Re: [ccp4bb] PyMOL v. Coot map 'level'
Hi James, carving and normalization in PyMOL are really independent things. Normalization happens during map loading (if normalize_ccp4_maps is on). Carving happens during mesh generation (it's an argument of the isomesh command) and is really just a way to limit mesh display to an area of interest. You can do a simple test and create a mesh of an entire map, and a carved mesh around a ligand or residue, and both should match perfectly. Example: fetch 1rx1, async=0 fetch 1rx1, async=0, type=2fofc isomesh meshfull, 1rx1_2fofc, 1.0 isomesh meshcarve, 1rx1_2fofc, 1.0, organic, 2.0, 1, 2.0 set grid_mode disable 1rx1 set_view (\ 0.929457247,0.368711948,0.012666196,\ -0.360624999,0.900760233,0.242035180,\ 0.077831753, -0.229529440,0.970184207,\ 0.16911,0.72468, -31.454853058,\ 26.290172577, 59.373352051, 15.045225143,\ 29.803743362, 33.103614807, -20.0 ) Expanding the map also happens during mesh generation and does nothing to the data, except replicating it. Using your tool of choice to normalize a map before loading into PyMOL is for sure a good practice and solves the issue that PyMOL doesn't normalize across the asymmetric unit, but the raw data (if raw data != integral number of asymmetric units). Cheers, Thomas On 03 Jun 2015, at 14:14, James Holton jmhol...@lbl.gov wrote: I have never trusted Pymol's normalization of maps, because it has never been clear to me if it does the normalization before or after the carve. If it is after, then you have a serious interpretation problem: the 1 sigma level will be MUCH lower than if the rest of the map were not set to zero. In this situation if you set the carve right the map will look a LOT more like the coordinates than it should. In fact, if you normalize a map using anything but an integral number of asymmetric units your 1 sigma level will not be the same as if it were done properly. With pymol you usually have to extend the map to cover the protein of interest, and this extended map is seldom an integral number of asymmetric units. So, I have always taken to normalizing the map myself (using mapmask) with a single ASU or single cell as the map extent, and THEN extending the map to cover the PDB (using a completely different run of mapmask) and only then load it into pymol. I always turn off map normalization in pymol. I have also never used carve, as my thesis adviser strongly disapproved of the practice. Mostly because of the potential for bias mentioned above. Do you really have to carve for your density to be clear? -James Holton MAD Scientist On 5/29/2015 1:15 PM, Emilia C. Arturo (Emily) wrote: Hello. I am struggling with an old question--old because I've found several discussions and wiki bits on this topic, e.g. on the PyMOL mailing list (http://sourceforge.net/p/pymol/mailman/message/26496806/ and http://www.pymolwiki.org/index.php/Display_CCP4_Maps), but the suggestions about how to fix the problem are not working for me, and I cannot figure out why. Perhaps someone here can help: I'd like to display (for beauty's sake) a selection of a model with the map about this selection. I've fetched the model from the PDB, downloaded its 2mFo-DFc CCP4 map, loaded both the map and model into both PyMOL (student version) and Coot (0.8.2-pre EL (revision 5592)), and decided that I would use PyMOL to make the figure. I notice, though, that the map 'level' in PyMOL is not equivalent to the rmsd level in Coot, even when I set normalization off in PyMOL. I expected that a 1.0 rmsd level in Coot would look identical to a 1.0 level in PyMOL, but it does not; rather, a 1.0 rmsd level in Coot looks more like a 0.5 level in PyMOL. Does anyone have insight they could share about the difference between how Coot and PyMOL loads maps? Maybe the PyMOL 'level' is not a rmsd? is there some other normalization factor in PyMOL that I should set? Or, perhaps there is a mailing list post out there that I've missed, to which you could point me. :-) Alternatively, does anyone have instructions on how to use Coot to do what I'm trying to do in PyMOL? In PyMOL I displayed the mesh of the 2Fo-Fc map, contoured at 1.0 about a 3-residue-long 'selection' like so: isomesh map, My_2Fo-Fc.map, 1.0, selection, carve=2.0, and after hiding everything but the selection, I have a nice picture ... but with a map at a level I cannot interpret in PyMOL relative to Coot :-/ Regards, Emily. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc.
