Re: [ccp4bb] Problems with CCP4MG
Dear Regina, On 5 Jul 2012, at 17:51, Regina Kettering wrote: > Dear All; > > I have two problems with the visualization program that I am hoping people > can help me with: > 1) I downloaded a model from the Swiss-Model repository that I have been > trying to open on CCP4MG version 2.4.2. I have it saved as a .pdb file but > when it loads, CCP4MG hangs and appears to convert the file into a .pdb.html > file. I can remove any spurious lines in the file, resave, reload, to no > avail. I can open the .pdb file without problems in Coot and Pymol. Could you send me a (a link to) the pdb file so that I can llnk to see what is wrong. I am sure this must be something quite simple to fix. > 2) I decided to try opening on a Windows machine (don't judge), so downloaded > CCP4MG executable today (version 2.5.2). When installing, I received two > messages indicating that the executable is a virus. Is anyone aware of this > problem; am I missing a program necessary to open the files? This is simply your anti-virus really thinking that CCP4MG is a virus. It is not. You need to tell your anti-virus program that CCP4MG is not a virus. How you do that depends on which anti-virus program you have. Then you need to search the web to find out how to deal with false positives. If you know what your anti-virus program is, I might be able to help you with fixing the problem. Best wishes, Stuart McNicholas
[ccp4bb] Accessing CCP4MG applications via python scripts
Hi, I can't see any documentation on the CCP4MG web site that shows how to access applications using python scripts. If someone could e-mail me basic script that uses SSM to automatically superimpose all loaded PDBs I'd be very grateful. Thanks!
Re: [ccp4bb] Accessing CCP4MG applications via python scripts
Dear Mo, On 6 Jul 2012, at 09:09, Mo Wong wrote: > Hi, > > I can't see any documentation on the CCP4MG web site that shows how to access > applications using python scripts. > > If someone could e-mail me basic script that uses SSM to automatically > superimpose all loaded PDBs I'd be very grateful. > > Thanks! > I am afraid that scripting this kind of thing is not currently possible. You have to use Applications->Superpose models and then jsut press superpose. This will achieve same result, but probably with more button presses. I will add scripting ability in the future. Best wishes, Stuart McNicholas
[ccp4bb] Hi
Hope you get this on time, I made a trip to Aberdeen in Scotland and had my bag stolen from me with my passport,cash and credit cards in it. unfortunately for me,I have made contact with my bank but they are not providing a fast solution. I need you to lend me some money to sort my self out of this predicament,i will pay back as soon as i return. Western Union transfer is the best option to send money to me. Let me know if you need my details(Full names location) to make the transfer. You can reach me via email or the hotel's desk phone the numbers are,+447031804805 I await your response Thanks Afshan
[ccp4bb] electron density peak volume
Hi, Is there a way to ask peakmax to output the volume of each electron density peak that it detects (or is there a reasonably straightforward way to do this via an alternative command line runnable approach?) Cheers, Alan
Re: [ccp4bb] Problems with CCP4MG
The model is a theoretical model of Q766C3 (nepenthesin 1), link to the download below: http://swissmodel.expasy.org/?pid=smf02&source=repository&tid=file_model&mid=7d1184184e0086123cd94070ab861eb2_1 For the virus problem, it gives me the automatic "You have downloaded a file from the internet. It could be a virus" error, but then gives me two further errors when installing and automatically quarantines the files. The program does not work because it then cannot find the two quarantined files. The computer contains two sets of virus protection software: Symantic and Windows Defender. Thank you for the help. Regina From: Stuart McNicholas To: Regina Kettering Cc: CCP4BB@JISCMAIL.AC.UK Sent: Friday, July 6, 2012 3:33 AM Subject: Re: [ccp4bb] Problems with CCP4MG Dear Regina, On 5 Jul 2012, at 17:51, Regina Kettering wrote: Dear All; > > >I have two problems with the visualization program that I am hoping people can >help me with: >1) I downloaded a model from the Swiss-Model repository that I have been >trying to open on CCP4MG version 2.4.2. I have it saved as a .pdb file but >when it loads, CCP4MG hangs and appears to convert the file into a .pdb.html >file. I can