly the older ones, and it sounds like this is your case. My understanding is that these days they should have - and if you find such examples, they should be reported to the wwPDB authorities. Paul.
Re: [ccp4bb] dm: Error in opening input map file.
Hi Eleanor, You are right, I just need a mask per domain. In my case, the protein has more than 10 domains, and I want to input their masks at the same time. It seems that I have to re-compile DM to run large proteins. Yu On Thu, May 17, 2012 at 4:38 AM, Eleanor Dodson eleanor.dod...@york.ac.ukwrote: i should rtfm but don't you just need a mask per domain? On 16 May 2012 22:54, Yu Feng yufengc...@gmail.com wrote: Hi Eleanor, If you have a large protein and want to apply different ncs operations to different domains, then you might need to give multiple masks and matrices. Yu On Wed, May 16, 2012 at 8:26 AM, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: It is a long time since I did this, but don't you need just one master mask - then that is converted using your rotation matrix to mask the related part of the structure ? Eleanor Dodson On 15 May 2012 15:56, Yu Feng yufengc...@gmail.com wrote: Dear De-Feng Li, Thank you for your reply. Actually, I already used the script. The script and the log file are at the bottom of the email. Best wishes, Yu On Tue, May 15, 2012 at 3:18 AM, lidefeng lidef...@moon.ibp.ac.cnwrote: Dear Yu Feng, You could try it in script, but not in the CCP4i. The same problem could be found in DMMulti. Your sincerely De-Feng Li 2012-05-15 De-Feng Li, Ph.D, National Laboratory of Biomacromolecules Institute of Biophysics, Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101, PR China === 2012-05-15 18:44:48 You writed in your letter:=== Dear CCP4ers, I have a problem when I use DM to do NCS averaging. If I input 9 NCS averaging masks, DM works OK. However, if I input 10 NCS averaging masks, DM can not open input map file. The masks should be OK because they are generated by the same method. Do you have any idea how to solve the problem? Thank you in advance! Yu DM script is as below: /usr/share/CCP4-6.0.2/ccp4-6.2.0/bin/dm \ hklin /home/crystal/Documents/Ecoli/datasets/F111062011/130_10/reprocess/DM/x_refine33_phase.mtz \ ncsin1 E.msk \ ncsin2 F1.msk \ ncsin3 F2.msk \ ncsin4 D4.msk \ ncsin5 D5.msk \ ncsin6 D3.msk \ ncsin7 D2.msk \ ncsin8 D1.msk \ ncsin9 C5.msk \ ncsin10 C6.msk \ hklout x_dm.mtz EOF-dm SOLC 0.62 #RESOL 50 4.0 #NCSMASK SIZE 1 #NCSMASK UPDATE 3 #GRID 144 144 144 MODE SOLV hist AVER MULTI combine weight 0.15 combine pert scheme res from 4.5 NCYCLE 10 ncsmask overlap AVER DOMAIN 1 REFINE ROTATE EULER 0.0000.0000.000 TRANSLATION0.0000.0000.000 AVER DOMAIN 1 REFINE ROTA MATRIX -0.26665 0.52763 0.80654 0.60893 -0.55642 0.56533 0.74706 0.64187 -0.17293 TRAN -31.41600 172.23766 -96.59856 AVER DOMAIN 1 REFINE ROTA MATRIX 0.82271 0.34200 -0.45406 -0.55866 0.63407 -0.53465 0.10506 0.69353 0.71272 TRAN -141.48692 39.40455 -17.81890 AVER DOMAIN 1 REFINE ROTA MATRIX -0.35001 0.06658 0.93438 0.03939 -0.99554 0.08569 0.93592 0.06679 0.34582 TRAN -75.12174 220.50938 35.16329 AVER DOMAIN 2 REFIN ROTATE EULER 0.0000.0000.000 TRANSLATION0.0000.0000.000 AVER DOMAIN 2 REFINE ROTA MATRIX -0.42731 0.24363 0.87066 0.39149 -0.81818 0.42109 0.81494 0.52080 0.25424 TRAN -7.42336 185.84557 -68.83428 AVER DOMAIN 2 REFINE ROTA MATRIX -0.42918 0.04126 0.90228 0.01801 -0.99837 0.05422 0.90304 0.03952 0.42774 TRAN -74.51554 219.69878 39.63858 AVER DOMAIN 2 REFINE ROTA MATRIX 0.94716 0.32039 -0.01558 -0.30765 0.89358 -0.32691 -0.09082 0.31442 0.94493 TRAN -121.99072 28.41423 20.60830 AVER DOMAIN 3 REFINE ROTATE EULER 0.0000.0000.000 TRANSLATION0.0000.0000.000 AVER DOMAIN 3 REFINE ROTA MATRIX -0.42590 0.08845 0.90044 -0.00887 -0.99557 0.09361 0.90473 0.03188 0.42480 TRAN -77.38764 220.87816 40.52480 AVER DOMAIN 4 REFINE ROTATE EULER 0.0000.0000.000 TRANSLATION0.0000.0000.000 AVER DOMAIN 4 REFINE ROTA MATRIX -0.34404 0.07038 0.93631 -0.03070 -0.99750 0.06370 0.93845 -0.00683 0.34534 TRAN -79.74300 222.43433 43.52758 AVER DOMAIN 5 REFINE ROTATE EULER 0.0000.0000.000 TRANSLATION0.0000.0000.000 AVER DOMAIN 5 REFINE ROTA MATRIX -0.35957 -0.00781 0.93309 -0.00716 -0.1 -0.01113 0.93309 -0.01068 0.35948 TRAN -70.14525 224.81303 43.77335 AVER DOMAIN 6 REFINE ROTATE EULER 0.0000.0000.000 TRANSLATION0.0000.0000.000 AVER DOMAIN 6 REFINE ROTA MATRIX -0.35957 -0.00781 0.93309 -0.00716 -0.1 -0.01113 0.93309 -0.01068 0.35948 TRAN -70.14525 224.81303 43.77335 AVER DOMAIN 7 REFINE ROTATE EULER 0.0000.0000.000 TRANSLATION0.0000.000
