<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi,<div><br></div><div>I am getting the following error from AutoMR, which I am fairly certain is due to the deficiencies of my machine:</div><div><br></div><div><div>Python(2624) malloc: *** mmap(size=1665024000) failed (error code=12)</div><div>*** error: can't allocate region</div><div>*** set a breakpoint in malloc_error_break to debug</div><div><br></div><div>While using the prior release of phenix, I was able to get a similar job to complete, which makes me curious.</div><div><br></div><div>I am running phenix 1.7-650 (GUI) on an Intel Mac with 4GB of RAM and OS 10.6.6.</div><div><br></div><div>Any suggestions?</div><div><br></div><div>Thanks!</div><div><br></div><div>Erik</div><div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px;"><br></span></font></div></span></div></span></div></span></div></span></div>
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<br><div><div>On Feb 17, 2011, at 11:29 AM, <<a href="mailto:phenixbb-request@phenix-online.org">phenixbb-request@phenix-online.org</a>> <<a href="mailto:phenixbb-request@phenix-online.org">phenixbb-request@phenix-online.org</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Send phenixbb mailing list submissions to<br> <a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br><br>To subscribe or unsubscribe via the World Wide Web, visit<br> <a href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>or, via email, send a message with subject or body 'help' to<br> <a href="mailto:phenixbb-request@phenix-online.org">phenixbb-request@phenix-online.org</a><br><br>You can reach the person managing the list at<br> <a href="mailto:phenixbb-owner@phenix-online.org">phenixbb-owner@phenix-online.org</a><br><br>When replying, please edit your Subject line so it is more specific<br>than "Re: Contents of phenixbb digest..."<br><br><br>Today's Topics:<br><br> 1. Re: At what percentage of saturated peaks is acceptable?<br> (Mischa Machius)<br> 2. Re: At what percentage of saturated peaks is acceptable?<br> (Ed Pozharski)<br> 3. Unrealistic number of waters found by phenix? (Ina Lindemann)<br> 4. Re: Unrealistic number of waters found by phenix?<br> (Folmer Fredslund)<br> 5. Re: Unrealistic number of waters found by phenix? (Felix Frolow)<br> 6. EMBO 2011 Practical Course - Exploiting Anomalous Scattering<br> - ESRF - 6 - 10 June 2011 (Daniele de Sanctis)<br> 7. IUCr Travel Fellowships Available (Gloria Borgstahl)<br><br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Wed, 16 Feb 2011 20:42:55 -0500<br>From: "Mischa Machius" <<a href="mailto:machius@med.unc.edu">machius@med.unc.edu</a>><br>To: "PHENIX user mailing list" <<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>><br>Subject: Re: [phenixbb] At what percentage of saturated peaks is<br> acceptable?<br>Message-ID: <<a href="mailto:91F63968-BF15-47B4-A15E-FB73279AD18C@med.unc.edu">91F63968-BF15-47B4-A15E-FB73279AD18C@med.unc.edu</a>><br>Content-Type: text/plain; charset=us-ascii<br><br>I would recommend taking two passes; a low-resolution pass with short exposures and a high-resolution pass with longer exposures. Then merge the two, and you've got a complete dataset. If applicable, take three or more passes. MM<br><br>On Feb 16, 2011, at 8:39 PM, Jason wrote:<br><br><blockquote type="cite">Hi,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I have a technical question that is not related to phenix, but I hope some expertise around may help me out.<br></blockquote><blockquote type="cite">I am intending to increase the exposure time to gain some resolution. At the same time I do not want too many over exposed peak. The question comes to at what percentage of the saturated peaks is acceptable? Many thanks.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">======================<br></blockquote><blockquote type="cite">Jason<br></blockquote><blockquote type="cite">Structural Biology Department<br></blockquote><blockquote type="cite">University of Pittsburgh<br></blockquote><blockquote type="cite">======================<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">phenixbb mailing list<br></blockquote><blockquote type="cite"><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br></blockquote><blockquote type="cite"><a href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a><br></blockquote><br><br><br><br>------------------------------<br><br>Message: 2<br>Date: Wed, 16 Feb 2011 20:45:47 -0500<br>From: Ed Pozharski <<a href="mailto:epozh001@umaryland.edu">epozh001@umaryland.edu</a>><br>To: PHENIX user mailing list <<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>><br>Subject: Re: [phenixbb] At what percentage of saturated peaks is<br> acceptable?