Re: [ccp4bb] PyMOL v. Coot map 'level'
Tim is making a very good point (as usual!) The RMSD of the whole asymmetric unit is only a rough guide to a useful map contour - that depends on the relative B values of the feature you want to display. It is pretty obvious that features with lower than average B factors show up at higher Sig level than perfectly well defined features which have higher B values. One of the best COOT features is being able so easily to adjust the contour to something sensible .. Eleanor On 3 June 2015 at 19:14, James Holton jmhol...@lbl.gov wrote: I have never trusted Pymol's normalization of maps, because it has never been clear to me if it does the normalization before or after the carve. If it is after, then you have a serious interpretation problem: the 1 sigma level will be MUCH lower than if the rest of the map were not set to zero. In this situation if you set the carve right the map will look a LOT more like the coordinates than it should. In fact, if you normalize a map using anything but an integral number of asymmetric units your 1 sigma level will not be the same as if it were done properly. With pymol you usually have to extend the map to cover the protein of interest, and this extended map is seldom an integral number of asymmetric units. So, I have always taken to normalizing the map myself (using mapmask) with a single ASU or single cell as the map extent, and THEN extending the map to cover the PDB (using a completely different run of mapmask) and only then load it into pymol. I always turn off map normalization in pymol. I have also never used carve, as my thesis adviser strongly disapproved of the practice. Mostly because of the potential for bias mentioned above. Do you really have to carve for your density to be clear? -James Holton MAD Scientist On 5/29/2015 1:15 PM, Emilia C. Arturo (Emily) wrote: Hello. I am struggling with an old question--old because I've found several discussions and wiki bits on this topic, e.g. on the PyMOL mailing list ( http://sourceforge.net/p/pymol/mailman/message/26496806/ and http://www.pymolwiki.org/index.php/Display_CCP4_Maps), but the suggestions about how to fix the problem are not working for me, and I cannot figure out why. Perhaps someone here can help: I'd like to display (for beauty's sake) a selection of a model with the map about this selection. I've fetched the model from the PDB, downloaded its 2mFo-DFc CCP4 map, loaded both the map and model into both PyMOL (student version) and Coot (0.8.2-pre EL (revision 5592)), and decided that I would use PyMOL to make the figure. I notice, though, that the map 'level' in PyMOL is not equivalent to the rmsd level in Coot, even when I set normalization off in PyMOL. I expected that a 1.0 rmsd level in Coot would look identical to a 1.0 level in PyMOL, but it does not; rather, a 1.0 rmsd level in Coot looks more like a 0.5 level in PyMOL. Does anyone have insight they could share about the difference between how Coot and PyMOL loads maps? Maybe the PyMOL 'level' is not a rmsd? is there some other normalization factor in PyMOL that I should set? Or, perhaps there is a mailing list post out there that I've missed, to which you could point me. :-) Alternatively, does anyone have instructions on how to use Coot to do what I'm trying to do in PyMOL? In PyMOL I displayed the mesh of the 2Fo-Fc map, contoured at 1.0 about a 3-residue-long 'selection' like so: isomesh map, My_2Fo-Fc.map, 1.0, selection, carve=2.0, and after hiding everything but the selection, I have a nice picture ... but with a map at a level I cannot interpret in PyMOL relative to Coot :-/ Regards, Emily.
[ccp4bb] Postdoctoral position available
A postdoctoral position is immediately available in the laboratory of Dr. Jung-Ja Kim at the Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI. The project entails an interdisciplinary approach to studying the catalytic mechanisms of cytochrome P450 reductase and nitric oxide synthase isozymes, using various biophysical techniques, including time-resolved structure/function studies in solution and time-resolved crystallography. This is a collaborative project under the NSF Program International Collaboration in Chemistry between US NSF and French ANR. Applications are invited from candidates with prior experience in protein X-ray crystallography, with strong background in protein biochemistry and enzymology. Preference will be given to candidates who received their Ph.D. degree recently. For more information on the Kim laboratory research, please visit http://www.mcw.edu/biochemistry/faculty/JungJaKim.htm Interested applicants should submit their CV, publication record, and contact information of three references to: Interested candidates should send their CV, brief description of prior research accomplishments and contact information for three references to Jung-Ja Kim (jj...@mcw.edumailto:jj...@mcw.edu). Jung-Ja Kim, Ph.D. Professor Department of Biochemistry Medical College of Wisconsin Milwaukee, WI 53226
