Re: [ccp4bb] xds crashes

igure your system to avoid that. Maybe the systems-oomd package can simply be removed. Hope that helps, Kay On Tue, 29 Nov 2022 10:25:17 +0200, Demetres D. Leonidas wrote: Dear Kay, you are right and I do apologize for the misunderstanding. Point 1 and 2 are sufficient. best Demetres On

Re: [ccp4bb] xds crashes

Tue, 29 Nov 2022 09:34:49 +0200, Demetres D. Leonidas wrote: Dear Kay, after some digging and help from Max Nanao we found that the problem was the memory.  It was fulling rapidly. The workaround was to: 1. unzip the cbf files prior to processing 2. use maximum number of jobs 1 3. use number

Re: [ccp4bb] xds crashes

ms, I fixed it by editing /etc/security/limits.d/20-nproc.conf so that users are allowed ~10x more pids than normal.  This tends to prevent these mysterious "Killed" errors. HTH? -James Holton MAD Scientist On 11/28/2022 7:44 AM, Demetres D. Leonidas wrote: Dear all, I do not know if

[ccp4bb] xds crashes

echo "$itask"   3428 Killed  | $amain We are trying to process data from P13 at EMBL-Hamburg. We are running XDS version Jan 10, 2022 BUILT=20220820 Any ideas ? Demetres -- --- Dr. Demetres D. Leonidas Professor in Bi

Re: [ccp4bb] CCP4Mg problems

se happen after that message? One way to possibly help is to run it as follows: ccp4mg -noredirect This way all messages should be sent to the terminal output and we might see something more helpful. Sorry for your difficulties, Stuart On Mon, 27 Sept 2021 at 13:24, Demetres D. Leonidas mailto:d

[ccp4bb] CCP4Mg problems

and such a file does not exist but I thought it will be created automatically once you run the program. Any ideas ? Demetres -- --- Dr. Demetres D. Leonidas Professor in Biochemistry Department of Biochemistry & Biotechnology University of Thessaly

[ccp4bb] Postdoctoral research position

genomics studies. His/her research could also lead to a PhD. Curriculum Vitae, a brief letter describing interests and prior experience and names of three references should be sent to: kmath...@bio.uth.gr. -- --- Dr. Demetres D. Leonidas Professor of

Re: [ccp4bb] X-ray pattern has streaks

streaking. The streaks are many wide spread and there are no high resolution spots or streaks as we might expect in salt crystals. -- --- Dr. Demetres D. Leonidas Associate Professor of Biochemistry Department of Biochemistry & Biotechnology Univer

Re: [ccp4bb] Off topic: Crystallization screening robot

ystems. Best, Jinyi -- ------- Dr. Demetres D. Leonidas Associate Professor of Biochemistry Department of Biochemistry & Biotechnology University of Thessaly 26 Ploutonos Str. 41221 Larissa, Greece -

Re: [ccp4bb] a challenge

-- --- Dr. Demetres D. Leonidas Associate Professor of Biochemistry Department of Biochemistry & Biotechnology University of Thessaly 26 Ploutonos Str. 41221 Larissa, Greece - Tel. +302410 565278 Tel. +302410 565297 (Lab)

[ccp4bb] Post-Doctoral position in Molecular Biology

2002). -- --- Dr. Demetres D. Leonidas Associate Professor of Biochemistry Department of Biochemistry & Biotechnology University of Thessaly 26 Ploutonos Str. 41221 Larissa, Greece - Tel. +302410 565278 Tel. +302410 565297 (Lab) Fax. +302410

Re: [ccp4bb] Unusually low B factors with phenix

, Demetres D. Leonidas wrote: Hello, I am experiencing a weird problem with B factor refinement (individual, isotropic) in phenix.refine (1.8.1.-1168) and a structure at 1.9 A resolution. The ADP values after the refinement are very very low, less than 2 and sometimes 0. I am getting the same result

[ccp4bb] Unusually low B factors with phenix

optimization of the X-ray/ADP weight. Has anyone else noticed that and is there a workaround ? Demetres -- --- Dr. Demetres D. Leonidas Associate Professor of Biochemistry Department of Biochemistry & Biotechnology University of Thessaly 26 Ploutonos

Re: [ccp4bb] Somewhat OT: question of professional courtesy

hanks! Evette Evette S. Radisky, Ph.D. Assistant Professor Mayo Clinic Cancer Center Griffin Cancer Research Building, Rm 310 4500 San Pablo Road Jacksonville, FL 32224 (904) 953-6372 -- --- Dr. Demetres D. Leonidas Associate Professor of Biochem