<br>Message-ID: <1297907147.30587.17.camel@thunderclap><br>Content-Type: text/plain; charset="UTF-8"<br><br>If you start losing completeness at low resolution, just collect a low<br>resolution pass (i.e. exactly the same frames but with short exposures).<br>Be mindful of radiation damage though.<br><br>On Wed, 2011-02-16 at 20:39 -0500, Jason wrote:<br><blockquote type="cite">Hi,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I have a technical question that is not related to phenix, but I hope<br></blockquote><blockquote type="cite">some expertise around may help me out.<br></blockquote><blockquote type="cite">I am intending to increase the exposure time to gain some resolution.<br></blockquote><blockquote type="cite">At the same time I do not want too many over exposed peak. The<br></blockquote><blockquote type="cite">question comes to at what percentage of the saturated peaks is<br></blockquote><blockquote type="cite">acceptable? Many thanks.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">======================<br></blockquote><blockquote type="cite">Jason<br></blockquote><blockquote type="cite">Structural Biology Department<br></blockquote><blockquote type="cite">University of Pittsburgh<br></blockquote><blockquote type="cite">======================<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">phenixbb mailing list<br></blockquote><blockquote type="cite"><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br></blockquote><blockquote type="cite"><a href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a><br></blockquote><br><br><br><br>------------------------------<br><br>Message: 3<br>Date: Thu, 17 Feb 2011 08:52:26 +0100<br>From: Ina Lindemann <<a href="mailto:lindema2@staff.uni-marburg.de">lindema2@staff.uni-marburg.de</a>><br>To: <a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>Cc: <a href="mailto:heinea@mailer.uni-marburg.de">heinea@mailer.uni-marburg.de</a><br>Subject: [phenixbb] Unrealistic number of waters found by phenix?<br>Message-ID:<br> <<a href="mailto:20110217085226.106944rzydtyujeo@home.staff.uni-marburg.de">20110217085226.106944rzydtyujeo@home.staff.uni-marburg.de</a>><br>Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";<br> format="flowed"<br><br><br>Hi,<br><br>I am refining a crystal structure of a protein with 198 amino acids at<br>1.59 A resolution.<br>I have used the function Update waters in phenix. After visual<br>inspection of the found water molecules I deleted some of them, but<br>there are still 334 water molecules left which show reasonable<br>electron density. Many of them interacts just with other water<br>molecules and not with the protein.<br>I calculated the average B of water molecules = 26.3 and protein = 12.6.<br>Now I am wondering if the number of water molecules and their average<br>B value is to high with respect to the protein and would be very<br>pleased about your answers.<br><br>With best regards,<br>Ina<br><br><br><br><br>Ina Lindemann<br>Philipps-Universit?t Marburg<br>Pharmazeutische Chemie<br>AG Klebe<br>Marbacher Weg 6<br>35032 Marburg<br>Tel.: 06421/2825908<br><br><br><br>------------------------------<br><br>Message: 4<br>Date: Thu, 17 Feb 2011 09:14:41 +0100<br>From: Folmer Fredslund <<a href="mailto:folmerf@gmail.com">folmerf@gmail.com</a>><br>To: PHENIX user mailing list <<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>><br>Subject: Re: [phenixbb] Unrealistic number of waters found by phenix?<br>Message-ID:<br> <<a href="mailto:AANLkTimXZUDZQMxf70jRSMPxi+=9dFKHB6OAoVV6wGuw@mail.gmail.com">AANLkTimXZUDZQMxf70jRSMPxi+=9dFKHB6OAoVV6wGuw@mail.gmail.com</a>><br>Content-Type: text/plain; charset=ISO-8859-1<br><br>Dear Ina<br><br>Have a look here (from the CCP4BB)<br><br><a href="http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg19631.html">http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg19631.html</a><br><br>Best regards,<br>Folmer Fredslund<br><br>2011/2/17 Ina Lindemann <lindema2@staff.uni-marburg.de>:<br><blockquote type="cite"><br></blockquote><blockquote type="cite">Hi,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I am refining a crystal structure of a protein with 198 amino acids at 1.59<br></blockquote><blockquote type="cite">A resolution.