[ccp4bb] Postdoctoral Position
A postdoctoral position is available in the structural biology group of Dr. Bret D. Freudenthal studying genomic stability and DNA damage processing at the University of Kansas Medical Center, Kansas City, Kansas. The candidate should have experience in structural biology, enzyme kinetics, protein purification, and/or biochemistry. Applicants should have excellent written and verbal communication skills, and ability to conduct research independently and with a team. A detailed notebook and organizational skills will be required. The selected individual will work as part of a team employing multiple structural and biochemical approaches to investigate how genome stability is maintained in response to DNA damage. The group has in lab crystallization facilities with a new x-ray diffraction system that complements molecular biology and protein chemistry laboratories. The lab has ready access to multiple cutting edge core facilities. The Freudenthal group is in both the department of Biochemistry and Molecular biology, and Cancer Biology. These departments are within the University of Kansas Medical Center-NCI designated Cancer Center with investigators renowned for their contributions to the area of biochemistry, protein-protein interactions, and cancer biology. The exceptional training environment offers a highly supportive and interactive scientific environment with many diverse areas of expertise KUMC is located in an especially attractive part of Kansas City that is central to prominent research institutions and maintains an affordable high quality of life. Kansas City is often ranked as top place to live in America. Applicants must possess a doctoral level degree. To apply, please send your CV, description of research experience, and contact information for three references to bfreudent...@kumc.edu or apply directly at http://www.kumc.edu/human-resources/jobs-at-kumc.html, Position #J0010798. The University of Kansas Medical Center is an Equal Opportunity/Affirmative Action employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, protected veteran status or status as a qualified individual with a disability. Dr. Bret Freudenthal Assistant Professor bfreudent...@kumc.edu Department of Biochemistry and Molecular Biology Department of Cancer Biology University of Kansas Medical Center 1. Freudenthal, B.D., et al. (2015) Uncovering the Polymerase-induced Cytotoxicity of an Oxidized Nucleotide. *Nature *517:635-9. 2. Freudenthal, B.D., et al. (2013) Observing a DNA Polymerase in Action. *Cell *154:157-68.
[ccp4bb] PhD Scholarship: Structural and functional studies of eukaryotic membrane proteins involved in cholesterol and sugar transport.
PhD Scholarship: Structural and functional studies of eukaryotic membrane proteins involved in cholesterol and sugar transport. A PhD position is available in membrane protein biochemistry and X-ray crystallography in the newly established research group of Dr. Bjorn P Pedersen at the Department of Molecular Biology and Genetics, Aarhus University, Denmark. Our group studies the structure-function relationship of membrane proteins involved in metabolite uptake in the human body, primarily cholesterol and sugar uptake, as well as their regulation from a structural perspective. The PhD project will involve expression, purification and structural/functional characterization of membrane proteins involved in metabolite transport. Methods learned and used will be X-ray crystallography and cryo-electron microscopy as well as various biochemical methods to elucidate function. The project is fully funded by the Danish Council for Independent Research for 3 years (3-year PhD), and will be based in the laboratory of Dr. Bjorn P. Pedersen. It would ideally suit an outstanding biochemistry graduate with a strong interest in structural biology. The candidate should have molecular biology, protein production and purification experience. Experience with membrane proteins or protein structure determination will be an advantage. Full training will be provided in all necessary areas of protein biochemistry and structural biology. Good English language skills are essential. Salary will be according to the collective agreement between the Danish Confederation of Professional Associations and the Danish State. The position will be filled as soon as a suitable candidate is identified. Applicant should send a CV, cover letter and names of 2 referees to Dr. Bjorn P Pedersen (b...@mbg.au.dk).