[ccp4bb] Postdoctoral Position in synthesis of glucopyranonucleosides

Dear all, please follow the link http://www.hecra.gr/vacancies/21_6.pdf for a posdoctoral position in Organic Synthesis at the Department of Biochemistry and Biotechnology, University of Thessaly. Demetres -- --- Dr. Demetres D. Leonidas

Re: [ccp4bb] Devices Suitable to Concentrate Protein Solutions in Liter Scale

(typically 2~4 litters). It was problematic when I wanted to concentrate the solution to at least less than 500ml. If you know any device appropriate for such task, please help me out:) Thanks in advance! Sincerely, Xuan Yang -- Demetres D. Leonidas, Ph.D. Senior Researcher Structural

[ccp4bb] Marie Curie Fellowship

handbook at: http://ec.europa.eu/research/fp6/mariecurie-actions/action/stage_en.html Applications should be e-mailed to Dr. MN Alexis (mnale...@eie.gr) till 1st of March 2009 and should include a full CV and the names and addresses of 1-2 referees. -- Demetres D. Leonidas, Ph.D. Senior

[ccp4bb] Nikos Oikonomakos

Dear all, it is with great sadness that we announce the passing of Nikos Oikonomakos yesterday. Nikos was a dear friend, a passionate researcher and an innovative teacher. We will all miss him . -- Dr. Demetres D. Leonidas

[ccp4bb] ccp4mg doesn't start in windows error in startup script

? Demetres -- Demetres D. Leonidas, Ph.D. Structural Biology & Chemistry Group Institute of Organic and Pharmaceutical Chemistry The National Hellenic Research Foundation 48, Vassileos Constantinou Avenue Athens 116 35, Greece == Tel. +30 210 7273841 (of

Re: [ccp4bb] crystallization incubators

Kalman Dock 415 South St. Waltham, MA 02454 USA -- Demetres D. Leonidas, Ph.D. Structural Biology & Chemistry Group Institute of Organic and Pharmaceutical Chemistry The National Hellenic Research Foundation 48, Vassileos Constantinou Avenue Athens 116 35, Gr

Re: [ccp4bb] crystallisation robot

good wash whilst still on the machine will clear the blockage. Dave -- David C. Briggs PhD Father & Crystallographer http://www.dbriggs.talktalk.net <http://www.dbriggs.talktalk.net> AIM ID: dbassophile -- Demetres D.

[ccp4bb] Postdoc protein crystallographer in Greece

y an EC grant. Please send a preliminary request with a CV and a summary of research experience and interests to Prof. Socrates Tzartos, emails: [EMAIL PROTECTED] and [EMAIL PROTECTED] -- Demetres D. Leonidas, Ph.D. Structural Biology & Chemistry Group Institute of Organic and Pharma

[ccp4bb] Postdoc protein crystallographer in Greece

y an EC grant. Please send a preliminary request with a CV and a summary of research experience and interests to Prof. Socrates Tzartos, emails: [EMAIL PROTECTED] and [EMAIL PROTECTED] -- Demetres D. Leonidas, Ph.D. Structural Biology & Chemistry Group Institute of Organic and Pharma

Re: [ccp4bb] Twinning in C2 ?

- is that feasible? I think I would generate P1 data Demetres D. Leonidas wrote: Dear Eleanor, Yes the native is a dimer and we did the search using the dimer as a model but we had similar results (i.e. all programs find one molecule). The graphs from TRUNCATE show rather "normal"

Re: [ccp4bb] Twinning in C2 ?

er there is a pseudo translation vector in the mutant form.. Or what the data analysis graphs from TRUNCATE show - are they "normal"? Eleanor Demetres D. Leonidas wrote: Dear all, we have encountered a problem in solving one mutant structure. The mutant protein crystallizes in the same

[ccp4bb] Twinning in C2 ?

Demetres -- Demetres D. Leonidas, Ph.D. Structural Biology & Chemistry Group Institute of Organic and Pharmaceutical Chemistry The National Hellenic Research Foundation 48, Vassileos Constantinou Avenue Athens 116 35, Greece == Tel. +30 210 727

[ccp4bb]

dvance Sajid Download prohibited? No problem! To chat from any browser without download, Click Here: http://in.messenger.yahoo.com/webmessengerpromo.php -- Demetres D. Leonidas, Ph.D. Structural Biology & Chemistry Group Institute of Organic and Pharmaceutical Chemistry The Nation