<br></blockquote><blockquote type="cite">I have used the function Update waters in phenix. After visual inspection of<br></blockquote><blockquote type="cite">the found water molecules I deleted some of them, but there are still 334<br></blockquote><blockquote type="cite">water molecules left which show reasonable electron density. Many of them<br></blockquote><blockquote type="cite">interacts just with other water molecules and not with the protein.<br></blockquote><blockquote type="cite">I calculated the average B of water molecules = 26.3 and protein = 12.6.<br></blockquote><blockquote type="cite">Now I am wondering if the number of water molecules and their average B<br></blockquote><blockquote type="cite">value is to high with respect to the protein and would be very pleased about<br></blockquote><blockquote type="cite">your answers.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">With best regards,<br></blockquote><blockquote type="cite">Ina<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Ina Lindemann<br></blockquote><blockquote type="cite">Philipps-Universit?t Marburg<br></blockquote><blockquote type="cite">Pharmazeutische Chemie<br></blockquote><blockquote type="cite">AG Klebe<br></blockquote><blockquote type="cite">Marbacher Weg 6<br></blockquote><blockquote type="cite">35032 Marburg<br></blockquote><blockquote type="cite">Tel.: 06421/2825908<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">phenixbb mailing list<br></blockquote><blockquote type="cite">phenixbb@phenix-online.org<br></blockquote><blockquote type="cite">http://phenix-online.org/mailman/listinfo/phenixbb<br></blockquote><br><br>------------------------------<br><br>Message: 5<br>Date: Thu, 17 Feb 2011 10:23:58 +0200<br>From: Felix Frolow <mbfrolow@post.tau.ac.il><br>To: PHENIX user mailing list <phenixbb@phenix-online.org><br>Cc: heinea@mailer.uni-marburg.de<br>Subject: Re: [phenixbb] Unrealistic number of waters found by phenix?<br>Message-ID: <D3ACED80-CB0C-4043-BB4A-CF8E8A936195@post.tau.ac.il><br>Content-Type: text/plain; charset=iso-8859-1<br><br>Dear Ina Lindemann<br>These are problems of the rich people...<br>Be happy and why not, after all your resolution is ~1.6 A<br>I would say that you have not enough water molecules. In such resolution and such molecular size<br>I would expect about 2 or even 3 water molecules per residue. So you are missing 198*2-334=62 water molecules.<br>As a frequent reviewer I would not let a paper describing such structure to pass! ;-) ;-)<br><br>Dr Felix Frolow<br>Professor of Structural Biology and Biotechnology<br>Department of Molecular Microbiology<br>and Biotechnology<br>Tel Aviv University 69978, Israel<br><br>Acta Crystallographica F, co-editor<br><br>e-mail: mbfrolow@post.tau.ac.il<br>Tel: ++972-3640-8723<br>Fax: ++972-3640-9407<br>Cellular: 0547 459 608<br><br>On Feb 17, 2011, at 09:52 , Ina Lindemann wrote:<br><br><blockquote type="cite"><br></blockquote><blockquote type="cite">Hi,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I am refining a crystal structure of a protein with 198 amino acids at 1.59 A resolution.<br></blockquote><blockquote type="cite">I have used the function Update waters in phenix. After visual inspection of the found water molecules I deleted some of them, but there are still 334 water molecules left which show reasonable electron density. Many of them interacts just with other water molecules and not with the protein.<br></blockquote><blockquote type="cite">I calculated the average B of water molecules = 26.3 and protein = 12.6.<br></blockquote><blockquote type="cite">Now I am wondering if the number of water molecules and their average B value is to high with respect to the protein and would be very pleased about your answers.