Re: [ccp4bb] Fine Phi Slicing
I could be wrong here, but isn't the case that fine slicing is an option with a CCD and a necessity on a PAD b/c of dead time and/or counter dynamic range issues? (no current and/or former financial ties to any manufacturer) Fred [32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred ***[m
[ccp4bb] Molrep
Dear All, Does anyone know by any chance what to do when Molrep crashes with: Radius of gyration : 27.85 WARNING: Radius of integration >42.40 Radius of integration : 42.40 Resolution : 29.824.00 --- rfcoef for model --- --- rfcoef for Fobs --- NCS (from Self rotation Function): 1 ERROR: in RFROT: RF overflow ERR: in CALC_SRF This is with "anisothermal correction of Fobs" whatever that means. It runs fine with "default scaling". Data are very anisotropic, so "anisothermal correction of Fobs" sounded attractive. Thanks. Fred [32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred ***[m
Re: [ccp4bb] Parallelization?
Am I correct that OpenMP parallelized crystallographic software is in Fortran? While I think there is OpenMP extensions for C and variants, but not so for python. Is this correct? Fred [32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred ***[m
Re: [ccp4bb] How to create electrostatic surface of modified DNA by APBS?
Hi Xiaoming, I would download pdb2pqr 1.8 from the apbs website and install it. (linux) It can handle nucleic acid, (3 letter code) . After you installed it run it with python /whereeveritis/pdb2pqr-1.8/pdb2pqr.py -h it will print the options. Hope this helps. Fred [32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred ***[m
Re: [ccp4bb] Align linux version
Please correct me if I'm wrong, but I think lsqman implements G. Cohen's operator improvement in DP_improve. Assuming of course if that was the reason why someone wanted to use align. Fred [32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred ***[m
Re: [ccp4bb] CCP4 Update victim of own success
Or nx, which works very well, although the server has to be installed at the remote end and client on the local. www.nomachine.com Fred [32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred ***[m
Re: [ccp4bb] PNAS on fraud
I think that the jump between fraud and other quality indicators is a bit too steep for me. Poor quality indicators may suggest poor data that the xtal was willing to diffract, a concept that to me is very orthogonal to fraud. Fred [32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred ***[m
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
I suspect that pure MIR (without anomalous) was always a fiction. I doubt that anyone has ever used it. Heavy atoms always give an anomalous signal Phil I suspect that there was a time when the anomalous signal in data sets was fictional. Before the invent of flash freezing, systematic errors due to decay and the need of scaling together many derivative data sets collected on multiple crystals could render weak anomalous signal useless. Therefore MIR was needed. Also, current hardware/software produces much better reduced data, so weak signals can become useful. Fred [32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred ***[m
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
Just for clarification: I didn't try to claim that there was no anomalous signal, simply that in some cases it was difficult use it, because the data weren't that great. fred [32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred ***[m
Re: [ccp4bb] very informative - Trends in Data Fabrication
I think that to review a paper containing a structure derived from crystallographic data should indeed involve the referee having access to coordinates and to the electron density. Without this access it is not possible to judge the quality and very often even the soundness of statements in the paper. I think the argument that this may give a competitive advantage to the referee who him or herself maybe working on the same thing should be mute, as I thought article refereeing was supposed to be a confidential process. Breaching this would be a serious ethical violation. In my experience, before agreeing to review, we see the abstract, I was always thought that I was supposed to decline if there is a potential conflict with my own work. Perhaps naively, but I always assumed that everyone acts like this. Unfortunately however, there is another serious issue. After a very troubling experience with a paper I reviewed, I discussed this issue with journal editors. What they said was that they already have a hell of time to find people who agree to referee, by raising the task level (asking refs to look at coords and density) they feared that no one would agree. Actually, perhaps many have noticed the large number of 5 liner referee reports saying really not much about a full length research article. People simply don't have the time to put the effort in. So I am not sure how realistic is to ask even more, for something that at some level, is pro bono work. Fred [32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred ***[m
[ccp4bb] pdb-l: Retraction of 12 Structures....
On Sat, 12 Dec 2009 11:58:27 +0530 Dr. Anthony Addlagatta wrote: Bernhard, I would be worried about sending the structure factors and the coordinates along with the manuscript. I wonder why? Cheers Fred [32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred ***[m