remove any spurious lines in the file, resave, reload, to no >avail. I can open the .pdb file without problems in Coot and Pymol. > Could you send me a (a link to) the pdb file so that I can llnk to see what is wrong. I am sure this must be something quite simple to fix. 2) I decided to try opening on a Windows machine (don't judge), so downloaded CCP4MG executable today (version 2.5.2). When installing, I received two messages indicating that the executable is a virus. Is anyone aware of this problem; am I missing a program necessary to open the files? > This is simply your anti-virus really thinking that CCP4MG is a virus. It is not. You need to tell your anti-virus program that CCP4MG is not a virus. How you do that depends on which anti-virus program you have. Then you need to search the web to find out how to deal with false positives. If you know what your anti-virus program is, I might be able to help you with fixing the problem. Best wishes, Stuart McNicholas
Re: [ccp4bb] electron density peak volume
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Alan, do you think the notion of 'volume of a peak' makes sense? You are probably asking for the number of connected pixels around a local maximum above a certain threshold - again, not sure whether this is a useful concept and I am not aware of a program doing this calculation. Regards, Tim On 07/06/12 15:40, Andrew Pannifer wrote: > Hi, Is there a way to ask peakmax to output the volume of each > electron density peak that it detects (or is there a reasonably > straightforward way to do this via an alternative command line > runnable approach?) Cheers, Alan > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFP9vaLUxlJ7aRr7hoRAi4uAJ4vO3QwPeg4zDIduTKhGgMN1tytXgCguCUr Jo3h/z4RMXcWFJI9MzMku5A= =/8p9 -END PGP SIGNATURE-
[ccp4bb] Workshop on Advanced Data Collection with Multi-axis Goniometer and Single-photon Counting Detector
Workshop on Advanced Data Collection with Multi-axis Goniometer and Single-photon Counting Detector http://indico.psi.ch/multiaxisgonio2012 Swiss Light Source, Paul Scherrer Institut, Switzerland Nov. 6th - 8th, 2012 This workshop will address aspects including application of multi-axis goniometer for difficult phasing experiments, data collection optimization for single-photon counting detectors, as well as data processing optimization to take full advantage of crystal geometry and detector properties. Hardware and software developments, as well as user applications will be covered. The workshop contains both lectures and practicals. Data collection practicals will be performed at beamline X06DA at the Swiss Light Source on a multi-axis goniometer PRIGo and a PILATUS 2M detector. Data processing tutorials will be on the following programs: AutoPROC (XDS/SCALA), PROTEUM, and CrysAlisPro. There will be no registration fee and all local expenses will be covered, but participants are requested to take care of their travel arrangements. The workshop is limited to 20 participants. http://indico.psi.ch/multiaxisgonio2012 This workshop is funded by BioStruct-X (WP10.7). Speakers Gerard Bricogne, Global Phasing Ltd. Sandor Brockhauser, ESRF Kay Diederichs, Uni. Konstanz Gwyndaf Evans, Diamond Light Source Pierre Legrand, SOLEIL Andrew McCarthy, ESRF Marcus Muller, Dectris, Ltd. Vincent Olieric, SLS Michael Ruf, Bruker AXS Thomas Schneider, PETRAIII Clemens Schulze-Briese, Dectris, Ltd. Tadeusz Skarzynski, Agilent Technologies Andrew Thompson, SOLEIL Clemens Vonrhein, Global Phasing Ltd. Sandro Waltersperger, SLS Manfred Weiss, BESSY __ Meitian Wang Swiss Light Source at Paul Scherrer Institut CH-5232 Villigen PSI - http://www.psi.ch/sls/ Phone: +41 56 310 4175 Fax: +41 56 310 5292
Re: [ccp4bb] electron density peak volume
Hi Tim, a possible way of thinking about this is: say you have N (=nx*ny*nz) nodes of the grid on which you sampled the map, and the unit cell volume is Vcell, and you are looking at a blob identified at some level. Then the volume of this blob can be defined as Vblob = np*Vcell/N, where np is the number of grid nodes inside the blob. Pavel On Fri, Jul 6, 2012 at 7:30 AM, Tim Gruene wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Dear Alan, > > do you think the notion of 'volume of a peak' makes sense? You are > probably asking for the number of connected pixels around a local > maximum above a certain threshold - again, not sure whether this is a > useful concept and I am not aware of a program doing this calculation. > > Regards, > Tim > > On 07/06/12 15:40, Andrew Pannifer wrote: > > Hi, Is there a way to ask peakmax to output the volume of each > > electron density peak that it detects (or is there a reasonably > > straightforward way to do this via an alternative command line > > runnable approach?) Cheers, Alan > > > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -BEGIN PGP SIGNATURE- > Version: GnuPG v1.4.12 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFP9vaLUxlJ7aRr7hoRAi4uAJ4vO3QwPeg4zDIduTKhGgMN1tytXgCguCUr > Jo3h/z4RMXcWFJI9MzMku5A= > =/8p9 > -END PGP SIGNATURE- >