Re: [ccp4bb] Problem regarding output in ccp4i 6.5
I thought thearound the fil name were meant to fix this? Eleanor On 3 June 2015 at 06:57, Andreas Forster docandr...@gmail.com wrote: Dear Deepa, there was a time when spaces in the names of foldera and files was a big nono in ccp4. Maybe it still is. Try changing New Folder to New_Folder or something else without a space. Best Andreas On Wed, Jun 3, 2015 at 6:09 AM, Deepa Raju deepakmraj...@gmail.com wrote: Dear all, I have installed ccp4i 6.5 version, I need to find out the contacts between the atoms of SAM and amino acid residues of the protein. But I'm not getting the output. Output is showing like this #CCP4I VERSION CCP4Interface 6.5.0 #CCP4I SCRIPT LOG contact #CCP4I DATE 02 Jun 2015 17:33:09 #CCP4I USER 'UNKNOWN' #CCP4I PROJECT deepasam #CCP4I JOB_ID 64 #CCP4I SCRATCH C:/ccp4temp/ #CCP4I HOSTNAME DEEPA-PC #CCP4I PID 7176 *** * Information from CCP4Interface script *** The program run with command: contact XYZIN D:/sum_proj/New Folder/structure analysis/5.6.2014/1XDS_chain_A.pdb has failed with error message couldn't execute contact: invalid argument *** #CCP4I TERMINATION STATUS 0 couldn't execute contact: invalid argument #CCP4I TERMINATION TIME 02 Jun 2015 17:33:09 #CCP4I MESSAGE Task failed please suggest the solution for this problem. Thank you in advance With Regards, Deepa
Re: [ccp4bb] calculation of map correlation coefficient
You can try EDSTATS in CCP4 to get the numbers you want. This works very well for us. Cheers, Robbie Sent with my Windows Phone Van: Andreas Heinemailto:hei...@mailer.uni-marburg.de Verzonden: 3-6-2015 15:43 Aan: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] calculation of map correlation coefficient Hi, I tried to use the program map correlation to calculate the correlation between a small molecule ligand and the corresponding electron density on a per residue basis. Even so the ligand is non-peptidic, the program lists values for main- and side-chain. Is there a command which can be used to calculate a combined overall correlation coefficient? Thanks in advance for any advice, Andreas
[ccp4bb] calculation of map correlation coefficient
Hi, I tried to use the program map correlation to calculate the correlation between a small molecule ligand and the corresponding electron density on a per residue basis. Even so the ligand is non-peptidic, the program lists values for main- and side-chain. Is there a command which can be used to calculate a combined overall correlation coefficient? Thanks in advance for any advice, Andreas
Re: [ccp4bb] PyMOL v. Coot map 'level'
I have never trusted Pymol's normalization of maps, because it has never been clear to me if it does the normalization before or after the carve. If it is after, then you have a serious interpretation problem: the 1 sigma level will be MUCH lower than if the rest of the map were not set to zero. In this situation if you set the carve right the map will look a LOT more like the coordinates than it should. In fact, if you normalize a map using anything but an integral number of asymmetric units your 1 sigma level will not be the same as if it were done properly. With pymol you usually have to extend the map to cover the protein of interest, and this extended map is seldom an integral number of asymmetric units. So, I have always taken to normalizing the map myself (using mapmask) with a single ASU or single cell as the map extent, and THEN extending the map to cover the PDB (using a completely different run of mapmask) and only then load it into pymol. I always turn off map normalization in pymol. I have also never used carve, as my thesis adviser strongly disapproved of the practice. Mostly because of the potential for bias mentioned above. Do you really have to carve for your density to be clear? -James Holton MAD Scientist On 5/29/2015 1:15 PM, Emilia C. Arturo (Emily) wrote: Hello. I am struggling with an old question--old because I've found several discussions and wiki bits on this topic, e.g. on the PyMOL mailing list (http://sourceforge.net/p/pymol/mailman/message/26496806/ and http://www.pymolwiki.org/index.php/Display_CCP4_Maps), but the suggestions about how to fix the problem are not working for me, and I cannot figure out why. Perhaps someone here can help: I'd like to display (for beauty's sake) a selection of a model with the map about this selection. I've fetched the model from the PDB, downloaded its 2mFo-DFc CCP4 map, loaded both the map and model into both PyMOL (student version) and Coot (0.8.2-pre EL (revision 5592)), and decided that I would use PyMOL to make the figure. I notice, though, that the map 'level' in PyMOL is not equivalent to the rmsd level in Coot, even when I set normalization off in PyMOL. I expected that a 1.0 rmsd level in Coot would look identical to a 1.0 level in PyMOL, but it does not; rather, a 1.0 rmsd level in Coot looks more like a 0.5 level in PyMOL. Does anyone have insight they could share about the difference between how Coot and PyMOL loads maps? Maybe the PyMOL 'level' is not a rmsd? is there some other normalization factor in PyMOL that I should set? Or, perhaps there is a mailing list post out there that I've missed, to which you could point me. :-) Alternatively, does anyone have instructions on how to use Coot to do what I'm trying to do in PyMOL? In PyMOL I displayed the mesh of the 2Fo-Fc map, contoured at 1.0 about a 3-residue-long 'selection' like so: isomesh map, My_2Fo-Fc.map, 1.0, selection, carve=2.0, and after hiding everything but the selection, I have a nice picture ... but with a map at a level I cannot interpret in PyMOL relative to Coot :-/ Regards, Emily.