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">With best regards,<br></blockquote><blockquote type="cite">Ina<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Ina Lindemann<br></blockquote><blockquote type="cite">Philipps-Universit?t Marburg<br></blockquote><blockquote type="cite">Pharmazeutische Chemie<br></blockquote><blockquote type="cite">AG Klebe<br></blockquote><blockquote type="cite">Marbacher Weg 6<br></blockquote><blockquote type="cite">35032 Marburg<br></blockquote><blockquote type="cite">Tel.: 06421/2825908<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">phenixbb mailing list<br></blockquote><blockquote type="cite">phenixbb@phenix-online.org<br></blockquote><blockquote type="cite">http://phenix-online.org/mailman/listinfo/phenixbb<br></blockquote><br><br><br>------------------------------<br><br>Message: 6<br>Date: Thu, 17 Feb 2011 16:23:16 +0100<br>From: Daniele de Sanctis <de.sanctisd@gmail.com><br>To: phenixbb@phenix-online.org<br>Subject: [phenixbb] EMBO 2011 Practical Course - Exploiting Anomalous<br> Scattering - ESRF - 6 - 10 June 2011<br>Message-ID:<br> <AANLkTikigUeBYgzF9wuJg7z5jTkZcKO0sh8j+AGUWDf6@mail.gmail.com><br>Content-Type: text/plain; charset=UTF-8<br><br>Deadline in 10 days!!<br><br><br>DEADLINE TO APPLY FEBRUARY 28th<br><br><br>COURSE ANNOUCEMENT<br><br>EMBO 2011 Practical Course - Exploiting Anomalous Scattering in<br>Macromolecular Structure Determination<br>ESRF-EMBL, Grenoble, France, 6 - 10 June 2011<br><br><br>The EMBO 2011 Practical Course on Exploiting Anomalous Scattering in<br>Macromolecular Structure Determination will be hosted by the ESRF in<br>Grenoble, France from 6 to 10, June 2011. The course aims to impart<br>the theoretical and practical basis for the 3-dimensional structure<br>determination of bio-macromolecules using Anomalous Dispersion<br>techniques (SAD & MAD) to young scientists who intend to apply these<br>methods in macromolecular crystallography.<br><br>Through a series of lectures, software demonstrations, practicals on<br>the ESRF beamlines and tutorials, participants will get insights into<br>all aspects of the structure determination process including beamline<br>instrumentation, data collection and processing, heavy atom<br>substructure determination, phasing and model building. There will<br>also be sessions focusing on automated structure solution procedures<br>and newer methods. Additional sessions will include presentations of<br>distinguished structures solved with these techniques.<br><br><br>Confirmed invited speakers include:<br>G. Bunkoczi, A. Cameron, D. Chirgadze, Z. Dauter, P. Evans, M.<br>Grininger, T. Gruene,<br>W. Kabsch, S. Panjikar, N. Pannu, A. Popov, H. Powell, L. Sazanov, G.<br>Sheldrick, T. Terwilliger, C. Vonrhein<br><br><br>The number of participants is limited to 20 and the deadline for<br>application is February 28th, 2011.<br>Additional information, course programme and instructions to apply to<br>the course can be found in the course webpages:<br>http://cwp.embo.org/pc11-03/<br><br>--<br>?????<br>---------------------------------------<br>Daniele de Sanctis, PhD<br><br>Structural Biology Group<br>ESRF, Grenoble, France<br>Tel 33 (0)4 76 88 2869<br><br><br>------------------------------<br><br>Message: 7<br>Date: Thu, 17 Feb 2011 10:42:00 -0600<br>From: Gloria Borgstahl <gborgstahl@gmail.com><br>To: phenixbb@phenix-online.org<br>Subject: [phenixbb] IUCr Travel Fellowships Available<br>Message-ID:<br> <AANLkTik3EecaF_MB8avPPs5jZbVWjoA+s__6k067mDAD@mail.gmail.com><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>Please see the attachment<br>The deadline is 15 days away.<br><br><br>************************************************************************<br>Gloria Borgstahl<br>Eppley Institute for Cancer Research and Allied Diseases<br>987696 Nebraska Medical Center<br>10732A Lied Transplant Center<br>Omaha, NE 68198-7696<br><br>http://sbl.unmc.edu<br>Office (402) 559-8578<br>FAX (402) 559-3739<br><br>Professor<br>Hobbies: ?Protein Crystallography, Cancer, Biochemistry,<br>DNA Metabolism, Modulated Crystals, ?Crystal Perfection<br>Interests: ?Manga, Led Zeppelin, Cold Play, piano, BRAN,<br>RAGBRAI, golf and lately superspace groups<br>************************************************************************<br>-------------- next part --------------<br>A non-text attachment was scrubbed...<br>Name: Travel Fellowship.Announcement.pdf<br>Type: application/octet-stream<br>Size: 140192 bytes<br>Desc: not available<br>URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20110217/eaff9de9/attachment.obj><br><br>------------------------------<br><br>_______________________________________________<br>phenixbb mailing list<br>phenixbb@phenix-online.org<br>http://phenix-online.org/mailman/listinfo/phenixbb<br><br><br>End of phenixbb Digest, Vol 63, Issue 7<br>***************************************<br></div></blockquote></div><br></div></body></html>