Re: [ccp4bb] electron density peak volume
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Pavel, that's probably how I'd program it, too. Still I am not aware of an existing (command line) program which does that, and I am not sure of its benefit from a users point of view. I can imagine that many programs internally make use of the 'blob' volume for various purposes. Cheers, Tim On 07/06/12 17:01, Pavel Afonine wrote: > Hi Tim, > > a possible way of thinking about this is: > > say you have N (=nx*ny*nz) nodes of the grid on which you sampled > the map, and the unit cell volume is Vcell, and you are looking at > a blob identified at some level. Then the volume of this blob can > be defined as Vblob = np*Vcell/N, where np is the number of grid > nodes inside the blob. > > Pavel > > On Fri, Jul 6, 2012 at 7:30 AM, Tim Gruene > wrote: > > Dear Alan, > > do you think the notion of 'volume of a peak' makes sense? You are > probably asking for the number of connected pixels around a local > maximum above a certain threshold - again, not sure whether this is > a useful concept and I am not aware of a program doing this > calculation. > > Regards, Tim > > On 07/06/12 15:40, Andrew Pannifer wrote: Hi, Is there a way to ask peakmax to output the volume of each electron density peak that it detects (or is there a reasonably straightforward way to do this via an alternative command line runnable approach?) Cheers, Alan > >> > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFP9v+qUxlJ7aRr7hoRAmEGAKDlWqKmeL3Woq3RG2kLdH+KMjue6ACgruAg 8Jy2MOq1OigufOsO+ud/uJQ= =tBk4 -END PGP SIGNATURE-
Re: [ccp4bb] Problems with CCP4MG
On 6 Jul 2012, at 15:10, Regina Kettering wrote: > The model is a theoretical model of Q766C3 (nepenthesin 1), link to the > download below: > > http://swissmodel.expasy.org/?pid=smf02&source=repository&tid=file_model&mid=7d1184184e0086123cd94070ab861eb2_1 > This is a very silly bug in CCP4MG, you need to delete the line: REMARK 1 http://swissmodel.expasy.org/repository/license.html or send an email in the PDB (line 24 when I downloaded). I will fix this asap. > For the virus problem, it gives me the automatic "You have downloaded a file > from the internet. It could be a virus" error, but then gives me two further > errors when installing and automatically quarantines the files. The program > does not work because it then cannot find the two quarantined files. The > computer contains two sets of virus protection software: Symantic and Windows > Defender. Then you need to go into your anti-virus setup and "unquarantine" or restore them. For windows defender see: http://windows.microsoft.com/en-US/windows7/Remove-or-restore-items-quarantined-by-Windows-Defender For symantic: https://www-secure.symantec.com/norton-support/jsp/help-solutions.jsp?docid=v6200305_NIS_Retail_2012_en_us&product=home&pvid=f-home&version=1&lg=english&ct=us Hope this helps. Best wishes, Stuart
Re: [ccp4bb] electron density peak volume
On 07/06/2012 09:40 AM, Andrew Pannifer wrote: Hi, Is there a way to ask peakmax to output the volume of each electron density peak that it detects (or is there a reasonably straightforward way to do this via an alternative command line runnable approach?) Cheers, Alan There might be a way to do it using some of the brilliant USF tools. A somewhat convoluted workaround would be to cut the piece of the map surrounding the peak, then converting it to mask using MAPMAN with cutoff of your choosing. You can then use MAMA's island_erase method to identify the main blob of density and count the nodes to get the volume. You may want to look into MAPMAN peek command too. It allows both getting the interpolated density value at the peak position and integral density over volume surrounding it. If you make certain assumptions about the peak shape (gaussian?) you can deduce the peak "volume" from these two numbers. Cheers, Ed. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
